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Pagli C, Chamizo S, Migliore G, Rugnini L, De Giudici G, Braglia R, Canini A, Cantón Y. Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174020. [PMID: 38897475 DOI: 10.1016/j.scitotenv.2024.174020] [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: 03/23/2024] [Revised: 04/30/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.
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Affiliation(s)
- Carlotta Pagli
- Department of Biology, University of Rome Tor Vergata, Italy; Department of Agronomy, University of Almería, Spain; PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, Italy.
| | - Sonia Chamizo
- Department of Agronomy, University of Almería, Spain; Department of Desertification and Geo-Ecology, Experimental Station of Arid Zones (EEZA-CSIC), Almería, Spain
| | - Giada Migliore
- ENEA, Territorial and Production Systems Sustainability Department, Italy
| | - Lorenza Rugnini
- Department of Biology, University of Rome Tor Vergata, Italy
| | - Giovanni De Giudici
- Department of Chemical and Geological Sciences, University of Cagliari, Italy
| | - Roberto Braglia
- Department of Biology, University of Rome Tor Vergata, Italy
| | | | - Yolanda Cantón
- Department of Agronomy, University of Almería, Spain; Center for Research on Scientific Collections of the University of Almeria (CECOUAL), Spain
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Çiftçi N, Ayas D. Elemental Composition and Health Risk Assessment of Deep-Sea Teleost's of the Levantine Basin. Biol Trace Elem Res 2024:10.1007/s12011-024-04298-y. [PMID: 38970712 DOI: 10.1007/s12011-024-04298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024]
Abstract
The determination of metal(loid) (As, Fe, Al, Sr, Zn, Pb, Mn, Cu, Cr, and Cd) levels in the muscle tissue of 23 different deep-sea bony fish sampled off Mersin Bay (NE Levantine Basin) and the assessment of health risks for human consumption were aimed. Tissue metal(loid) concentrations were determined as dry weight and analyzed by inductively coupled plasma mass spectrometry (ICP-MS). The tissue metal(loid) concentrations (µg g dw) were converted to wet weight prior to health risk assessment calculations. Standard mathematical formulas were used to determine the health risk assessment. There was a statistically significant difference between the fish species in terms of tissue metal(loid) levels (p < 0.05). The highest metal(loid) level was found in C. sloani among other species. As and Fe had the highest and Cd the lowest tissue concentrations in the examined species (p < 0.05). The relationships between the metal(loid)s analyzed in the tissue were significant (p < 0.01;0.05). Fe had an antagonistic effect with Cd, while other metal(loid)s had a synergetic effect with each other. Risk assessment analyses were performed for the consumable species, and it was found that the estimated daily and weekly intakes were below the tolerable limits established by the Food and Agriculture Organization (FAO) and the World Health Organization (WHO). The target hazard quotient (THQ) values exceeded the threshold of 1 (THQ > 1) only for As. The target cancer risk (TCR) was below the tolerable limits (> 10-5) except for As, Cd, and Al.
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Affiliation(s)
- Nuray Çiftçi
- Faculty of Fisheries, Mersin University, Mersin, Turkey.
| | - Deniz Ayas
- Faculty of Fisheries, Mersin University, Mersin, Turkey
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Parades-Aguilar J, Calderon K, Agustin-Salazar S, Cerruti P, Ambrogi V, Gamez-Meza N, Medina-Juarez LA. Isolation and identification of metallotolerant bacteria with a potential biotechnological application. Sci Rep 2024; 14:3663. [PMID: 38351239 PMCID: PMC10864330 DOI: 10.1038/s41598-024-54090-0] [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: 12/04/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
Mining has led to severe environmental pollution in countries with exhaustive mining production and inadequate industrial waste regulation. Microorganisms in contaminated sites, like mine tailings, have adapted to high concentrations of heavy metals, developing the capacity of reducing or removing them from these environments. Therefore, it is essential to thoroughly characterize bacteria present in these sites to find different ways of bioremediation. In this regard, in this study, an enrichment and isolation procedure were performed to isolate bacteria with lower nutritional requirements and high tolerance to Cu(II) and Fe(II) from two Sonoran River basin mining tails. Two Staphylococcus species and a Microbacterium ginsengisoli strain were isolated and identified from the San Felipe de Jesús mining tail. Also, three strains were isolated from the Nacozari de García mining tail: Burkholderia cenocepacia, Sphingomonas sp. and Staphylococcus warneri. Significant microbiological differences were found between the two sites. All these species exhibited tolerance up to 300 mg/L for Cu (II)-Fe (II) solutions, indicating their capacity to grow in these conditions. Moreover, a consortium of isolated bacteria was immobilized in two different biocomposites and the biocomposite with larger pore size achieved greater bacterial immobilization showcasing the potential of these bacteria in biotechnological applications.
