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Pozarycki C, Seaton KM, C Vincent E, Novak Sanders C, Nuñez N, Castillo M, Ingall E, Klempay B, Pontefract A, Fisher LA, Paris ER, Buessecker S, Alansson NB, Carr CE, Doran PT, Bowman JS, Schmidt BE, Stockton AM. Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration. ASTROBIOLOGY 2024; 24:795-812. [PMID: 39159437 DOI: 10.1089/ast.2023.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl2-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects. Bioluminescence assays show that adenosine triphosphate (ATP) concentrations are higher in NaCl-rich, low water activity (aw) samples (<0.85) from SBSW. This is consistent with the accumulation and preservation of ATP at low aw as described in past laboratory studies. The water-soluble small organic molecule inventory was determined by using microchip capillary electrophoresis paired with high-resolution mass spectrometry (µCE-HRMS). We analyzed the relative distribution of proteinogenic amino acids with a recently developed quantitative method using CE-separation and laser-induced fluorescence (LIF) detection of amino acids in hypersaline brines. Salinity trends for dissolved free amino acids were consistent with amino acid residue abundance determined from the proteome of the microbial community predicted from metagenomic data. This highlights a tangible connection up and down the "-omics" ladder across changing geochemical conditions. The detection of water-soluble organic compounds, specifically proteinogenic amino acids at high abundance (>7 mM) in concentrated brines, demonstrates that potential organic biomarkers accumulate at hypersaline sites and suggests the possibility of long-term preservation. The detection of such molecules in high abundance when using diverse analytical tools appropriate for spacecraft suggests that life detection within hypersaline environments, such as evaporates on Mars and the surface or subsurface brines of ocean world Europa, is plausible and argues such environments should be a high priority for future exploration. Key Words: Salts-Analytical chemistry-Amino acids-Biosignatures-Capillary electrophoresis-Preservation. Astrobiology 24, 795-812.
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Affiliation(s)
- Chad Pozarycki
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kenneth M Seaton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Emily C Vincent
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Carlie Novak Sanders
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nickie Nuñez
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mariah Castillo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ellery Ingall
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Benjamin Klempay
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | | | - Luke A Fisher
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | - Emily R Paris
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Steffen Buessecker
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Nikolas B Alansson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Christopher E Carr
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter T Doran
- Geology and Geophysics, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | - Britney E Schmidt
- Departments of Astronomy and Earth & Atmospheric Sciences, Cornell University, Ithaca, New York, USA
| | - Amanda M Stockton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
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Kashani M, Engle MA, Kent DB, Gregston T, Cozzarelli IM, Mumford AC, Varonka MS, Harris CR, Akob DM. Illegal dumping of oil and gas wastewater alters arid soil microbial communities. Appl Environ Microbiol 2024; 90:e0149023. [PMID: 38294246 PMCID: PMC10880632 DOI: 10.1128/aem.01490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024] Open
Abstract
The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.
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Affiliation(s)
- Mitra Kashani
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Mark A Engle
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Douglas B Kent
- U.S. Geological Survey, Earth Systems Processes Division, Menlo Park, California, USA
| | | | - Isabelle M Cozzarelli
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Adam C Mumford
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, Maryland, USA
| | - Matthew S Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Cassandra R Harris
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
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Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
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Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
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Wood C, Bruinink A, Trembath-Reichert E, Wilhelm MB, Vidal C, Balaban E, McKay CP, Swan R, Swan B, Goordial J. Active microbiota persist in dry permafrost and active layer from Elephant Head, Antarctica. ISME COMMUNICATIONS 2024; 4:ycad002. [PMID: 38304082 PMCID: PMC10833075 DOI: 10.1093/ismeco/ycad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/03/2023] [Accepted: 11/07/2023] [Indexed: 02/03/2024]
Abstract
Dry permafrost is a challenging environment for microbial life due to cold, dry, and often oligotrophic conditions. In 2016, Elephant Head, Antarctica, was confirmed as the second site on Earth to contain dry permafrost. It is geographically distinct from the McMurdo Dry Valleys where dry permafrost has been studied previously. Here, we present the first study of the microbial activity, diversity, and functional potential of Elephant Head dry permafrost. Microbial activity was measured using radiorespiration assays with radiolabeled acetate as a carbon source at 5, 0, and -5°C. Low, but detectable, rates of microbial activity were measured in some samples at 0 and -5°C. This is distinct from previous studies of McMurdo Dry Valley dry permafrost which concluded that dry permafrost represents a cold-arid limit to life on the planet. The isolation of cold-adapted organisms from these soils, including one capable of subzero growth, further supports that the Elephant Head dry active layer and dry permafrost harbor viable microbial life, which may be active in situ. Metagenomic, 16S rRNA gene, and internal transcribed spacer and amplicon sequencing identified similar microbial communities to other Antarctic and cold environments. The Elephant Head microbial community appears to be adapted for survival in cold, dry, and oligotrophic conditions based on the presence of cold adaptation and stress response genes in the metagenomes. Together, our results show that dry permafrost environments do not exclude active microbial life at subzero temperatures, suggesting that the cold, dry soils of Mars may also not be as inhospitable as previously thought.
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Affiliation(s)
- Claudia Wood
- School of Environmental Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
| | - Alyssa Bruinink
- School of Environmental Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
| | - Elizabeth Trembath-Reichert
- School of Earth and Space Exploration, Arizona State University, 781 Terrace Mall, Tempe, AZ 85287, United States
| | - Mary Beth Wilhelm
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, United States
| | - Chanel Vidal
- School of Earth and Space Exploration, Arizona State University, 781 Terrace Mall, Tempe, AZ 85287, United States
| | - Edward Balaban
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, United States
| | - Christopher P McKay
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, United States
| | - Robert Swan
- 2041 Foundation, 130 Wescott Ct, Auburn, CA 95603, United States
| | - Barney Swan
- 2041 Foundation, 130 Wescott Ct, Auburn, CA 95603, United States
| | - Jackie Goordial
- School of Environmental Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G 2W1, Canada
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Moreno-Paz M, dos Santos Severino RS, Sánchez-García L, Manchado JM, García-Villadangos M, Aguirre J, Fernández-Martínez MA, Carrizo D, Kobayashi L, Dave A, Warren-Rhodes K, Davila A, Stoker CR, Glass B, Parro V. Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert. ASTROBIOLOGY 2023; 23:1259-1283. [PMID: 37930382 PMCID: PMC10825288 DOI: 10.1089/ast.2021.0174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/02/2023] [Indexed: 11/07/2023]
Abstract
The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.
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Affiliation(s)
- Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Rita Sofia dos Santos Severino
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Departament of Física y Matemáticas y de Automática, University of Alcalá de Henares (UAH), Madrid, Spain
| | - Laura Sánchez-García
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Juan Manuel Manchado
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | | | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Miguel Angel Fernández-Martínez
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Department of Natural Resource Sciences, McGill University, Québec, Canada
| | - Daniel Carrizo
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Linda Kobayashi
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Arwen Dave
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Kim Warren-Rhodes
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
| | - Alfonso Davila
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Carol R. Stoker
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Brian Glass
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
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Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
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Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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Lian WH, Mohamad OAA, Dong L, Zhang LY, Wang D, Liu L, Han MX, Li S, Wang S, Antunes A, Fang BZ, Jiao JY, Li WJ. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems. ENVIRONMENTAL MICROBIOME 2023; 18:4. [PMID: 36639807 PMCID: PMC9840269 DOI: 10.1186/s40793-023-00463-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/08/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Yu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong Wang
- College of Life Science and Technology, Honghe University, Mengzi, 661199, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, People's Republic of China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Bacterial Diversity Profiling of Desert Sand from Tierra Caliente, Mexico, Based on 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2022; 11:e0078222. [PMID: 36000857 PMCID: PMC9476955 DOI: 10.1128/mra.00782-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Tierra Caliente is an arid region in Mexico, representing a reservoir of understudied xerophilic bacteria. Here, we report the bacterial amplicon sequencing characterization of desert sand collected from the Zicuirán-Infiernillo Biosphere Reserve within Tierra Caliente. Bacteria known to be resistant to desiccation and high radiation were detected.
