1
|
Ghezzi D, Salvi L, Costantini PE, Firrincieli A, Iorio M, Lopo E, Sosio M, Elbanna AH, Khalil ZG, Capon RJ, De Waele J, Vergara F, Sauro F, Cappelletti M. Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiol Res 2024; 286:127793. [PMID: 38901277 DOI: 10.1016/j.micres.2024.127793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
Collapse
Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Luca Salvi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Paolo E Costantini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Ettore Lopo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Ahmed H Elbanna
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Pharmacognosy, Cairo University, Cairo 11562, Egypt
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Freddy Vergara
- La Venta Geographic Explorations Association, Treviso 31100, Italy; Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - Francesco Sauro
- La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy.
| |
Collapse
|
2
|
Zada S, Khan M, Su Z, Sajjad W, Rafiq M. Cryosphere: a frozen home of microbes and a potential source for drug discovery. Arch Microbiol 2024; 206:196. [PMID: 38546887 DOI: 10.1007/s00203-024-03899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
The world is concerned about the emergence of pathogens and the occurrence and spread of antibiotic resistance among pathogens. Drug development requires time to combat these issues. Consequently, drug development from natural sources is unavoidable. Cryosphere represents a gigantic source of microbes that could be the bioprospecting source of natural products with unique scaffolds as molecules or drug templates. This review focuses on the novel source of drug discovery and cryospheric environments as a potential source for microbial metabolites having potential medicinal applications. Furthermore, the problems encountered in discovering metabolites from cold-adapted microbes and their resolutions are discussed. By adopting modern practical approaches, the discovery of bioactive compounds might fulfill the demand for new drug development.
Collapse
Affiliation(s)
- Sahib Zada
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Mohsin Khan
- Department of Biological Sciences, Ohio University Athens, Athens, OH, USA
| | - Zheng Su
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, 87650, Pakistan.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
Collapse
Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| |
Collapse
|
5
|
Karatay KB, Dogruoz Gungor N, Colak B, Biber Muftuler FZ, Aras O. Bacterial production of ciprofloxacin and potential usage as a radiotracer. PLoS One 2023; 18:e0291342. [PMID: 37943851 PMCID: PMC10635501 DOI: 10.1371/journal.pone.0291342] [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: 05/01/2023] [Accepted: 08/29/2023] [Indexed: 11/12/2023] Open
Abstract
Infectious diseases caused by bacteria that have become resistant to antibiotics have increased in prevalence, necessitating new methods for their diagnosis and treatment. The aim of this study was to compare the efficacy of synthetic ciprofloxacin to that of organic ciprofloxacin produced by cave microorganisms, as well as to evaluate the feasibility of using organic ciprofloxacin radiolabeled with technetium-99m as an imaging agent. Organic ciprofloxacin produced by cave bacteria isolated from sediment taken from the dark zone of Antalya's "Yark Sinkhole," (Turkey's 14th deepest cave), was purified using high-performance liquid chromatography. Purified organic ciprofloxacin and standard ciprofloxacin were radiolabeled with technetium-99m (99mTc), and their uptake by pathogenic microorganisms as well as potential as an imaging agent were examined. According to thin-layer radiochromatography, radiolabeling efficiencies were 98.99 ± 0.34 (n = 7) and 91.25 ± 1.84 (n = 7) for radiolabeled organic ciprofloxacin and standard ciprofloxacin respectively. The binding efficiency of radiolabeled organic ciprofloxacin at the 240th minute was higher compared with radiolabeled standard ciprofloxacin, especially with P.aeruginosa, MRSA, VRE and E.coli. The results demonstrate that radiolabeling with 99mTc does not alter the biological behavior of organic ciprofloxacin, and radiolabeled organic ciprofloxacin has potential as an imaging agent for the detection of bacterial infection. The original value of the study is the monitoring of the antibiofilm effects of untouched cave-derived organic antibiotics by radiolabeling with a radionuclide.
Collapse
Affiliation(s)
- Kadriye Busra Karatay
- Department of Nuclear Applications, Institute of Nuclear Sciences, Ege University, Izmir, Turkey
| | - Nihal Dogruoz Gungor
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Batu Colak
- Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey
| | | | - Omer Aras
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Pipite A, Lockhart PJ, McLenachan PA, Christi K, Kumar D, Prasad S, Subramani R. Isolation, antibacterial screening, and identification of bioactive cave dwelling bacteria in Fiji. Front Microbiol 2022; 13:1012867. [PMID: 36605510 PMCID: PMC9807670 DOI: 10.3389/fmicb.2022.1012867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria are well known producers of bioactive secondary metabolites, including some of the most effective antibiotics in use today. While the caves of Oceania are still largely under-explored, they form oligotrophic and extreme environments that are a promising source for identifying novel species of bacteria with biologically active compounds. By using selective media that mimicked a cave environment, and pretreatments that suppressed the growth of fast-growing bacteria, we have cultured genetically diverse bacteria from a limestone cave in Fiji. Partial 16S rRNA gene sequences from isolates were determined and compared with 16S rRNA gene sequences in EzBioCloud and SILVA data bases. Fifty-five isolates purified from culture had Actinomycete-like morphologies and these were investigated for antibacterial activity. Initial screening using a cross streak test with pathogenic bacteria indicated that 34 of the isolates had antibacterial properties. The best matches for the isolates are bacteria with potential uses in the manufacture of antibiotics and pesticides, in bioremediation of toxic waste, in biomining, in producing bioplastics, and in plant growth promotion. Nineteen bacteria were confirmed as Actinomycetes. Thirteen were from the genus Streptomyces and six from genera considered to be rare Actinomycetes from Pseudonocardia, Kocuria, Micromonospora, Nonomuraea. Ten isolates were Firmicutes from the genera Bacillus, Lysinbacillus, Psychrobacillus and Fontibacillus. Two were Proteobacteria from the genera Mesorhizobium and Cupriavidus. Our findings identify a potentially rich source of microbes for applications in biotechnologies.
