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Duan Y, Li Y, Zhao J, Zhang J, Luo C, Jia R, Liu X. Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China. MICROBIAL ECOLOGY 2024; 87:43. [PMID: 38363394 PMCID: PMC10873229 DOI: 10.1007/s00248-024-02359-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.
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Affiliation(s)
- Yulong Duan
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, 730000, China
| | - Yuqiang Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Strategic Mineral Resources of the Upper Yellow River, Ministry of Natural Resources, Lanzhou, 730000, China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Junbiao Zhang
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Chun Luo
- Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai, 200120, China
| | - Rongliang Jia
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Zhongwei, 755007, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xinping Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, 028300, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ding Y, Geng Y, Zhou W, Li D. Habitat-specific environmental factors regulate the spatial variability of biological soil crust microbial communities on the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165937. [PMID: 37532035 DOI: 10.1016/j.scitotenv.2023.165937] [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: 05/30/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/04/2023]
Abstract
Biological soil crusts (BSCs) are an important biological component of the soil surface, covering approximately 12 % of the Earth's land surface. Although BSCs are closely related to habitats, the microbial diversity and spatial variability of BSCs in different ecosystems are still unclear, especially on the Qinghai-Tibet Plateau (QTP), where climate is changeable and habitats are complex. Here, we investigated the diversity, assembly processes, spatial distribution pattern and driving factors of prokaryotic and eukaryotic microbial communities in BSCs in four habitats on the QTP. It was found that habitat-specific environmental factors regulated the composition, diversity and spatial variability of BSC microbial communities. Soil organic carbon and soil water content were the most important factors (R2 = 0.9024, P = 0.001; R2 = 0.8004, P = 0.001) affecting the spatial differences in prokaryotes and eukaryotes, respectively. Under the specific climate of the QTP, the spatial pattern of microbial communities in BSCs was controlled by precipitation rather than temperature. In addition, ecological processes further explained the effects of habitat specificity, and environmental filtering explained microbial community differences better than dispersal limitation. The results of the neutral community model and the normalized stochastic ratio index revealed that the assembly of prokaryotic communities was determined by deterministic processes at the regional scale, and at the local scale, the assembly process was mainly determined by habitat type, while the assembly of eukaryotic communities was determined by stochastic processes at both the regional and local scales. This study provided a scientific reference for the prediction of BSC distribution and resource conservation under future climate change scenarios.
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Affiliation(s)
- Yuang Ding
- School of Ecology and Environment, Tibet University, Lhasa 850001, PR China; Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuchen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weicheng Zhou
- School of Chemistry and Environmental Science, Xiangnan University, Chenzhou 423000, PR China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Abstract
Biological soil crusts are thin, inconspicuous communities along the soil atmosphere ecotone that, until recently, were unrecognized by ecologists and even more so by microbiologists. In its broadest meaning, the term biological soil crust (or biocrust) encompasses a variety of communities that develop on soil surfaces and are powered by photosynthetic primary producers other than higher plants: cyanobacteria, microalgae, and cryptogams like lichens and mosses. Arid land biocrusts are the most studied, but biocrusts also exist in other settings where plant development is constrained. The minimal requirement is that light impinge directly on the soil; this is impeded by the accumulation of plant litter where plants abound. Since scientists started paying attention, much has been learned about their microbial communities, their composition, ecological extent, and biogeochemical roles, about how they alter the physical behavior of soils, and even how they inform an understanding of early life on land. This has opened new avenues for ecological restoration and agriculture.
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Affiliation(s)
- Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, Arizona, USA;
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Hansen FA, James DK, Anderson JP, Meredith CS, Dominguez AJ, Pombubpa N, Stajich JE, Romero-Olivares AL, Salley SW, Pietrasiak N. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert. Front Microbiol 2023; 14:1135800. [PMID: 37350785 PMCID: PMC10282155 DOI: 10.3389/fmicb.2023.1135800] [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: 01/01/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.
