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Ghezzi D, Jiménez-Morillo NT, Foschi L, Donini E, Chiarini V, De Waele J, Miller AZ, Cappelletti M. The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter. ENVIRONMENTAL MICROBIOME 2024; 19:25. [PMID: 38659019 PMCID: PMC11040949 DOI: 10.1186/s40793-024-00562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Moonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota. RESULTS Three moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development. CONCLUSIONS The moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Nicasio Tomás Jiménez-Morillo
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Pólo da Mitra Apartado 94, Évora, 7006-554, Portugal
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. de la Reina Mercedes, 10, Sevilla, 41012, Spain
| | - Lisa Foschi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Eva Donini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Veronica Chiarini
- Department of Geosciences, University of Padova, via Gradenigo 6, Padua, 35131, Italy
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy
| | - Ana Zélia Miller
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Av. de la Reina Mercedes, 10, Sevilla, 41012, Spain.
- HERCULES Laboratory, University of Évora, Largo dos Colegiais 2, Évora, 7004-516, Portugal.
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy.
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Gutierrez‐Patricio S, Osman JR, Gonzalez‐Pimentel JL, Jurado V, Laiz L, Concepción AL, Saiz‐Jimenez C, Miller AZ. Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13245. [PMID: 38643985 PMCID: PMC11033209 DOI: 10.1111/1758-2229.13245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/15/2024] [Indexed: 04/23/2024]
Abstract
Cueva del Viento, located in the Canary Islands, Spain, is the Earth's sixth-longest lava tube, spanning 18,500 m, and was formed approximately 27,000 years ago. This complex volcanic cave system is characterized by a unique geomorphology, featuring an intricate network of galleries. Despite its geological significance, the geomicrobiology of Cueva del Viento remains largely unexplored. This study employed a combination of culture-dependent techniques and metabarcoding data analysis to gain a comprehensive understanding of the cave's microbial diversity. The 16S rRNA gene metabarcoding approach revealed that the coloured microbial mats (yellow, red and white) coating the cave walls are dominated by the phyla Actinomycetota, Pseudomonadota and Acidobacteriota. Of particular interest is the high relative abundance of the genus Crossiella, which is involved in urease-mediated biomineralization processes, along with the presence of genera associated with nitrogen cycling, such as Nitrospira. Culture-dependent techniques provided insights into the morphological characteristics of the isolated species and their potential metabolic activities, particularly for the strains Streptomyces spp., Paenarthrobacter sp. and Pseudomonas spp. Our findings underscore the potential of Cueva del Viento as an ideal environment for studying microbial diversity and for the isolation and characterization of novel bacterial species of biotechnological interest.
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Affiliation(s)
| | - Jorge R. Osman
- Instituto de Geología Económica Aplicada (GEA)Universidad de ConcepciónConcepciónChile
| | - José Luis Gonzalez‐Pimentel
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
- Laboratorio HERCULESUniversidade de ÉvoraÉvoraPortugal
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | | | - Cesareo Saiz‐Jimenez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | - Ana Zélia Miller
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
- Laboratorio HERCULESUniversidade de ÉvoraÉvoraPortugal
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3
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Turrini P, Chebbi A, Riggio FP, Visca P. The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives. Front Microbiol 2024; 15:1370520. [PMID: 38572233 PMCID: PMC10987966 DOI: 10.3389/fmicb.2024.1370520] [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: 01/14/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.
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Affiliation(s)
- Paolo Turrini
- Department of Science, Roma Tre University, Rome, Italy
| | - Alif Chebbi
- Department of Science, Roma Tre University, Rome, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- National Biodiversity Future Center, Palermo, Italy
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4
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Lange-Enyedi NT, Borsodi AK, Németh P, Czuppon G, Kovács I, Leél-Őssy S, Dobosy P, Felföldi T, Demény A, Makk J. Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves. FEMS Microbiol Ecol 2023; 99:fiad161. [PMID: 38066687 DOI: 10.1093/femsec/fiad161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023] Open
Abstract
The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.
