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Zapata-Peñasco I, Avelino-Jiménez I, Mendoza-Pérez J, Vázquez Guevara M, Gutiérrez-Ladrón de Guevara M, Valadez- Martínez M, Hernández-Maya L, Garibay-Febles V, Fregoso-Aguilar T, Fonseca-Campos J. Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00834. [PMID: 38948351 PMCID: PMC11211098 DOI: 10.1016/j.btre.2024.e00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 07/02/2024]
Abstract
The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or encapsulated indigenous hydrocarbonoclastic species selected under laboratory conditions to improve degradation rates. The environmental factors that act as stressors and impact the effectiveness of hydrocarbon removal are one of the challenges associated with these applications. Understanding how native microbes react to environmental stresses is necessary for effective bioaugmentation. Herein, Micrococcus luteus and M. yunnanensis isolated from a marine oil spill mooring system showed hydrocarbonoclastic activity on Maya crude oil in a short time by means of total petroleum hydrocarbons (TPH) at 144 h: M. luteus up to 98.79 % and M. yunnanensis 97.77 % removal. The assessment of Micrococcus biofilms at different temperature (30 °C and 50 °C), pH (5, 6, 7, 8, 9), salinity (30, 50, 60, 70, 80 g/L), and crude oil concentration (1, 5, 15, 25, 35 %) showed different response to the stressors depending on the strain. According to response surface analysis, the main effect was temperature > salinity > hydrocarbon concentration. The hydrocarbonoclastic biofilm architecture was characterised using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Subtle but significant differences were observed: pili in M. luteus by SEM and the topographical differences measured by AFM Power Spectral Density (PSD) analysis, roughness was higher in M. luteus than in M. yunnanensis. In all three domains of life, the Universal Stress Protein (Usp) is crucial for stress adaptation. Herein, the uspA gene expression was analysed in Micrococcus biofilm under environmental stressors. The uspA expression increased up to 2.5-fold in M. luteus biofilms at 30 °C, and 1.3-fold at 50 °C. The highest uspA expression was recorded in M. yunnanensis biofilms at 50 °C with 2.5 and 3-fold with salinities of 50, 60, and 80 g/L at hydrocarbon concentrations of 15, 25, and 35 %. M. yunnanensis biofilms showed greater resilience than M. luteus biofilms when exposed to harsh environmental stressors. M. yunnanensis biofilms were thicker than M. luteus biofilms. Both biofilm responses to environmental stressors through uspA gene expression were consistent with the behaviours observed in the response surface analyses. The uspA gene is a suitable biomarker for assessing environmental stressors of potential microorganisms for bioremediation of marine oil spills and for biosensing the ecophysiological status of native microbiota in a marine petroleum environment.
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Affiliation(s)
- I. Zapata-Peñasco
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - I.A. Avelino-Jiménez
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - J. Mendoza-Pérez
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - M. Vázquez Guevara
- Facultad de Química, Universidad de Guanajuato, Noria Alta, Guanajuato, 36050, Mexico
| | - M. Gutiérrez-Ladrón de Guevara
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - M. Valadez- Martínez
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - L. Hernández-Maya
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - V. Garibay-Febles
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas Norte 152, Gustavo A. Madero, Ciudad de México, 07730, Mexico
| | - T. Fregoso-Aguilar
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu 399, Nueva Industrial Vallejo, Gustavo A. Madero, 07738, Mexico
| | - J. Fonseca-Campos
- Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av Instituto Politécnico Nacional, Gustavo A. Madero, 07340, Mexico
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Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [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: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
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Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
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Si H, Zhou K, Zhao T, Cui B, Liu F, Zhao M. The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves. BIORESOUR BIOPROCESS 2023; 10:74. [PMID: 38647588 PMCID: PMC10992852 DOI: 10.1186/s40643-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 04/25/2024] Open
Abstract
Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.
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Affiliation(s)
- Hongyang Si
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Kun Zhou
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Tingyi Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Bing Cui
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China.
| | - Fang Liu
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China
| | - Mingqin Zhao
- College of Tobacco Science, Flavors and Fragrance Engineering & Technology Research Center of Henan Province, Henan Agricultural University, No.218 Ping An Avenue, Zhengdong New District, Zhengzhou, 450046, Henan, China.