Collapse
Affiliation(s)
- Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji,*Correspondence: Atanas Pipite,
| | - Peter J. Lockhart
- School of Natural Sciences, Massey University, Palmerston North, New Zealand,Peter J. Lockhart,
| | | | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Dinesh Kumar
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Surendra Prasad
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Suva, Fiji
| |
Collapse
|
9
|
The Rare Actinobacterium Crossiella sp. Is a Potential Source of New Bioactive Compounds with Activity against Bacteria and Fungi. Microorganisms 2022; 10:microorganisms10081575. [PMID: 36013993 PMCID: PMC9415966 DOI: 10.3390/microorganisms10081575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance has become a global problem in recent decades. A gradual reduction in drug discoveries has led to the current antimicrobial resistance crisis. Caves and other subsurface environments are underexplored thus far, and they represent indispensable ecological niches that could offer new molecules of interest to medicine and biotechnology. We explored Spanish show caves to test the bioactivity of the bacteria dwelling in the walls and ceilings, as well as airborne bacteria. We reported the isolation of two strains of the genus Crossiella, likely representing a new species, isolated from Altamira Cave, Spain. In vitro and in silico analyses showed the inhibition of pathogenic Gram-positive and Gram-negative bacteria, and fungi, as well as the taxonomical distance of both strains from their closest relative, Crossiella cryophila. The presence of an exclusive combination of gene clusters involved in the synthesis of lanthipeptides, lasso peptides, nonribosomal peptides and polyketides indicates that species of this genus could represent a source of new compounds. Overall, there is promising evidence for antimicrobial discovery in subterranean environments, which increases the possibility of identifying new bioactive molecules.
Collapse
|
10
|
Haidău C, Năstase-Bucur R, Bulzu P, Levei E, Cadar O, Mirea IC, Faur L, Fruth V, Atkinson I, Constantin S, Moldovan OT. A 16S rRNA Gene-Based Metabarcoding of Phosphate-Rich Deposits in Muierilor Cave, South-Western Carpathians. Front Microbiol 2022; 13:877481. [PMID: 35663904 PMCID: PMC9161362 DOI: 10.3389/fmicb.2022.877481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Muierilor Cave is one of Romania's most important show caves, with paleontological and archeological deposits. Recently, a new chamber was discovered in the cave, with unique yellow calcite crystals, fine-grained crusts, and black sediments. The deposits in this chamber were related to a leaking process from the upper level that contains fossil bones and a large pile of guano. Samples were taken from the new chamber and another passage to investigate the relationship between the substrate and microbial community. Chemical, mineralogical, and whole community 16S rRNA gene-based metabarcoding analyses were undertaken, and the base of the guano deposit was radiocarbon dated. Our study indicated bacteria linked to the presence of high phosphate concentration, most likely due to the nature of the substrate (hydroxyapatite). Bacteria involved in Fe, Mn, or N cycles were also found, as these elements are commonly identified in high concentrations in guano. Since no bat colonies or fossil bones were present in the new chamber, a high concentration of these elements could be sourced by organic deposits inside the cave (guano and fossil bones) even after hundreds of years of their deposition and in areas far from both deposits. Metabarcoding of the analyzed samples found that ∼0.7% of the identified bacteria are unknown to science, and ∼47% were not previously reported in caves or guano. Moreover, most of the identified human-related bacteria were not reported in caves or guano before, and some are known for their pathogenic potential. Therefore, continuous monitoring of air and floor microbiology should be considered in show caves with organic deposits containing bacteria that can threaten human health. The high number of unidentified taxa in a small sector of Muierilor Cave indicates the limited knowledge of the bacterial diversity in caves that can have potential applications in human health and biotechnology.
Collapse
Affiliation(s)
- Catalina Haidău
- Department of Biospeleology and Karst Edaphobiology, Emil Racovita Institute of Speleology, Bucureşti, Romania
| | - Ruxandra Năstase-Bucur
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Paul Bulzu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Erika Levei
- Research Institute for Analytical Instrumentation Subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Cluj-Napoca, Romania
| | - Oana Cadar
- Research Institute for Analytical Instrumentation Subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Cluj-Napoca, Romania
| | - Ionuţ Cornel Mirea
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
| | - Luchiana Faur
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
- Faculty of Geology and Geophysics, University of Bucharest, Bucureşti, Romania
| | - Victor Fruth
- Institute of Physical Chemistry “Ilie Murgulescu” of the Romanian Academy, Bucuresti, Romania
| | - Irina Atkinson
- Institute of Physical Chemistry “Ilie Murgulescu” of the Romanian Academy, Bucuresti, Romania
| | - Silviu Constantin
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucureşti, Romania
- Centro Nacional Sobre la Evolucion Humana, Burgos, Spain
| | - Oana Teodora Moldovan
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
- Centro Nacional Sobre la Evolucion Humana, Burgos, Spain
| |
Collapse
|
11
|
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.
Collapse
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.)
| |
Collapse
|
12
|
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.
Collapse
|