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Affiliation(s)
- Frederick A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Darren K. James
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | - John P. Anderson
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | | | - Andrew J. Dominguez
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | | | - Shawn W. Salley
- U.S. Department of Agriculture-Natural Resources Conservation Service, Jornada Experimental Range, Las Cruces, NM, United States
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere. Microorganisms 2022; 10:microorganisms10061252. [PMID: 35744770 PMCID: PMC9230428 DOI: 10.3390/microorganisms10061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/17/2022] [Indexed: 12/10/2022] Open
Abstract
How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities.
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Glaser K, Van AT, Pushkareva E, Barrantes I, Karsten U. Microbial Communities in Biocrusts Are Recruited From the Neighboring Sand at Coastal Dunes Along the Baltic Sea. Front Microbiol 2022; 13:859447. [PMID: 35783389 PMCID: PMC9245595 DOI: 10.3389/fmicb.2022.859447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022] Open
Abstract
Biological soil crusts occur worldwide as pioneer communities stabilizing the soil surface. In coastal primary sand dunes, vascular plants cannot sustain due to scarce nutrients and the low-water-holding capacity of the sand sediment. Thus, besides planted dune grass, biocrusts are the only vegetation there. Although biocrusts can reach high coverage rates in coastal sand dunes, studies about their biodiversity are rare. Here, we present a comprehensive overview of the biodiversity of microorganisms in such biocrusts and the neighboring sand from sampling sites along the Baltic Sea coast. The biodiversity of Bacteria, Cyanobacteria, Fungi, and other microbial Eukaryota were assessed using high-throughput sequencing (HTS) with a mixture of universal and group-specific primers. The results showed that the biocrusts recruit their microorganisms mainly from the neighboring sand rather than supporting a universal biocrust microbiome. Although in biocrusts the taxa richness was lower than in sand, five times more co-occurrences were identified using network analysis. This study showed that by comparing neighboring bare surface substrates with biocrusts holds the potential to better understand biocrust development. In addition, the target sequencing approach helps outline potential biotic interactions between different microorganisms groups and identify key players during biocrust development.
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Affiliation(s)
- Karin Glaser
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
- *Correspondence: Karin Glaser
| | - Ahn Tu Van
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ekaterina Pushkareva
- Department of Biology, Botanical Institute, University of Cologne, Cologne, Germany
| | - Israel Barrantes
- Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Ulf Karsten
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
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7
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Weber B, Belnap J, Büdel B, Antoninka AJ, Barger NN, Chaudhary VB, Darrouzet-Nardi A, Eldridge DJ, Faist AM, Ferrenberg S, Havrilla CA, Huber-Sannwald E, Malam Issa O, Maestre FT, Reed SC, Rodriguez-Caballero E, Tucker C, Young KE, Zhang Y, Zhao Y, Zhou X, Bowker MA. What is a biocrust? A refined, contemporary definition for a broadening research community. Biol Rev Camb Philos Soc 2022; 97:1768-1785. [PMID: 35584903 PMCID: PMC9545944 DOI: 10.1111/brv.12862] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/22/2022]
Abstract
Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as ‘biocrust’, it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. In this review, we synthesize the literature with the views of new and experienced biocrust researchers, to provide a refined and fully elaborated definition of biocrusts. In doing so, we illustrate the ecological relevance and ecosystem services provided by them. We demonstrate that biocrusts are defined by four distinct elements: physical structure, functional characteristics, habitat, and taxonomic composition. We describe outgroups, which have some, but not all, of the characteristics necessary to be fully consistent with our definition and thus would not be considered biocrusts. We also summarize the wide variety of different types of communities that fall under our definition of biocrusts, in the process of highlighting their global distribution. Finally, we suggest the universal use of the Belnap, Büdel & Lange definition, with minor modifications: Biological soil crusts (biocrusts) result from an intimate association between soil particles and differing proportions of photoautotrophic (e.g. cyanobacteria, algae, lichens, bryophytes) and heterotrophic (e.g. bacteria, fungi, archaea) organisms, which live within, or immediately on top of, the uppermost millimetres of soil. Soil particles are aggregated through the presence and activity of these often extremotolerant biota that desiccate regularly, and the resultant living crust covers the surface of the ground as a coherent layer. With this detailed definition of biocrusts, illustrating their ecological functions and widespread distribution, we hope to stimulate interest in biocrust research and inform various stakeholders (e.g. land managers, land users) on their overall importance to ecosystem and Earth system functioning.