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Pittino F, Zawierucha K, Poniecka E, Buda J, Rosatelli A, Zordan S, Azzoni RS, Diolaiuti G, Ambrosini R, Franzetti A. Functional and Taxonomic Diversity of Anaerobes in Supraglacial Microbial Communities. Microbiol Spectr 2023; 11:e0100422. [PMID: 36939373 PMCID: PMC10100660 DOI: 10.1128/spectrum.01004-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 02/16/2023] [Indexed: 03/21/2023] Open
Abstract
Cryoconite holes are small ponds present on the surface of most glaciers filled with meltwater and sediment at the bottom. Although they are characterized by extreme conditions, they host bacterial communities with high taxonomic and functional biodiversity. Despite that evidence for a potential niche for anaerobic microorganisms and anaerobic processes has recently emerged, the composition of the microbial communities of the cryoconite reported so far has not shown the relevant presence of anaerobic taxa. We hypothesize that this is due to the lower growth yield of anaerobes compared to aerobic microorganisms. In this work, we aim at evaluating whether the anaerobic bacterial community represents a relevant fraction of the biodiversity of the cryoconite and at describing its structure and functions. We collected sediment samples from cryoconite holes on the Forni Glacier (Italy) and sequenced both 16S rRNA amplicon genes and 16S rRNA amplicon transcripts at different times of the day along a clear summer day. Results showed that a relevant fraction of taxa has been detected only by 16S rRNA transcripts and was undetectable in 16S rRNA gene amplicons. Furthermore, in the transcript approach, anaerobic taxa were overrepresented compared with DNA sequencing. The metatranscriptomics approach was used also to investigate the expression of the main metabolic functions. Results showed the occurrence of syntrophic and commensalism relationships among fermentative bacteria, hydrogenothrophs, and consumers of fermentation end products, which have never been reported so far in cryoconite. IMPORTANCE Recent evidence disclosed the presence of a potential niche for anaerobic microorganisms and anaerobic processes in supraglacial sediments (cryoconite), but a detailed description of the structure and functions of the anaerobic population is still lacking. This work used rRNA and mRNA sequencing and demonstrated that anaerobes are very active in these environments and represent a relevant albeit neglected part of the ecosystem functions in these environments.
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Affiliation(s)
- Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Ewa Poniecka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Asia Rosatelli
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Simone Zordan
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
| | - Roberto S. Azzoni
- Department of Earth Science “Ardito Desio,” University of Milan, Milano, Italy
| | - Guglielmina Diolaiuti
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy (ESP), University of Milan, Milano, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT)–University of Milano-Bicocca, Milano, Italy
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Exploration of actinobacteria communities in seawater and sediments of mediterranean basin from Algerian coast displays hight diversity with new taxa and antibacterial potential. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01353-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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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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Kang J, Yin Z, Pei F, Ye Z, Song G, Ling H, Gao D, Jiang X, Zhang C, Ge J. Aerobic composting of chicken manure with penicillin G: Community classification and quorum sensing mediating its contribution to humification. BIORESOURCE TECHNOLOGY 2022; 352:127097. [PMID: 35367602 DOI: 10.1016/j.biortech.2022.127097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Chicken manure containing antibiotics is a hazardous biological waste. The purpose of our study was to investigate how different concentrations of penicillin G alter the bacterial community to affect humification during aerobic composting of chicken manure. The effect of quorum sensing on the bacterial community was also evaluated. Penicillin G mainly affects low fold changes (within 4) for low-abundance (within 200) microbial genera. We found that the bacterial community cooperated to regulate humus and humic acid synthesis. The microbial genera that make up the bacterial community are different, but each bacterial community may have the same ecological function. Quorum sensing affects humic acid synthesis by regulating carbohydrate metabolism and amino acid metabolism in bacterial communities through mechanisms such as the pentose phosphate pathway and the shikimate pathway. This work presents an understanding of the impact of quorum sensing on the collaboration between bacterial communities during composting.
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Affiliation(s)
- Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Ziliang Yin
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Fangyi Pei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Zeming Ye
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Gang Song
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Hongzhi Ling
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dongni Gao
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xueyong Jiang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China.
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Li W, Li Y, Zheng N, Ge C, Yao H. Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152756. [PMID: 34990667 DOI: 10.1016/j.scitotenv.2021.152756] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.
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Affiliation(s)
- Wei Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Yaying Li
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Ningguo Zheng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Chaorong Ge
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
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Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals. ENERGIES 2021. [DOI: 10.3390/en14164903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.
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10
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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11
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Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China. PLoS One 2020; 15:e0236006. [PMID: 32649724 PMCID: PMC7351256 DOI: 10.1371/journal.pone.0236006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Halophiles are relatively unexplored as potential sources of novel species.