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Busse L, Tisza M, DiRuggiero J. Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities. Viruses 2022; 14:v14091983. [PMID: 36146789 PMCID: PMC9500819 DOI: 10.3390/v14091983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Viruses are key players in the environment, and recent metagenomic studies have revealed their diversity and genetic complexity. Despite progress in understanding the ecology of viruses in extreme environments, viruses’ dynamics and functional roles in dryland ecosystems, which cover about 45% of the Earth’s land surfaces, remain largely unexplored. This study characterizes virus sequences in the metagenomes of endolithic (within rock) microbial communities ubiquitously found in hyper-arid deserts. Taxonomic classification and network construction revealed the presence of novel and diverse viruses in communities inhabiting calcite, gypsum, and ignimbrite rocks. Viral genome maps show a high level of protein diversity within and across endolithic communities and the presence of virus-encoded auxiliary metabolic genes. Phage-host relationships were predicted by matching tRNA, CRISPR spacer, and protein sequences in the viral and microbial metagenomes. Primary producers and heterotrophic bacteria were found to be putative hosts to some viruses. Intriguingly, viral diversity was not correlated with microbial diversity across rock substrates.
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Affiliation(s)
- Leora Busse
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mike Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
- Correspondence:
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10
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Laboratory experiment of ATP measurement using Mars soil simulant: as a method for extraterrestrial life detection. ANAL SCI 2022; 38:725-730. [PMID: 35286642 PMCID: PMC9013681 DOI: 10.1007/s44211-022-00081-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/06/2022] [Indexed: 12/04/2022]
Abstract
We present a laboratory experiment of ATP measurement using Mars soil simulant and Escherichia coli (E. coli) with a point of view for future application to searching extraterrestrial life. We used Mars Global Simulant MGS-1 (Exolith Lab) as soil simulant, added E. coli suspension to it, then the soil simulant with E. coli was dried. Various configurations of samples with different E. coli density, 1.75 × 102, 1.75 × 103, 1.75 × 104, 1.75 × 105, and 1.75 × 106 cells (g soil)−1, were prepared together with controls. ATP extraction reagent and luminescence reagent were added to the sample, and bioluminescence measurement was performed. The result suggests significant detection of ATP for samples with E. coli density used in this work. Similar experiments but without the soil simulant were carried out, and results with and without the soil simulant are compared. Based on the ATP measurement studied in this work, we discussed extraterrestrial life search, planetary protection, relation with the panspermia hypothesis, and also other applications.
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11
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Fuentes B, Choque A, Gómez F, Alarcón J, Castro-Nallar E, Arenas F, Contreras D, Mörchen R, Amelung W, Knief C, Moradi G, Klumpp E, Saavedra CP, Prietzel J, Klysubun W, Remonsellez F, Bol R. Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert. Front Microbiol 2022; 12:794743. [PMID: 35197940 PMCID: PMC8859261 DOI: 10.3389/fmicb.2021.794743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
The extreme environmental conditions and lack of water on the soil surface in hyperarid deserts hamper microbial life, allowing only highly specialized microbial communities to the establish colonies and survive. Until now, the microbial communities that inhabit or have inhabited soils of hyperarid environments at greater depths have been poorly studied. We analyzed for the first time the variation in microbial communities down to a depth of 3.4 m in one of the driest places of the world, the hyperarid Yungay region in the Atacama Desert, and we related it to changes in soil physico-chemical characteristics. We found that the moisture content changed from 2 to 11% with depth and enabled the differentiation of three depth intervals: (i) surface zone A (0–60 cm), (ii) intermediate zone B (60–220 cm), and (iii) deep zone C (220–340 cm). Each zone showed further specific physicochemical and mineralogical features. Likewise, some bacterial phyla were unique in each zone, i.e., members of the taxa Deinococcota, Halobacterota, and Latescibacterota in zone A; Crenarchaeota, Fusobacteriota, and Deltaproteobacterium Sva0485 in zone B; and Fervidibacteria and Campilobacterota in zone C, which indicates taxon-specific preferences in deep soil habitats. Differences in the microbiota between the zones were rather abrupt, which is concomitant with abrupt changes in the physical-chemical parameters. Overall, moisture content, total carbon (TC), pH, and electric conductivity (EC) were most predictive of microbial richness and diversity, while total sulfur (TS) and total phosphorous (TP) contents were additionally predictive of community composition. We also found statistically significant associations between taxa and soil properties, most of which involved moisture and TC contents. Our findings show that under-explored habitats for microbial survival and existence may prevail at greater soil depths near water or within water-bearing layers, a valuable substantiation also for the ongoing search for biosignatures on other planets, such as Mars.
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Affiliation(s)
- Bárbara Fuentes
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Alessandra Choque
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Francisco Gómez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - Franko Arenas
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Contreras
- Programa de Doctorado en Ciencias Mención Geología, Universidad Católica del Norte, Antofagasta, Chile
| | - Ramona Mörchen
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Wulf Amelung
- Institute of Crop Science and Resource Conservation, Soil Science and Soil Ecology, University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Ghazal Moradi
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Erwin Klumpp
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jörg Prietzel
- Wissenschaftszentum Weihenstephan, Technical University München, Freising, Germany
| | - Wantana Klysubun
- Synchrotron Light Research Institute, Nakhon Ratchasima, Thailand
| | - Francisco Remonsellez
- Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
- *Correspondence: Francisco Remonsellez,
| | - Roland Bol
- Institute of Bio and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- Roland Bol,
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12
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Schulze-Makuch D, Lipus D, Arens FL, Baqué M, Bornemann TLV, de Vera JP, Flury M, Frösler J, Heinz J, Hwang Y, Kounaves SP, Mangelsdorf K, Meckenstock RU, Pannekens M, Probst AJ, Sáenz JS, Schirmack J, Schloter M, Schmitt-Kopplin P, Schneider B, Uhl J, Vestergaard G, Valenzuela B, Zamorano P, Wagner D. Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. Microorganisms 2021; 9:microorganisms9051038. [PMID: 34065975 PMCID: PMC8151210 DOI: 10.3390/microorganisms9051038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
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Affiliation(s)
- Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
| | - Felix L. Arens
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Mickael Baqué
- German Aerospace Center (DLR), Institute of Planetary Research, 12489 Berlin, Germany;
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Microgravity User Support Center (MUSC), 51147 Cologne, Germany;
| | - Markus Flury
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
- Department of Crop and Soil Science, Washington State University, Puyallup, WA 98371, USA
| | - Jan Frösler
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jacob Heinz
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Yunha Hwang
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Samuel P. Kounaves
- Department of Chemistry, Tufts University, Boston, MA 02155, USA;
- Department of Earth Science & Engineering, Imperial College London, London SW7 2AZ, UK
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, 14473 Potsdam, Germany;
| | - Rainer U. Meckenstock
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Johan S. Sáenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Janosch Schirmack
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Beate Schneider
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Jenny Uhl
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
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13
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Abstract
Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR. IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.