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Affiliation(s)
- Bettina Weber
- Division of Plant Sciences, Institute for Biology, University of Graz, Holteigasse 6, 8010, Graz, Austria.,Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - Jayne Belnap
- Southwest Biological Science Center, U.S. Geological Survey, 2290 S. Resource Blvd, Moab, UT, 84532, USA
| | - Burkhard Büdel
- Biology Institute, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Anita J Antoninka
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
| | - Nichole N Barger
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Campus Box 334, Boulder, CO, 80309, USA
| | - V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, 6182 Steele Hall, 39 College Street, Hanover, NH, 03755, USA
| | - Anthony Darrouzet-Nardi
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79968, USA
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Akasha M Faist
- Department of Animal and Range Sciences, New Mexico State University, PO Box 30003, MSC 3-I, Las Cruces, NM, 88003, USA
| | - Scott Ferrenberg
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA
| | - Caroline A Havrilla
- Department of Forest and Rangeland Stewardship, Colorado State University, 1472 Campus Delivery, Colorado State University, Fort Collins, CO, 80521, USA
| | - Elisabeth Huber-Sannwald
- Division of Environmental Sciences, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Col. 4ta Sección, CP 78216, San Luis Potosi, SLP, Mexico
| | - Oumarou Malam Issa
- Institute of Ecology and Environmental Sciences of Paris (IEES-Paris), SU/IRD/CNRS/INRAE/UPEC, 32, Avenue Henry Varagnat, F-93143, Bondy Cedex, France
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Spain.,Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Spain
| | - Sasha C Reed
- Southwest Biological Science Center, U.S. Geological Survey, 2290 S. Resource Blvd, Moab, UT, 84532, USA
| | - Emilio Rodriguez-Caballero
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany.,Department of Agronomy and Centro de Investigación de Colecciones Científicas (CECOUAL), Universidad de Almería, carretera Sacramento s/n, 04120, La cañada de San Urbano, Almeria, Spain
| | - Colin Tucker
- USDA Forest Service, Northern Research Station, 410 MacInnes Drive, Houghton, MI, 49931-1134, USA
| | - Kristina E Young
- Extension Agriculture and Natural Resources, Utah State University, 1850 S. Aggie Blvd, Moab, UT, 84532, USA
| | - Yuanming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Bejing Road, Urumqi City, 830011, Xinjiang, China
| | - Yunge Zhao
- Institute of Soil and Water Conservation, Northwest A & F University, 26 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Bejing Road, Urumqi City, 830011, Xinjiang, China
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
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Glaser K, Albrecht M, Baumann K, Overmann J, Sikorski J. Biological Soil Crust From Mesic Forests Promote a Specific Bacteria Community. Front Microbiol 2022; 13:769767. [PMID: 35369523 PMCID: PMC8966483 DOI: 10.3389/fmicb.2022.769767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/19/2022] [Indexed: 12/03/2022] Open
Abstract
Biological soil crusts (biocrusts) harbor a diverse community of various microorganisms with microalgae as primary producers and bacteria living in close association. In mesic regions, biocrusts emerge rapidly on disturbed surface soil in forest, typically after clear-cut or windfall. It is unclear whether the bacterial community in biocrusts is similar to the community of the surrounding soil or if biocrust formation promotes a specific bacterial community. Also, many of the interactions between bacteria and algae in biocrusts are largely unknown. Through high-throughput-sequencing analysis of the bacterial community composition, correlated drivers, and the interpretation of biological interactions in a biocrust of a forest ecosystem, we show that the bacterial community in the biocrust represents a subset of the community of the neighboring soil. Bacterial families connected with degradation of large carbon molecules, like cellulose and chitin, and the bacterivore Bdellovibrio were more abundant in the biocrust compared to bulk soil. This points to a closer interaction and nutrient recycling in the biocrust compared to bulk soil. Furthermore, the bacterial richness was positively correlated with the content of mucilage producing algae. The bacteria likely profit from the mucilage sheaths of the algae, either as a carbon source or protectant from grazing or desiccation. Comparative sequence analyses revealed pronounced differences between the biocrust bacterial microbiome. It seems that the bacterial community of the biocrust is recruited from the local soil, resulting in specific bacterial communities in different geographic regions.