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Affiliation(s)
- Jonathan Parades-Aguilar
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio s/n, Entre Reforma y Sahuaripa, Edificio 7G, Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico
| | - Kadiya Calderon
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio s/n, Entre Reforma y Sahuaripa, Edificio 7G, Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico.
| | - Sarai Agustin-Salazar
- Institute for Polymers, Composites and Biomaterials (IPCB-CNR), Via Campi Flegrei 34, 80078, Pozzuoli, NA, Italy
| | - Pierfrancesco Cerruti
- Institute for Polymers, Composites and Biomaterials (IPCB-CNR), Via Campi Flegrei 34, 80078, Pozzuoli, NA, Italy
| | - Veronica Ambrogi
- Department of Chemical, Materials and Production Engineering (DICMAPI), University of Naples Federico II, Piazzale Tecchio 80, 80125, Naples, Italy
| | - Nohemi Gamez-Meza
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio s/n, Entre Reforma y Sahuaripa, Edificio 7G, Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico
| | - Luis Angel Medina-Juarez
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio s/n, Entre Reforma y Sahuaripa, Edificio 7G, Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico.
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Rahman Z, Thomas L, Chetri SPK, Bodhankar S, Kumar V, Naidu R. A comprehensive review on chromium (Cr) contamination and Cr(VI)-resistant extremophiles in diverse extreme environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:59163-59193. [PMID: 37046169 DOI: 10.1007/s11356-023-26624-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/20/2023] [Indexed: 05/10/2023]
Abstract
Chromium (Cr) compounds are usually toxins and exist abundantly in two different forms, Cr(VI) and Cr(III), in nature. Their contamination in any environment is a major problem. Many extreme environments including cold climate, warm climate, acidic environment, basic/alkaline environment, hypersaline environment, radiation, drought, high pressure, and anaerobic conditions have accumulated elevated Cr contamination. These harsh physicochemical conditions associated with Cr(VI) contamination damage biological systems in various ways. However, several unique microorganisms belonging to phylogenetically distant taxa (bacteria, fungi, and microalgae) owing to different and very distinct physiological characteristics can withstand extremities of Cr(VI) in different physicochemical environments. These challenging situations offer great potential and extended proficiencies in extremophiles for environmental and biotechnological applications. On these issues, the present review draws attention to Cr(VI) contamination from diverse extreme environmental regions. The study gives a detailed account on the ecology and biogeography of Cr(VI)-resistant microorganisms in inhospitable environments, and their use for detoxifying Cr(VI) and other applications. The study also focuses on physiological, multi-omics, and genetic engineering approaches of Cr(VI)-resistant extremophiles.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, India.
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Siva P K Chetri
- Department of Botany, Dimoria College, Gauhati University, Guwahati, Assam, India
| | - Shrey Bodhankar
- Department of Agriculture Microbiology, School of Agriculture Sciences, Anurag University, Hyderabad, Telangana, India
| | - Vikas Kumar
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Ravi Naidu
- Global Centre for Environmental Remediation, University of Newcastle, Newcastle, Australia
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González Plaza JJ, Hradecký J. The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests. Front Microbiol 2023; 14:1089525. [PMID: 36998409 PMCID: PMC10043212 DOI: 10.3389/fmicb.2023.1089525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023] Open
Abstract
Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.
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Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62. Mar Drugs 2023; 21:md21020095. [PMID: 36827136 PMCID: PMC9961484 DOI: 10.3390/md21020095] [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: 12/17/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (-)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC50 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations.
