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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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Mugnai G, Borruso L, Wu YL, Gallinaro M, Cappitelli F, Zerboni A, Villa F. Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168026. [PMID: 37907101 DOI: 10.1016/j.scitotenv.2023.168026] [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: 08/10/2023] [Revised: 09/18/2023] [Accepted: 10/20/2023] [Indexed: 11/02/2023]
Abstract
Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.
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Affiliation(s)
- Gianmarco Mugnai
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, I-06121 Perugia (PG), IT, Italy.
| | - Luigimaria Borruso
- Free University of Bolzano, Faculty of Agricultural, Environmental and Food Sciences, Piazza Universitá 5, 39100 Bolzano, Italy.
| | - Ying-Li Wu
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, 20133 Milan, Italy.
| | - Marina Gallinaro
- Dipartimento di Scienze dell'Antichità, Università di Roma La Sapienza, 00185 Rome, Italy.
| | - Francesca Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, 20133 Milan, Italy.
| | - Federica Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
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Liu X, Qian Y, Wu F, Wang Y, Wang W, Gu JD. Biofilms on stone monuments: biodeterioration or bioprotection? Trends Microbiol 2022; 30:816-819. [PMID: 35752563 DOI: 10.1016/j.tim.2022.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 10/17/2022]
Abstract
Debate on whether biofilms on stone monuments are biodeteriorative or bioprotective is long-standing. We propose a criterion of 'relative bioprotective ratio' for assessing the ambivalent role of the biofilms by comparing biodeterioration with weathering. A boundary between biodeterioration and bioprotection exists and fluctuates with dynamic microflora influenced by environmental conditions.
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Affiliation(s)
- Xiaobo Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, Jiangsu 210094, China; Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou, Guangdong 515063, China.
| | - Youfen Qian
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, China
| | - Yali Wang
- Guangdong Conservation Centre, Guangdong Museum, 2 Zhujiang East Road, Guangzhou, Guangdong 510623, China
| | - Wanfu Wang
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China.
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Black Fungi and Stone Heritage Conservation: Ecological and Metabolic Assays for Evaluating Colonization Potential and Responses to Traditional Biocides. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Identifying species involved in biodeterioration processes is helpful, however further effort is needed to assess their ecological requirements and actual activity. Black fungi (BF) represent one of the most underestimated threats to stone cultural heritage in the Mediterranean basin; they are difficult to kill or remove due to their ability to grow inside the rock and cope with several stresses. Despite this, little is known about BF and factors favoring their growth on stone surfaces. Eighteen BF species were here investigated for temperature and salt tolerance, and metabolic traits by plate assays. The relation between some highly damaged monuments and their BF settlers was assessed using X-ray diffraction analysis, mercury intrusion porosimetry, and SEM. The sensitiveness to four commonly used traditional biocides was also tested. All strains were able to grow within the range of 5–25 °C and in the presence of 3.5% NaCl. Instrumental analyses were fundamental in discovering the relation between halophilic strains and weathered marble sculptures. The acid, cellulase, esterase, and protease production recorded proved BF’s potential to produce a chemical action on carbonate stones and likely affect other materials/historical artefacts. Besides, the use of carboxymethylcellulose and Tween 20 should be evaluated in restoration practice to prevent tertiary bioreceptivity. Agar diffusion tests helped identify the most resistant species to biocides, opening the perspective of its use as reference organisms in material testing procedures.
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Ding X, Lan W, Yan A, Li Y, Katayama Y, Gu JD. Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114041. [PMID: 34741944 DOI: 10.1016/j.jenvman.2021.114041] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/11/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The surfaces of historical stone monuments are visibly covered with a layer of colonizing microorganisms and their degradation products. In this study, a metadata analysis was conducted using the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential and functionality of the stone microbiome on important world cultural heritage sites under four different climatic conditions. The retrieved stone microbial community composition in these metagenomes shows a clear association between climate types of the historical monuments and the diversity and taxonomic composition of the stone microbiomes. Shannon diversity values showed that microbial communities on stone monuments exposed to dry climate were more diverse than those under humid ones. In particular, functions associated with photosynthesis and UV resistance were identified from geographical locations under different climate types. The distribution of key microbial determinants responsible for stone deterioration was linked to survival under extreme environmental conditions and biochemical capabilities and reactions. Among them, biochemical reactions of the microbial nitrogen and sulfur cycles were most predominant. These stone-dwelling microbiomes on historical stone monuments were highly diverse and self-sustaining driven by energy metabolism and biomass accumulation. And metabolic products of the internal geomicrobiological nitrogen cycling on these ancient monuments play a unique role in the biodeterioration of stone monuments. These results highlight the significance of identifying the essential microbial biochemical reactions to advance the understanding of stone biodeterioration for protection management.
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Affiliation(s)
- Xinghua Ding
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Inspection and Quarantine, Food Inspection and Quarantine Center of Shenzhen Custom, 1011 Fuqiang Road, Shenzhen, 518045, People's Republic of China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Yiliang Li
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Yoko Katayama
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan; Tokyo National Research Institute for Cultural Properties, 13-43 Ueno Park, Taito-ku, Tokyo, 110-8713, Japan
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, People's Republic of China.
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Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem. Microbiol Spectr 2021; 9:e0115221. [PMID: 34494852 PMCID: PMC8557908 DOI: 10.1128/spectrum.01152-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.
