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Manyatsi TS, Lin YH, Jou YT. The isolation and identification of Bacillus velezensis ZN-S10 from vanilla (V. planifolia), and the microbial distribution after the curing process. Sci Rep 2024; 14:16339. [PMID: 39014002 PMCID: PMC11252412 DOI: 10.1038/s41598-024-66753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The market value of vanilla beans (Vanilla planifolia) is constantly increasing due to their natural aroma and flavor properties that improve after a curing process, where bacteria colonization plays a critical role. However, a few publications suggest that bacteria play a role in the curing process. Hence, this study aimed to isolate Bacillus sp. that could be used for fermenting V. planifolia while analyzing their role in the curing process. Bacillus velezensis ZN-S10 identified with 16S rRNA sequencing was isolated from conventionally cured V. planifolia beans. A bacteria culture solution of B. velezensis ZN-S10 (1 mL of 1 × 107 CFU mL-1) was then coated on 1 kg of non-cured vanilla pods that was found to ferment and colonize vanilla. PCA results revealed distinguished bacterial communities of fermented vanilla and the control group, suggesting colonization of vanilla. Phylogenetic analysis showed that ZN-S10 was the dominant Bacillus genus member and narrowly correlated to B. velezensis EM-1 and B. velezensis PMC206-1, with 78% and 73% similarity, respectively. The bacterial taxonomic profiling of cured V. planifolia had a significant relative abundance of Firmicutes, Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes phyla according to the predominance. Firmicutes accounted for 55% of the total bacterial sequences, suggesting their colonization and effective fermentation roles in curing vanilla.
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Affiliation(s)
- Thabani Sydney Manyatsi
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan
| | - Yu-Hsin Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan
| | - Ying-Tzy Jou
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu Shuefu Road 1, 91201, Pingtung, Taiwan.
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Ganie ZA, Mandal A, Arya L, T S, Talib M, Darbha GK. Assessment and accumulation of microplastics in the Indian riverine systems: Risk assessment and implications of translocation across the water-to-fish continuum. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 272:106944. [PMID: 38823071 DOI: 10.1016/j.aquatox.2024.106944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Microplastic (MP) pollution has engulfed global aquatic systems, and the concerns about microplastic translocation and bioaccumulation in fish and other aquatic organisms are now an unpleasant truth. In the past few years, MP pollution in freshwater systems, particularly rivers and subsequently in freshwater organisms, especially in fish, has caught the attention of researchers. Rivers provide livelihood to approximately 40 % of the global population through food and potable water. Hence, assessment of emerging contaminants like microplastics in rivers and the associated fauna is crucial. This study assessed microplastics (MPs) in fish, sediment and freshwater samples across the third largest riverine system of peninsular India, the Mahanadi River. The number concentrations of MPs measured in water, sediment and fish ranged from 337.5 ± 54.4-1333.3 ± 557.2 MPs/m3, 14.7 ± 3.7-69.3 ± 10.1 MPs/kg. Dry weight and 0.4-3.2 MPs/Fish, respectively. Surprisingly, MPs were found in every second fish sample, with a higher MP number in the gut than in the gills. Black and blue coloured filaments with <0.5 mm size were the dominant MPs with polypropylene and polyethylene polymers in abundance. The Polymer Hazard Index (PHI) and the Potential Ecological Risk Index (PERI) studies revealed that the majority of the sampling sites fell in Risk category V (dangerous category). An irregular trend in the MP concentration was observed downstream of the river, though relatively elevated MP concentrations in water and fish samples were observed downstream of the river. t-Distributed Stochastic Neighbour Embedding (t-SNE) unveiled distinct patterns in MP distribution with a higher similarity exhibited in the MPs found in fish gill and gut samples, unlike water and sediment, which shared certain characteristics. The findings in the current study contribute to filling the knowledge gap of MP assessment and accumulation in global freshwater systems and highlight the microplastic contamination and accumulation in fish with its potential implications on human health.
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Affiliation(s)
- Zahid Ahmad Ganie
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India
| | - Abhishek Mandal
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India
| | - Lavish Arya
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India
| | - Sangeetha T
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India
| | - Mohmmed Talib
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India
| | - Gopala Krishna Darbha
- Environmental Nanoscience Laboratory, Department of Earth Sciences, Indian Institute of Science Education and Research- Kolkata, Mohanpur, West Bengal, 741246, India; Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India.
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Awad MA, Hammad SF, El-Mashtoly SF, El-Deeb B, Soliman HSM. Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel. BMC Complement Med Ther 2024; 24:205. [PMID: 38796482 PMCID: PMC11128111 DOI: 10.1186/s12906-024-04482-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 04/24/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND The plant roots excrete a large number of organic compounds into the soil. The rhizosphere, a thin soil zone around the roots, is a hotspot for microbial activity, making it a crucial component of the soil ecosystem. Secondary metabolites produced by rhizospheric Sphingomonas sanguinis DM have sparked significant curiosity in investigating their possible biological impacts. METHODS A bacterial strain has been isolated from the rhizosphere of Datura metel. The bacterium's identification, fermentation, and working up have been outlined. The ethyl acetate fraction of the propagated culture media of Sphingomonas sanguinis DM was fractioned and purified using various chromatographic techniques. The characterization of the isolated compounds was accomplished through the utilization of various spectroscopic techniques, such as UV, MS, 1D, and 2D-NMR. Furthermore, the evaluation of their antimicrobial activity was conducted using the agar well diffusion method, while cytotoxicity was assessed using the MTT test. RESULTS The extract from Sphingomonas sanguinis DM provided two distinct compounds: n-dibutyl phthalic acid (1) and Bis (2-methyl heptyl) phthalate (2) within its ethyl acetate fraction. Furthermore, the 16S rRNA gene sequence of Sphingomonas sanguinis DM has been registered under the NCBI GenBank database with the accession number PP422198. The bacterial extract exhibited its effect against gram-positive bacteria, inhibiting Streptococcus mutans (12.6 ± 0.6 mm) and Staphylococcus aureus (10.6 ± 0.6 mm) compared to standard antibiotics. Conversely, compound 1 showed a considerable effect against phytopathogenic fungi such as Alternaria alternate (56.3 ± 10.6 mm) and Fusarium oxysporum (21.3 ± 1.5 mm) with a MIC value of 17.5 µg/mL. However, it was slightly active against Klebsiella pneumonia (11.0 ± 1.0 mm). Furthermore, compound 2 was the most active metabolite, having a significant antimicrobial efficacy against Rhizoctonia solani (63.6 ± 1.1 mm), Pseudomonas aeruginosa (16.7 ± 0.6 mm), and Alternaria alternate (20.3 ± 0.6 mm) with MIC value at 15 µg/mL. In addition, compound 2 exhibited the most potency against hepatocellular (HepG-2) and skin (A-431) carcinoma cell lines with IC50 values of 107.16 µg/mL and 111.36 µg/mL, respectively. CONCLUSION Sphingomonas sanguinis DM, a rhizosphere bacterium of Datura metel, was studied for its phytochemical and biological characteristics, resulting in the identification of two compounds with moderate antimicrobial and cytotoxic activities.
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Affiliation(s)
- Mohamed A Awad
- Biotechnology Program, Institute of Basic and Applied Science, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Sherif F Hammad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
- PharmD Program, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
| | - Samir F El-Mashtoly
- Biotechnology Program, Institute of Basic and Applied Science, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt
| | - Bahig El-Deeb
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Hesham S M Soliman
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt.
- PharmD Program, Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City, Alexandria, 21934, Egypt.
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Shang Y, Wang X, Wu X, Dou H, Wei Q, Wang Q, Liu G, Sun G, Wang L, Zhang H. Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors. Microbiol Spectr 2024; 12:e0324523. [PMID: 38602397 PMCID: PMC11064641 DOI: 10.1128/spectrum.03245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/12/2024] Open
Abstract
Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.
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Affiliation(s)
- Yongquan Shang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Gang Liu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Guolei Sun
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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Ahmad T, Erum Ishaq S, Liang L, Hou J, Xie R, Dong Y, Yu T, Wang F. Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea. Syst Appl Microbiol 2024; 47:126490. [PMID: 38330528 DOI: 10.1016/j.syapm.2024.126490] [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: 12/23/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01T (= CGMCC 1.61593T = KCTC 92913T).