However, little is known about the culturable bacterial diversity thrive in
hypersaline lakes. In this work, a total of 343 bacteria from sediment samples
of Aiding Lake, China, were isolated using nine different media supplemented
with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria
recovered from the different media varied, indicating the need to optimize the
isolation conditions. The results showed an unexpected level of bacterial
diversity, with four phyla (Actinobacteria,
Firmicutes, Proteobacteria, and
Rhodothermaeota), fourteen orders
(Actinopolysporales, Alteromonadales,
Bacillales, Balneolales,
Chromatiales, Glycomycetales,
Jiangellales, Micrococcales,
Micromonosporales, Oceanospirillales,
Pseudonocardiales, Rhizobiales,
Streptomycetales, and
Streptosporangiales), including 17 families, 43 genera
(including two novel genera), and 71 species (including four novel species). The
predominant phyla included Actinobacteria and Firmicutes and the predominant
genera included Actinopolyspora,
Gracilibacillus, Halomonas,
Nocardiopsis, and Streptomyces. To our
knowledge, this is the first time that members of phylum
Rhodothermaeota were identified in sediment samples from a
salt lake.
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12
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Millán-Aguiñaga N, Soldatou S, Brozio S, Munnoch JT, Howe J, Hoskisson PA, Duncan KR. Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential. MICROBIOLOGY-SGM 2020; 165:1169-1180. [PMID: 31592756 DOI: 10.1099/mic.0.000845] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare A ctinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.
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Affiliation(s)
- Natalie Millán-Aguiñaga
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, Baja California, México
| | - Sylvia Soldatou
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Science, Glasgow, UK
| | - Sarah Brozio
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Science, Glasgow, UK
| | - John T Munnoch
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Science, Glasgow, UK
| | - John Howe
- The Scottish Association for Marine Science, The Scottish Marine Institute, ObanArgyll, UK
| | - Paul A Hoskisson
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Science, Glasgow, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Science, Glasgow, UK
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13
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Zhang B, Wu X, Tai X, Sun L, Wu M, Zhang W, Chen X, Zhang G, Chen T, Liu G, Dyson P. Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China. Front Microbiol 2019; 10:2209. [PMID: 31608036 PMCID: PMC6769177 DOI: 10.3389/fmicb.2019.02209] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
Actinobacteria are known for their metabolic potential of producing diverse secondary metabolites such as antibiotics. Actinobacteria also playimportant roles in biogeochemical cycling and how soils develop. However, little is known about the effect of the vegetation type on the actinobacterial community structures in soils from arid regions. For these reasons, we have analyzed the actinobacterial communities of five types of ecosystem (tree grove, shrub, meadow, desert, and farm) in the Heihe river basin. Using 16S rRNA high-throughput sequencing, we found 11 classes of Actinobacteria, with dominant classes of Actinobacteria (36.2%), Thermoleophilia (28.3%), Acidimicrobiia (19.4%). Five classes, 15 orders, 20 families and 36 genera were present in all samples. The dominant generalist genera were Gaiella, Solirubrobacter, Nocardioides, Mycobacterium, and Pseudonocardia. The actinobacterial community structures were significantly affected by the environment and vegetation type. The diversity of the actinobacterial community in the desert ecosystem was high, and this ecosystem harbored the highest proportion of unclassified sequences, representing rare Actinobacteria. Functional metagenomic prediction, using PICRUSt, indicated that Actinobacteria play an important role in nitrogen cycling in both desert and cultivated farm ecosystems.
