101
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Chang BV, Chang YT, Chao WL, Yeh SL, Kuo DL, Yang CW. Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:305-316. [PMID: 31158659 DOI: 10.1016/j.envpol.2019.05.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
Intensive farming practices are typically used for aquaculture. To prevent disease outbreaks, antibiotics are often used to reduce pathogenic bacteria in aquaculture animals. However, the effects of antibiotics on water quality and microbial communities in euryhaline fish culture ponds are largely unknown. The aim of this study was to investigate the interactions between sulfamethoxazole (SMX), water quality and microbial communities in milkfish (Chanos chanos) culture ponds. The results of small-scale milkfish pond experiments indicated that the addition of SMX decreased the abundance of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and photosynthetic bacteria. Consequently, the levels of ammonia and total phosphorus in the fish pond water increased, causing algal and cyanobacterial blooms to occur. In contrast, the addition of the SMX-degrading bacterial strains A12 and L effectively degraded SMX and reduced the levels of ammonia and total phosphorus in fish pond water. Furthermore, the abundances of AOB, NOB and photosynthetic bacteria were restored, and algal and cyanobacterial blooms were inhibited. This study demonstrate the influences of SMX on water quality and microbial community composition in milkfish culture ponds. Moreover, the use of the bacterial strains A12 and L as dual function (bioaugmentation and water quality maintenance) beneficial bacteria was shown to provide an effective approach for the bioremediation of SMX-contaminated euryhaline milkfish culture ponds.
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Affiliation(s)
- Bea-Ven Chang
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yi-Tang Chang
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Wei-Liang Chao
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Shinn-Lih Yeh
- Mariculture Research Center, Council of Agriculture, Tainan City, Taiwan
| | - Dong-Lin Kuo
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Chu-Wen Yang
- Department of Microbiology, Soochow University, Taipei, Taiwan.
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102
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Sayyadi F, Rastegar-Pouyani N, Azadbakht M, Chehri K. First comprehensive report of bacteria spp. associated with cloaca of Laudakia nupta (Sauria: Agamidae) in Iran using molecular studies. Lab Anim Res 2019; 35:3. [PMID: 31463222 PMCID: PMC6707428 DOI: 10.1186/s42826-019-0001-5] [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: 03/21/2019] [Accepted: 04/29/2019] [Indexed: 11/30/2022] Open
Abstract
Iran bears a remarkable variety of reptiles. One of the lizard families occurring in Iran is the Family Agamidae which is widely are distributed throughout the old world. The large-scaled rock agamid, Laudakia nupta, is one of the well-known agamid. There are few reports of cloacal microbial on reptiles hence their function in cloacae remains unknown. Laudakia nupta usually live in rural and urban areas and close vicinity to man, they are likely to play an important role in the spread of disease that may be caused by these microorganisms and their transmission to man. Therefore, the aim of this study was to identify the bacterial flora colonizing the cloacal region of Laudakia nupta using molecular studies. The cloacal fluids were directly placed on nutrient agar (NA) plates and incubated at 25 ± 2 °C for 48 h. The resulting bacterial colonies were transferred to fresh nutrient agar (NA) plates for molecular studies. Twelve isolates were obtained from 17 specimens of Laudakia nupta. All bacteria isolates were identified as Bacillus subtillis (5), Bacillus cereus (4), Bacillus sp. (1), Pseudomonas putida (1), and Pseudomonas sp. (1) based on partial sequences of the 16 s rRNA gene. This is the first comprehensive report of bacteria spp. associated with cloaca of Laudakia nupta using molecular studies. In this research, we found that Laudakia nupta can be a carrier of bacteria which can transfer microorganisms to hosts.