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14
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Saona LA, Soria M, Durán-Toro V, Wörmer L, Milucka J, Castro-Nallar E, Meneses C, Contreras M, Farías ME. Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes. MICROBIAL ECOLOGY 2021; 81:941-953. [PMID: 33388944 DOI: 10.1007/s00248-020-01673-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.
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Affiliation(s)
- L A Saona
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina.
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
| | - M Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - V Durán-Toro
- Hydrothermal Geomicrobiology Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - L Wörmer
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, 28359, Bremen, Germany
| | - J Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - E Castro-Nallar
- Facultad de Ciencias de la Vida, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
| | - C Meneses
- Centro de Biotecnología Vegetal (CBV), FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - M Contreras
- Centro de Ecología Aplicada, Santiago, Chile
| | - M E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina.
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15
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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16
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Zhang W, Bahadur A, Zhang G, Zhang B, Wu X, Chen T, Liu G. Diverse Bacterial Communities From Qaidam Basin of the Qinghai-Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions. Front Microbiol 2020; 11:554105. [PMID: 33042062 PMCID: PMC7530167 DOI: 10.3389/fmicb.2020.554105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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17
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Saona LA, Soria M, Villafañe PG, Lencina AI, Stepanenko T, Farías ME. Andean Microbial Ecosystems: Traces in Hypersaline Lakes About Life Origin. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-46087-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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18
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Carrier B, Beaty D, Meyer M, Blank J, Chou L, DasSarma S, Des Marais D, Eigenbrode J, Grefenstette N, Lanza N, Schuerger A, Schwendner P, Smith H, Stoker C, Tarnas J, Webster K, Bakermans C, Baxter B, Bell M, Benner S, Bolivar Torres H, Boston P, Bruner R, Clark B, DasSarma P, Engelhart A, Gallegos Z, Garvin Z, Gasda P, Green J, Harris R, Hoffman M, Kieft T, Koeppel A, Lee P, Li X, Lynch K, Mackelprang R, Mahaffy P, Matthies L, Nellessen M, Newsom H, Northup D, O'Connor B, Perl S, Quinn R, Rowe L, Sauterey B, Schneegurt M, Schulze-Makuch D, Scuderi L, Spilde M, Stamenković V, Torres Celis J, Viola D, Wade B, Walker C, Wiens R, Williams A, Williams J, Xu J. Mars Extant Life: What's Next? Conference Report. ASTROBIOLOGY 2020; 20:785-814. [PMID: 32466662 PMCID: PMC7307687 DOI: 10.1089/ast.2020.2237] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/24/2020] [Indexed: 05/19/2023]
Abstract
On November 5-8, 2019, the "Mars Extant Life: What's Next?" conference was convened in Carlsbad, New Mexico. The conference gathered a community of actively publishing experts in disciplines related to habitability and astrobiology. Primary conclusions are as follows: A significant subset of conference attendees concluded that there is a realistic possibility that Mars hosts indigenous microbial life. A powerful theme that permeated the conference is that the key to the search for martian extant life lies in identifying and exploring refugia ("oases"), where conditions are either permanently or episodically significantly more hospitable than average. Based on our existing knowledge of Mars, conference participants highlighted four potential martian refugium (not listed in priority order): Caves, Deep Subsurface, Ices, and Salts. The conference group did not attempt to reach a consensus prioritization of these candidate environments, but instead felt that a defensible prioritization would require a future competitive process. Within the context of these candidate environments, we identified a variety of geological search strategies that could narrow the search space. Additionally, we summarized a number of measurement techniques that could be used to detect evidence of extant life (if present). Again, it was not within the scope of the conference to prioritize these measurement techniques-that is best left for the competitive process. We specifically note that the number and sensitivity of detection methods that could be implemented if samples were returned to Earth greatly exceed the methodologies that could be used at Mars. Finally, important lessons to guide extant life search processes can be derived both from experiments carried out in terrestrial laboratories and analog field sites and from theoretical modeling.
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Affiliation(s)
- B.L. Carrier
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - D.W. Beaty
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - J.G. Blank
- NASA Ames Research Center, Moffett Field, California, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - L. Chou
- Georgetown University, Washington, DC, USA
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - S. DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - N.L. Lanza
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - A.C. Schuerger
- University of Florida/Space Life Sciences Laboratory, Kennedy Space Center, Florida, USA
| | - P. Schwendner
- University of Florida/Space Life Sciences Laboratory, Kennedy Space Center, Florida, USA
| | - H.D. Smith
- NASA Ames Research Center, Moffett Field, California, USA
| | - C.R. Stoker
- NASA Ames Research Center, Moffett Field, California, USA
| | - J.D. Tarnas
- Brown University, Providence, Rhode Island, USA
| | - K.D. Webster
- Planetary Science Institute, Tucson, Arizona, USA
| | - C. Bakermans
- Pennsylvania State University, Altoona, Pennsylvania, USA
| | - B.K. Baxter
- Westminster College, Salt Lake City, Utah, USA
| | - M.S. Bell
- NASA Johnson Space Center, Houston, Texas, USA
| | - S.A. Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - H.H. Bolivar Torres
- Universidad Nacional Autonoma de Mexico, Coyoacan, Distrito Federal Mexico, Mexico
| | - P.J. Boston
- NASA Astrobiology Institute, NASA Ames Research Center, Moffett Field, California, USA
| | - R. Bruner
- Denver Museum of Nature and Science, Denver, Colorado, USA
| | - B.C. Clark
- Space Science Institute, Littleton, Colorado, USA
| | - P. DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Z.E. Gallegos
- University of New Mexico, Albuquerque, New Mexico, USA
| | - Z.K. Garvin
- Princeton University, Princeton, New Jersey, USA
| | - P.J. Gasda
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - J.H. Green
- Texas Tech University, Lubbock, Texas, USA
| | - R.L. Harris
- Princeton University, Princeton, New Jersey, USA
| | - M.E. Hoffman
- University of New Mexico, Albuquerque, New Mexico, USA
| | - T. Kieft
- New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA
| | | | - P.A. Lee
- College of Charleston, Charleston, South Carolina, USA
| | - X. Li
- University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - K.L. Lynch
- Lunar and Planetary Institute/USRA, Houston, Texas, USA
| | - R. Mackelprang
- California State University Northridge, Northridge, California, USA
| | - P.R. Mahaffy
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - L.H. Matthies
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - H.E. Newsom
- University of New Mexico, Albuquerque, New Mexico, USA
| | - D.E. Northup
- University of New Mexico, Albuquerque, New Mexico, USA
| | | | - S.M. Perl
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - R.C. Quinn
- NASA Ames Research Center, Moffett Field, California, USA
| | - L.A. Rowe
- Valparaiso University, Valparaiso, Indiana, USA
| | | | | | | | - L.A. Scuderi
- University of New Mexico, Albuquerque, New Mexico, USA
| | - M.N. Spilde
- University of New Mexico, Albuquerque, New Mexico, USA
| | - V. Stamenković
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - J.A. Torres Celis
- Universidad Nacional Autonoma de Mexico, Coyoacan, Distrito Federal Mexico, Mexico
| | - D. Viola
- NASA Ames Research Center, Moffett Field, California, USA
| | - B.D. Wade
- Michigan State University, East Lansing, Michigan, USA
| | - C.J. Walker
- Delaware State University, Dover, Delaware, USA
| | - R.C. Wiens
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - J.M. Williams
- University of New Mexico, Albuquerque, New Mexico, USA
| | - J. Xu
- University of Texas, El Paso, Texas, USA
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19
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Amin A, Ahmed I, Khalid N, Khan IU, Ali A, Dahlawi SM, Li WJ. Insights on comparative bacterial diversity between different arid zones of Cholistan Desert, Pakistan. 3 Biotech 2020; 10:224. [PMID: 32373416 DOI: 10.1007/s13205-020-02204-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/10/2020] [Indexed: 11/30/2022] Open
Abstract
The present study was conducted to analyze bacterial diversity profile of Cholistan desert located in Pakistan. The study investigates the influence of physicochemical parameters of soil on distribution of different bacteria at all taxonomic levels and also study the distribution pattern between different desert environments, particularly rhizospheric and bulk desert sands. Species richness showed phyla Proteobacteria and Chloroflexi as the dominant OTUs in all the samples. Besides the two phyla, the rhizospheric soils with root remnants were dominated by Firmicutes, Deinococcus-Thermus, Actinobacteria and Acidobacteri, while phylum Thermotogae was present in significant quantity in rhizosheaths devoid of roots. In non-rhizospheric desert soils, a considerable number of OTUs belonged to phyla Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. An important finding from this study is that a bulk portion of the OTUs were assigned to unclassified taxa, indicating a large repertoire of unexplored taxa in the desert ecology of Pakistan. Distribution of taxonomic groups among various regions of the desert was collaborating well with the physicochemical parameters of the sites. The findings of this study establish the fundamental relationships between desert ecosystem, specific native plant and the total bacterial flora. This is the first study of microbial community analysis of any desert in Pakistan and thus, will serve as a future platform to explore further on desert ecosystem functioning by employing the ever-changing biotechnological tools.