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Affiliation(s)
- Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xisheng Tai
- College of Geography and Environmental Engineering, Lanzhou City University, Lanzhou, China
| | - Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, China
| | - Minghui Wu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Paul Dyson
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
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14
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Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
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Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
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15
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Yamamura H, Hayashi T, Hamada M, Kohda T, Serisawa Y, Matsuyama-Serisawa K, Nakagawa Y, Otoguro M, Yanagida F, Tamura T, Hayakawa M. Cellulomonas algicola sp. nov., an actinobacterium isolated from a freshwater alga. Int J Syst Evol Microbiol 2019; 69:2723-2728. [PMID: 31232683 DOI: 10.1099/ijsem.0.003549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain, TKZ-21T, was isolated from a freshwater alga (Chetophoraceae) collected from the Takizawa River, Yamanashi, Japan, and examined using a polyphasic taxonomic approach. Cells were Gram-stain positive, aerobic, non-sporulating, motile, and coccoid or short rod-shaped. The strain grew in the presence of 0-4 % (w/v) NaCl, between pH 6-9.4, and over a temperature range of 15-40 °C, with optimum growth at 30 °C. The peptidoglycan type of strain TKZ-21T was A4β, containing l-ornithine as diagnostic diamino acid and d-glutamic acid as the interpeptide bridge. The predominant menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, ninhydrin-positive glycolipid, and unidentified phospholipids. The major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0, and the DNA G+C content was 75.6 mol%. On the basis of 16S rRNA gene sequence analysis, strain TKZ-21T was closely related to Cellulomonas fimi (98.5 % sequence similarity) and Cellulomonas biazotea (98.3 %). The genome orthoANI value between strain TKZ-21T and C. biazotea and C. fimi were 84.7 and 84.2 %, respectively. On the basis of fatty acid and MALDI-TOF MS profile analysis, phylogenetic analyses, genomic analysis, and phenotypic data, it is proposed that the isolate be classified as a representative of a novel species of the genus Cellulomonas, with the name Cellulomonas algicola sp. nov. The type strain is TKZ-21T (=NBRC 112905T=TBRC 8129T).
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Affiliation(s)
- Hideki Yamamura
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Takuma Hayashi
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center, National Institute of Technology and Evaluation, Kazusakamatari 2-5-8, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Kohda
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Yukihiko Serisawa
- Graduate School of Education, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | | | - Youji Nakagawa
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Misa Otoguro
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Fujitoshi Yanagida
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
| | - Tomohiko Tamura
- NITE Biological Resource Center, National Institute of Technology and Evaluation, Kazusakamatari 2-5-8, Kisarazu, Chiba 292-0818, Japan
| | - Masayuki Hayakawa
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Takeda-4-3-11, Kofu 400-8511, Japan
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16
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Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants. Probiotics Antimicrob Proteins 2019; 10:284-292. [PMID: 28560514 DOI: 10.1007/s12602-017-9293-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
As potential probiotic candidates, plant vertically transmitted actinobacteria are beneficial to growth and health of host plants. New methods to isolate the actinobacterial taxa with low growth rates should be developed. Based on the actinobacterial population information, the probiotic actinobacterial taxa could be directly isolated from healthy banana shoot tips. However, actinobacterial DNAs with high GC contents could bias estimates of actinobacteria by PCR. In the study, two amplicon sequencing strategies were adopted to elucidate the endophytic actinobacterial community of banana plants. More than 92.5% bacterial OTUs were affiliated with actinobacteria by these two strategies, and total 14,289 actinobacterial OTUs with above 97% similarity were detected in banana shoot tips. Although the libraries generated by the two strategies differed in the abundance of some genera, Mycobacterium and Nocardia dominated both libraries and most actinobacterial taxa were overlapped. Higher phylogenetic resolution actinobacteriome of banana plants was successfully established. Based on the endophytic actinobacterial community information, the streptomycetes were isolated from shoot tips. Pot experiments illustrated that the strain could promote banana plantlet growth and elevate resistance to Fusarium oxysporum f. sp. cubense (FOC) under FOC infested soils. The results suggested that the selection for probiotic agents based on actinobacteriome analysis is reliable and feasible compared with present greenhouse selection.
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17
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Cuthbertson L, Amores-Arrocha H, Malard LA, Els N, Sattler B, Pearce DA. Characterisation of Arctic Bacterial Communities in the Air above Svalbard. BIOLOGY 2017; 6:biology6020029. [PMID: 28481257 PMCID: PMC5485476 DOI: 10.3390/biology6020029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/09/2023]
Abstract
Atmospheric dispersal of bacteria is increasingly acknowledged as an important factor influencing bacterial community biodiversity, biogeography and bacteria–human interactions, including those linked to human health. However, knowledge about patterns in microbial aerobiology is still relatively scarce, and this can be attributed, in part, to a lack of consensus on appropriate sampling and analytical methodology. In this study, three different methods were used to investigate aerial biodiversity over Svalbard: impaction, membrane filtration and drop plates. Sites around Svalbard were selected due to their relatively remote location, low human population, geographical location with respect to air movement and the tradition and history of scientific investigation on the archipelago, ensuring the presence of existing research infrastructure. The aerial bacterial biodiversity found was similar to that described in other aerobiological studies from both polar and non-polar environments, with Proteobacteria, Actinobacteria, and Firmicutes being the predominant groups. Twelve different phyla were detected in the air collected above Svalbard, although the diversity was considerably lower than in urban environments elsewhere. However, only 58 of 196 bacterial genera detected were consistently present, suggesting potentially higher levels of heterogeneity. Viable bacteria were present at all sampling locations, showing that living bacteria are ubiquitous in the air around Svalbard. Sampling location influenced the results obtained, as did sampling method. Specifically, impaction with a Sartorius MD8 produced a significantly higher number of viable colony forming units (CFUs) than drop plates alone.