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Zárate A, Molina V, Valdés J, Icaza G, Vega SE, Castillo A, Ugalde JA, Dorador C. Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline. Front Microbiol 2023; 13:1020491. [PMID: 36726571 PMCID: PMC9885135 DOI: 10.3389/fmicb.2022.1020491] [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: 08/16/2022] [Accepted: 12/31/2022] [Indexed: 01/17/2023] Open
Abstract
Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Biotecnología en Ambientes Extremos, Centro de Excelencia en Medicina Traslacional, Universidad de la Frontera, Temuco, Chile,*Correspondence: Ana Zárate, ✉
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile,Verónica Molina, ✉
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Facultad de Ciencias del Mar y de Recursos Biológicos, Instituto de Ciencias Naturales A. von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | | | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados del Maule, Vicerrectoría de Investigación de Investigación y Posgrado, Universidad Católica del Maule, Campus San Miguel, Talca, Chile,J’EAI CHARISMA (IRD-France, UMNG-Colombia, UA-Chile, UCM-Chile, UCH-Chile, IGP-Peru, UPCH-Peru) and Nucleo Milenio UPWELL, Concepción, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile,Cristina Dorador, ✉
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Li Q, Pei L, Huang Z, Shu W, Li Q, Song Y, Zhao H, Schäfer M, Nordhaus I. Ecological risk assessment of heavy metals in the sediments and their impacts on bacterial community structure: A case study of Bamen Bay in China. MARINE POLLUTION BULLETIN 2023; 186:114482. [PMID: 36565579 DOI: 10.1016/j.marpolbul.2022.114482] [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: 10/18/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Heavy metal pollution associated with human activity is of big concern in tropical bays. Microorganisms may be highly sensitive to heavy metals. Nonetheless, little is known about effects of heavy metals on microbial structure in tropical bay sediments. In this study, 16S rRNA gene sequencing and potential ecological risk index analysis were used to analyze the relationships between nine metals (arsenic, lead, cadmium, cobalt, chromium, copper, zinc, manganese, and nickel) and bacterial communities in the sediments of Bamen Bay, China. Our results showed that Bamen Bay was under a considerable ecological risk and cadmium had the highest monomial potential ecological risk. In addition, individual metal contamination correlated with bacterial community composition but not with bacterial α-diversity. Arsenic was the metal influencing bacterial community structure the most. Our findings provide a novel insight into the monitoring and remediation of heavy metal pollution in tropical bays.
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Affiliation(s)
- Qipei Li
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China; Center for Eco-Environment Restoration of Hainan Province, School of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Lixin Pei
- Haikou Marine Geological Survey Center, China Geological Survey, Haikou 571127, China
| | - Zanhui Huang
- Haikou Marine Geological Survey Center, China Geological Survey, Haikou 571127, China
| | - Wei Shu
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, China; Center for Eco-Environment Restoration of Hainan Province, School of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Qiuli Li
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yanwei Song
- Haikou Marine Geological Survey Center, China Geological Survey, Haikou 571127, China.
| | - Hongwei Zhao
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, China; Center for Eco-Environment Restoration of Hainan Province, School of Ecology and Environment, Hainan University, Haikou 570228, China.
| | - Marvin Schäfer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen 28359, Germany
| | - Inga Nordhaus
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen 28359, Germany
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Anand KP, Suthindhiran K. Microbial signature and biosynthetic gene cluster profiling of poly extremophilic marine actinobacteria isolated from Vhan Island, Tamil Nadu, India. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2023.101742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Ribeiro I, Antunes JT, Alexandrino DAM, Tomasino MP, Almeida E, Hilário A, Urbatzka R, Leão PN, Mucha AP, Carvalho MF. Actinobacteria from Arctic and Atlantic deep-sea sediments-Biodiversity and bioactive potential. Front Microbiol 2023; 14:1158441. [PMID: 37065153 PMCID: PMC10100589 DOI: 10.3389/fmicb.2023.1158441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
The deep-sea covers over 70% of the Earth's surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.