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Affiliation(s)
- Arshia Amin
- 1State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People's Republic of China
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500 Pakistan
| | - Iftikhar Ahmed
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
| | - Nauman Khalid
- 4School of Food and Agricultural Sciences, University of Management and Technology, Lahore, 54000 Pakistan
| | - Inam Ullah Khan
- 5Institute of Microbiology, Faculty of Veterinary and Animal Sciences,, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ahmad Ali
- 2National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Islamabad, 45500 Pakistan
| | - Saad Mohammad Dahlawi
- 6Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Wen-Jun Li
- 1State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People's Republic of China
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20
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Gadkari PS, McGuinness LR, Männistö MK, Kerkhof LJ, Häggblom MM. Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing. FEMS Microbiol Ecol 2019; 96:5645228. [DOI: 10.1093/femsec/fiz192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.
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Affiliation(s)
- Preshita S Gadkari
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Minna K Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
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21
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Ruginescu R, Purcărea C, Dorador C, Lavin P, Cojoc R, Neagu S, Lucaci I, Enache M. Exploring the hydrolytic potential of cultured halophilic bacteria isolated from the Atacama Desert. FEMS Microbiol Lett 2019; 366:5613365. [DOI: 10.1093/femsle/fnz224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
ABSTRACTConsidering that most industrial processes are carried out under harsh physicochemical conditions, which would inactivate enzymes from commonly isolated mesophilic organisms, current studies are geared toward the identification of extremophilic microorganisms producing enzymes resistant to extreme salt concentrations, temperature and pH. Among the extremophiles, halophilic microorganisms are an important source of salt-tolerant enzymes that can be used in varying biotechnological applications. In this context, the aim of the present work was to isolate and identify halophiles producing hydrolases from the Atacama Desert, one of the harshest environments on Earth. Isolates were recovered from halite samples and screened for the presence of seven different hydrolase activities (amylase, caseinase, gelatinase, lipase, pectinase, cellulase and inulinase) using agar plate-based assays. From a total of 23 halophilic bacterial isolates, most showed lipolytic (19 strains) and pectinolytic (11 strains) activities. The molecular identification of eight selected isolates showed a strong similarity to members of the Halomonas and Idiomarina genera. Therefore, the present study represents a preliminary, but essential, step to identify novel biological sources of extremozymes in an environment once thought to be devoid of life.
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Affiliation(s)
- Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Purcărea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Roxana Cojoc
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Simona Neagu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Ioana Lucaci
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Mădălin Enache
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
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22
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Shen J, Zerkle AL, Stueeken E, Claire MW. Nitrates as a Potential N Supply for Microbial Ecosystems in a Hyperarid Mars Analog System. Life (Basel) 2019; 9:life9040079. [PMID: 31635024 PMCID: PMC6958444 DOI: 10.3390/life9040079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022] Open
Abstract
Nitrate is common in Mars sediments owing to long-term atmospheric photolysis, oxidation, and potentially, impact shock heating. The Atacama Desert in Chile, which is the driest region on Earth and rich in nitrate deposits, is used as a Mars analog in this study to explore the potential effects of high nitrate levels on growth of extremophilic ecosystems. Seven study sites sampled across an aridity gradient in the Atacama Desert were categorized into 3 clusters—hyperarid, middle, and arid sites—as defined by essential soil physical and chemical properties. Intriguingly, the distribution of nitrate concentrations in the shallow subsurface suggests that the buildup of nitrate is not solely controlled by precipitation. Correlations of nitrate with SiO2/Al2O3 and grain sizes suggest that sedimentation rates may also be important in controlling nitrate distribution. At arid sites receiving more than 10 mm/yr precipitation, rainfall shows a stronger impact on biomass than nitrate does. However, high nitrate to organic carbon ratios are generally beneficial to N assimilation, as evidenced both by soil geochemistry and enriched culturing experiments. This study suggests that even in the absence of precipitation, nitrate levels on a more recent, hyperarid Mars could be sufficiently high to benefit potentially extant Martian microorganisms.
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Affiliation(s)
- Jianxun Shen
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Aubrey L Zerkle
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Eva Stueeken
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
| | - Mark W Claire
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews KY16 9AL, Scotland, UK.
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Onstott T, Ehlmann B, Sapers H, Coleman M, Ivarsson M, Marlow J, Neubeck A, Niles P. Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration. ASTROBIOLOGY 2019; 19:1230-1262. [PMID: 31237436 PMCID: PMC6786346 DOI: 10.1089/ast.2018.1960] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/25/2019] [Indexed: 05/19/2023]
Abstract
Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.
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Affiliation(s)
- T.C. Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Address correspondence to: T.C. Onstott, Department of Geosciences, Princeton University,, Princeton, NJ 008544
| | - B.L. Ehlmann
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- B.L. Ehlmann, Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - H. Sapers
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - M. Coleman
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- NASA Astrobiology Institute, Pasadena, California, USA
| | - M. Ivarsson
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - J.J. Marlow
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - A. Neubeck
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - P. Niles
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, Texas, USA
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24
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Moreira-Grez B, Tam K, Cross AT, Yong JWH, Kumaresan D, Nevill P, Farrell M, Whiteley AS. The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil. Front Microbiol 2019; 10:2143. [PMID: 31608023 PMCID: PMC6768011 DOI: 10.3389/fmicb.2019.02143] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/30/2019] [Indexed: 02/01/2023] Open
Abstract
Biocrusts are aggregated crusts that exist on the soil surface of arid environments. They are complex microbial communities comprised of cyanobacteria, lichens, mosses, algae and fungi. Recently, biocrusts have gained significant attention due to their ubiquitous distribution and likely important ecological roles, including soil stabilization, soil moisture retention, carbon (C) and nitrogen (N) fixation, as well as microbial engineers for semi-arid ecosystem restoration. Here, we collected three co-occurring types of biocrust (Cyanobacterial crust, Crustose lichen, and Foliose lichen) and their underlying soil from arid zones within Western Australia. Bacterial microbiome composition was determined through 16S rRNA gene amplicon sequencing to assess the extent of microbiome selection within the crusts versus underlying soil and biogeochemical measures performed to determine whether the crusts had significant impact upon the underlying soil for nutrient input. We determined that the bacterial communities of native biocrusts are distinct from those in their underlying soil, where dominant bacterial taxa differed according to crust morphologies. δ15N revealed that N-fixation appeared most evident in Foliose lichen crust (1.73 ± 1.04‰). Consequently, depending upon the crust type, biocrusts contained higher concentrations of organic C (2 to 50 times), total N (4 to 16 times) and available ammonium (2 to 4 times), though this enrichment did not extend to the soils underneath them. These findings demonstrate that biocrust communities are seemingly islands of biological activity in an arid landscape, uniquely different from their surrounding and underlying soil.