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Affiliation(s)
- Lewis Cuthbertson
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria at Newcastle, Ellison Building, Newcastle-upon-Tyne NE1 8ST, UK.
| | - Herminia Amores-Arrocha
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria at Newcastle, Ellison Building, Newcastle-upon-Tyne NE1 8ST, UK.
| | - Lucie A Malard
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria at Newcastle, Ellison Building, Newcastle-upon-Tyne NE1 8ST, UK.
| | - Nora Els
- Institute of Ecology, Austrian Polar Research Institute, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria.
| | - Birgit Sattler
- Institute of Ecology, Austrian Polar Research Institute, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria.
| | - David A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, University of Northumbria at Newcastle, Ellison Building, Newcastle-upon-Tyne NE1 8ST, UK.
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18
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Smith SL, Boothman C, Williams HA, Ellis BL, Wragg J, West JM, Lloyd JR. Microbial impacts on 99mTc migration through sandstone under highly alkaline conditions relevant to radioactive waste disposal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 575:485-495. [PMID: 27751688 DOI: 10.1016/j.scitotenv.2016.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
Geological disposal of intermediate level radioactive waste in the UK is planned to involve the use of cementitious materials, facilitating the formation of an alkali-disturbed zone within the host rock. The biogeochemical processes that will occur in this environment, and the extent to which they will impact on radionuclide migration, are currently poorly understood. This study investigates the impact of biogeochemical processes on the mobility of the radionuclide technetium, in column experiments designed to be representative of aspects of the alkali-disturbed zone. Results indicate that microbial processes were capable of inhibiting 99mTc migration through columns, and X-ray radiography demonstrated that extensive physical changes had occurred to the material within columns where microbiological activity had been stimulated. The utilisation of organic acids under highly alkaline conditions, generating H2 and CO2, may represent a mechanism by which microbial processes may alter the hydraulic conductivity of a geological environment. Column sediments were dominated by obligately alkaliphilic H2-oxidising bacteria, suggesting that the enrichment of these bacteria may have occurred as a result of H2 generation during organic acid metabolism. The results from these experiments show that microorganisms are able to carry out a number of processes under highly alkaline conditions that could potentially impact on the properties of the host rock surrounding a geological disposal facility for intermediate level radioactive waste.
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Affiliation(s)
- Sarah L Smith
- Research Centre for Radwaste and Decommissioning & Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, United Kingdom; British Geological Survey, Environmental Science Centre, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Christopher Boothman
- Research Centre for Radwaste and Decommissioning & Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Heather A Williams
- Department of Nuclear Medicine, Manchester Royal Infirmary, Oxford Road, M13 9WL, United Kingdom
| | - Beverly L Ellis
- Department of Nuclear Medicine, Manchester Royal Infirmary, Oxford Road, M13 9WL, United Kingdom
| | - Joanna Wragg
- British Geological Survey, Environmental Science Centre, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Julia M West
- British Geological Survey, Environmental Science Centre, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Jonathan R Lloyd
- Research Centre for Radwaste and Decommissioning & Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, United Kingdom
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19
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Maciejewska M, Adam D, Martinet L, Naômé A, Całusińska M, Delfosse P, Carnol M, Barton HA, Hayette MP, Smargiasso N, De Pauw E, Hanikenne M, Baurain D, Rigali S. A Phenotypic and Genotypic Analysis of the Antimicrobial Potential of Cultivable Streptomyces Isolated from Cave Moonmilk Deposits. Front Microbiol 2016; 7:1455. [PMID: 27708627 PMCID: PMC5030222 DOI: 10.3389/fmicb.2016.01455] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical properties, thereby suggesting that its filamentous endemic actinobacterial population might be a source of natural products useful in human treatment. In this work, a screening approach was undertaken in order to isolate cultivable Actinobacteria from moonmilk of the Grotte des Collemboles in Belgium, to evaluate their taxonomic profile, and to assess their potential in biosynthesis of antimicrobials. Phylogenetic analysis revealed that all 78 isolates were exclusively affiliated to the genus Streptomyces and clustered into 31 distinct phylotypes displaying various pigmentation patterns and morphological features. Phylotype representatives were tested for antibacterial and antifungal activities and their genomes were mined for secondary metabolite biosynthetic genes coding for non-ribosomal peptide synthetases (NRPSs), and polyketide synthases (PKS). The moonmilk Streptomyces collection was found to display strong inhibitory activities against a wide range of reference organisms, as 94, 71, and 94% of the isolates inhibited or impaired the growth of Gram-positive, Gram-negative bacteria, and fungi, respectively. Interestingly, 90% of the cave strains induced strong growth suppression against the multi-drug resistant Rasamsonia argillacea, a causative agent of invasive mycosis in cystic fibrosis and chronic granulomatous diseases. No correlation was observed between the global antimicrobial activity of an individual strain and the number of NRPS and PKS genes predicted in its genome, suggesting that approaches for awakening cryptic metabolites biosynthesis should be applied to isolates with no antimicrobial phenotype. Overall, our work supports the common belief that moonmilk might effectively treat various infectious diseases thanks to the presence of a highly diverse population of prolific antimicrobial producing Streptomyces, and thus may indeed constitute a promising reservoir of potentially novel active natural compounds.