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Affiliation(s)
- Karin Glaser
- Applied Ecology and Phycology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Martin Albrecht
- Applied Ecology and Phycology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Karen Baumann
- Department of Soil Science, Faculty of Agricultural and Environmental Science, University of Rostock, Rostock, Germany
| | - Jörg Overmann
- Department of Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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9
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Barrera A, Acuña-Rodríguez IS, Ballesteros GI, Atala C, Molina-Montenegro MA. Biological Soil Crusts as Ecosystem Engineers in Antarctic Ecosystem. Front Microbiol 2022; 13:755014. [PMID: 35391734 PMCID: PMC8981465 DOI: 10.3389/fmicb.2022.755014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 01/11/2022] [Indexed: 01/04/2023] Open
Abstract
Biological soil crusts (BSC) are considered as pivotal ecological elements among different ecosystems of the world. The effects of these BSC at the micro-site scale have been related to the development of diverse plant species that, otherwise, might be strongly limited by the harsh abiotic conditions found in environments with low water availability. Here, we describe for the first time the bacterial composition of BSCs found in the proximities of Admiralty Bay (Maritime Antarctica) through 16S metabarcoding. In addition, we evaluated their effect on soils (nutrient levels, enzymatic activity, and water retention), and on the fitness and performance of Colobanthus quitensis, one of the two native Antarctic vascular plants. This was achieved by comparing the photochemical performance, foliar nutrient, biomass, and reproductive investment between C. quitensis plants growing with or without the influence of BSC. Our results revealed a high diversity of prokaryotes present in these soil communities, although we found differences in terms of their abundances. We also found that the presence of BSCs is linked to a significant increase in soils' water retention, nutrient levels, and enzymatic activity when comparing with control soils (without BSCs). In the case of C. quitensis, we found that measured ecophysiological performance parameters were significantly higher on plants growing in association with BSCs. Taken together, our results suggest that BSCs in Antarctic soils are playing a key role in various biochemical processes involved in soil development, while also having a positive effect on the accompanying vascular flora. Therefore, BSCs would be effectively acting as ecosystem engineers for the terrestrial Antarctic ecosystem.
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Affiliation(s)
- Andrea Barrera
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | | | - Cristian Atala
- Facultad de Ciencias, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Marco A. Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Facultad de Ciencias del Mar, Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile
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Yang H, Hu C. Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau. MICROBIAL ECOLOGY 2022; 83:100-113. [PMID: 33733304 DOI: 10.1007/s00248-021-01734-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl-, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl-. Chlorophyceae and Bacillariophyceae were positively correlated with CO32-. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.
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Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Microbial Diversity in Subarctic Biocrusts from West Iceland following an Elevation Gradient. Microorganisms 2021; 9:microorganisms9112195. [PMID: 34835321 PMCID: PMC8624075 DOI: 10.3390/microorganisms9112195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/16/2022] Open
Abstract
Biological soil crusts (biocrusts) are essential communities of organisms in the Icelandic soil ecosystem, as they prevent erosion and cryoturbation and provide nutrients to vascular plants. However, biocrust microbial composition in Iceland remains understudied. To address this gap in knowledge, we applied high-throughput sequencing to study microbial community composition in biocrusts collected along an elevation gradient (11–157 m a.s.l.) stretching away perpendicular to the marine coast. Four groups of organisms were targeted: bacteria and cyanobacteria (16S rRNA gene), fungi (transcribed spacer region), and other eukaryotes (18S rRNA gene). The amplicon sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Within the cyanobacteria, filamentous forms from the orders Synechococcales and Oscillatoriales prevailed. Furthermore, fungi in the biocrusts were dominated by Ascomycota, while the majority of reads obtained from sequencing of the 18S rRNA gene belonged to Archaeplastida. In addition, microbial photoautotrophs isolated from the biocrusts were assigned to the cyanobacterial genera Phormidesmis, Microcoleus, Wilmottia, and Oscillatoria and to two microalgal phyla Chlorophyta and Charophyta. In general, the taxonomic diversity of microorganisms in the biocrusts increased following the elevation gradient and community composition differed among the sites, suggesting that microclimatic and soil parameters might shape biocrust microbiota.