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Affiliation(s)
- Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Kang Tam
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Adam T. Cross
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Jean W. H. Yong
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
- School of Biological Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Deepak Kumaresan
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paul Nevill
- Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Mark Farrell
- CSIRO Agriculture and Food, Urrbrae, SA, Australia
| | - Andrew S. Whiteley
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
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25
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Contador CA, Veas-Castillo L, Tapia E, Antipán M, Miranda N, Ruiz-Tagle B, García-Araya J, Andrews BA, Marin M, Dorador C, Asenjo JA. Atacama Database: a platform of the microbiome of the Atacama Desert. Antonie van Leeuwenhoek 2019; 113:185-195. [PMID: 31535335 DOI: 10.1007/s10482-019-01328-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/07/2019] [Indexed: 11/30/2022]
Abstract
The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.
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Affiliation(s)
- Carolina A Contador
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile.
| | - Luis Veas-Castillo
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Emilio Tapia
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Marcela Antipán
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Noemi Miranda
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Benjamín Ruiz-Tagle
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan García-Araya
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Mauricio Marin
- Centre for Biotechnology and Bioengineering (CeBiB), Departamento de Ingeniería Informática (DIINF), Universidad de Santiago de Chile, Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology and Bioengineering (CeBiB), Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
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New genus-specific primers for PCR identification of Rubrobacter strains. Antonie Van Leeuwenhoek 2019; 112:1863-1874. [PMID: 31407134 PMCID: PMC6834744 DOI: 10.1007/s10482-019-01314-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/01/2019] [Indexed: 12/02/2022]
Abstract
A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.
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Kaur S, Kurtz HD. Core bacterial community composition of a cryptoendolithic ecosystem in the Grand Staircase-Escalante National Monument, Utah. Microbiologyopen 2019; 8:e00707. [PMID: 30079546 PMCID: PMC6528646 DOI: 10.1002/mbo3.707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/12/2018] [Accepted: 07/04/2018] [Indexed: 11/21/2022] Open
Abstract
Cryptoendolithic bacterial communities in the Jurassic Navajo Sandstones play an important ecological role in this ecosystem. Developing a better understanding of the role of these cryptoendolithic communities required a deeper knowledge of the microbial diversity present. We analyzed the bacterial diversity in eight sandstones samples from several microgeological features associated with a large sandstone dome. Cryptoendolithic bacterial diversity is clustered into three distinct groups which correlated with topography, suggesting the duration of water retention might be a factor. Comparisons of diversity between each cluster showed that a core bacterial community exists in this habitat. The overall bacterial community structure was dominated by Cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria. The most prevalent genera in cyanobacteria were Leptolyngbya, Chroococcidiopsis, and unclassified cyanobacteria accounting for the bulk of cyanobacterial sequences. Within the Proteobacteria, Alphaproteobacteria were the largest class detected, with members of the Acetobacteraceae, particularly the genus Acidiphilium, being the most abundant. Acidiphilium spp. are capable of aerobic ferric iron reduction under moderately acidic conditions, explaining the high levels of iron (II) in this system. This study highlights the extent of unexplored bacterial diversity in this habitat system and sets the premise for elaborating on the ecological function of cryptoendolithic communities.
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Affiliation(s)
- Sukhpreet Kaur
- Department of Biological SciencesClemson UniversityClemsonSouth Carolina
| | - HD Kurtz
- Department of Biological SciencesClemson UniversityClemsonSouth Carolina
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Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman. Sci Rep 2019; 9:6468. [PMID: 31015576 PMCID: PMC6478931 DOI: 10.1038/s41598-019-42911-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/09/2019] [Indexed: 11/08/2022] Open
Abstract
Biological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. The results were interpreted based on the environmental parameters of the different sites. Whereas at lowland sites, mainly cyanobacteria-dominated biocrusts were observed, both cyanobacteria- and lichen-dominated biocrusts occurred at mountain sites. The majority of bacterial sequences (32–83% of total sequences) belonged to Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes, whereas fungal sequences belonged to Ascomycota, Basidiomycota, and Chytridiomycota (>95%). With biocrust development, a notable increase in cyanobacterial and decrease in actinobacterial proportions was observed for cyanobacteria-dominated crusts. In coastal areas, where salinity is high, biocrusts were replaced by a unique marine mat-like microbial community, dominated by halotolerant taxa. Redundancy analysis revealed a significant contribution of soil texture, cover type, carbon content, and elevation to the variations in bacterial and fungal communities. Multivariate analysis placed microbial communities in significantly separated clusters based on their carbon content, elevation and electrical conductivity. We conclude that Oman hosts a variety of cyanobacteria- and lichen-dominated crusts with their bacterial and fungal communities being largely dictated by soil properties and environmental parameters.
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Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA. Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems. MICROBIAL ECOLOGY 2019; 77:713-725. [PMID: 30209585 DOI: 10.1007/s00248-018-1251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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Affiliation(s)
- Aicha Asma Houfani
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Oscar U Navarrete
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
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30
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Warren-Rhodes KA, Lee KC, Archer SDJ, Cabrol N, Ng-Boyle L, Wettergreen D, Zacny K, Pointing SB. Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment. Front Microbiol 2019; 10:69. [PMID: 30873126 PMCID: PMC6403490 DOI: 10.3389/fmicb.2019.00069] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/15/2019] [Indexed: 02/03/2023] Open
Abstract
Sediments in the hyper-arid core of the Atacama Desert are a terrestrial analog to Mars regolith. Understanding the distribution and drivers of microbial life in the sediment may give critical clues on how to search for biosignatures on Mars. Here, we identify the spatial distribution of highly specialized bacterial communities in previously unexplored depth horizons of subsurface sediments to a depth of 800 mm. We deployed an autonomous rover in a mission-relevant Martian drilling scenario with manual sample validation. Subsurface communities were delineated by depth related to sediment moisture. Geochemical analysis indicated soluble salts and minerology that influenced water bio-availability, particularly in deeper sediments. Colonization was also patchy and uncolonized sediment was associated with indicators of extreme osmotic challenge. The study identifies linkage between biocomplexity, moisture and geochemistry in Mars-like sediments at the limit of habitability and demonstrates feasibility of the rover-mounted drill for future Mars sample recovery.