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Affiliation(s)
- Marta Maciejewska
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège Liège, Belgium
| | - Delphine Adam
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège Liège, Belgium
| | - Loïc Martinet
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège Liège, Belgium
| | - Aymeric Naômé
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège Liège, Belgium
| | - Magdalena Całusińska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology Belvaux, Luxembourg
| | - Philippe Delfosse
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology Belvaux, Luxembourg
| | - Monique Carnol
- InBioS - Plant and Microbial Ecology, Botany B22, University of Liège Liège, Belgium
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron OH, USA
| | - Marie-Pierre Hayette
- Department of Clinical Microbiology, University Hospital of Liège Liège, Belgium
| | - Nicolas Smargiasso
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège Liège, Belgium
| | - Edwin De Pauw
- MolSys Research Unit, Mass Spectrometry Laboratory, University of Liège Liège, Belgium
| | - Marc Hanikenne
- InBioS - Functional Genomics and Plant Molecular Imaging, University of LiègeLiège, Belgium; PhytoSYSTEMS, University of LiègeLiège, Belgium
| | - Denis Baurain
- PhytoSYSTEMS, University of LiègeLiège, Belgium; InBioS - Eukaryotic Phylogenomics, University of LiègeLiège, Belgium
| | - Sébastien Rigali
- InBioS - Centre for Protein Engineering, Institut de Chimie B6a, University of Liège Liège, Belgium
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Chen P, Zhang L, Guo X, Dai X, Liu L, Xi L, Wang J, Song L, Wang Y, Zhu Y, Huang L, Huang Y. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge. Front Microbiol 2016; 7:1340. [PMID: 27621725 PMCID: PMC5002886 DOI: 10.3389/fmicb.2016.01340] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/15/2016] [Indexed: 02/01/2023] Open
Abstract
The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.
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Affiliation(s)
- Ping Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Xiaoxuan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Li Liu
- Information Network Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Lijun Xi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai Shanghai, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
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Influence of Chicken Manure Fertilization on Antibiotic-Resistant Bacteria in Soil and the Endophytic Bacteria of Pakchoi. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13070662. [PMID: 27376311 PMCID: PMC4962203 DOI: 10.3390/ijerph13070662] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 11/17/2022]
Abstract
Animal manure is commonly used as fertilizer for agricultural crops worldwide, even though it is believed to contribute to the spread of antibiotic resistance from animal intestines to the soil environment. However, it is unclear whether and how there is any impact of manure fertilization on populations and community structure of antibiotic-resistant endophytic bacteria (AREB) in plant tissues. To investigate the effect of manure and organic fertilizer on endophytic bacterial communities, pot experiments were performed with pakchoi grown with the following treatments: (1) non-treated; (2) chicken manure-treated and (3) organic fertilizer-treated. Manure or organic fertilizer significantly increased the abundances of total cultivable endophytic bacteria (TCEB) and AREB in pakchoi, and the effect of chicken manure was greater than that of organic fertilizer. Further, 16S rDNA sequencing and the phylogenetic analysis indicated that chicken manure or organic fertilizer application increased the populations of multiple antibiotic-resistant bacteria (MARB) in soil and multiple antibiotic-resistant endophytic bacteria (MAREB) in pakchoi. The identical multiple antibiotic-resistant bacterial populations detected in chicken manure, manure- or organic fertilizer-amended soil and the vegetable endophytic system were Brevundimonas diminuta, Brachybacterium sp. and Bordetella sp., suggesting that MARB from manure could enter and colonize the vegetable tissues through manure fertilization. The fact that some human pathogens with multiple antibiotic resistance were detected in harvested vegetables after growing in manure-amended soil demonstrated a potential threat to human health.