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Del Moral Á, Garrido-Benavent I, Durán J, Lehmann JR, Rodríguez A, Heiðmarsson S, de Los Ríos A. Are recently deglaciated areas at both poles colonised by the same bacteria? FEMS Microbiol Lett 2021; 368:6122588. [PMID: 33507249 DOI: 10.1093/femsle/fnab011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 01/05/2023] Open
Abstract
Polar glacier forefields offer an unprecedented framework for studying community assembly processes in regions that are geographically and climatically isolated. Through amplicon sequence variant (ASV) inference, we compared the composition and structure of soil bacterial communities from glacier forefields in Iceland and Antarctica to assess overlap between communities and the impact of established cryptogamic covers on the uniqueness of their taxa. These pioneer microbial communities were found to share only 8% of ASVs and each taxonomic group's contribution to the shared ASV data subset was heterogeneous and independent of their relative abundance. Although the presence of ASVs specific to one glacier forefield and/or different cryptogam cover values confirms the existence of habitat specialist bacteria, our data show that the influence of cryptogams on the edaphic bacterial community structure also varied also depending on the taxonomic group. Hence, the establishment of distinct cryptogamic covers is probably not the only factor driving the uniqueness of bacterial communities at both poles. The structure of bacterial communities colonising deglaciated areas seems also conditioned by lineage-specific limitations in their dispersal capacity and/or their establishment and persistence in these isolated and hostile regions.
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Affiliation(s)
- Álvaro Del Moral
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain.,AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, STEM Faculty, The Open University, Walton Hall, Kents Hill, MK7 6AA, Milton Keynes, UK
| | - Isaac Garrido-Benavent
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain
| | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calzada Martin de Freitas, 3000-456 Coimbra, Portugal
| | - Jan R Lehmann
- Remote Sensing and Spatial Modelling, Institute of Landscape Ecology, University of Münster, Heisenbergstrasse 2, 48149 Münster, Germany
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calzada Martin de Freitas, 3000-456 Coimbra, Portugal
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Borgir vio Noroursloo 600-Akureyri, Iceland
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain
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Abstract
Oman is a desert country in the south of the Middle East. Springs and other water sources that harbor aquatic organisms can be separated by hundreds of kilometers. In Oct 2019, we isolated four freshwater aquatic fungi (Chytridiomycota) from benthic detritus baited with pine pollen on a general nutrient medium near Salalah, Oman. Database queries of nuc 28S rRNA (28S) and internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) revealed that one of these strains was Dinochytrium kinnereticum, a recently described algal pathogen from the Sea of Galilee. The other three strains had low molecular identity to available ITS sequences. These unknown strains varied in size and released endogenously swarming zoospores through papillae from mature zoosporangia. Zoospore ultrastructure was consistent with described species in the Rhizophydiales, and molecular phylogenetic results grouped these three strains into a clade in the genus Rhizophydium. We circumscribe these three strains as a sp. nov., thereby expanding the diversity within Rhizophydium described as the new species R. jobii. In doing so, we provide the first report of Chytridiomycota from Oman.
