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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. Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ghezzi D, Foschi L, Firrincieli A, Hong PY, Vergara F, De Waele J, Sauro F, Cappelletti M. Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela). Front Microbiol 2022; 13:930302. [PMID: 36212823 PMCID: PMC9537377 DOI: 10.3389/fmicb.2022.930302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022] Open
Abstract
Microbial communities inhabiting caves in quartz-rich rocks are still underexplored, despite their possible role in the silica cycle. The world’s longest orthoquartzite cave, Imawarì Yeuta, represents a perfect arena for the investigation of the interactions between microorganisms and silica in non-thermal environments due to the presence of extraordinary amounts of amorphous silica speleothems of different kinds. In this work, the microbial diversity of Imawarì Yeuta was dissected by analyzing nineteen samples collected from different locations representative of different silica amorphization phases and types of samples. Specifically, we investigated the major ecological patterns in cave biodiversity, specific taxa enrichment, and the main ecological clusters through co-occurrence network analysis. Water content greatly contributed to the microbial communities’ composition and structures in the cave leading to the sample clustering into three groups DRY, WET, and WATER. Each of these groups was enriched in members of Actinobacteriota, Acidobacteriota, and Gammaproteobacteria, respectively. Alpha diversity analysis showed the highest value of diversity and richness for the WET samples, while the DRY group had the lowest. This was accompanied by the presence of correlation patterns including either orders belonging to various phyla from WET samples or orders belonging to the Actinobacteriota and Firmicutes phyla from DRY group samples. The phylogenetic analysis of the dominant species in WET and DRY samples showed that Acidobacteriota and Actinobacteriota strains were affiliated with uncultured bacteria retrieved from various oligotrophic and silica/quartz-rich environments, not only associated with subterranean sites. Our results suggest that the water content greatly contributes to shaping the microbial diversity within a subterranean quartzite environment. Further, the phylogenetic affiliation between Imawarì Yeuta dominant microbes and reference strains retrieved from both surface and subsurface silica- and/or CO2/CO-rich environments, underlines the selective pressure applied by quartz as rock substrate. Oligotrophy probably in association with the geochemistry of silica/quartz low pH buffering activity and alternative energy sources led to the colonization of specific silica-associated microorganisms. This study provides clues for a better comprehension of the poorly known microbial life in subsurface and surface quartz-dominated environments.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- *Correspondence: Daniele Ghezzi,
| | - Lisa Foschi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Pei-Ying Hong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Freddy Vergara
- Teraphosa Exploring Team, Puerto Ordaz, Venezuela
- La Venta Geographic Explorations Association, Treviso, Italy
| | - Jo De Waele
- La Venta Geographic Explorations Association, Treviso, Italy
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Francesco Sauro
- Teraphosa Exploring Team, Puerto Ordaz, Venezuela
- La Venta Geographic Explorations Association, Treviso, Italy
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Martina Cappelletti,
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Chiciudean I, Russo G, Bogdan DF, Levei EA, Faur L, Hillebrand-Voiculescu A, Moldovan OT, Banciu HL. Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments. Environ Microbiome 2022; 17:44. [PMID: 35978381 PMCID: PMC9386943 DOI: 10.1186/s40793-022-00438-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water. RESULTS A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities. CONCLUSIONS These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.
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Affiliation(s)
- Iulia Chiciudean
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Giancarlo Russo
- EMBL Partner Institute for Genome Editing, Life Sciences Center–Vilnius University, Vilnius, Lithuania
| | - Diana Felicia Bogdan
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Doctoral School of Integrative Biology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- National Institute for Research and Development for Optoelectronics, Research Institute for Analytical Instrumentation Subsidiary, Cluj-Napoca, Romania
| | - Luchiana Faur
- Emil Racovita Institute of Speleology, Geospeleology and Paleontology Department, Bucharest, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Alexandra Hillebrand-Voiculescu
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Biospeology and Edaphobiology Department, Emil Racovita Institute of Speleology, Bucharest, Romania
| | - Oana Teodora Moldovan
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
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Meyer-Dombard DR, Malas J. Advances in Defining Ecosystem Functions of the Terrestrial Subsurface Biosphere. Front Microbiol 2022; 13:891528. [PMID: 35722320 PMCID: PMC9201636 DOI: 10.3389/fmicb.2022.891528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
The subsurface is one of the last remaining 'uncharted territories' of Earth and is now accepted as a biosphere in its own right, at least as critical to Earth systems as the surface biosphere. The terrestrial deep biosphere is connected through a thin veneer of Earth's crust to the surface biosphere, and many subsurface biosphere ecosystems are impacted by surface topography, climate, and near surface groundwater movement and represent a transition zone (at least ephemerally). Delving below this transition zone, we can examine how microbial metabolic functions define a deep terrestrial subsurface. This review provides a survey of the most recent advances in discovering the functional and genomic diversity of the terrestrial subsurface biosphere, how microbes interact with minerals and obtain energy and carbon in the subsurface, and considers adaptations to the presented environmental extremes. We highlight the deepest subsurface studies in deep mines, deep laboratories, and boreholes in crystalline and altered host rock lithologies, with a focus on advances in understanding ecosystem functions in a holistic manner.