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Affiliation(s)
- Inês Ribeiro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
- *Correspondence: Inês Ribeiro,
| | - Jorge T. Antunes
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Diogo A. M. Alexandrino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Environmental Health, School of Health, Polytechnic of Porto, Porto, Portugal
| | - Maria Paola Tomasino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Eduarda Almeida
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Ana Hilário
- Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Ralph Urbatzka
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pedro N. Leão
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Ana P. Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Maria F. Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
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Pan Y, Xie J, Yan W, Zhang TC, Chen C. Response of microbial community to different land-use types, nutrients and heavy metals in urban river sediment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115855. [PMID: 35994962 DOI: 10.1016/j.jenvman.2022.115855] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 05/27/2023]
Abstract
Nutrients and heavy metals (HM) in the sediment have an impact on microbial diversity and community structure. In this study, the distribution characteristics of nutrients, HM, and microbial community in the sediments along the Longsha River, a tributary of the Pearl River (or Zhu Jiang), China were investigated by analyzing samples from 11 sites. On the basis of the HM-contamination level, the 11 sampling sites were divided into three groups to explore the changes in microbial communities at different ecological risk levels. Results indicated that nutrient concentrations were higher near farmlands and residential lands, while the ecological risk of HM at the 11 sampling sites was from high to low as S10 > S2 > S9 > S6 > S11 > S7 > S5 > S8 > S3 > S4 > S1. Among these HM, Cu, Cr, and Ni had intense ecological risks. In addition, the results of Variance Partitioning Analysis (VPA) revealed a higher contribution of HM (35.93%) to microbial community variation than nutrients (12.08%) and pH (4.08%). Furthermore, the HM-tolerant microbial taxa (Clostridium_sensu_stricto_1, Romboutsia, norank_o__Gaiellales, and etc.) were the dominant genera, and they were more dynamic around industrial lands, while microbes involved in the C, N, and S cycles (e.g., Smithella, Thiobacillus, Dechloromonas, Bacter oidetes_vadinHA17, and Syntrophorhabdus) were inhibited by HM, while their abundance was lower near industrial lands and highway but higher around residential lands. A three-unit monitoring program of land-use types, pollutants, and microbial communities was proposed. These results provide a new perspective on the control of riparian land-use types based on contaminants and microbes, and different microbial community response patterns may provide a reference for contaminant control in sediments with intensive industrial activities.
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Affiliation(s)
- Yuwei Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Jiawei Xie
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Weixing Yan
- Foshan Nanhai Suzhou University of Science and Technology Environmental Research Institute, Foshan 528226, PR China
| | - Tian C Zhang
- Civil & Environmental Engineering Dept., University of Nebraska-Lincoln (Omaha Campus), Omaha, NE 68182-0178, USA
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, PR China; Foshan Nanhai Suzhou University of Science and Technology Environmental Research Institute, Foshan 528226, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215009, PR China.
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12
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Wang C, Jia Y, Wang Q, Yan F, Wu M, Li X, Fang W, Xu F, Liu H, Qiu Z. Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China. ENVIRONMENTAL RESEARCH 2022; 214:113748. [PMID: 35750128 DOI: 10.1016/j.envres.2022.113748] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 05/27/2023]
Abstract
In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.
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Affiliation(s)
- Can Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil&Water Pollution, PR China
| | - Yinxue Jia
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Qiqi Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Fangfang Yan
- Panzhihua City Company, Sichuan Tobacco Company, China National Tobacco Corporation, Panzhihua, 617000, Sichuan, PR China
| | - Minghui Wu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Xing Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Weizhen Fang
- Analysis & Testing Center, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Fei Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Huakang Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China.
| | - Zhongping Qiu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China.
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13
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Thalassobacillus, a genus of extreme to moderate environmental halophiles with biotechnological potential. World J Microbiol Biotechnol 2021; 37:147. [PMID: 34363544 DOI: 10.1007/s11274-021-03116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/29/2021] [Indexed: 01/09/2023]
Abstract
Thalassobacillus is a moderately halophilic genus that has been isolated from several sites worldwide, such as hypersaline lakes, saline soils, salt flats, and volcanic mud. Halophilic bacteria have provided functional stable biomolecules in harsh conditions for industrial purposes. Despite its potential biotechnological applications, Thalassobacillus has not been fully characterized yet. This review describes the Thalassobacillus genus, with the few species reported, pointing out its possible applications in enzymes (amylases, cellulases, xylanases, and others), biosurfactants, bioactive compounds, biofuels production, bioremediation, and plant growth promotion. The Thalassobacillus genus represents a little-explored biological resource but with a high potential.