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Affiliation(s)
- Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Lewen Liang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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Dolatabad HK, Mahjenabadi VAJ. Geographical and climatic distribution of lentil-nodulating rhizobia in Iran. FEMS Microbiol Ecol 2024; 100:fiae046. [PMID: 38587812 PMCID: PMC11044965 DOI: 10.1093/femsec/fiae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Lentil is one of the most important legumes cultivated in various provinces of Iran. However, there is limited information about the symbiotic rhizobia of lentils in this country. In this study, molecular identification of lentil-nodulating rhizobia was performed based on 16S-23S rRNA intergenic spacer (IGS) and recA, atpD, glnII, and nodC gene sequencing. Using PCR-RFLP analysis of 16S-23S rRNA IGS, a total of 116 rhizobia isolates were classified into 20 groups, leaving seven strains unclustered. Phylogenetic analysis of representative isolates revealed that the rhizobia strains belonged to Rhizobium leguminosarum and Rhizobium laguerreae, and the distribution of the species is partially related to geographical location. Rhizobium leguminosarum was the dominant species in North Khorasan and Zanjan, while R. laguerreae prevailed in Ardabil and East Azerbaijan. The distribution of the species was also influenced by agroecological climates; R. leguminosarum thrived in cold semiarid climates, whereas R. laguerreae adapted to humid continental climates. Both species exhibited equal dominance in the Mediterranean climate, characterized by warm, dry summers and mild, wet winters, in Lorestan and Kohgiluyeh-Boyer Ahmad provinces.
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Affiliation(s)
- Hossein Kari Dolatabad
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
| | - Vahid Alah Jahandideh Mahjenabadi
- Soil Biology and Biotechnology Department, Soil and Water Research Institute, Agriculture Research, Education and Extension Organization, Meshkin Dasht Road, Karaj 31785-311, Iran
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Pal U, Bachmann D, Pelzer C, Christiansen J, Blank LM, Tiso T. A genetic toolbox to empower Paracoccus pantotrophus DSM 2944 as a metabolically versatile SynBio chassis. Microb Cell Fact 2024; 23:53. [PMID: 38360576 PMCID: PMC10870620 DOI: 10.1186/s12934-024-02325-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND To contribute to the discovery of new microbial strains with metabolic and physiological robustness and develop them into successful chasses, Paracoccus pantotrophus DSM 2944, a Gram-negative bacterium from the phylum Alphaproteobacteria and the family Rhodobacteraceae, was chosen. The strain possesses an innate ability to tolerate high salt concentrations. It utilizes diverse substrates, including cheap and renewable feedstocks, such as C1 and C2 compounds. Also, it can consume short-chain alkanes, predominately found in hydrocarbon-rich environments, making it a potential bioremediation agent. The demonstrated metabolic versatility, coupled with the synthesis of the biodegradable polymer polyhydroxyalkanoate, positions this microbial strain as a noteworthy candidate for advancing the principles of a circular bioeconomy. RESULTS The study aims to follow the chassis roadmap, as depicted by Calero and Nikel, and de Lorenzo, to transform wild-type P. pantotrophus DSM 2944 into a proficient SynBio (Synthetic Biology) chassis. The initial findings highlight the antibiotic resistance profile of this prospective SynBio chassis. Subsequently, the best origin of replication (ori) was identified as RK2. In contrast, the non-replicative ori R6K was selected for the development of a suicide plasmid necessary for genome integration or gene deletion. Moreover, when assessing the most effective method for gene transfer, it was observed that conjugation had superior efficiency compared to electroporation, while transformation by heat shock was ineffective. Robust host fitness was demonstrated by stable plasmid maintenance, while standardized gene expression using an array of synthetic promoters could be shown. pEMG-based scarless gene deletion was successfully adapted, allowing gene deletion and integration. The successful integration of a gene cassette for terephthalic acid degradation is showcased. The resulting strain can grow on both monomers of polyethylene terephthalate (PET), with an increased growth rate achieved through adaptive laboratory evolution. CONCLUSION The chassis roadmap for the development of P. pantotrophus DSM 2944 into a proficient SynBio chassis was implemented. The presented genetic toolkit allows genome editing and therewith the possibility to exploit Paracoccus for a myriad of applications.
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Affiliation(s)
- Upasana Pal
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Denise Bachmann
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Chiara Pelzer
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Julia Christiansen
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Till Tiso
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany.
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Hosseini S, Sharifi R, Habibi A. Simultaneous removal of aliphatic and aromatic crude oil hydrocarbons by Pantoea agglomerans isolated from petroleum-contaminated soil in the west of Iran. Arch Microbiol 2024; 206:98. [PMID: 38351169 DOI: 10.1007/s00203-023-03819-y] [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: 10/26/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
Hydrocarbons are considered as one of the most common and harmful environmental pollutants affecting human health and the environment. Bioremediation as an environmentally friendly, highly efficient, and cost-effective method in remediating oil-contaminated environments has been interesting in recent decades. In this study, hydrocarbon degrader bacterial strains were isolated from the highly petroleum-contaminated soils in the Dehloran oil field in the west of Iran. Out of 37 isolates, 15 can grow on M9 agar medium that contains 1.5 g L-1 of crude oil as the sole carbon source. The morphological, biochemical, and 16SrRNA sequencing analyses were performed for the isolates. The choosing of the isolates as the hydrocarbon degrader was examined by evaluating the efficacy of their crude oil removal at a concentration of 10 g L-1 in an aqueous medium. The results showed that five isolates belonging to Pseudomonas sp., Pseudomonas oryzihabitans, Roseomonas aestuarii, Pantoea agglomerans, and Arthrobacter sp. had a hyper hydrocarbon-degrading activity and they could remove more than 85% of the total petroleum hydrocarbon (TPH) after 96 h. The highest TPH removal of about 95.75% and biodegradation rate of 0.0997 g L-1 h-1 was observed for P. agglomerans. The gas chromatography-mass spectroscopy (GC-MS) analysis was performed during the biodegradation process by P. agglomerans to detect the degradation intermediates and final products. The results confirmed the presence of intermediates such as alcohols and fatty acids in the terminal oxidation pathway of alkanes in this biodegradation process. A promising P. agglomerans NB391 strain can remove aliphatic and aromatic hydrocarbons simultaneously.
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Affiliation(s)
- Saman Hosseini
- Department of Plant Protection, Razi University, Kermanshah, Iran
| | | | - Alireza Habibi
- Faculty of Petroleum and Chemical Engineering, Razi University, Kermanshah, Iran
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Díaz-Díaz M, Antón-Domínguez BI, Raya MC, Bernal-Cabrera A, Medina-Marrero R, Trapero A, Agustí-Brisach C. Streptomyces spp. Strains as Potential Biological Control Agents against Verticillium Wilt of Olive. J Fungi (Basel) 2024; 10:138. [PMID: 38392810 PMCID: PMC10890128 DOI: 10.3390/jof10020138] [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: 01/02/2024] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Verticillium wilt of olive (VWO) caused by Verticillium dahliae is considered a major olive (Olea europaea) disease in Mediterranean-type climate regions. The lack of effective chemical products against VWO makes it necessary to search for alternatives such as biological control. The main goal of this study was to evaluate the effect of six Streptomyces spp. strains as biological control agents (BCAs) against VWO. All of them were molecularly characterized by sequencing 16S or 23S rRNA genes and via phylogenetic analysis. Their effect was evaluated in vitro on the mycelial growth of V. dahliae (isolates V004 and V323) and on microsclerotia (MS) viability using naturally infested soils. Bioassays in olive plants inoculated with V. dahliae were also conducted to evaluate their effect against disease progress. In all the experiments, the reference BCAs Fusarium oxysporum FO12 and Aureobasidium pullulans AP08 were included for comparative purposes. The six strains were identified as Streptomyces spp., and they were considered as potential new species. All the BCAs, including Streptomyces strains, showed a significant effect on mycelial growth inhibition for both V. dahliae isolates compared to the positive control, with FO12 being the most effective, followed by AP08, while the Streptomyces spp. strains showed an intermediate effect. All the BCAs tested also showed a significant effect on the inhibition of germination of V. dahliae MS compared to the untreated control, with FO12 being the most effective treatment. Irrigation treatments with Streptomyces strain CBQ-EBa-21 or FO12 were significantly more effective in reducing disease severity and disease progress in olive plants inoculated with V. dahliae compared to the remaining treatments. This study represents the first approach to elucidating the potential effect of Streptomyces strains against VWO.