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Addesso R, Bellino A, Baldantoni D. Underground Ecosystem Conservation Through High-resolution Air Monitoring. Environ Manage 2022; 69:982-993. [PMID: 35190855 PMCID: PMC8860376 DOI: 10.1007/s00267-022-01603-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/30/2022] [Indexed: 05/19/2023]
Abstract
In cave ecosystems tourists represent moving sources of discontinuous disturbances, able to induce transient system responses whose knowledge is crucial in defining appropriate conservation measures. Here we propose an approach to evaluate the amplitude and scales of cave alterations based on high-resolution air monitoring, through the use of purposely developed low-cost monitoring stations and a consistent analytical framework for information retrieval based on time series analysis. In particular, monitoring stations adopt a modular structure based on physical computing platforms acquiring data through several sensors, with means of preventing humidity damages and guaranteeing their continuous operation. Data are then analyzed using wavelet periodograms and cross-periodograms to extract the scales of tourism-induced alterations. The approach has been exemplified in the Pertosa-Auletta Cave, one of the most important underground environments in Southern Italy, highlighting the development of monitoring stations and the information obtainable with the proposed analytical workflow. Here, 2 monitoring stations acquiring data for 1 year at 1' sampling time on temperature, relative humidity, CO2, VOCs, and particulate matter were deployed in trails subjected to different levels of tourism. In terms of Pertosa-Auletta Cave air dynamics, the approach allowed estimating the temporal and spatial scales of tourism-induced alterations in the order of minutes and meters, respectively, with parameter-dependent variations. On more general terms, the approach proved reliable and effective, with its modularity and low-cost fostering its straightforward adoption in other underground ecosystems, where it can support the development of tailored management strategies.
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Affiliation(s)
- Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano (SA), Italy
| | - Alessandro Bellino
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano (SA), Italy.
| | - Daniela Baldantoni
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano (SA), Italy
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Ai J, Guo J, Li Y, Zhong X, Lv Y, Li J, Yang A. The diversity of microbes and prediction of their functions in karst caves under the influence of human tourism activities-a case study of Zhijin Cave in Southwest China. Environ Sci Pollut Res Int 2022; 29:25858-25868. [PMID: 34854002 DOI: 10.1007/s11356-021-17783-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms, sensitive to the surrounding environment changes, show how the cave environment can be impacted by human activities. Zhijin Cave, featured with the most well-developed karst landform in China, has been open to tourists for more than 30 years. This study explored the microbial diversity in a karst cave and the impacts of tourism activities on the microbial communities and the community structures of bacteria and archaea in three niches in Zhijin Cave, including the mixture of bacteria and cyanobacteria on the rock wall, the aquatic sediments, and the surface sediments, using 16S rRNA high-throughput sequencing technology. It was found that Actinobacteriota and Proteobacteria were the dominant bacteria in the cave and Crenarchaeota and Thermoplasmatota were the dominant archaea. The correlation between microorganisms and environmental variables in the cave showed that archaea were more affected by pH and ORP than bacteria and F-, Cl-, NO3-, and SO42- were all positively relevant to the distribution of most bacteria and archaea in the cave. PICRUSt's prediction of microbial functions also indicated that abundance of the bacteria's functions was higher than that of the archaea. The intention of this study was to improve the understanding, development, and protection of microbial resources in caves.