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Affiliation(s)
- Nóra Tünde Lange-Enyedi
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Péter Németh
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
- Research Institute of Biomolecular and Chemical Engineering, Nanolab, University of Pannonia, Egyetem út 10, H-8200 Veszprém, Hungary
| | - György Czuppon
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Ivett Kovács
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Szabolcs Leél-Őssy
- Department of Physical and Applied Geology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Péter Dobosy
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Attila Demény
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Judit Makk
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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5
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Theodorescu M, Bucur R, Bulzu PA, Faur L, Levei EA, Mirea IC, Cadar O, Ferreira RL, Souza-Silva M, Moldovan OT. Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves. MICROBIAL ECOLOGY 2023; 86:2847-2857. [PMID: 37606696 DOI: 10.1007/s00248-023-02286-8] [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: 05/12/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023]
Abstract
Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.
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Affiliation(s)
- Mihail Theodorescu
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania
| | - Ruxandra Bucur
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, 37005, České Budějovice, Czech Republic
| | - Luchiana Faur
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
- Emil Racovita Institute of Speleology, 13 Septembrie 13, 050711, Bucharest, Romania
| | - Erika Andrea Levei
- Research Institute for Analytical Instrumentation subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Donath 67, 400293, Cluj-Napoca, Romania
| | - Ionuț Cornel Mirea
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
- Emil Racovita Institute of Speleology, 13 Septembrie 13, 050711, Bucharest, Romania
| | - Oana Cadar
- Research Institute for Analytical Instrumentation subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Donath 67, 400293, Cluj-Napoca, Romania
| | - Rodrigo Lopes Ferreira
- Centro de Estudos em Biologia Subterrânea, Setor de Biodiversidade Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Campus Universitário, Lavras, Minas Gerais, 37202-553, Brazil
| | - Marconi Souza-Silva
- Centro de Estudos em Biologia Subterrânea, Setor de Biodiversidade Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Campus Universitário, Lavras, Minas Gerais, 37202-553, Brazil
| | - Oana Teodora Moldovan
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania.
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania.
- Centro Nacional sobre la Evolucion Humana, Paseo Sierra de Atapuerca 3, 09002, Burgos, Spain.
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6
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Samanta B, Sharma S, Budhwar R. Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity. Curr Microbiol 2023; 80:317. [PMID: 37561193 DOI: 10.1007/s00284-023-03431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.
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Affiliation(s)
- Brajogopal Samanta
- Department of Microbiology and FST, GITAM School of Science, GITAM (Deemed to Be University), Rushikonda, Visakhapatnam, Andhra Pradesh, 530045, India.
| | - Shivasmi Sharma
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
| | - Roli Budhwar
- Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India
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Van Wylick A, Vandersanden S, Jonckheere K, Rahier H, De Laet L, Peeters E. Screening fungal strains isolated from a limestone cave on their ability to grow and precipitate CaCO 3 in an environment relevant to concrete. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000764. [PMID: 37223428 PMCID: PMC10202147 DOI: 10.17912/micropub.biology.000764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 05/02/2023] [Indexed: 05/25/2023]
Abstract
Fungi-mediated self-healing concrete is a novel approach that promotes the precipitation of calcium carbonate (CaCO 3 ) on fungal hyphae to heal the cracks in concrete. In this study, we set out to explore the potential of fungal species isolated from a limestone cave by investigating their ability to precipitate CaCO 3 and to survive and grow in conditions relevant to concrete. Isolated strains belonging to the genera Botryotrichum sp. , Trichoderma sp. and Mortierella sp. proved to be promising candidates for fungi-mediated self-healing concrete attributed to their growth properties and CaCO 3 precipitation capabilities in the presence of cement.