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Affiliation(s)
- Miriam Díaz-Díaz
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Begoña I Antón-Domínguez
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - María Carmen Raya
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Alexander Bernal-Cabrera
- Centro de Investigaciones Agropecuarias (CIAP), Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
- Departamento de Agronomía, Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Ricardo Medina-Marrero
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Antonio Trapero
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Carlos Agustí-Brisach
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
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Ben Abdallah M, Chamkha M, Karray F, Sayadi S. Microbial diversity in polyextreme salt flats and their potential applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11371-11405. [PMID: 38180652 DOI: 10.1007/s11356-023-31644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.
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Affiliation(s)
- Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia.
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Sami Sayadi
- Biotechnology Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, 2713, Doha, Qatar
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Yang ZZ, Xiong LS, Yuan Q, Zuo SY, Chen XM, Jiang MG, Tian XP, Jiang CL, Jiang Y. Marinimicrococcus flavescens gen. nov., sp. nov., a new member of the family Geminicoccaceae, isolated from a marine sediment of the South China Sea. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240641 DOI: 10.1099/ijsem.0.006241] [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] [Indexed: 01/23/2024] Open
Abstract
A Gram-stain-negative, catalase-positive and oxidase-positive, nonmotile, aerobic, light yellow, spherical-shaped bacterial strain with no flagella, designated strain YIM 152171T, was isolated from sediment of the South China Sea. Colonies were smooth and convex, light yellow and circular, and 1.0-1.5×1.0-1.5 µm in cell diameter after 7 days of incubation at 28°C on YIM38 media supplemented with sea salt. Colonies could grow at 20-45°C (optimum 28-35°C) and pH 6.0-11.0 (optimum, pH 7.0-9.0), and they could proliferate in the salinity range of 0-6.0 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C18 : 1 ω7c 11-methyl, C16 : 0, C16 : 1 ω11c, C16 : 1 ω5c, C17 : 1 ω6c and C18 : 1 ω5c. The respiratory quinone was ubiquinone 10, and the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified aminolipid. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain YIM 152171T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus. The 16S rRNA gene sequence similarities of YIM 152171T to those of Arboricoccus pini, Geminicoccus roseus and Constrictibacter antarcticus were 92.17, 89.25 and 88.91 %, respectively. The assembled draft genome of strain YIM 152171T had 136 contigs with an N50 value of 134704 nt, a total length of 3 001 346 bp and a G+C content of 70.27 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain YIM 152171T (=MCCC 1K08488T=KCTC 92884T) represents a type of novel species and genus for which we propose the name Marinimicrococcus gen. nov., sp. nov.
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Affiliation(s)
- Zu-Zhen Yang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Lian-Shuang Xiong
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Qing Yuan
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Shu-Ya Zuo
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Xue-Mei Chen
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Ming-Guo Jiang
- School of Marine Science and Biotechnology, Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning 530008, PR China
| | - Xin-Peng Tian
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cheng-Lin Jiang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
| | - Yi Jiang
- The Lab for Research and Development of Actinomycete Resources, Yunnan Institute of Microbiology, Chenggong campus of Yunnan University, Kunming, 650500, PR China
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12
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Bueno de Mesquita CP, Hartman WH, Ardón M, Tringe SG. Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME COMMUNICATIONS 2024; 4:ycae040. [PMID: 38628812 PMCID: PMC11020224 DOI: 10.1093/ismeco/ycae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Wyatt H Hartman
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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13
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Yuan J, Deng X, Xie X, Chen L, Wei C, Feng C, Qiu G. Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems. ISME COMMUNICATIONS 2024; 4:ycae011. [PMID: 38524765 PMCID: PMC10958769 DOI: 10.1093/ismeco/ycae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (<36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.
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Affiliation(s)
- Jing Yuan
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chunhua Feng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
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14
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Yang Q, Yan Y, Huang J, Wang Z, Feng M, Cheng H, Zhang P, Zhang H, Xu J, Zhang M. The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms. Microorganisms 2023; 11:2807. [PMID: 38004818 PMCID: PMC10672829 DOI: 10.3390/microorganisms11112807] [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: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.
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Affiliation(s)
- Qian Yang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Yifeng Yan
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Jinhe Huang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Zhaolei Wang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Mingjun Feng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Haowu Cheng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Peiyu Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Huan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Min Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
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15
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Bähr T, Baumhögger A, Geis G, Gatermann S. Complete genome sequences of eight Auritidibacter ignavus strains isolated from ear infections in Germany. Microbiol Resour Announc 2023; 12:e0066623. [PMID: 37847045 PMCID: PMC10652893 DOI: 10.1128/mra.00666-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/14/2023] [Indexed: 10/18/2023] Open
Abstract
Here, we present the complete genome sequences of eight Auritidibacter ignavus strains isolated from clinical samples of patients with ear infections in Bochum, Germany. The sequence information will give assistance to greater knowledge about the virulence potential of this unfamiliar putative pathogen.
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Affiliation(s)
- Tobias Bähr
- Institute of Medical Laboratory Diagnostics, Bochum, Germany
| | | | - Gabriele Geis
- Institute of Medical Laboratory Diagnostics, Bochum, Germany
| | - Sören Gatermann
- Institute of Medical Laboratory Diagnostics, Bochum, Germany
- Department of Medical Microbiology, Ruhr University Bochum, Bochum, Germany
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16
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Manara S, Beghini F, Masetti G, Armanini F, Geat D, Galligioni G, Segata N, Farina S, Cristofolini M. Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome. Dermatol Ther (Heidelb) 2023; 13:2769-2783. [PMID: 37768448 PMCID: PMC10613183 DOI: 10.1007/s13555-023-01036-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
INTRODUCTION Psoriasis is a systemic immune-mediated disease primarily manifesting as skin redness and inflammation. Balneotherapy proved to be a successful non-pharmacological option to reduce the skin areas affected by the disease, but the specific mechanisms underlying this effect have not been elucidated yet. Here we test the hypothesis that the effect of thermal treatments on psoriatic lesions could be partially mediated by changes in the resident microbial population, i.e., the microbiome. METHODS In this study, we enrolled patients with psoriasis and monitored changes in their skin and gut microbiome after a 12-bath balneotherapy course with a combination of 16S rRNA amplicon sequencing and metagenomics. Changes in the resident microbiome were then correlated with thermal therapy outcomes evaluated as changes in Psoriasis Area and Severity Index (PASI) and Body Surface Area index (BSA). RESULTS The amplicon sequencing analysis of the skin microbiome showed that after thermal treatment the microbiome composition of affected areas improved to approach that typical of unaffected skin. We moreover identified some low-abundance bacterial biomarkers indicative of disease status and treatment efficacy, and we showed via metagenomic sequencing that thermal treatments and thermal water drinking affect the fecal microbiome to host more species associated with favorable metabolic health. CONCLUSIONS Changes in lower-abundance microbial taxa presence and abundance could be the basis for the positive effect of thermal water treatment and drinking on the cutaneous and systemic symptomatology of psoriasis.
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Affiliation(s)
- Serena Manara
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Francesco Beghini
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Giulia Masetti
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Federica Armanini
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy
| | - Davide Geat
- Department of Dermatology, ASST Spedali Civili Di Brescia, Brescia, Italy
| | - Giulia Galligioni
- Clinical Unit of Occupational Medicine, Health Agency Trento, Trento, Italy
| | - Nicola Segata
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy.
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Liu SW, Zhai XX, Liu D, Liu YY, Sui LY, Luo KK, Yang Q, Li FN, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang BY, Zhang DJ, Xue CM, Sun CH. Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau. Microorganisms 2023; 11:2475. [PMID: 37894133 PMCID: PMC10609225 DOI: 10.3390/microorganisms11102475] [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: 09/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.