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Affiliation(s)
- Kimberley A Warren-Rhodes
- NASA Ames Research Center, Mountain View, CA, United States.,The SETI Institute, Mountain View, CA, United States
| | - Kevin C Lee
- School of Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Stephen D J Archer
- School of Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Nathalie Cabrol
- NASA Ames Research Center, Mountain View, CA, United States.,The SETI Institute, Mountain View, CA, United States
| | - Linda Ng-Boyle
- College of Engineering, University of Washington, Seattle, WA, United States
| | - David Wettergreen
- Institute of Robotics, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Kris Zacny
- Honeybee Robotics Spacecraft Mechanisms Corp., Pasadena, CA, United States
| | - Stephen B Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Maza F, Maldonado J, Vásquez-Dean J, Mandakovic D, Gaete A, Cambiazo V, González M. Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability. Front Bioeng Biotechnol 2019; 7:10. [PMID: 30805333 PMCID: PMC6371850 DOI: 10.3389/fbioe.2019.00010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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Affiliation(s)
- Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Javiera Vásquez-Dean
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
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Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep 2019; 9:1042. [PMID: 30705356 PMCID: PMC6355873 DOI: 10.1038/s41598-018-37776-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 12/12/2018] [Indexed: 12/23/2022] Open
Abstract
The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1426-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Hahn MW, Koll U, Schmidt J. Isolation and Cultivation of Bacteria. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2019. [DOI: 10.1007/978-3-030-16775-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Orellana R, Macaya C, Bravo G, Dorochesi F, Cumsille A, Valencia R, Rojas C, Seeger M. Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation. Front Microbiol 2018; 9:2309. [PMID: 30425685 PMCID: PMC6218600 DOI: 10.3389/fmicb.2018.02309] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., Methanofollis tationis from Tatio Geyser), acidophiles (e.g., Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum from Atacama Desert and Central Chile copper ores), halophiles (e.g., Shewanella sp. Asc-3 from Altiplano, Streptomyces sp. HKF-8 from Patagonia), alkaliphiles (Exiguobacterium sp. SH31 from Altiplano), xerotolerant bacteria (S. atacamensis from Atacama Desert), UV- and Gamma-resistant bacteria (Deinococcus peraridilitoris from Atacama Desert) and psychrophiles (e.g., Pseudomonas putida ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | - Constanza Macaya
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Guillermo Bravo
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Ricardo Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Claudia Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
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Powers LS, Smith HD, Kilungo AP, Ellis WR, McKay CP, Bonaccorsi R, Roveda JW. In situ real-time quantification of microbial communities: Applications to cold and dry volcanic habitats. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Huang T, Wang R, Xiao L, Wang H, Martínez JM, Escudero C, Amils R, Cheng Z, Xu Y. Dalangtan Playa (Qaidam Basin, NW China): Its microbial life and physicochemical characteristics and their astrobiological implications. PLoS One 2018; 13:e0200949. [PMID: 30067805 PMCID: PMC6070256 DOI: 10.1371/journal.pone.0200949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/04/2018] [Indexed: 01/29/2023] Open
Abstract
Dalangtan Playa is the second largest salt playa in the Qaidam Basin, north-western China. The hyper saline deposition, extremely arid climate and high UV radiation make Dalangtan a Mars analogue both for geomorphology and life preservation. To better understand microbial life at Dalangtan, both culture-dependent and culture-independent methods were examined and simultaneously, environment conditions and the evaporitic mineral assemblages were investigated. Ten and thirteen subsurface samples were collected along a 595-cm deep profile (P1) and a 685-cm deep profile (P2) respectively, and seven samples were gathered from surface sediments. These samples are composed of salt minerals, minor silicate mineral fragments and clays. The total bacterial cell numbers are (1.54±0.49) ×10(5) g-1 for P1 and (3.22±0.95) ×10(5) g-1 for P2 as indicated by the CAtalyzed Reporter Deposition- Fluorescent in situ Hybridization (CARD-FISH). 76.6% and 75.7% of the bacteria belong to Firmicutes phylum respectively from P1 and P2. In total, 47 bacteria and 6 fungi were isolated from 22 subsurface samples. In contrast, only 3 bacteria and 1 fungus were isolated from 3 surface samples. The isolated bacteria show high homology (≥97%) with members of the Firmicutes phylum (47 strains, 8 genera) and the Actinobacteria phylum (3 strains, 2 genera), which agrees with the result of CARD-FISH. Isolated fungi showed ≥98% ITS1 homology with members of the phylum Ascomycota. Moisture content and TOC values may control the sediments colonization. Given the deliquescence of salts, evaporites may provide refuge for microbial life, which merits further investigation. Halotolerant and spore-forming microorganisms are the dominant microbial groups capable of surviving under extreme conditions. Our results offer brand-new information on microbial biomass in Dalangtan Playa and shed light on understanding the potential microbial life in the dried playa or paleo-lakes on Mars.
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Affiliation(s)
- Ting Huang
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Long Xiao
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
- Space Science Institute, Macau University of Science and Technology, Macau, China
- * E-mail: (LX); (HW)
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
- * E-mail: (LX); (HW)
| | - José M. Martínez
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
| | - Cristina Escudero
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Ziye Cheng
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
| | - Yi Xu
- Space Science Institute, Macau University of Science and Technology, Macau, China
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38
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Pershina EV, Ivanova EA, Korvigo IO, Chirak EL, Sergaliev NH, Abakumov EV, Provorov NA, Andronov EE. Investigation of the core microbiome in main soil types from the East European plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1421-1430. [PMID: 29727966 DOI: 10.1016/j.scitotenv.2018.03.136] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 05/12/2023]
Abstract
The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing. Soils of different types varied in the taxonomic composition of microbial communities. Their core microbiomes comprised 47 taxa within the orders Solirubrobacteriales and Hyphomicrobiaceae and the Gaiellaceae family. Two species from Bradyrhizobiaceae and Solirubrobactriaceae were present in all samples, whereas most other taxa were soil-type specific. Multiple resampling analysis revealed that two random soil samples from the same soil type shared more taxa than two samples from different types. The differences in community composition were mostly affected by the variation in pH values and exchangeable potassium content. The results show that data on the soil microbiome could be used for soil identification and clarification of their taxonomic position.
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Affiliation(s)
- Elizaveta V Pershina
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Department of Microbiology, Saint-Petersburg State University, Saint-Petersburg, Russia.
| | - Ekaterina A Ivanova
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Ilia O Korvigo
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny L Chirak
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nurlan H Sergaliev
- West Kazakhstan Agrarian Technical University, Zhangir Khan, Uralsk, Kazakhstan
| | | | - Nikolai A Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
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39
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Perera I, Subashchandrabose SR, Venkateswarlu K, Naidu R, Megharaj M. Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota. Appl Microbiol Biotechnol 2018; 102:7351-7363. [PMID: 29982925 DOI: 10.1007/s00253-018-9192-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
Desert ecosystem is generally considered as a lifeless habitat with extreme environmental conditions although it is colonized by extremophilic microorganisms. Cyanobacteria, microalgae, and bacteria in these habitats could tolerate harsh and rapidly fluctuating environmental conditions, intense ultraviolet radiation, and lack of water, leading to cell desiccation. They possess valuable metabolites withstanding extreme environmental conditions and make them good candidates for industrial applications. Moreover, most natural microorganisms in these extreme habitats exist as consortia that provide robustness and extensive metabolic capabilities enabling them to establish important relationships in desert environments. Engineering of such consortia of cyanobacteria, microalgae, and bacteria would be functional in the sustainable development of deserts through improving soil fertility, water preservation, primary production, pollutant removal, and maintaining soil stability. Modern tools and techniques would help in constructing highly functional cyanobacterial/microalgal-bacterial consortia that are greatly useful in the establishment of vegetation in deserts as well as in biotechnological applications.