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Ettoumi B, Chouchane H, Guesmi A, Mahjoubi M, Brusetti L, Neifar M, Borin S, Daffonchio D, Cherif A. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea. Microbiol Res 2016; 186-187:71-80. [DOI: 10.1016/j.micres.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
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23
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Liao L, Chen R, Jiang M, Tian X, Liu H, Yu Y, Fan C, Chen B. Bioprospecting potential of halogenases from Arctic marine actinomycetes. BMC Microbiol 2016; 16:34. [PMID: 26964536 PMCID: PMC4785625 DOI: 10.1186/s12866-016-0662-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/05/2016] [Indexed: 11/14/2022] Open
Abstract
Background Halometabolites, an important group of natural products, generally require halogenases for their biosynthesis. Actinomycetes from the Arctic Ocean have rarely been investigated for halogenases and their gene clusters associated, albeit great potential of halometabolite production has been predicted. Therefore, we initiated this research on the screening of halogenases from Arctic marine actinomycetes isolates to explore their genetic potential of halometabolite biosynthesis. Results Nine halogenase genes were discovered from sixty Arctic marine actinomycetes using in-house designed or previously reported PCR primers. Four representative genotypes were further cloned to obtain full coding regions through genome walking. The resulting halogenases were predicted to be involved in halogenation of indole groups, antitumor agent ansamitocin-like substrates, or unknown peptide-like compounds. Genome sequencing revealed a potential gene cluster containing the halogenase predicted to catalyze peptide-like compounds. However, the gene cluster was probably silent under the current conditions. Conclusions PCR-based screening of halogenase genes is a powerful and efficient tool to conduct bioprospecting of halometabolite-producing actinomycetes from the Arctic. Genome sequencing can also identify cryptic gene clusters potentially producing new halometabolites, which might be easily missed by traditional isolation and chemical characterization. In addition, our study indicates that great genetic potential of new halometabolites can be expected from mostly untapped actinomycetes from the polar regions. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0662-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Liao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Ruiqin Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Bioengineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20030, China
| | - Xiaoqing Tian
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Huan Liu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Chenqi Fan
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.
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Sun W, Zhang F, He L, Karthik L, Li Z. Actinomycetes from the South China Sea sponges: isolation, diversity, and potential for aromatic polyketides discovery. Front Microbiol 2015; 6:1048. [PMID: 26483773 PMCID: PMC4589764 DOI: 10.3389/fmicb.2015.01048] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
Marine sponges often harbor dense and diverse microbial communities including actinobacteria. To date no comprehensive investigation has been performed on the culturable diversity of the actinomycetes associated with South China Sea sponges. Structurally novel aromatic polyketides were recently discovered from marine sponge-derived Streptomyces and Saccharopolyspora strains, suggesting that sponge-associated actinomycetes can serve as a new source of aromatic polyketides. In this study, a total of 77 actinomycete strains were isolated from 15 South China Sea sponge species. Phylogenetic characterization of the isolates based on 16S rRNA gene sequencing supported their assignment to 12 families and 20 genera, among which three rare genera (Marihabitans, Polymorphospora, and Streptomonospora) were isolated from marine sponges for the first time. Subsequently, β-ketoacyl synthase (KSα) gene was used as marker for evaluating the potential of the actinomycete strains to produce aromatic polyketides. As a result, KSα gene was detected in 35 isolates related to seven genera (Kocuria, Micromonospora, Nocardia, Nocardiopsis, Saccharopolyspora, Salinispora, and Streptomyces). Finally, 10 strains were selected for small-scale fermentation, and one angucycline compound was detected from the culture extract of Streptomyces anulatus strain S71. This study advanced our knowledge of the sponge-associated actinomycetes regarding their diversity and potential in producing aromatic polyketides.