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Affiliation(s)
- Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jianeng Guo
- Management Office of Zhijin Cave Scenic Area, Bijie, 552100, Guizhou, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xiong Zhong
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Yang Lv
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
| | - Aijiang Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 500025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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Saraba V, Dragisic V, Janakiev T, Obradovic V, Copic M, Knezevic B, Dimkic I. Bacteriome composition analysis of selected mineral water occurrences in Serbia. ARCH BIOL SCI 2022. [DOI: 10.2298/abs211223005s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacterial metabarcoding analysis by 16S rDNA of five occurrences of mineral
waters in Serbia (Torda, Slankamen Banja, Lomnicki Kiseljak, Velika Vrbnica
and Obrenovacka Banja) indicated the presence of a high percentage of the
Proteobacteria phylum, followed by the Bacteroidetes phylum. The families
Rhodobacteraceae, Burkholderiaceae, Pseudomonadaceae, Methylophilaceae and
Moraxellaceae were the most dominant in the bacterial flora of the selected
occurrences, whereas the most represented genera were Acinetobacter,
Pseudorhodobacter, Pseudomonas, Limnohabitans, Massilia, Limnobacter and
Methylotenera. The presence of coliform bacteria was not detected. Alpha
diversity analysis revealed that Slankamen Banja and Lomnicki Kiseljak were
the richest of the selected occurrences, while the mineral waters of Torda,
Velika Vrbnica and Obrenovacka Banja were characterized by similar diversity
of bacterial communities determined by beta diversity analysis.
Physical-chemical analysis revealed the value of total dissolved solids
above 1 g/L, as well as elevated concentrations of some metals and
non-metals. The research concluded that specific bacteria contribute to the
development of biocorrosion and biofouling processes of water intake
facilities. In addition, some of these bacteria might be potential
indicators of the organic sources of pollution and/or biotechnological
natural remediators in the treatment of contaminated waters.
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Iwanowicz DD, Jonas RB, Schill WB, Marano-Briggs K. Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas. PLoS One 2021; 16:e0256305. [PMID: 34411155 PMCID: PMC8375975 DOI: 10.1371/journal.pone.0256305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022] Open
Abstract
Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.
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Affiliation(s)
- Deborah D. Iwanowicz
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Robert B. Jonas
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, United States of America
- * E-mail:
| | - William B. Schill
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
| | - Kay Marano-Briggs
- Eastern Ecological Science Center, United States Geological Survey, Kearneysville, West Virginia, United States of America
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Gonzalez-Pimentel JL, Martin-Pozas T, Jurado V, Miller AZ, Caldeira AT, Fernandez-Lorenzo O, Sanchez-Moral S, Saiz-Jimenez C. Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PeerJ 2021; 9:e11386. [PMID: 34026356 PMCID: PMC8121065 DOI: 10.7717/peerj.11386] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/10/2021] [Indexed: 11/21/2022] Open
Abstract
Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37-89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72-96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.
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Affiliation(s)
| | | | - Valme Jurado
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
| | | | | | | | | | - Cesareo Saiz-Jimenez
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
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11
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Addesso R, Gonzalez-Pimentel JL, D'Angeli IM, De Waele J, Saiz-Jimenez C, Jurado V, Miller AZ, Cubero B, Vigliotta G, Baldantoni D. Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation. Microb Ecol 2021; 81:884-896. [PMID: 33156395 PMCID: PMC8062384 DOI: 10.1007/s00248-020-01623-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/12/2020] [Indexed: 05/07/2023]
Abstract
The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.
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Affiliation(s)
- Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Jose L Gonzalez-Pimentel
- HERCULES Laboratory, University of Évora, Largo Marques de Marialva 8, 7000-809, Évora, Portugal
| | - Ilenia M D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni, 67, 40126, Bologna, Italy
| | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni, 67, 40126, Bologna, Italy
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, IRNAS-CSIC, Av. Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiología de Sevilla, IRNAS-CSIC, Av. Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Ana Z Miller
- HERCULES Laboratory, University of Évora, Largo Marques de Marialva 8, 7000-809, Évora, Portugal
| | - Beatriz Cubero
- Instituto de Recursos Naturales y Agrobiología de Sevilla, IRNAS-CSIC, Av. Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Giovanni Vigliotta
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Daniela Baldantoni
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
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12
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Morse KV, Richardson DR, Brown TL, Vangundy RD, Cahoon AB. Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession. PeerJ 2021; 9:e10757. [PMID: 33732542 PMCID: PMC7950216 DOI: 10.7717/peerj.10757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave's aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave.
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13
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Ghezzi D, Sauro F, Columbu A, Carbone C, Hong PY, Vergara F, De Waele J, Cappelletti M. Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment. Sci Rep 2021; 11:3921. [PMID: 33594175 PMCID: PMC7887251 DOI: 10.1038/s41598-021-83416-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical-chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.