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Affiliation(s)
- Aurélie Van Wylick
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Simon Vandersanden
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
- Current Address: Centre for Environmental Sciences, Hasselt University, Hasselt, Flanders, Belgium
| | - Karl Jonckheere
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Hubert Rahier
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Lars De Laet
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Brussels Capital, Belgium
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8
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Martin-Pozas T, Cuezva S, Fernandez-Cortes A, Cañaveras JC, Benavente D, Jurado V, Saiz-Jimenez C, Janssens I, Seijas N, Sanchez-Moral S. Role of subterranean microbiota in the carbon cycle and greenhouse gas dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154921. [PMID: 35364174 DOI: 10.1016/j.scitotenv.2022.154921] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/15/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Subterranean ecosystems play an active role in the global carbon cycle, yet only a few studies using indirect methods have focused on the role of the cave microbiota in this critical cycle. Here we present pioneering research based on in situ real-time monitoring of CO2 and CH4 diffusive fluxes and concurrent δ13C geochemical tracing in caves, combined with 16S microbiome analysis. Our findings show that cave sediments are promoting continuous CH4 consumption from cave atmosphere, resulting in a significant removal of 65% to 90%. This research reveals the most effective taxa and metabolic pathways in consumption and uptake of greenhouse gases. Methanotrophic bacteria were the most effective group involved in CH4 consumption, namely within the families Methylomonaceae, Methylomirabilaceae and Methylacidiphilaceae. In addition, Crossiella and Nitrosococcaceae wb1-P19 could be one of the main responsible of CO2 uptake, which occurs via the Calvin-Benson-Bassham cycle and reversible hydration of CO2. Thus, syntrophic relationships exist between Crossiella and nitrifying bacteria that capture CO2, consume inorganic N produced by heterotrophic ammonification in the surface of sediments, and induce moonmilk formation. Moonmilk is found as the most evolved phase of the microbial processes in cave sediments that fixes CO2 as calcite and intensifies CH4 oxidation. From an ecological perspective, cave sediments act qualitatively as soils, providing fundamental ecosystem services (e.g. nutrient cycling and carbon sequestration) with direct influence on greenhouse gas emissions.
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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 Alcalá, Scientific Technological Campus, 28802 Alcalá de Henares, Spain; Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | | | - Juan Carlos Cañaveras
- Department of Environmental and Earth Sciences, University of Alicante, San Vicente del Raspeig Campus, 03690 Alicante, Spain.
| | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, San Vicente del Raspeig Campus, 03690 Alicante, Spain.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Ivan Janssens
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Naomi Seijas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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9
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Miller AZ, Jiménez-Morillo NT, Coutinho ML, Gazquez F, Palma V, Sauro F, Pereira MF, Rull F, Toulkeridis T, Caldeira AT, Forti P, Calaforra JM. Organic geochemistry and mineralogy suggest anthropogenic impact in speleothem chemistry from volcanic show caves of the Galapagos. iScience 2022; 25:104556. [PMID: 35789844 PMCID: PMC9250005 DOI: 10.1016/j.isci.2022.104556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The network of lava tubes is one of the most unexploited natural wonders of the Galapagos Islands. Here, we provide the first morphological, mineralogical, and biogeochemical assessment of speleothems from volcanic caves of the Galapagos to understand their structure, composition, and origin, as well as to identify organic molecules preserved in speleothems. Mineralogical analyses revealed that moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves were composed of calcite, opal-A, and minor amounts of clay minerals. Extracellular polymeric substances, fossilized bacteria, silica microspheres, and cell imprints on siliceous minerals evidenced microbe-mineral interactions and biologically-mediated silica precipitation. Alternating depositional layers between siliceous and carbonate minerals and the detection of biomarkers of surface vegetation and anthropogenic stressors indicated environmental and anthropogenic changes (agriculture, human waste, and cave visits) on these unique underground resources. Stable isotope analysis and Py-GC/MS were key to robustly identify biomarkers, allowing for implementation of future protection policies. Speleothems from lava tubes of Galapagos are archives of anthropogenic stressors Moonmilk and coralloids are composed of calcite, opal-A, and clay minerals Microbe-mineral interactions promote mineral dissolution and precipitation Biomarkers of surface vegetation and anthropogenic impacts detected by Py-GC/MS
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Affiliation(s)
- Ana Z. Miller