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Affiliation(s)
- Isiri Perera
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ATC Building, University Drive, Callaghan, Newcastle, NSW, 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ATC Building, University Drive, Callaghan, Newcastle, NSW, 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, Newcastle, NSW, 2308, Australia
| | | | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ATC Building, University Drive, Callaghan, Newcastle, NSW, 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, Newcastle, NSW, 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, ATC Building, University Drive, Callaghan, Newcastle, NSW, 2308, Australia. .,Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, Newcastle, NSW, 2308, Australia.
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40
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Wilhelm MB, Davila AF, Parenteau MN, Jahnke LL, Abate M, Cooper G, Kelly ET, Parro García V, Villadangos MG, Blanco Y, Glass B, Wray JJ, Eigenbrode JL, Summons RE, Warren-Rhodes K. Constraints on the Metabolic Activity of Microorganisms in Atacama Surface Soils Inferred from Refractory Biomarkers: Implications for Martian Habitability and Biomarker Detection. ASTROBIOLOGY 2018; 18:955-966. [PMID: 30035640 DOI: 10.1089/ast.2017.1705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dryness is one of the main environmental challenges to microbial survival. Understanding the threshold of microbial tolerance to extreme dryness is relevant to better constrain the environmental limits of life on Earth and critically evaluate long-term habitability models of Mars. Biomolecular proxies for microbial adaptation and growth were measured in Mars-like hyperarid surface soils in the Atacama Desert that experience only a few millimeters of precipitation per decade, and in biologically active soils a few hundred kilometers away that experience two- to fivefold more precipitation. Diversity and abundance of lipids and other biomolecules decreased with increasing dryness. Cyclopropane fatty acids (CFAs), which are indicative of adaptive response to environmental stress and growth in bacteria, were only detected in the wetter surface soils. The ratio of trans to cis isomers of an unsaturated fatty acid, another bacterial stress indicator, decreased with increasingly dry conditions. Aspartic acid racemization ratios increased from 0.01 in the wetter soils to 0.1 in the driest soils, which is indicative of racemization rates comparable to de novo biosynthesis over long timescales (∼10,000 years). The content and integrity of stress proteins profiled by immunoassays were additional indicators that biomass in the driest soils is not recycled at significant levels. Together, our results point to minimal or no in situ microbial growth in the driest surface soils of the Atacama, and any metabolic activity is likely to be basal for cellular repair and maintenance only. Our data add to a growing body of evidence that the driest Atacama surface soils represent a threshold for long-term habitability (i.e., growth and reproduction). These results place constraints on the potential for extant life on the surface of Mars, which is 100-1000 times drier than the driest regions in the Atacama. Key Words: Atacama Desert-Dryness-Growth-Habitability-Biomarker-Mars. Astrobiology 18, 955-966.
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Affiliation(s)
- Mary Beth Wilhelm
- 1 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | - Alfonso F Davila
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | - Mary N Parenteau
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | - Linda L Jahnke
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | - Mastewal Abate
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | - George Cooper
- 2 Space Science and Astrobiology Division, NASA Ames Research Center , Moffett Field, California
| | | | - Victor Parro García
- 4 Departamento Evolución Molecular, Centro de Astrobiologia (INTA-CSIC) , Madrid, Spain
| | - Miriam G Villadangos
- 4 Departamento Evolución Molecular, Centro de Astrobiologia (INTA-CSIC) , Madrid, Spain
| | - Yolanda Blanco
- 4 Departamento Evolución Molecular, Centro de Astrobiologia (INTA-CSIC) , Madrid, Spain
| | - Brian Glass
- 5 Intelligent Systems Division, NASA Ames Research Center , Moffett Field, California
| | - James J Wray
- 1 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia
| | - Jennifer L Eigenbrode
- 6 Planetary Environments Laboratory, NASA Goddard Space Flight Center , Greenbelt, Maryland
| | - Roger E Summons
- 7 Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts
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41
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Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow M. Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol 2018; 41:427-436. [PMID: 29789182 DOI: 10.1016/j.syapm.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 01/20/2023]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12T and G. obscurus DSM 43160T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12T (CECT 9483T=NCIMB 15089T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.
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Affiliation(s)
- Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | | | - Tara Rahmani
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, United Kingdom
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.
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42
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Ren M, Zhang Z, Wang X, Zhou Z, Chen D, Zeng H, Zhao S, Chen L, Hu Y, Zhang C, Liang Y, She Q, Zhang Y, Peng N. Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin. Front Microbiol 2018; 9:431. [PMID: 29593680 PMCID: PMC5855357 DOI: 10.3389/fmicb.2018.00431] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/26/2018] [Indexed: 11/14/2022] Open
Abstract
Arid and semi-arid regions comprise nearly one-fifth of the earth's terrestrial surface. However, the diversities and functions of their soil microbial communities are not well understood, despite microbial ecological importance in driving biogeochemical cycling. Here, we analyzed the geochemistry and microbial communities of the desert soils from Tarim Basin, northwestern China. Our geochemical data indicated half of these soils are saline. Metagenomic analysis showed that bacterial phylotypes (89.72% on average) dominated the community, with relatively small proportions of Archaea (7.36%) and Eukaryota (2.21%). Proteobacteria, Firmicutes, Actinobacteria, and Euryarchaeota were most abundant based on metagenomic data, whereas genes attributed to Proteobacteria, Actinobacteria, Euryarchaeota, and Thaumarchaeota most actively transcribed. The most abundant phylotypes (Halobacterium, Halomonas, Burkholderia, Lactococcus, Clavibacter, Cellulomonas, Actinomycetospora, Beutenbergia, Pseudomonas, and Marinobacter) in each soil sample, based on metagenomic data, contributed marginally to the population of all microbial communities, whereas the putative halophiles, which contributed the most abundant transcripts, were in the majority of the active microbial population and is consistent with the soil salinity. Sample correlation analyses according to the detected and active genotypes showed significant differences, indicating high diversity of microbial communities among the Tarim soil samples. Regarding ecological functions based on the metatranscriptomic data, transcription of genes involved in various steps of nitrogen cycling, as well as carbon fixation, were observed in the tested soil samples. Metatranscriptomic data also indicated that Thaumarchaeota are crucial for ammonia oxidation and Proteobacteria play the most important role in other steps of nitrogen cycle. The reductive TCA pathway and dicarboxylate-hydroxybutyrate cycle attributed to Proteobacteria and Crenarchaeota, respectively, were highly represented in carbon fixation. Our study reveals that the microbial communities could provide carbon and nitrogen nutrients for higher plants in the sandy saline soils of Tarim Basin.