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Ranalli G, Bosch-Roig P, Crudele S, Rampazzi L, Corti C, Zanardini E. Dry biocleaning of artwork: an innovative methodology for Cultural Heritage recovery? MICROBIAL CELL 2021; 8:91-105. [PMID: 33981761 PMCID: PMC8080898 DOI: 10.15698/mic2021.05.748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An innovative methodology is proposed, based on applied biotechnology to the recovery of altered stonework: the “dry biocleaning”, which envisages the use of dehydrated microbial cells without the use of free water or gel-based matrices. This methodology can be particularly useful for the recovery of highly-ornamented stoneworks, which cannot be treated using the conventional cleaning techniques. The experimental plan included initial laboratory tests on Carrara marble samples, inoculated with dehydrated Saccharomyces cerevisiae yeast cells, followed by on-site tests performed on “Quattro Fontane” (The Four Fountains), a travertine monumental complex in Rome (Italy), on altered highly ornamented areas of about 1,000 cm2. The mechanism is based on the spontaneous re-hydration process due to the environmental humidity and on the metabolic fermentative activity of the yeast cells. Evaluation by physical-chemical analyses, after 18 hours of the biocleaning, confirmed a better removal of salts and pollutants, compared to both nebulization treatment and control tests (without cells). The new proposed on-site dry biocleaning technique, adopting viable yeast cells, represents a promising method that can be further investigated and optimized for recovering specific altered Cultural Heritage stoneworks.
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Affiliation(s)
- Giancarlo Ranalli
- Department of Bioscience and Territory, University of Molise, Pesche, Italy
| | - Pilar Bosch-Roig
- Department of Conservation and Restoration of Cultural Heritage, Instituto de Restauration de Patrimonio, Universitat Politècnica de València, Valencia, Spain
| | - Simone Crudele
- Department of Bioscience and Territory, University of Molise, Pesche, Italy
| | - Laura Rampazzi
- Department of Human Sciences, Innovation and Territory, Università degli Studi dell'Insubria, Como, Italy.,The Institute of Heritage Science, National Research Council of Italy, Milan, Italy
| | - Cristina Corti
- Department of Human Sciences, Innovation and Territory, Università degli Studi dell'Insubria, Como, Italy
| | - Elisabetta Zanardini
- Department of Science and High Technology, Università degli Studi dell'Insubria, Como, Italy
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Ranalli G, Zanardini E. Biocleaning on Cultural Heritage: new frontiers of microbial biotechnologies. J Appl Microbiol 2021; 131:583-603. [PMID: 33404159 DOI: 10.1111/jam.14993] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023]
Abstract
Over the last two decades, the biotechnologies applied to Cultural heritage (CH) have become a successful novel alternative to the traditional approaches in the CH conservation and preservation. From these new perspectives, microorganisms and their metabolisms can be used for the safeguarding of artworks. Biocleaning is a field with a growing interest, based on eco-friendly processes and safe procedures, where biological reactions occurring in natural habitats are optimized in artificial conditions with the aim of CH conservation. This represents a new tool and opportunity for the development and improvement of the sector, with a great advantage for the CH conservation-restoration, in terms of safety, effectiveness, costs and environmental sustainability. This review focuses on the use of microbes and enzymes involved in biocleaning of CH artworks. The aim is to provide a comprehensive, critical and chronological view of the scientific works published until now where 'virtuous' microorganisms are applied on different CH materials, pointing out strength and drawback of the biocleaning treatments.
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Affiliation(s)
- G Ranalli
- Department of Bioscience and Territory, University of Molise, Pesche, Italy
| | - E Zanardini
- Department of Sciences and High Technology, University of Insubria, Como, Italy
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Marvasi M, Mastromei G, Perito B. Bacterial Calcium Carbonate Mineralization in situ Strategies for Conservation of Stone Artworks: From Cell Components to Microbial Community. Front Microbiol 2020; 11:1386. [PMID: 32714304 PMCID: PMC7341901 DOI: 10.3389/fmicb.2020.01386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Calcareous stones have been widely used in artworks and buildings by almost all human cultures. Now, more than ever, the increased environmental pollution and global warming are threatening the stone cultural heritage. Weathering due to physical, chemical and biological factors results in monumental calcareous stone deterioration. These agents induce a progressive dissolution of the mineral matrix, increase porosity, and lead to structural weakening. Bacterial Calcium Carbonate Mineralization is a widespread naturally occurring process which in the last decades was proposed as an environmentally friendly tool to protect monumental and ornamental calcareous stones. The advantage of this treatment is that it mimics the natural process responsible for stone formation, producing a mineral product similar to the stone substrate. This mini review highlights the milestones of the biomineralization approaches with focus on in situ stone artworks protection. The strategies explored to date are based on three main approaches: (i) the use of allochthonous and (ii) autochthonous alive cells that, due to the bacterial metabolism, foster biomineralization; (iii) the cell-free approach which uses fractionated cellular components inducing biomineralization. We discuss the challenging aspects of all these techniques, focusing on in situ applications and suggesting perspectives based on recent advances.
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Affiliation(s)
| | | | - Brunella Perito
- Department of Biology, University of Florence, Florence, Italy
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Villa F, Cappitelli F. The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments. Microorganisms 2019; 7:microorganisms7100380. [PMID: 31547498 PMCID: PMC6843906 DOI: 10.3390/microorganisms7100380] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
The ecological relationship between minerals and microorganisms arguably represents one of the most important associations in dry terrestrial environments, since it strongly influences major biochemical cycles and regulates the productivity and stability of the Earth’s food webs. Despite being inhospitable ecosystems, mineral substrata exposed to air harbor form complex and self-sustaining communities called subaerial biofilms (SABs). Using life on air-exposed minerals as a model and taking inspiration from the mechanisms of some microorganisms that have adapted to inhospitable conditions, we illustrate the ecology of SABs inhabiting natural and built environments. Finally, we advocate the need for the convergence between the experimental and theoretical approaches that might be used to characterize and simulate the development of SABs on mineral substrates and SABs’ broader impacts on the dry terrestrial environment.
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Affiliation(s)
- Federica Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
| | - Francesca Cappitelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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