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Affiliation(s)
- Farkhondeh Sayyadi
- Department of Biology, Faculty of Basic Sciences, Razi University, Taq-e Bostan, Bagh-e Abrasham, Kermanshah, 6714967346 Iran
| | - Nasrullah Rastegar-Pouyani
- Department of Biology, Faculty of Basic Sciences, Razi University, Taq-e Bostan, Bagh-e Abrasham, Kermanshah, 6714967346 Iran
| | - Mehri Azadbakht
- Department of Biology, Faculty of Basic Sciences, Razi University, Taq-e Bostan, Bagh-e Abrasham, Kermanshah, 6714967346 Iran
| | - Khosrow Chehri
- Department of Biology, Faculty of Basic Sciences, Razi University, Taq-e Bostan, Bagh-e Abrasham, Kermanshah, 6714967346 Iran
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103
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Mann BC, Bezuidenhout JJ, Bezuidenhout CC. Biocide resistant and antibiotic cross-resistant potential pathogens from sewage and river water from a wastewater treatment facility in the North-West, Potchefstroom, South Africa. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 80:551-562. [PMID: 31596266 DOI: 10.2166/wst.2019.300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Exposure to antibiotics, biocides, chemical preservatives, and heavy metals in different settings such as wastewater treatment plants (WWTPs) may apply selective pressure resulting in the enrichment of multiple resistant, co- and cross-resistant strains of bacteria. The purpose of this study was to identify and characterize potentially pathogenic triclosan (TCS) - and/or, chloroxylenol (PCMX) tolerant bacteria from sewage and river water in the North-West, Potchefstroom, South Africa. Several potential pathogens were identified, with Aeromonas isolates being most abundant. Clonal relationships between Aeromonas isolates found at various sampling points were elucidated using ERIC-PCR. Selected isolates were characterized for their minimum inhibitory concentrations against the biocides, as well as antibiotic resistance profiles, followed by an evaluation of synergistic and antagonistic interactions between various antimicrobials. Isolates were also screened for the presence of extracellular enzymes associated with virulence. High-performance liquid chromatography revealed the presence of both biocides in the wastewater, but fingerprinting methods did not reveal whether the WWTP is the source from which these organisms enter the environment. Isolates exhibited various levels of resistance to antimicrobials as well as several occurrences of synergy and antagonisms between the biocides and select antibiotics. Several isolates had a very high potential for virulence but further study is required to identify the specific virulence and resistance genes associated with the isolates in question.
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Affiliation(s)
- B C Mann
- Unit for Environmental Science and Management: Microbiology, North-West University, Potchefstroom Campus, Potchefstroom, South Africa E-mail:
| | - J J Bezuidenhout
- Unit for Environmental Science and Management: Microbiology, North-West University, Potchefstroom Campus, Potchefstroom, South Africa E-mail:
| | - C C Bezuidenhout
- Unit for Environmental Science and Management: Microbiology, North-West University, Potchefstroom Campus, Potchefstroom, South Africa E-mail:
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104
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Sogandi, Nilasari P. Isolation and molecular identification of Endophytic bacteria from Noni fruits (Morinda citrifolia l.) and their antibacterial activity. ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1755-1315/299/1/012020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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105
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Ren Z, Qu X, Peng W, Yu Y, Zhang M. Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China. PeerJ 2019; 7:e7318. [PMID: 31338262 PMCID: PMC6628883 DOI: 10.7717/peerj.7318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/18/2019] [Indexed: 02/04/2023] Open
Abstract
In river-lake systems, sediment and water column are two distinct habitats harboring different bacterial communities which play a crucial role in biogeochemical processes. In this study, we employed Phylogenetic Investigation of Communities by Reconstruction of Unobserved States to assess the potential functions and functional redundancy of the bacterial communities in sediment and water in a eutrophic river-lake ecosystem, Poyang Lake in China. Bacterial communities in sediment and water had distinct potential functions of carbon, nitrogen, and sulfur metabolisms as well as phosphorus cycle, while the differences between rivers and the lake were inconspicuous. Bacterial communities in sediment had a higher relative abundance of genes associated with carbohydrate metabolism, carbon fixation pathways in prokaryotes, methane metabolism, anammox, nitrogen fixation, and dissimilatory sulfate reduction than that of water column. Bacterial communities in water column were higher in lipid metabolism, assimilatory nitrate reduction, dissimilatory nitrate reduction, phosphonate degradation, and assimilatory sulfate reduction than that of sediment bacterial communities. Furthermore, the variations in functional composition were closely associated to the variations in taxonomic composition in both habitats. In general, the bacterial communities in water column had a lower functional redundancy than in sediment. Moreover, comparing to the overall functions, bacterial communities had a lower functional redundancy of nitrogen metabolism and phosphorus cycle in water column and lower functional redundancy of nitrogen metabolism in sediment. Distance-based redundancy analysis and mantel test revealed close correlations between nutrient factors and functional compositions. The results suggested that bacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column. The results enriched our understanding of the bacterial communities and major biogeochemical processes in the eutrophic river-lake ecosystems.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Flathead Lake Biological Station, University of Montana, Polson, MT, USA