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Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Xiao-Xu Zhai
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Di Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Yu-Yu Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Li-Ying Sui
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ke-Ke Luo
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Qin Yang
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Fei-Na Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing 100045, China;
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ben-Yin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - De-Jun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - Chun-Mei Xue
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
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18
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Zhao Y, Liu Z, Zhang B, Cai J, Yao X, Zhang M, Deng Y, Hu B. Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation. Nat Commun 2023; 14:5394. [PMID: 37669961 PMCID: PMC10480208 DOI: 10.1038/s41467-023-41224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress is thought to promote microbial mutualism, there is a paucity of research in this area. Here, we monitor microbial communities in a quasi-natural composting system, where temperature variation (20 °C-70 °C) is the main abiotic stress. Genomic analyses and culturing experiments provide evidence that temperature selects for slow-growing and stress-tolerant strains (i.e., Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and the remaining strains through the sharing of cobalamin. Comparison of 3000 bacterial pairings reveals that mutualism is common (~39.1%) and competition is rare (~13.9%) in pairs involving T. fusca and S. viridis. Overall, our work provides insights into how high temperature can favour mutualism and reduce competition at both the community and species levels.
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Affiliation(s)
- Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou, China
| | - Jingjie Cai
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Meng Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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19
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Yang Z, Lian Z, Liu L, Fang B, Li W, Jiao J. Cultivation strategies for prokaryotes from extreme environments. IMETA 2023; 2:e123. [PMID: 38867929 PMCID: PMC10989778 DOI: 10.1002/imt2.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/28/2023] [Indexed: 06/14/2024]
Abstract
The great majority of microorganisms are as-yet-uncultivated, mostly found in extreme environments. High-throughput sequencing provides data-rich genomes from single-cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of "microbial dark matter." However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long-term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi-omics-guided microbial cultivation approaches for culturing these as-yet-uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.
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Affiliation(s)
- Zi‐Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zheng‐Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Jian‐Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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20
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Chen M, Conroy JL, Sanford RA, Wyman-Feravich DA, Chee-Sanford JC, Connor LM. Tropical lacustrine sediment microbial community response to an extreme El Niño event. Sci Rep 2023; 13:6868. [PMID: 37106028 PMCID: PMC10140070 DOI: 10.1038/s41598-023-33280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.
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Affiliation(s)
- Mingfei Chen
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jessica L Conroy
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Joanne C Chee-Sanford
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
| | - Lynn M Connor
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
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21
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Farlow AJ, Rupasinghe DB, Naji KM, Capon RJ, Spiteller D. Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria. Microorganisms 2023; 11:microorganisms11041005. [PMID: 37110428 PMCID: PMC10142583 DOI: 10.3390/microorganisms11041005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rosenbergiella bacteria have been previously isolated predominantly from floral nectar and identified in metagenomic screenings as associated with bees. Here, we isolated three Rosenbergiella strains from the robust Australian stingless bee Tetragonula carbonaria sharing over 99.4% sequence similarity with Rosenbergiella strains isolated from floral nectar. The three Rosenbergiella strains (D21B, D08K, D15G) from T. carbonaria exhibited near-identical 16S rDNA. The genome of strain D21B was sequenced; its draft genome contains 3,294,717 bp, with a GC content of 47.38%. Genome annotation revealed 3236 protein-coding genes. The genome of D21B differs sufficiently from the closest related strain, Rosenbergiella epipactidis 2.1A, to constitute a new species. In contrast to R. epipactidis 2.1A, strain D21B produces the volatile 2-phenylethanol. The D21B genome contains a polyketide/non-ribosomal peptide gene cluster not present in any other Rosenbergiella draft genomes. Moreover, the Rosenbergiella strains isolated from T. carbonaria grew in a minimal medium without thiamine, but R. epipactidis 2.1A was thiamine-dependent. Strain D21B was named R. meliponini D21B, reflecting its origin from stingless bees. Rosenbergiella strains may contribute to the fitness of T. carbonaria.
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Affiliation(s)
- Anthony J Farlow
- Chemical Ecology/Biological Chemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Darshani B Rupasinghe
- Chemical Ecology/Biological Chemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Khalid M Naji
- Chemical Ecology/Biological Chemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Robert J Capon
- Centre for Drug Discovery, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Dieter Spiteller
- Chemical Ecology/Biological Chemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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22
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Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China. BMC Microbiol 2023; 23:47. [PMID: 36823577 PMCID: PMC9948317 DOI: 10.1186/s12866-023-02793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.
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23
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Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. ENVIRONMENTAL MICROBIOME 2023; 18:10. [PMID: 36805022 PMCID: PMC9938989 DOI: 10.1186/s40793-023-00470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Mark Grippo
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Negri
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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24
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Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A, Rattei T, Ostrovsky A, Zotchev SB. Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiol Spectr 2023; 11:e0435322. [PMID: 36728429 PMCID: PMC10100984 DOI: 10.1128/spectrum.04353-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.
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Affiliation(s)
- Sophie Graffius
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Rasmus Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Mathias Flieder
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational System Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Andrew Ostrovsky
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Vienna, Austria
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sergey B. Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
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25
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Bourhane Z, Cagnon C, Castañeda C, Rodríguez-Ochoa R, Álvaro-Fuentes J, Cravo-Laureau C, Duran R. Vertical organization of microbial communities in Salineta hypersaline wetland, Spain. Front Microbiol 2023; 14:869907. [PMID: 36778872 PMCID: PMC9911865 DOI: 10.3389/fmicb.2023.869907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.
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Affiliation(s)
- Zeina Bourhane
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rafael Rodríguez-Ochoa
- Departamento de Medio Ambiente y Ciencias del Suelo, Universidad de Lleida, Lleida, Spain
| | | | | | - Robert Duran
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
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26
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Mersinkova Y, Yemendzhiev H, Nenov V. Comparative study on the metabolic behaviour of anode biofilm in microbial fuel cell under different external resistance. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2055491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yana Mersinkova
- Department of Chemical Technology, Faculty of Technical Science, Burgas “Prof. Dr Asen Zlatarov” University, Burgas, Bulgaria
| | - Hyusein Yemendzhiev
- Department of Chemical Technology, Faculty of Technical Science, Burgas “Prof. Dr Asen Zlatarov” University, Burgas, Bulgaria
| | - Valentin Nenov
- Department of Chemical Technology, Faculty of Technical Science, Burgas “Prof. Dr Asen Zlatarov” University, Burgas, Bulgaria
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27
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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28
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Pan B, Liu X, Chen Q, Sun H, Zhao X, Huang Z. Hydrological connectivity promotes coalescence of bacterial communities in a floodplain. Front Microbiol 2022; 13:971437. [PMID: 36212880 PMCID: PMC9532515 DOI: 10.3389/fmicb.2022.971437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Floodplains play essential roles in the ecological functions of regional environments. The merging and coalescence of bacterial communities in aquatic environments results in periodic patterns driven by regular hydrological activities, which may, in turn, influence ecological activities. However, the degree of bacterial community coalescence in the lateral and vertical directions as well as the underlying hydrological mechanism of floodplain ecosystems is poorly understood. Therefore, we investigated the spatiotemporal patterns and coalescence processes of planktonic and sedimentary bacterial communities during normal and high-water periods in a floodplain ecosystem of the Yellow River source region. We classified bacterial operational taxonomic units (OTUs) based on 16S rRNA gene sequencing, and quantified community coalescence by calculating the proportions of overlapping OTUs, the contributions of upstream sources to downstream sinks, and positive/negative cohesion. The results revealed major differences in the composition and diversity of planktonic and sedimentary bacterial communities. Bacterial community diversity in the high-water period was higher than in the normal period. Laterally, hydrological connectivity promoted the immigration and coalescence of bacterial communities to oxbow lakes in both the mainstream and tributaries, with the coalescence degree of planktonic bacteria (2.9%) higher than that of sedimentary bacteria (1.7%). Vertically, the coalescence degree of mainstream planktonic and sedimentary bacterial communities was highest, reaching 2.9%. Co-occurrence network analysis revealed that hydrological connectivity increased the complexity of the bacterial network and enhanced the coalescence of keystone species to oxbow lakes. Furthermore, community coalescence improved the competitiveness and dispersal of bacterial communities. This study demonstrated that coalescence of bacterial communities is driven by hydrological connectivity in a floodplain ecosystem. Further studies should investigate the processes of bacterial community coalescence in floodplains in more detail, which could provide new approaches for environmental protection and ecological function preservation.