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Affiliation(s)
- D. Ghezzi
- grid.6292.f0000 0004 1757 1758Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy ,grid.419038.70000 0001 2154 6641Laboratory of NanoBiotechnology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - F. Sauro
- grid.6292.f0000 0004 1757 1758Department of Biological Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy ,La Venta Geographic Explorations Association, 31100 Treviso, Italy ,Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - A. Columbu
- grid.6292.f0000 0004 1757 1758Department of Biological Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - C. Carbone
- grid.5606.50000 0001 2151 3065Department of Earth, Environment and Life, University of Genoa, 16132 Genoa, Italy
| | - P.-Y. Hong
- grid.45672.320000 0001 1926 5090Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
| | - F. Vergara
- La Venta Geographic Explorations Association, 31100 Treviso, Italy ,Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - J. De Waele
- grid.6292.f0000 0004 1757 1758Department of Biological Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - M. Cappelletti
- grid.6292.f0000 0004 1757 1758Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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14
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Kelly H, Spilde MN, Jones DS, Boston PJ. Insights into the Geomicrobiology of Biovermiculations from Rock Billet Incubation Experiments. Life (Basel) 2021; 11:life11010059. [PMID: 33467599 PMCID: PMC7830032 DOI: 10.3390/life11010059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/03/2022] Open
Abstract
Biovermiculations are uniquely patterned organic rich sediment formations found on the walls of caves and other subterranean environments. These distinctive worm-like features are the combined result of physical and biological processes. The diverse microbial communities that inhabit biovermiculations may corrode the host rock, form secondary minerals, and produce biofilms that stabilize the sediment matrix, thus altering cave surfaces and contributing to the formation of these wall deposits. In this study, we incubated basalt, limestone, and monzonite rock billets in biovermiculation mixed natural community enrichments for 468–604 days, and used scanning electron microscopy (SEM) to assess surface textures and biofilms that developed over the course of the experiment. We observed alteration of rock billet surfaces associated with biofilms and microbial filaments, particularly etch pits and other corrosion features in olivine and other silicates, calcite dissolution textures, and the formation of secondary minerals including phosphates, clays, and iron oxides. We identified twelve distinct biofilm morphotypes that varied based on rock type and the drying method used in sample preparation. These corrosion features and microbial structures inform potential biological mechanisms for the alteration of cave walls, and provide insight into possible small-scale macroscopically visible biosignatures that could augment the utility of biovermiculations and similarly patterned deposits for astrobiology and life detection applications.
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Affiliation(s)
- Hilary Kelly
- Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA;
| | - Michael N. Spilde
- Institute of Meteoritics, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Daniel S. Jones
- Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA;
- National Cave and Karst Research Institute, Carlsbad, NM 88220, USA
- Correspondence: (P.J.B.); (D.S.J.)
| | - Penelope J. Boston
- Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA;
- National Cave and Karst Research Institute, Carlsbad, NM 88220, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- Correspondence: (P.J.B.); (D.S.J.)
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15
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Cirigliano A, Mura F, Cecchini A, Tomassetti MC, Maras DF, Di Paola M, Meriggi N, Cavalieri D, Negri R, Quagliariello A, Hallsworth JE, Rinaldi T. Active microbial ecosystem in
Iron‐Age
tombs of the Etruscan civilization. Environ Microbiol 2020; 23:3957-3969. [DOI: 10.1111/1462-2920.15327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Angela Cirigliano
- Department of Biology and Biotechnology Sapienza University of Rome Rome Italy
| | - Francesco Mura
- CNIS – Center for Nanotechnology Applied to Industry of La Sapienza Sapienza University of Rome Rome Italy
| | - Adele Cecchini
- Associazione No Profit ‘Amici Delle Tombe Dipinte di Tarquinia’ Tarquinia Italy
| | | | - Daniele Federico Maras
- Soprintendenza Archeologia Belle Arti e Paesaggio per l'Area Metropolitana di Roma, la Provincia di Viterbo e l'Etruria Meridionale Ministero dei Beni e delle Attività Culturali e del Turismo Rome Italy
| | | | | | | | - Rodolfo Negri
- Department of Biology and Biotechnology Sapienza University of Rome Rome Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science University of Padova Padova Italy
| | - John E. Hallsworth
- Institute for Global Food Security School of Biological Sciences, Queen's University Belfast Belfast UK
| | - Teresa Rinaldi
- Department of Biology and Biotechnology Sapienza University of Rome Rome Italy
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