| | - Xiaodong Qu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Wenqi Peng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Yang Yu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Min Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China.,Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing, China
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106
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Oyetibo GO, Miyauchi K, Huang Y, Ikeda-Ohtsubo W, Chien MF, Ilori MO, Amund OO, Endo G. Comparative geochemical evaluation of toxic metals pollution and bacterial communities of industrial effluent tributary and a receiving estuary in Nigeria. CHEMOSPHERE 2019; 227:638-646. [PMID: 31015084 DOI: 10.1016/j.chemosphere.2019.04.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/02/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
Toxic metals/metalloid contaminations of estuarine sediments due to compromised tributaries arouse significant interest in studying bacterial community that triggers natural attenuation processes. Geo-accumulation index (Igeo), contamination factor (CF), pollution load index (PLI), and Hakanson potential ecological risk index (RI) as a sum of risk factors (Er) were used to quantify toxic metal/metalloid-pollution status of Lagos Lagoon (2W) and 'Iya-Alaro' tributary (4W) sediments in comparison with pristine 'Lekki Conservation Centre' sediment (L1-B). Bacteriology of the ecosystems was based on culture-independent analyses using pyrosequencing. 2W and 4W were extremely contaminated with mercury (Igeo > 7), whereas, cadmium contamination was only observed in 4W. The two ecosystems were polluted with toxic metal based on PLI, where mercury (Er = 2900 and 1900 for 4W and 2W, respectively) posed very high ecological risks. Molecular fingerprinting revealed that Proteobacteria, Firmicutes, and Acidobacteria predominately contributed the 20 most abundant genera in the two ecosystems. The 240 and 310 species present in 2W and 4W, respectively, but absent in L1-B, thrive under the metal concentrations in the polluted hydrosphere. Whereas, the 58,000 species missing in 2W and 4W but found in L1-B would serve as indicators for systems impacted with metal eco-toxicity. Despite toxic metal pollution of the ecosystems understudied, bacterial communities play vital roles in self-recovery processes occurring in the hydrosphere.
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Affiliation(s)
- Ganiyu O Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria; Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan.
| | - Keisuke Miyauchi
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Yi Huang
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan; Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Wakako Ikeda-Ohtsubo
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Mei-Fang Chien
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
| | - Matthew O Ilori
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Lagos, Nigeria
| | - Ginro Endo
- Biotechnology Research Common, Faculty of Engineering, Tohoku Gakuin University, Tagajo, Miyagi, 985-8537, Japan
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107
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Das P, Chatterjee S, Behera BK, Dangar TK, Das BK, Mohapatra T. Isolation and characterization of marine bacteria from East Coast of India: functional screening for salt stress tolerance. Heliyon 2019; 5:e01869. [PMID: 31245639 PMCID: PMC6581878 DOI: 10.1016/j.heliyon.2019.e01869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/09/2019] [Accepted: 05/29/2019] [Indexed: 11/29/2022] Open
Abstract
Soil salinization has become a severe constraint for crop production world-wide which necessitated development or induced enhancement of salt stress tolerance in plant life to sustain production in saline lands. Recognition and prospecting of valuable stress tolerant genes from natural microbial resources of saline habitat is obscure to date. Therefore, the investigation was towards isolation and characterization of marine salt stress tolerant microbes along the East coast of India for revelation of effective salt stress tolerant genes. Salt stress tolerance was assessed from 98 bacterial isolates obtained from 28 water and soil samples. Among them, 35 isolates which failed to grow beyond 4% salt were discarded and remainder 63 isolates were selected for further functional analysis and only seven isolates recorded ≥8% NaCl stress tolerance. Phylogeny revealed that four isolates belong to Firmicutes and three isolates were members of Proteobacteria. Ribosomal Database Project Release-11 and SILVA SSU database based genotyping and taxonomic identity analysis confirmed that the higher (20%) salt stress tolerant bacteria were Staphylococcus sp., Enterococcus sp., Enterobacter sp. and Proteus sp. To investigate candidate, as well as, novel salt stress tolerant genes, the seven bacterial isolates would provide new horizon to focus on the recent developments of salinity stress tolerance. In addition, the findings evidently point out the diversity of salt stress tolerant marine bacteria in coastal Odisha and West Bengal, India.