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Affiliation(s)
- Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, China
- *Correspondence: Qiuwen Chen,
| | - He Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Zhenyu Huang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi, China
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Song ZQ, Wang L, Liang F, Zhou Q, Pei D, Jiang H, Li WJ. nifH gene expression and diversity in geothermal springs of Tengchong, China. Front Microbiol 2022; 13:980924. [PMID: 36160261 PMCID: PMC9493357 DOI: 10.3389/fmicb.2022.980924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Terrestrial hot springs have been suggested to harbor diverse diazotrophic lineages by using DNA-based nifH gene phylogenetic analysis. However, only a small amount of diazotrophs were ever confirmed to perform nitrogen fixation. In order to explore the compositions of active diazotrophic populations in hot springs, the in situ expression and diversity of nifH and 16S rRNA genes were investigated in the sediments of hot springs (pH 4.3-9.1; temperature 34-84°C) in Tengchong, China, by using high-throughput sequencing. The results showed that active diazotrophs were diverse in the studied Tengchong hot springs. The main active diazotrophs in high-temperature hot springs were affiliated with Aquificae, while those in low-temperature hot springs belonged to Cyanobacteria and Nitrospirae. Such dominance of Aquificae and Nitrospirae of diazotrophs has not been reported in other ecosystems. This suggests that hot springs may harbor unique active diazotrophs in comparison with other type of ecosystems. Furthermore, there were significant differences in the phylogenetic lineages of diazotrophs between hot springs of Tengchong and other regions, indicating that diazotrophs have geographical distribution patterns. Statistical analysis suggests that the expression and distribution of nifH gene were influenced by temperature and concentrations of ammonia and sulfur seem in Tengchong hot springs. These findings avail us to understand element cycling mediated by diazotrophs in hot spring ecosystems.
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Affiliation(s)
- Zhao-Qi Song
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Li Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Feng Liang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Dongli Pei
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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30
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Šurín Hudáková N, Kačírová J, Sondorová M, Šelianová S, Mucha R, Maďar M. Inhibitory Effect of Bacillus licheniformis Strains Isolated from Canine Oral Cavity. Life (Basel) 2022; 12:life12081238. [PMID: 36013417 PMCID: PMC9409769 DOI: 10.3390/life12081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Bacillus licheniformis is used in a broad spectrum of areas, including some probiotic preparations for human and veterinary health. Moreover, B. licheniformis strains are known producers of various bioactive substances with antimicrobial and antibiofilm effects. In searching for new potentially beneficial bacteria for oral health, the inhibitory effect of B. licheniformis strains isolated from canine dental biofilm against pathogenic oral bacteria was evaluated. The antimicrobial effect of neutralized cell-free supernatants (nCFS) was assessed in vitro on polystyrene microtiter plates. Furthermore, molecular and morphological analyses were executed to evaluate the production of bioactive substances. To determine the nature of antimicrobial substance present in nCFS of B. licheniformis A-1-5B-AP, nCFS was exposed to the activity of various enzymes. The nCFS of B. licheniformis A-1-5B-AP significantly (p < 0.0001) reduced the growth of Porphyromonas gulae 3/H, Prevotella intermedia 1/P and Streptococcus mutans ATCC 35668. On the other hand, B. licheniformis A-2-11B-AP only significantly (p < 0.0001) inhibited the growth of P. intermedia 1/P and S. mutans ATCC 35668. However, enzyme-treated nCFS of B. licheniformis A-1-5B-AP did not lose its antimicrobial effect and significantly (p < 0.0001) inhibited the growth of Micrococcus luteus DSM 1790. Further studies are needed for the identification of antimicrobial substances.
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Affiliation(s)
- Natália Šurín Hudáková
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Jana Kačírová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Miriam Sondorová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Svetlana Šelianová
- Clinic of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of Pavol Jozef Safarik in Kosice, 040 01 Kosice, Slovakia
| | - Rastislav Mucha
- Institute of Neurobiology, Biomedical Research Center of the Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
| | - Marián Maďar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
- Correspondence: ; Tel.: +421-9-4971-5632
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31
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Thompson TP, Megaw J, Kelly SA, Hopps J, Gilmore BF. Microbial communities of halite deposits and other hypersaline environments. ADVANCES IN APPLIED MICROBIOLOGY 2022; 120:1-32. [PMID: 36243451 DOI: 10.1016/bs.aambs.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom.
| | - Julianne Megaw
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen A Kelly
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Jason Hopps
- Irish Salt Mining & Exploration Company Ltd., Carrickfergus, United Kingdom
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
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32
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Wang Z, Guo L, Li J, Li J, Cui L, Dong J, Wang H. Case Report: The First Report on Moraxella canis Isolation From Corneal Ulcer in a Bulldog. Front Vet Sci 2022; 9:934081. [PMID: 35812875 PMCID: PMC9265251 DOI: 10.3389/fvets.2022.934081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
A 5-year-old castrated male bulldog was diagnosed with a corneal ulcer accompanied by edema and conjunctival hyperemia. Ophthalmic examination and microbiological analysis were performed, and the bacteria were found to be gram-negative and globular. The isolated clone was identified as Moraxella canis (MZ579539) via MALDI-TOF MS and 16S rDNA sequencing. Antimicrobial susceptibility testing showed that the bacteria were sensitive to tetracycline and chloramphenicol, but resistant to levofloxacin and ciprofloxacin. After a conjunctival flap was placed, tobramycin ophthalmic solution and 5% sodium hyaluronate were administered. Following surgery, the ulcer was effectively controlled, and after 3 weeks, the cornea healed. This is the first case report of a canine corneal ulcer associated with M. canis, which should be considered when corneal ulceration or keratitis were suspected.
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Affiliation(s)
- Zhihao Wang
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Long Guo
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Jun Li
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Jianji Li
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Luying Cui
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Junsheng Dong
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
| | - Heng Wang
- College of Veterinary Medicine, Yangzhou University, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou, China
- *Correspondence: Heng Wang
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Santini TC, Gramenz L, Southam G, Zammit C. Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments. Front Microbiol 2022; 13:920056. [PMID: 35756015 PMCID: PMC9221066 DOI: 10.3389/fmicb.2022.920056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 11/16/2022] Open
Abstract
Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L-1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L-1 NaCl between pH values 2-10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.
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Affiliation(s)
- Talitha C. Santini
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Lucy Gramenz
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Carla Zammit
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
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Draft Genome Sequence of Plesiomonas shigelloides Strain zfcc0051 (Phylum
Proteobacteria
). Microbiol Resour Announc 2022; 11:e0007422. [PMID: 35639031 PMCID: PMC9302144 DOI: 10.1128/mra.00074-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report a draft genome sequence of
Plesiomonas shigelloides
strain zfcc0051, an isolate derived from zebrafish (
Danio rerio
) feces. The genome consists of 115 contigs (>500 bp) and has a total assembly length of 4,041,537 bases.
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Salamandane A, Malfeito-Ferreira M, Brito L. A high level of antibiotic resistance in Klebsiella and Aeromonas isolates from street water sold in Mozambique, associated with the prevalence of extended-spectrum and AmpC ß-lactamases. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2022; 57:561-567. [PMID: 35603723 DOI: 10.1080/03601234.2022.2078627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aims to evaluate the resistance profile and the prevalence of antibiotic resistance genes in 30 isolates of Klebsiella spp. and Aeromonas spp. recovered from water sold in the streets of Maputo. Susceptibility profiles to 15 antibiotics were performed according to Clinical Laboratory Standard Institute guidelines with antibiotic disks on Mueller-Hinton agar plates. Multiplex PCRs were performed targeting 10 ß-lactamase genes, five ESBL (blaTEM-variants, blaOXA-variants, BlaSHV-variants, MCTX-M Group 1 and Group 9 variants) and five AmpC (ACC variants, FOX variants, MOX variants, CIT variants and DHA variants). The results showed a high prevalence of Klebsiella resistance to ß-lactam antibiotics, such as amoxicillin/clavulanic acid (62.5%), amoxicillin (56.3%), ampicillin (50%), cefoxitin (43.8%), and cefotaxime (43.8%). Aeromonas showed resistance to cefoxitin and ampicillin (71.4%), amoxicillin/clavulanic acid (57.1%) and imipenem (42.9%). ESBL blaOXA-variants, blaSVH-variants, MCTX-M Group 1 variants, and MCTX-M Group 9 variants were the most prevalent b-lactam genes, followed by the b-lactams AmpC, ACC variants and FOX variants. It is extremely important to improve waterborne disease control strategies, especially in terms of public awareness of the potential health implications of multidrug-resistant strains of Klebsiella and Aeromonas, which are often neglected.