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Seville, Spain
- HERCULES Laboratory, University of Évora, Évora, Portugal
- Corresponding author
| | - Nicasio T. Jiménez-Morillo
- MED—Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
| | | | - Fernando Gazquez
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for the Monitoring and Assessment of Global Change (CAESCG), University of Almería, Almería, Spain
| | - Vera Palma
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | - Francesco Sauro
- Department of Earth Sciences and Environmental Geology, University of Bologna, Bologna, Italy
| | | | - Fernando Rull
- CSIC-CAB Associated Unit ERICA, Department of Condensed Matter Physics, Mineralogy and Crystallography, University of Valladolid, Boecillo, Spain
| | | | | | - Paolo Forti
- Department of Earth Sciences and Environmental Geology, University of Bologna, Bologna, Italy
| | - José M. Calaforra
- Department of Biology and Geology, University of Almería, Almería, Spain
- Andalusian Centre for the Monitoring and Assessment of Global Change (CAESCG), University of Almería, Almería, Spain
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10
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Farda B, Djebaili R, Vaccarelli I, Del Gallo M, Pellegrini M. Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments. Microorganisms 2022; 10:453. [PMID: 35208907 PMCID: PMC8875103 DOI: 10.3390/microorganisms10020453] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/21/2022] Open
Abstract
The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.
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Affiliation(s)
| | - Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy; (B.F.); (I.V.); (M.D.G.)
| | | | | | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy; (B.F.); (I.V.); (M.D.G.)
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11
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Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use. Microorganisms 2022; 10:microorganisms10020222. [PMID: 35208677 PMCID: PMC8877592 DOI: 10.3390/microorganisms10020222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 02/05/2023] Open
Abstract
Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.
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12
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Van Wylick A, Monclaro AV, Elsacker E, Vandelook S, Rahier H, De Laet L, Cannella D, Peeters E. A review on the potential of filamentous fungi for microbial self-healing of concrete. Fungal Biol Biotechnol 2021; 8:16. [PMID: 34794517 PMCID: PMC8600713 DOI: 10.1186/s40694-021-00122-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.
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Affiliation(s)
- Aurélie Van Wylick
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Antonielle Vieira Monclaro
- PhotoBioCatalysis Unit-BTL-Ecole interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Center for Microbial Ecology and Technology (CMET), Department of Biotechnology Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.,Center for Advanced Process Technology and Urban Resource Efficiency (CAPTURE), Frieda Saeysstraat, B-9052, Ghent, Belgium
| | - Elise Elsacker
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.,Newcastle University, Hub for Biotechnology in the Built Environment, Devonshire Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Simon Vandelook
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Hubert Rahier
- Research Group of Physical Chemistry and Polymer Science, Department of Materials and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - Lars De Laet
- Research Group of Architectural Engineering, Department of Architectural Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
| | - David Cannella
- PhotoBioCatalysis Unit-BTL-Ecole interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.
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13
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Colored Microbial Coatings in Show Caves from the Galapagos Islands (Ecuador): First Microbiological Approach. COATINGS 2020. [DOI: 10.3390/coatings10111134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Galapagos Islands (Ecuador) have a unique ecosystem on Earth due to their outstanding biodiversity and geological features. This also extends to their subterranean heritage, such as volcanic caves, with plenty of secondary mineral deposits, including coralloid-type speleothems and moonmilk deposits. In this study, the bacterial communities associated with speleothems from two lava tubes of Santa Cruz Island were investigated. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features associated with moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves. Microbial cells, especially filamentous bacteria in close association with extracellular polymeric substances (EPS), were abundant in both types of speleothems. Furthermore, reticulated filaments and Actinobacteria-like cells were observed by FESEM. The analysis of 16S rDNA revealed the presence of different bacterial phylotypes, many of them associated with the carbon, nitrogen, iron and sulfur cycles, and some others with pollutants. This study gives insights into subsurface microbial diversity of the Galapagos Islands and further shows the interest of the conservation of these subterranean geoheritage sites used as show caves.
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