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Horstmann L, Lipus D, Bartholomäus A, Arens F, Airo A, Ganzert L, Zamorano P, Schulze-Makuch D, Wagner D. Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis. PNAS NEXUS 2024; 3:pgae123. [PMID: 38655503 PMCID: PMC11037274 DOI: 10.1093/pnasnexus/pgae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.
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Affiliation(s)
- Lucas Horstmann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, 37073 Göttingen, Germany
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Felix Arens
- Zentrum für Astronomie und Astrophysik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alessandro Airo
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Lars Ganzert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, University of Antofagasta, Antofagasta 02800, Chile
| | - Dirk Schulze-Makuch
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Zentrum für Astronomie und Astrophysik, Technische Universität Berlin, 10623 Berlin, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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Rodríguez V, Bartholomäus A, Witzgall K, Riveras-Muñoz N, Oses R, Liebner S, Kallmeyer J, Rach O, Mueller CW, Seguel O, Scholten T, Wagner D. Microbial impact on initial soil formation in arid and semiarid environments under simulated climate change. Front Microbiol 2024; 15:1319997. [PMID: 38298893 PMCID: PMC10827993 DOI: 10.3389/fmicb.2024.1319997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence for its relevance is scarce. To fill this gap, we investigated the impact of in situ microbial communities and their interrelationship with biocrust and plants compared to abiotic controls on soil formation in initial arid and semiarid soils. Additionally, we assessed the response of bacterial communities to climate change. Topsoil and subsoil samples from arid and semiarid sites in the Chilean Coastal Cordillera were incubated for 16 weeks under diurnal temperature and moisture variations to simulate humid climate conditions as part of a climate change scenario. Our findings indicate that microorganism-plant interaction intensified aggregate formation and stabilized soil structure, facilitating initial soil formation. Interestingly, microorganisms alone or in conjunction with biocrust showed no discernible patterns compared to abiotic controls, potentially due to water-masking effects. Arid soils displayed reduced bacterial diversity and developed a new community structure dominated by Proteobacteria, Actinobacteriota, and Planctomycetota, while semiarid soils maintained a consistently dominant community of Acidobacteriota and Proteobacteria. This highlighted a sensitive and specialized bacterial community in arid soils, while semiarid soils exhibited a more complex and stable community. We conclude that microorganism-plant interaction has measurable impacts on initial soil formation in arid and semiarid regions on short time scales under climate change. Additionally, we propose that soil and climate legacies are decisive for the present soil microbial community structure and interactions, future soil development, and microbial responses.
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Affiliation(s)
- Victoria Rodríguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | | | - Kristina Witzgall
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, Tübingen, Germany
| | - Romulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copiapó, Chile
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Oliver Rach
- GFZ German Research Centre for Geosciences, Section Geomorphology, Potsdam, Germany
| | - Carsten W. Mueller
- Institute for Ecology, Chair of Soil Science, Technische Universitaet Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, Tübingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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Martin-Pozas T, Fernandez-Cortes A, Cuezva S, Cañaveras JC, Benavente D, Duarte E, Saiz-Jimenez C, Sanchez-Moral S. New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165218. [PMID: 37419360 DOI: 10.1016/j.scitotenv.2023.165218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | | | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, Campus Cientifico-Tecnologico, 28802 Alcala de Henares, Spain.
| | - Juan Carlos Cañaveras
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Elsa Duarte
- Department of History, University of Oviedo, 33011 Oviedo, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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McClure R. Editorial for Special Issue "Advances in Soil Microbiome". Microorganisms 2023; 11:2026. [PMID: 37630586 PMCID: PMC10459778 DOI: 10.3390/microorganisms11082026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The soil microbiome (the community of all soil microorganisms and their surrounding environment) is a critical part of our ecological network [...].
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Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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