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Affiliation(s)
- Acácio Salamandane
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Centre, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Ciências de Saúde, Universidade Lúrio, Nampula, Mozambique
| | - Manuel Malfeito-Ferreira
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Centre, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Luísa Brito
- Faculdade de Ciências de Saúde, Universidade Lúrio, Nampula, Mozambique
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36
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She W, Yang J, Wu G, Jiang H. The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153446. [PMID: 35092771 DOI: 10.1016/j.scitotenv.2022.153446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/16/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH4 and CO2), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH4 and CO2, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH4 and CO2 fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH4 fluxes and spatial variations of CO2, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.
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Affiliation(s)
- Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
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37
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Han Z, Qi P, Zhao Y, Guo N, Yan H, Tucker ME, Li D, Wang J, Zhao H. High Mg/Ca Molar Ratios Promote Protodolomite Precipitation Induced by the Extreme Halophilic Bacterium Vibrio harveyi QPL2. Front Microbiol 2022; 13:821968. [PMID: 35450281 PMCID: PMC9016281 DOI: 10.3389/fmicb.2022.821968] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/23/2022] [Indexed: 11/30/2022] Open
Abstract
Bacterial activities have been demonstrated as critical for protodolomite precipitation in specific aqueous conditions, whereas the relationship between the various hydrochemical factors and bacterial activity has not been fully explored. In this study, biomineralization experiments were conducted using a newly isolated extreme halophilic bacterium from salina mud, Vibrio harveyi QPL2, under various Mg/Ca molar ratios (0, 3, 6, 10, and 12) and a salinity of 200‰. The mineral phases, elemental composition, morphology, and crystal lattice structure of the precipitates were analyzed by XRD, SEM, and HRTEM, respectively. The organic weight and functional groups in the biominerals were identified by TG-DSC, FTIR, and XPS analysis. The amounts of amino acids and polysaccharides in the EPS of QPL2 cultured at various Mg/Ca molar ratios were quantified by an amino acid analyzer and high-performance liquid chromatography. The results confirm that disordered stoichiometric protodolomite was successfully precipitated through the activities of bacteria in a medium with relatively high Mg/Ca molar ratios (10 and 12) but it was not identified in cultures with lower Mg/Ca molar ratios (0, 3, and 6). That bacterial activity is critical for protodolomite formation as shown by the significant bacterial relicts identified in the precipitated spherulite crystals, including pinhole structures, a mineral coating around cells, and high organic matter content within the crystals. It was also confirmed that the high Mg/Ca molar ratio affects the composition of the organic components in the bacterial EPS, leading to the precipitation of the protodolomite. Specifically, not only the total EPS amount, but also other facilitators including the acidic amino acids (Glu and Asp) and polysaccharides in the EPS, increased significantly under the high Mg/Ca molar ratios. Combined with previous studies, the present findings suggest a clear link between high Mg/Ca molar ratios and the formation of protodolomite through halophilic bacterial activity.
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Affiliation(s)
- Zuozhen Han
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China.,Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peilin Qi
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Yanyang Zhao
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Na Guo
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Huaxiao Yan
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Maurice E Tucker
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.,Cabot Institute, University of Bristol, Bristol, United Kingdom
| | - Dan Li
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Jiajia Wang
- Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals, College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Hui Zhao
- Department of Bioengineering, College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, China
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38
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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Flores Pantoja LE, Briseño Silva E, Loeza Lara PD, Jiménez Mejía R. ACTIVIDAD ANTIFÚNGICA Y CARACTERÍSTICAS DE PROMOCIÓN DE CRECIMIENTO VEGETAL DE Pseudomonas aeruginosa y Enterobacter sp. DEGRADADORAS DE HIDROCARBUROS AISLADAS DE SUELO CONTAMINADO. ACTA BIOLÓGICA COLOMBIANA 2022. [DOI: 10.15446/abc.v27n3.92758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El diésel es una mezcla compleja de hidrocarburos alifáticos y aromáticos, que por su amplio uso se ha convertido en un contaminante ambiental muy frecuente. Debido a esto, es imperativo explorar alternativas viables y económicas para la remoción de dicho contaminante. El propósito del presente trabajo fue analizar la degradación de diésel por bacterias aisladas de suelo contaminado con esa mezcla de hidrocarburos, así como evaluar su actividad antagónica sobre hongos fitopatógenos, sus características de promoción del crecimiento vegetal y tolerancia a pesados. A partir del enriquecimiento en diésel como única fuente de carbono, se obtuvieron los aislados bacterianos J3 y S3, cuya identificación bioquímica y molecular reveló que corresponden a Pseudomonas aeruginosa y Enterobacter sp., respectivamente. Además, se observó que el crecimiento bacteriano fue mejor entre 2 y 5 % de diésel, mientras que el pH óptimo fue de 7,0 y 8,0 en presencia de 3 % de diésel. También, S3 mostró buen crecimiento a concentraciones de hasta 4 % de NaCl. Por otro lado, las bacterias mostraron inhibición del crecimiento micelial de los hongos fitopatógenos Alternaria sp., Botrytis cinerea, Colletotrichum siamense y Fusarium proliferatum. Además de características de promoción de crecimiento vegetal como producción de ácido indol acético (AIA), solubilización de fosfato, producción de sideróforos y surfactantes. También, se observó que las bacterias crecieron en presencia de metales como Zn, Cu, Ba y Pb, en concentraciones de entre 1,5 y >10 mM. En conclusión, las bacterias aisladas e identificadas en este estudio presentan características que las hacen excelentes candidatas para la remoción de hidrocarburos solas o mediante fitorremediación por sus características de promoción de crecimiento vegetal.
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40
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Yuan C, Li P, Qing C, Kou Z, Wang H. Different Regulatory Strategies of Arsenite Oxidation by Two Isolated Thermus tengchongensis Strains From Hot Springs. Front Microbiol 2022; 13:817891. [PMID: 35359718 PMCID: PMC8963470 DOI: 10.3389/fmicb.2022.817891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Arsenic is a ubiquitous constituent in geothermal fluids. Thermophiles represented by Thermus play vital roles in its transformation in geothermal fluids. In this study, two Thermus tengchongensis strains, named as 15Y and 15W, were isolated from arsenic-rich geothermal springs and found different arsenite oxidation behaviors with different oxidation strategies. Arsenite oxidation of both strains occurred at different growth stages, and two enzyme-catalyzed reaction kinetic models were observed. The arsenite oxidase of Thermus strain 15W performed better oxidation activity, exhibiting typical Michaelis–Menten kinetics. The kinetic parameter of arsenite oxidation in whole cell showed a Vmax of 18.48 μM min–1 and KM of 343 μM. Both of them possessed the arsenite oxidase-coding genes aioB and aioA. However, the expression of gene aioBA was constitutive in strain 15W, whereas it was induced by arsenite in strain 15Y. Furthermore, strain 15Y harbored an intact aio operon including the regulatory gene of the ArsR family, whereas a genetic inversion of an around 128-kbp fragment produced the inactivation of this regulator in strain 15W, leading to the constitutive expression of aioBA genes. This study provides a valuable insight into the adaption of thermophiles to extreme environments.
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Affiliation(s)
- Changguo Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
- *Correspondence: Ping Li,
| | - Chun Qing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Zhu Kou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
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41
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Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes. WATER 2022. [DOI: 10.3390/w14050723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO3−-N, NH4+-N, PO43−, and CODcr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO3−-N, and NH4+-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment.