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Affiliation(s)
- Min Ren
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhufeng Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuelian Wang
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Zhiwei Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Hui Zeng
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lingling Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yuanliang Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Edible Wild Plants Conservation & Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- Department of Biology, Archaeal Centre, University of Copenhagen, Copenhagen, Denmark
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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43
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Corrosion of bare carbon steel as a passive sensor to assess moisture availability for biological activity in Atacama Desert soils. Antonie van Leeuwenhoek 2018; 111:1293-1299. [PMID: 29492771 DOI: 10.1007/s10482-018-1037-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/29/2018] [Indexed: 10/17/2022]
Abstract
Here we consider that the corrosion of polished bared metal coupons can be used as a passive sensor to detect or identify the lower limit of water availability suitable for biological activity in Atacama Desert soils or solid substrates. For this purpose, carbon steel coupons were deposited at selected sites along a west-east transect and removed at predetermined times for morphological inspection. The advantage of this procedure is that the attributes of the oxide layer (corrosion extent, morphology and oxide phases) can be considered as a fingerprint of the atmospheric moisture history at a given time interval. Two types of coupons were used, long rectangular shaped ones that were half-buried in a vertical position, and square shaped ones that were deposited on the soil surface. The morphological attributes observed by SEM inspection were found to correlate to the so-called humectation time which is determined from local meteorological parameters. The main finding was that the decreasing trend of atmospheric moisture along the transect was closely related to corrosion behaviour and water soil penetration. For instance, at the coastal site oxide phases formed on the coupon surface rapidly evolve into well-crystallized species, while at the driest inland site Lomas Bayas only amorphous oxide was observed on the coupons.
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44
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Del Rocío Bustillos-Cristales M, Corona-Gutierrez I, Castañeda-Lucio M, Águila-Zempoaltécatl C, Seynos-García E, Hernández-Lucas I, Muñoz-Rojas J, Medina-Aparicio L, Fuentes-Ramírez LE. Culturable Facultative Methylotrophic Bacteria from the Cactus Neobuxbaumia macrocephala Possess the Locus xoxF and Consume Methanol in the Presence of Ce 3+ and Ca 2. Microbes Environ 2017; 32:244-251. [PMID: 28855445 PMCID: PMC5606694 DOI: 10.1264/jsme2.me17070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5. The sequences included Asp301, the REE-coordinating amino acid, present in all known XoxF dehydrogenases and absent in MxaF methanol dehydrogenases. The quantity of the isolates showed positive hybridization with a xoxF probe, but not with a mxaF probe. Isolates of all taxonomic groups showed methylotrophic growth in the presence of Ce3+ or Ca2+. The presence of xoxF-like sequences in methylotrophic bacteria from N. macrocephala and its potential relationship with their adaptability to xerophytic plants are discussed.
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45
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Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B. The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity. Annu Rev Microbiol 2017; 70:215-34. [PMID: 27607552 DOI: 10.1146/annurev-micro-102215-095236] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom;
| | - Juan A Asenjo
- Center for Biotechnology and Bioengineering, University of Chile, Santiago, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile;
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;
| | - Benito Gómez-Silva
- Biochemistry Laboratory, Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Chile;
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46
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Pulschen AA, Bendia AG, Fricker AD, Pellizari VH, Galante D, Rodrigues F. Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media. Front Microbiol 2017; 8:1346. [PMID: 28769908 PMCID: PMC5509766 DOI: 10.3389/fmicb.2017.01346] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
Uncultured microorganisms comprise most of the microbial diversity existing on our planet. Despite advances in environmental sequencing and single-cell genomics, in-depth studies about bacterial metabolism and screening of novel bioproducts can only be assessed by culturing microbes in the laboratory. Here we report uncultured, or recalcitrant, microorganisms from an Antarctic soil sample, using relatively simple methods: oligotrophic media, extended incubation periods, observation under stereo microscopy, and selection of slow-growing bacteria. We managed to isolate several rare microorganisms belonging to infrequently isolated or recently described genera, for example Lapillicoccus, Flavitalea, Quadrisphaera, Motilibacter, and Polymorphobacter. Additionally, we obtained isolates presenting 16S rRNA sequence similarity ranging from 92.08 to 94.46% with any other known cultured species, including two distinct isolates from the class Thermoleophilia, that although common in Antarctic soils (as identified by metagenomics), was never reported to be isolated from such samples. Our data indicates that simple methods are still useful for cultivating recalcitrant microorganisms, even when dealing with samples from extreme environments.
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Affiliation(s)
| | - Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | | | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | - Douglas Galante
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e MateriaisCampinas, Brazil
| | - Fabio Rodrigues
- Departamento de Química Fundamental, Instituto de Química, Universidade de São PauloButantã, Brazil
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47
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Azua-Bustos A, González-Silva C, Corsini G. The Hyperarid Core of the Atacama Desert, an Extremely Dry and Carbon Deprived Habitat of Potential Interest for the Field of Carbon Science. Front Microbiol 2017. [PMID: 28642741 PMCID: PMC5463503 DOI: 10.3389/fmicb.2017.00993] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The Atacama Desert in Chile is the driest and oldest desert on Earth, also considered one of the best Mars analog models. Here, several heterotrophic microbial communities have been discovered in its driest regions, with the ones present in the soil subsurface being one of the most interesting due to its existence in a habitat with almost no water available and almost undetectable organic carbon sources. Our recent discovery of the driest site of the Atacama known to date (and the heterotrophic microbial species that are able to survive in this site) reaffirms the opportunity to better characterize the physiological and molecular mechanisms that these species use to detect, mobilize, incorporate and use carbon under these extremely harsh conditions. Here we summarize what has been reported up to date on the organic carbon concentrations in different sites of the hyperarid core of the Atacama Desert, proposing that due to the meager amounts of carbon and extremely dry conditions, the microbial communities of the hyperarid core of the Atacama Desert may be of interest for the field of carbon science.
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Affiliation(s)
- Armando Azua-Bustos
- Centro de Astrobiología (Consejo Superior de Investigaciones Científicas-Instituto Nacional de Técnica Aeroespacial)Madrid, Spain.,Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de ChileSantiago, Chile
| | | | - Gino Corsini
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de ChileSantiago, Chile
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48
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Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems 2017; 2:mSystems00195-16. [PMID: 28593197 PMCID: PMC5451488 DOI: 10.1128/msystems.00195-16] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/03/2017] [Indexed: 02/04/2023] Open
Abstract
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. Global deserts occupy one-third of the Earth’s surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman’s rank correlation [rs] = >0.81; false-discovery rate [q] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE 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.
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Lacap-Bugler DC, Lee KK, Archer S, Gillman LN, Lau MCY, Leuzinger S, Lee CK, Maki T, McKay CP, Perrott JK, de Los Rios-Murillo A, Warren-Rhodes KA, Hopkins DW, Pointing SB. Global Diversity of Desert Hypolithic Cyanobacteria. Front Microbiol 2017; 8:867. [PMID: 28559886 PMCID: PMC5432569 DOI: 10.3389/fmicb.2017.00867] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/28/2017] [Indexed: 12/02/2022] Open
Abstract
Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts.
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Affiliation(s)
- Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Kevin K Lee
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Stephen Archer
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Len N Gillman
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, PrincetonNJ, USA
| | - Sebastian Leuzinger
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of WaikatoHamilton, New Zealand
| | - Teruya Maki
- Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
| | - Christopher P McKay
- National Aeronautics and Space Administration Ames Research Center, Moffett FieldCA, USA
| | - John K Perrott
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | | | | | | | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand.,Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
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Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, Knight R, Gilbert JA, Quade J, Caporaso JG, Maier RM. Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems 2017. [PMID: 28593197 DOI: 10.1128/msystems.00195-16/suppl_file/sys003172106st5.pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman's rank correlation [rs] = >0.81; false-discovery rate [q] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE 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.
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Affiliation(s)
- Julia W Neilson
- Department of Soil Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Katy Califf
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Audrey Copeland
- Department of Soil Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Will van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Karen L Josephson
- Department of Soil Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering and Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Jay Quade
- Department of Geosciences, University of Arizona, Tucson, Arizona, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Raina M Maier
- Department of Soil Water and Environmental Science, University of Arizona, Tucson, Arizona, USA
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