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Bosch J, Lebre PH, Marais E, Maggs‐Kölling G, Cowan DA. Kinetics and pathways of sub-lithic microbial community (hypolithon) development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13290. [PMID: 38923208 PMCID: PMC11194044 DOI: 10.1111/1758-2229.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
- Institute of Microbiology of the Czech Academy of SciencesCzech Academy of SciencesPrahaCzech Republic
| | - Pedro H. Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
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James N, Adkinson A, Mast A. Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11547. [PMID: 37915433 PMCID: PMC10617317 DOI: 10.1002/aps3.11547] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/31/2023] [Accepted: 04/16/2023] [Indexed: 11/03/2023]
Abstract
Premise We recognized the need for a customized imaging protocol for plant specimens at the time of collection for the purpose of three-dimensional (3D) modeling, as well as the lack of a broadly applicable photogrammetry protocol that encompasses the heterogeneity of plant specimen geometries and the challenges introduced by processes such as wilting. Methods and Results We developed an equipment list and set of detailed protocols describing how to capture images of plant specimens in the field prior to their deformation (e.g., with pressing) and how to produce a 3D model from the image sets in Agisoft Metashape Professional. Conclusions The equipment list and protocols represent a foundation on which additional improvements can be made for specimen geometries outside of the range of the six types considered, and an easy entry into photogrammetry for those who have not previously used it.
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Affiliation(s)
- Nicole James
- Department of ArtFlorida State University540 West Call StreetTallahassee32301FloridaUSA
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
| | - Alex Adkinson
- Department of ArtFlorida State University540 West Call StreetTallahassee32301FloridaUSA
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
| | - Austin Mast
- Institute for Digital Information and Scientific Communication (iDigInfo)Florida State University142 Collegiate LoopTallahassee32306FloridaUSA
- Department of Biological ScienceFlorida State University319 Stadium DriveTallahassee32306FloridaUSA
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Cowan DA, Cary SC, DiRuggiero J, Eckardt F, Ferrari B, Hopkins DW, Lebre PH, Maggs-Kölling G, Pointing SB, Ramond JB, Tribbia D, Warren-Rhodes K. 'Follow the Water': Microbial Water Acquisition in Desert Soils. Microorganisms 2023; 11:1670. [PMID: 37512843 PMCID: PMC10386458 DOI: 10.3390/microorganisms11071670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.
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Affiliation(s)
- Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - S Craig Cary
- School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand
| | - Jocelyne DiRuggiero
- Departments of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Frank Eckardt
- Department of Environmental and Geographical Science, University of Cape Town, Cape Town 7701, South Africa
| | - Belinda Ferrari
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh EH9 3JG, UK
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | | | - Stephen B Pointing
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Dana Tribbia
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Kidron GJ, Kronenfeld R, Tal SY, Temina M, Starinsky A, McKay CP. The effect of the water source on niche partioning of chlorolichens and cyanobacteria-implications for resilience? PLANTA 2023; 258:8. [PMID: 37227529 DOI: 10.1007/s00425-023-04165-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023]
Abstract
MAIN CONCLUSION Microclimate determines lichens and cyanobacteria distribution in the Negev, with lichens and cyanobacteria inhabit dewy and dewless habitats, respectively. Lichens experiences more frequent and extensive environmental fluctuations than cyanobacteria. The spatial partitioning of chlorolichens (eukaryotes) and cyanobacteria (prokaryotes) are intriguing, especially following recent intense search for extraterrestrial life. This is especially relevant for deserts, where both lithobionts are thought to use rain and dew but may differ in their resilience to environmental extremes and fluctuations. Following the different spatial distribution of lithobionts in a south-facing slope of the Negev Highlands (with cyanobacteria-inhabiting rocks and chlorolichen-inhabiting cobbles), measurements of temperature, non-rainfall water (NRW) and biomass were carried out within the drainage basin aiming to test the hypotheses that (i) cobble-inhabiting lichens may access more water (through NRW) and may be subjected to more extensive environmental fluctuations of temperature and water than bedrock-inhabiting cyanobacteria, and (ii) will therefore have a greater contribution to the ecosystem productivity. In contrast to cyanobacteria, cobble-inhabiting chlorolichens were found to access NRW (up to 0.20 mm of daily amounts in comparison to < 0.04 mm of the cyanobacteria) and to experience higher fluctuations of temperatures (up to 4.1 °C higher and 5.3 °C lower). With lichens and cyanobacteria inhabiting dewy and dewless habitats, respectively, NRW was found responsible for contributing 6.8-fold higher organic carbon to the lithobiontic community. At this site, chlorolichens experience more extensive environmental fluctuations than cyanobacteria, possibly indicating a higher tolerance for environmental fluctuations. These observations may assist in the interpretation of the abiotic conditions responsible for past or present lithobiontic life on Mars.
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Affiliation(s)
- Giora J Kidron
- Institute of Earth Sciences, The Hebrew University, 91904, Jerusalem, Israel.
| | - Rafael Kronenfeld
- Meteorological Unit, Israel Meteorological Service, 84993, Kibbutz Sde Boker, Israel
| | - Shimon Y Tal
- Sheshet Company LTD, 5 Mevo Rimon, 91043, Mevaseret Zion, Israel
| | - Marina Temina
- Institute of Evolution, University of Haifa, Mount Carmel, 3498838, Haifa, Israel
| | - Abraham Starinsky
- Institute of Earth Sciences, The Hebrew University, 91904, Jerusalem, Israel
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de Los Ríos A, Garrido-Benavent I, Limón A, Cason ED, Maggs-Kölling G, Cowan D, Valverde A. Novel lichen-dominated hypolithic communities in the Namib Desert. MICROBIAL ECOLOGY 2022; 83:1036-1048. [PMID: 34312709 PMCID: PMC9015988 DOI: 10.1007/s00248-021-01812-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.
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Affiliation(s)
- Asunción de Los Ríos
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain.
| | - Isaac Garrido-Benavent
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València (UV), C. Doctor Moliner 50, 46100, Burjassot, València, Spain
| | - Alicia Limón
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Errol D Cason
- Department of Animal Science, University of the Free State, Bloemfontein, South Africa
| | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008, Salamanca, Spain
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Estimating Net Photosynthesis of Biological Soil Crusts in the Atacama Using Hyperspectral Remote Sensing. REMOTE SENSING 2018. [DOI: 10.3390/rs10060891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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