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Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Fengli Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Loganathan Karthik
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
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25
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Duran R, Bielen A, Paradžik T, Gassie C, Pustijanac E, Cagnon C, Hamer B, Vujaklija D. Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15215-29. [PMID: 25712885 DOI: 10.1007/s11356-015-4240-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/13/2015] [Indexed: 05/27/2023]
Abstract
The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
- Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1155, 64013, Pau Cedex, France.
| | - Ana Bielen
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Tina Paradžik
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
| | - Claire Gassie
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Emina Pustijanac
- Juraj Dobrila University of Pula, Zagrebačka 30, 52100, Pula, Croatia
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Bojan Hamer
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210, Rovinj, Croatia
| | - Dušica Vujaklija
- Division of Molecular Biology, Institute Ruđer Bošković, Bijenička 54, 10000, Zagreb, Croatia
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26
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Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile. Front Microbiol 2015; 6:737. [PMID: 26284034 PMCID: PMC4516979 DOI: 10.3389/fmicb.2015.00737] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds.
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Affiliation(s)
| | | | | | | | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea. Appl Microbiol Biotechnol 2015; 99:5939-50. [PMID: 25820602 DOI: 10.1007/s00253-015-6547-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/05/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.
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28
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Nguyen D, Maranger R, Balagué V, Coll-Lladó M, Lovejoy C, Pedrós-Alió C. Winter diversity and expression of proteorhodopsin genes in a polar ocean. ISME JOURNAL 2015; 9:1835-45. [PMID: 25700336 DOI: 10.1038/ismej.2015.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 12/25/2022]
Abstract
Mixotrophy is a valuable functional trait used by microbes when environmental conditions vary broadly or resources are limited. In the sunlit waters of the ocean, photoheterotrophy, a form of mixotrophy, is often mediated by proteorhodopsin (PR), a seven helices transmembrane protein binding the retinal chromophore. Altogether, they allow bacteria to capture photic energy for sensory and proton gradient formation cell functions. The seasonal occurrence and diversity of the gene coding for PR in cold oligotrophic polar oceans is not known and PR expression has not yet been reported. Here we show that PR is widely distributed among bacterial taxa, and that PR expression decreased markedly during the winter months in the Arctic Ocean. Gammaproteobacteria-like PR sequences were always dominant. However, within the second most common affiliation, there was a transition from Flavobacteria-like PR in early winter to Alphaproteobacteria-like PR in late winter. The phylogenetic shifts followed carbon dynamics, where patterns in expression were consistent with community succession, as identified by DNA community fingerprinting. Although genes for PR were always present, the trend in decreasing transcripts from January to February suggested reduced functional utility of PR during winter. Under winter darkness, sustained expression suggests that PR may continue to be useful for non-ATP forming functions, such as environmental sensing or small solute transport. The persistence of PR expression in winter among some bacterial groups may offer a competitive advantage, where its multifunctionality enhances microbial survival under harsh polar conditions.
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Affiliation(s)
- Dan Nguyen
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Roxane Maranger
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Vanessa Balagué
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Montserrat Coll-Lladó
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Connie Lovejoy
- Département de biologie, Québec-Océan, Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, Québec, Canada
| | - Carlos Pedrós-Alió
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
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Duncan KR, Haltli B, Gill KA, Correa H, Berrué F, Kerr RG. Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada. J Ind Microbiol Biotechnol 2014; 42:57-72. [PMID: 25371290 DOI: 10.1007/s10295-014-1529-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
Marine sediments from Newfoundland, Canada were explored for biotechnologically promising Actinobacteria using culture-independent and culture-dependent approaches. Culture-independent pyrosequencing analyses uncovered significant actinobacterial diversity (H'-2.45 to 3.76), although the taxonomic diversity of biotechnologically important actinomycetes could not be fully elucidated due to limited sampling depth. Assessment of culturable actinomycete diversity resulted in the isolation of 360 actinomycetes representing 59 operational taxonomic units, the majority of which (94 %) were Streptomyces. The biotechnological potential of actinomycetes from NL sediments was assessed by bioactivity and metabolomics-based screening of 32 representative isolates. Bioactivity was exhibited by 41 % of isolates, while 11 % exhibited unique chemical signatures in metabolomics screening. Chemical analysis of two isolates resulted in the isolation of the cytotoxic metabolite 1-isopentadecanoyl-3β-D-glucopyranosyl-X-glycerol from Actinoalloteichus sp. 2L868 and sungsanpin from Streptomyces sp. 8LB7. These results demonstrate the potential for the discovery of novel bioactive metabolites from actinomycetes isolated from Atlantic Canadian marine sediments.
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Affiliation(s)
- K R Duncan
- Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3, Canada
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