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Affiliation(s)
- Brandon T Hassett
- UiT-The Arctic University of Norway , Framstredet 6, Tromsø 9019, Norway
| | - Badriya K Al-Shaibi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
| | - Abdulrahman Al-Nabhani
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University , P.O. Box-34, Al-Khod 123, Oman
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Su YG, Liu J, Zhang BC, Zhao HM, Huang G. Habitat-specific environmental factors regulate spatial variability of soil bacterial communities in biocrusts across northern China's drylands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 719:137479. [PMID: 32135332 DOI: 10.1016/j.scitotenv.2020.137479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Biocrusts are common biotic components in dryland ecosystems worldwide, they contain diverse soil organisms and effectively enhance soil stability and perform a series of key ecological functions. However, the geographical pattern of microbial communities in biocrusts is rarely assessed, despite it is closely related to the spatial variation of ecosystem functions in drylands. We assessed soil bacterial communities in biocrusts across four ecosystems (Gobi, desert, desert steppe and grassland) in a precipitation gradient (16-566 mm yr-1) in northern China. Bacterial OTU number and phylogenetic diversity did not linearly increase with decreasing aridity, they were significantly lower in Gobi and similar among desert, desert steppe and grassland. Soil bacterial community composition in Gobi and desert were different than those in desert steppe and grassland, and they were similar between Gobi and desert, this suggests the key role of habitat in structuring soil bacterial communities. The geographic pattern of soil bacterial communities was strongly influenced by both geographic distance and environmental factors. The first explanatory factor for the geographic variation of bacterial community dissimilarity differed among four ecosystems, being aridity in Gobi and desert, precipitation in desert steppe, and soil inorganic nitrogen in grassland. The geographic pattern of the bacterial functional group profile showed a similar pattern with community composition across four ecosystems, and the groups of containing mobile elements and gram negative bacteria were more abundant in drier habitats of Gobi and desert. Our results reveal the non-linear changes in diversity, composition and functional group of soil bacterial communities in biocrusts across the precipitation gradient from hyper-arid to semi-humid regions, and suggest that the geographic distance and habitat-specific environmental factors determine the distribution of soil bacterial communities in different ecosystems.
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Affiliation(s)
- Yan-Gui Su
- Institute of Geography Science, Fujian Normal University, 8 Shangshan Road, Cang shan District, Fuzhou, Fujian 350007, China
| | - Jie Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, South Beijing Road 818, Urumqi, Xinjiang 830011, China
| | - Bing-Chang Zhang
- College of Geographical Science, Shanxi Normal University, Gongyuan Street 1, Linfeng, Shan'xi 041000, China
| | - Hong-Mei Zhao
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Nongdong Road 311, Urumqi, Xinjiang 830052, China
| | - Gang Huang
- Institute of Geography Science, Fujian Normal University, 8 Shangshan Road, Cang shan District, Fuzhou, Fujian 350007, China.
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Leung PM, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C. Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems. mSystems 2020; 5:e00495-19. [PMID: 32291352 PMCID: PMC7159902 DOI: 10.1128/msystems.00495-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.
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Affiliation(s)
- Pok Man Leung
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Sean K Bay
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Dimitri V Meier
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Eleonora Chiri
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
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Aanderud ZT, Bahr J, Robinson DM, Belnap J, Campbell TP, Gill RA, McMillian B, St. Clair S. The Burning of Biocrusts Facilitates the Emergence of a Bare Soil Community of Poorly-Connected Chemoheterotrophic Bacteria With Depressed Ecosystem Services. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Villa F, Cappitelli F. The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments. Microorganisms 2019; 7:microorganisms7100380. [PMID: 31547498 PMCID: PMC6843906 DOI: 10.3390/microorganisms7100380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
The ecological relationship between minerals and microorganisms arguably represents one of the most important associations in dry terrestrial environments, since it strongly influences major biochemical cycles and regulates the productivity and stability of the Earth’s food webs. Despite being inhospitable ecosystems, mineral substrata exposed to air harbor form complex and self-sustaining communities called subaerial biofilms (SABs). Using life on air-exposed minerals as a model and taking inspiration from the mechanisms of some microorganisms that have adapted to inhospitable conditions, we illustrate the ecology of SABs inhabiting natural and built environments. Finally, we advocate the need for the convergence between the experimental and theoretical approaches that might be used to characterize and simulate the development of SABs on mineral substrates and SABs’ broader impacts on the dry terrestrial environment.
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Affiliation(s)
- Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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