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Wang C, Liu S, Wang P, Chen J, Wang X, Yuan Q, Ma J. How sediment bacterial community shifts along the urban river located in mining city. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42300-42312. [PMID: 33811632 DOI: 10.1007/s11356-020-12031-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Jingjie Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
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Maquia ISA, Fareleira P, Videira e. Castro I, Soares R, Brito DRA, Mbanze AA, Chaúque A, Máguas C, Ezeokoli OT, Ribeiro NS, Marques I, Ribeiro-Barros AI. The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique. Microorganisms 2021; 9:microorganisms9081562. [PMID: 34442641 PMCID: PMC8400031 DOI: 10.3390/microorganisms9081562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/14/2022] Open
Abstract
(1) Background: the Miombo woodlands comprise the most important vegetation from southern Africa and are dominated by tree legumes with an ecology highly driven by fires. Here, we report on the characterization of bacterial communities from the rhizosphere of Brachystegia boehmii in different soil types from areas subjected to different regimes. (2) Methods: bacterial communities were identified through Illumina MiSeq sequencing (16S rRNA). Vigna unguiculata was used as a trap to capture nitrogen-fixing bacteria and culture-dependent methods in selective media were used to isolate plant growth promoting bacteria (PGPB). PGP traits were analysed and molecular taxonomy of the purified isolates was performed. (3) Results: Bacterial communities in the Miombo rhizosphere are highly diverse and driven by soil type and fire regime. Independent of the soil or fire regime, the functional diversity was high, and the different consortia maintained the general functions. A diverse pool of diazotrophs was isolated, and included symbiotic (e.g., Mesorhizobium sp., Neorhizobium galegae, Rhizobium sp., and Ensifer adhaerens), and non-symbiotic (e.g., Agrobacterium sp., Burkholderia sp., Cohnella sp., Microvirga sp., Pseudomonas sp., and Stenotrophomonas sp.) bacteria. Several isolates presented cumulative PGP traits. (4) Conclusions: Although the dynamics of bacterial communities from the Miombo rhizosphere is driven by fire, the maintenance of high levels of diversity and functions remain unchanged, constituting a source of promising bacteria in terms of plant-beneficial activities such as mobilization and acquisition of nutrients, mitigation of abiotic stress, and modulation of plant hormone levels.
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Affiliation(s)
- Ivete Sandra Alberto Maquia
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- TropiKMan Doctoral Program, NOVA SBE, 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | - Paula Fareleira
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Isabel Videira e. Castro
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Ricardo Soares
- National Institute of Agricultural and Veterinary Research, I.P. (INIAV, I.P), 2780-157 Oeiras, Portugal; (P.F.); (I.V.e.C.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, Maputo 3453, Mozambique;
| | | | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Cristina Máguas
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Obinna T. Ezeokoli
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein 9300, South Africa;
| | - Natasha Sofia Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, Maputo 3453, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal;
- Correspondence: (I.M.); (A.I.R.-B.)