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42
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Zamora-Quintero AY, Torres-Beltrán M, Guillén Matus DG, Oroz-Parra I, Millán-Aguiñaga N. Rare actinobacteria isolated from the hypersaline Ojo de Liebre Lagoon as a source of novel bioactive compounds with biotechnological potential. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001144. [PMID: 35213299 PMCID: PMC8941997 DOI: 10.1099/mic.0.001144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022]
Abstract
The Ojo de Liebre Lagoon is a Marine Protected Area that lies within a UNESCO World Heritage Site and is a critical habitat for important migratory species such as the grey whale and bird species. Unique hypersaline environments, such as the Ojo de Liebre Lagoon, are underexplored in terms of their bacterial and chemical diversity, representing a potential source for new bioactive compounds with pharmacological properties. Actinobacteria are one of the most diverse and prolific taxonomic bacterial groups in terms of marine bioactive compounds. This study aimed to identify the culturable actinobacterial community inhabiting the Lagoon, as well as to test their potential as new sources of anticancer compounds with pharmacological potential. A selective isolation approach focused on spore-forming bacteria from 40 sediment samples generated a culture collection of 64 strains. The 16S rRNA gene analyses identified three phyla in this study, the Actinobacteria, Firmicutes and Proteobacteria, where the phylum Actinobacteria dominated (57%) the microbial community profiles. Within the Actinobacteria, nine different genera were isolated including the Actinomadura, Micromonospora, Nocardiopsis, Plantactinospora and Streptomyces sp. We observed seasonal differences on actinobacteria recovery. For instance, Micromonospora strains were recovered during the four sampling seasons, while Arthrobacter and Pseudokineococcus were only isolated in February 2018, and Blastococcus, Rhodococcus and Streptomyces were uniquely isolated in June 2018. Ethyl acetate crude extracts derived from actinobacterial cultures were generated and screened for cytotoxic activity against six cancer cell lines. Strains showed promising low percentages of viability on lung (H1299), cervical (SiHa), colon (Caco-2) and liver (HepG2) cancer lines. Molecular networking results suggest many of the metabolites produced by these strains are unknown and they might harbour novel chemistry. Our results showed the Ojo de Liebre Lagoon is a novel source for isolating diverse marine actinobacteria which produce promising bioactive compounds for potential biotechnological use as anticancer agents.
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Affiliation(s)
- Andrea Y. Zamora-Quintero
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Mónica Torres-Beltrán
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Dulce G. Guillén Matus
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Irasema Oroz-Parra
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Natalie Millán-Aguiñaga
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
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43
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Qin M, Xu H, Zhao D, Zeng J, Wu QL. Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes. Environ Microbiol 2022; 24:4079-4093. [PMID: 35099108 DOI: 10.1111/1462-2920.15922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/13/2021] [Accepted: 01/19/2022] [Indexed: 11/03/2022]
Abstract
Aquaculture would change the environmental condition in the lake ecosystem, affecting the structure and function of the aquatic ecosystem. However, little is known about the underlying mechanisms controlling the distribution patterns of bacterial community respond to aquaculture in water column and sediment. Here, we investigated the composition, co-occurrence patterns, and assembly processes of planktonic and sedimentary bacterial communities (PBC vs. SBC) from an aquaculture-influenced zone of the Eastern Lake Taihu, China. We found that aquaculture activity greatly influenced the diversity and composition of SBC by inducing excess nitrogen into the sediments. Meanwhile, network analysis revealed that aquaculture activity strengthened species interactions within the SBC network but weakened the species interactions within the PBC network. Aquaculture activity also increased the importance of deterministic processes governing the assembly of SBC by heightening the importance of environmental filtering, whereas it decreased the relative importance of deterministic processes within the assembly of PBC. In addition, ecological restoration with macrophytes increased the diversity of PBC and formed a more stable PBC network by increasing the number of network keystones. Overall, our results indicated that aquaculture drove distinct co-occurrence patterns and assembly mechanisms of PBC and SBC. This study has fundamental implications in the lake ecosystem for evaluating the microbially mediated ecological consequences of aquaculture.
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Affiliation(s)
- Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
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44
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Shi H, Wang K, Wang L, Sun S, Li B, Yao L. Case report of enterobacter hormaechei in sheep with respiratory disease and death. BMC Vet Res 2022; 18:57. [PMID: 35081969 PMCID: PMC8790845 DOI: 10.1186/s12917-022-03157-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background Enterobacter hormaechei is typically a opportunistic pathogenic bacterium in humans, and no pathological change of of Enterobacter hormaechei in diseased sheep has previously been documented. Case presentation Three free-range, four-month-old female sheep were ill with respiratory disease and died three days after receiving treatment with ceftiofur sodium. A frozen lung sample of one sheep was studied using bacterium isolation, and lung samples of the other two sheep were collected and analyzed by histopathological examination and bacterium isolation. The 16S rRNA gene sequences and biochemical characteristics of the isolates were analyzed. All results showed the isolated strain to be Enterobacter hormaechei. Phylogenetic analysis of the 16S rRNA sequence showed three representative strains were most closely related to the strains isolated from calf. Antimicrobial sensitivity tests indicated that no sensitivity to the β-lactam antimicrobials involved in treatment of sheep respiratory disease in China. Detection of the genes responsible for β-lactam resistance showed that all three isolates from sheep harbor blaSHV and blaKPC. Interstitial pneumonia, bronchial epithelial cells shedding, and massive mucous secretion were observed in the lung histopathological sections. Immunohistochemical staining showed that specific staining was mainly limited to the alveoli and alveolar septum. Conclusions This appears to be the first report of pathological changes in lungs of sheep with respiratory disease and death associated with Enterobacter hormaechei.
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Affiliation(s)
- Hongfei Shi
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, PR China.
| | - Kun Wang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Li Wang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Shiyu Sun
- Liao Ning Center for Animal Disease Control and Prevention, Shenyang, China
| | - Bozhen Li
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Lunguang Yao
- Henan Provincal Engineering and Technology Center of Health Products for Livestock and Poultry, Key Laboratory of Ecological Security and Collaborative Innovation Centre of Water Security for Water Source Region of Mid-Line of South-To-North Diversion Project of Henan Province, School of Agricultural Engineering, Nanyang Normal University, Nanyang, PR China.
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45
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Guo K, Wu N, Li W, Baattrup-Pedersen A, Riis T. Microbial biofilm community dynamics in five lowland streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149169. [PMID: 34329932 DOI: 10.1016/j.scitotenv.2021.149169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Stream biofilms are complex aggregates of diverse organism groups that play a vital role in global carbon and nitrogen cycles. Most of the current studies on stream biofilm focus on a limited number of organism groups (e.g., bacteria and algae), and few have included both prokaryote and eukaryote communities simultaneously. In this study, we incubated artificial substrates in five Danish lowland streams exhibiting different hydrological and physico-chemical conditions and explored the dynamics of community composition and diversity of the benthic biofilm, including both prokaryotes and eukaryotes. We found that few phyla in the prokaryote (Gammaproteobacteria and Bacteroidetes) and eukaryote (Cercozoa) communities accounted for over two-thirds of the total abundance at most of the sites. Both prokaryotic and eukaryotic diversity displayed the same temporal patterns, i.e., diversity peaked in July and January. We also found that hydrological and physico-chemical variables significantly explained the variation in the community composition at phylum level for both prokaryotes and eukaryotes. However, a large proportion of variation remained unexplained, which can be ascribed to important but unmeasured variables like light intensity and biological factors such as trophic and non-trophic interactions as revealed by network analysis. Therefore, we suggest that use of a multitrophic level perspective is needed to study biofilm i.e., the "microbial jungles", where high occurrences of trophic and non-trophic interactions are expected.