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16
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Wang F, Dong W, Zhao Z, Wang H, Li W, Chen G, Wang F, Zhao Y, Huang J, Zhou T. Heavy metal pollution in urban river sediment of different urban functional areas and its influence on microbial community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146383. [PMID: 34030363 DOI: 10.1016/j.scitotenv.2021.146383] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 05/22/2023]
Abstract
In this study, the Songgang River (SR) was selected as a typical contaminated urban river in a highly urbanized city (Shenzhen) that is extensively polluted by heavy metals (HMs). Five representative sampling sites were selected from different urban functional areas along the SR, and the spatial and vertical distributions of HMs and the related environmental risk were investigated. In addition, the distribution variability, composition, and abundance of microbial communities, as well as the correlation between the abundance of the operational taxonomic units (OTUs) and the HM contents were analyzed. The spatial distribution of HMs in the sediment revealed wide variation among the different urban functional areas. Industrial and residential areas had higher HM contents, following the order of Cu > Zn > Ni > Cr > Pb. In addition, the vertical characterization (5-300 cm) of HM content showed a decreasing trend with depth, with a distinct layer around 120-180 cm that might have been caused by anthropogenic activity. An ecological risk assessment indicated that Cu, Ni, and Cr pose high potential risks in these industrial and residential areas (at the depth of 5-180 cm). Furthermore, microbial community analysis indicated that some HM-tolerant bacteria (e.g., Gallionella, Acidovorax, Arenimonas, Curvibacter, and Sideroxydans) were dominant in the 5-120 cm layer, corresponding to high HM contents. A canonical correspondence analysis and co-occurrence network further confirmed that there was a strong correlation among the urban functional areas, HM contents, and the abundance of microorganisms in the urban river sediment. The results of this study have the potential to provide a bio-augmentation strategy for the in-situ bioremediation of sediment contaminated by HMs.
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Affiliation(s)
- Feng Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Wenyi Dong
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zilong Zhao
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Hongjie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Wenzheng Li
- School of Marine Science and Management, University of Sydney, Sydney, New South Wales 2220, Australia
| | - Guanhan Chen
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Feifei Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Yue Zhao
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Jie Huang
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Ting Zhou
- School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
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Cecchi G, Cutroneo L, Di Piazza S, Besio G, Capello M, Zotti M. Port Sediments: Problem or Resource? A Review Concerning the Treatment and Decontamination of Port Sediments by Fungi and Bacteria. Microorganisms 2021; 9:microorganisms9061279. [PMID: 34208305 PMCID: PMC8231108 DOI: 10.3390/microorganisms9061279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
Contamination of marine sediments by organic and/or inorganic compounds represents one of the most critical problems in marine environments. This issue affects not only biodiversity but also ecosystems, with negative impacts on sea water quality. The scientific community and the European Commission have recently discussed marine environment and ecosystem protection and restoration by sustainable green technologies among the main objectives of their scientific programmes. One of the primary goals of sustainable restoration and remediation of contaminated marine sediments is research regarding new biotechnologies employable in the decontamination of marine sediments, to consider sediments as a resource in many fields such as industry. In this context, microorganisms—in particular, fungi and bacteria—play a central and crucial role as the best tools of sustainable and green remediation processes. This review, carried out in the framework of the Interreg IT-FR Maritime GEREMIA Project, collects and shows the bioremediation and mycoremediation studies carried out on marine sediments contaminated with ecotoxic metals and organic pollutants. This work evidences the potentialities and limiting factors of these biotechnologies and outlines the possible future scenarios of the bioremediation of marine sediments, and also highlights the opportunities of an integrated approach that involves fungi and bacteria together.
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Affiliation(s)
- Grazia Cecchi
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Laura Cutroneo
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Simone Di Piazza
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
| | - Giovanni Besio
- DICCA, University of Genoa, 1 Via Montallegro, I-16145 Genoa, Italy;
| | - Marco Capello
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
- Correspondence:
| | - Mirca Zotti
- DISTAV, University of Genoa, 26 Corso Europa, I-16132 Genoa, Italy; (G.C.); (L.C.); (S.D.P.); (M.Z.)
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18
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Povedano-Priego C, Jroundi F, Lopez-Fernandez M, Shrestha R, Spanek R, Martín-Sánchez I, Villar MV, Ševců A, Dopson M, Merroun ML. Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124600. [PMID: 33339698 DOI: 10.1016/j.jhazmat.2020.124600] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm3 densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.
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Affiliation(s)
| | - Fadwa Jroundi
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
| | - Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Rojina Shrestha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Roman Spanek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Inés Martín-Sánchez
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
| | - María Victoria Villar
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Mohamed L Merroun
- Departmento de Microbiología, Facultad de Ciencias, University of Granada, Granada, Spain.
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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20
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Diversity and characterization of culturable haloalkaliphilic bacteria from two distinct hypersaline lakes in northern Egypt. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00609-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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