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Affiliation(s)
- Kun Guo
- Department of Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus, Denmark; School of Ecological and Environmental Sciences, East China Normal University, 200241 Shanghai, China
| | - Naicheng Wu
- Department of Geography and Spatial Information Techniques, Center for Land and Marine Spatial Utilization and Governance Research, Ningbo University, 315211 Ningbo, China.
| | - Wei Li
- Department of Land Resources and Environmental Sciences, Montana State University, 59717 Bozeman, MT, United States
| | | | - Tenna Riis
- Department of Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus, Denmark; WATEC, Aarhus University, Centre for Water Technology, 8000 Aarhus, Denmark
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46
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Mirzaee H, Ariens E, Blaskovich MAT, Clark RJ, Schenk PM. Biostimulation of Bacteria in Liquid Culture for Identification of New Antimicrobial Compounds. Pharmaceuticals (Basel) 2021; 14:1232. [PMID: 34959632 PMCID: PMC8706287 DOI: 10.3390/ph14121232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/05/2022] Open
Abstract
We hypothesized that environmental microbiomes contain a wide range of bacteria that produce yet uncharacterized antimicrobial compounds (AMCs) that can potentially be used to control pathogens. Over 600 bacterial strains were isolated from soil and food compost samples, and 68 biocontrol bacteria with antimicrobial activity were chosen for further studies based on inhibition assays against a wide range of food and plant pathogens. For further characterization of the bioactive compounds, a new method was established that used living pathogens in a liquid culture to stimulate bacteria to produce high amounts of AMCs in bacterial supernatants. A peptide gel electrophoresis microbial inhibition assay was used to concurrently achieve size separation of the antimicrobial peptides. Fifteen potential bioactive peptides were then further characterized by tandem MS, revealing cold-shock proteins and 50S ribosomal proteins. To identify non-peptidic AMCs, bacterial supernatants were analyzed by HPLC followed by GC/MS. Among the 14 identified bioactive compounds, 3-isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione and 2-acetyl-3-methyl-octahydropyrrolo[1,2-a]piperazine-1,4-dione were identified as new AMCs. Our work suggests that antimicrobial compound production in microbes is enhanced when faced with a threat from other microorganisms, and that this approach can rapidly lead to the development of new antimicrobials with the potential for upscaling.
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Affiliation(s)
- Hooman Mirzaee
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Emily Ariens
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Richard J. Clark
- Peptide Chemical Biology Laboratory, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
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Fariq A, Yasmin A, Blazier JC, Jannat S. Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing. Biodivers Data J 2021; 9:e68929. [PMID: 34744475 PMCID: PMC8551136 DOI: 10.3897/bdj.9.e68929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms thrive nearly everywhere including extreme environments where few other forms of life can exist. Geochemistry of extreme sites plays a major role in shaping these microbial communities and microbes thriving in such harsh conditions are untapped sources of novel biomolecules. To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. Barcoded amplicon sequencing technique was used to study the microbial communities. Physicochemical analysis of these sites was also conducted to study the dynamics of microbial communities under stressed conditions. Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. Proteobacteria were predominant in saline soil while Firmicutes were most abundant in hot spring sediment. The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. OTUs from genus Alkalibacillus were most abundant in hot spring sediments, whereas Haloarcula were more prevalent in saline soil. Some unidentified sequences were also present at each taxonomic level. Multivariate analysis indicated that electrical conductivity and pH are the major environmental factors involved in modelling microbial communities. This study revealed a poly-extremophilic microbial community in the Murtazaabad hot spring and characterised the unexplored halophilic microbial diversity of saline soil of Pakistan.
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Affiliation(s)
- Anila Fariq
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan.,Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
| | - Azra Yasmin
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan
| | - John C Blazier
- Texas A&M Institute of Genome Sciences and SocietyTexas A&M University,, College Station, Texas, United States of America Texas A&M Institute of Genome Sciences and SocietyTexas A&M University, College Station, Texas United States of America
| | - Sammyia Jannat
- Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
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Chen G, Kong C, Yang L, Zhuang M, Zhang Y, Wang Y, Ji J, Fang Z, Lv H. Genetic Diversity and Population Structure of the Xanthomonas campestris pv. campestris Strains Affecting Cabbages in China Revealed by MLST and Rep-PCR Based Genotyping. THE PLANT PATHOLOGY JOURNAL 2021; 37:476-488. [PMID: 34847634 PMCID: PMC8632610 DOI: 10.5423/ppj.oa.06.2021.0088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/15/2021] [Indexed: 05/09/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot for cruciferous vegetables worldwide, especially for the cole crops such as cabbage and cauliflower. Due to the lack of resistant cabbage cultivars, black rot has brought about considerable yield losses in recent years in China. Understanding of the pathogen features is a key step for disease prevention, however, the pathogen diversity, population structure, and virulence are largely unknown. In this study, we studied 50 Xcc strains including 39 Xcc isolates collected from cabbage in 20 regions across China, using multilocus sequence genotyping (MLST), repetitive DNA sequence-based PCR (rep-PCR), and pathogenicity tests. For MLST analysis, a total of 12 allelic profiles (AP) were generated, among which the largest AP was AP1 containing 32 strains. Further cluster analysis of rep-PCR divided all strains into 14 DNA groups, with the largest group DNA I comprising of 34 strains, most of which also belonged to AP1. Inoculation tests showed that the representative Xcc strains collected from diverse regions performed differential virulence against three brassica hosts compared with races 1 and 4. Interestingly, these results indicated that AP1/DNA I was not only the main pathotype in China, but also a novel group that differed from the previously reported type races in both genotype and virulence. To our knowledge, this is the first extensive genetic diversity survey for Xcc strains in China, which provides evidence for cabbage resistance breeding and opens the gate for further cabbage-Xcc interaction studies.
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Affiliation(s)
- Guo Chen
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Congcong Kong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Ji
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Fang
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Hunan Agricultural University, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Co-corresponding authors: Z. Fang, Phone, FAX) +86-01082105972, E-mail) . H. Lv, Phone, FAX) +86-01062135629, E-mail)
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Co-corresponding authors: Z. Fang, Phone, FAX) +86-01082105972, E-mail) . H. Lv, Phone, FAX) +86-01062135629, E-mail)
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Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius. Microorganisms 2021; 9:microorganisms9102038. [PMID: 34683359 PMCID: PMC8539994 DOI: 10.3390/microorganisms9102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/23/2022] Open
Abstract
Lactobacillus salivarius has drawn attention because of its promising probiotic functions. Tolerance to the gastrointestinal tract condition is crucial for orally administrated probiotics to exert their functions. However, previous studies of L. salivarius have only focused on the bile salt resistance of particular strains, without uncovering the common molecular mechanisms of this species. Therefore, in this study, we expanded our research to 90 L. salivarius strains to explore their common functional genes for bile salt resistance. First, the survival rates of the 90 L. salivarius strains in 0.3% bile salt solutions were determined. Comparative genomics analysis was then performed to screen for the potential functional genes related to bile salt tolerance. Next, real-time polymerase chain reaction and gene knockout experiments were conducted to further verify the tolerance-related functional genes. The results indicated that the strain-dependent bile salt tolerance of L. salivarius was mainly associated with four peptidoglycan synthesis-related genes, seven phosphotransferase system-related genes, and one chaperone-encoding gene involved in the stress response. Among them, the GATase1-encoding gene showed the most significant association with bile salt tolerance. In addition, four genes related to DNA damage repair and substance transport were redundant in the strains with high bile salt tolerance. Besides, cluster analysis showed that bile salt hydrolases did not contribute to the bile salt tolerance of L. salivarius. In this study, we determined the global regulatory genes, including LSL_1568, LSL_1716 and LSL_1709, for bile salt tolerance in L. salivarius and provided a potential method for the rapid screening of bile salt-tolerant L. salivarius strains, based on PCR amplification of functional genes.
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The identification and performance assessment of dominant bacterial species during linear alkylbenzene sulfonate (LAS)-biodegradation in a bioelectrochemical system. Bioprocess Biosyst Eng 2021; 44:2579-2590. [PMID: 34490522 DOI: 10.1007/s00449-021-02629-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/27/2021] [Indexed: 10/20/2022]
Abstract
The anionic surfactant linear alkylbenzene sulfonate (LAS) is a major chemical constituent of detergent formulation. Regarding the recalcitrant nature of sulfonoaromatic compounds, discharging these substances into wastewater collection systems is a real environmental issue. A study on LAS biodegradation based on bioelectrochemical treatment and in the form of developing a single-chamber microbial fuel cell with air cathode is reported in the present work. Pretreatment study showed LAS concentration of 60 ppm resulted in the highest anaerobic LAS removal of 57%; so, this concentration was chosen to run the MFC. After the sustained anodic biofilm was formed, LAS degradation rate during 4 days in MFC was roughly 76% higher than that in the serum bottle, which indicated the role of the bioelectrochemical process in improving anaerobic LAS removal. Additionally, through 16S rRNA gene sequencing, the dominant bacterial species in the biofilm was identified as Pseudomonas zhaodongensis NEAU-ST5-21(T) with about 98.9% phylogenetic similarity and then a pathway was proposed for LAS anaerobic biodegradation. The MFC characteristics were assessed by pH monitoring as well as scanning electron microscopy and current density evolution.
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