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Affiliation(s)
- Priyanka Das
- Biotechnology Laboratory, Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India.,Parasitology and Microbiology Research Laboratory, Department of Zoology, University of Burdwan, Burdwan, West Bengal, India
| | - Soumendranath Chatterjee
- Parasitology and Microbiology Research Laboratory, Department of Zoology, University of Burdwan, Burdwan, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
| | - Tushar Kanti Dangar
- Microbiology Laboratory, Crop Production Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, West Bengal, India
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108
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Laforest M, Bisaillon K, Ciotola M, Cadieux M, Hébert PO, Toussaint V, Svircev AM. Rapid identification of Erwinia amylovora and Pseudomonas syringae species and characterization of E. amylovora streptomycin resistance using quantitative PCR assays. Can J Microbiol 2019; 65:496-509. [PMID: 30901526 DOI: 10.1139/cjm-2018-0587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Erwinia amylovora and Pseudomonas syringae are bacterial phytopathogens responsible for considerable yield losses in commercial pome fruit production. The pathogens, if left untreated, can compromise tree health and economically impact entire commercial fruit productions. Historically, the choice of effective control methods has been limited. The use of antibiotics was proposed as an effective control method. The identification of these pathogens and screening for the presence of antibiotic resistance is paramount in the adoption and implementation of disease control methods. Molecular tests have been developed and accepted for identification and characterization of these disease-causing organisms. We improved existing molecular tests by developing methods that are equal or superior in robustness for identifying E. amylovora or P. syringae while being faster to execute. In addition, the real-time PCR-based detection method for E. amylovora provided complementary information on the susceptibility or resistance to streptomycin of individual isolates. Finally, we describe a methodology and results that compare the aggressiveness of the different bacterial isolates on four apple cultivars. We show that bacterial isolates exhibit different behaviors when brought into contact with various apple varieties and that the hierarchical clustering of symptom severity indicates a population structure, suggesting a genetic basis for host cultivar specificity.
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Affiliation(s)
- Martin Laforest
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Katherine Bisaillon
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Marie Ciotola
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Mélanie Cadieux
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Pierre-Olivier Hébert
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.,b Department of Biology, Sherbrooke University, 2500 University Boulevard, Sherbrooke, QC J1K 2R1, Canada
| | - Vicky Toussaint
- a Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
| | - Antonet M Svircev
- c Agriculture and Agri-Food Canada, 4902 Victoria Avenue North, P.O. Box 6000, Vineland, ON L0R 2E0, Canada
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109
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Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations. BMC Microbiol 2019; 19:65. [PMID: 30898089 PMCID: PMC6429831 DOI: 10.1186/s12866-019-1432-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Quantification of viable microorganisms is an important step in microbiological research as well as in microbial product formulation to develop biological control products or probiotics. Often, the efficiency of the resulting product is dependent on the microbial cell density and their viability, which may decrease over time. Commonly, the number of viable cells is determined by serial dilution and plating techniques or flow cytometry. In 2017, we developed a mathematical model for isothermal microcalorimetry (IMC) data analysis and showed that the new method allows for a more rapid quantification of viable fresh and freeze-dried anaerobic Lactobacillus reuteri cells than traditional viable count methods. RESULTS This study developed the new method further by applying it to well-known aerophilic plant-beneficial microbial species (Pseudomonas brassicacearum, Bacillus amyloliquefaciens subsp. plantarum and Clonostachys rosea) used in biological control products. We utilized IMC to quantify viable cells in microbial pure cultures as well as when coated onto wheat seeds. The results from this study confirmed that thermal viable count methods are more rapid and sensitive than traditional viable count techniques. Most interestingly, a thermal viable count method was able to quantify microbes coated on seeds despite the presence of the natural microbiota of the seeds. Our results also showed that, in contrast to plating techniques for which clustered cells skew the results, IMC does not require single cells for accurate viable counts. CONCLUSIONS Thermal viable count methods are novel methods for the rapid quantification of divergent bacterial and fungal species and enhance the speed, sensitivity, and accuracy of routine viable counts of pure cultures and controlled microbiomes such as plant seed coatings.
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110
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Kai S, Matsuo Y, Nakagawa S, Kryukov K, Matsukawa S, Tanaka H, Iwai T, Imanishi T, Hirota K. Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer. FEBS Open Bio 2019; 9:548-557. [PMID: 30868063 PMCID: PMC6396348 DOI: 10.1002/2211-5463.12590] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/27/2018] [Accepted: 12/27/2018] [Indexed: 12/15/2022] Open
Abstract
Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequencing has proven to be a powerful strategy for diagnosing bacterial infections. We have recently established a sequencing method and bioinformatics pipeline for 16S rRNA gene analysis utilizing the Oxford Nanopore Technologies MinION™ sequencer. In combination with our taxonomy annotation analysis pipeline, the system enabled the molecular detection of bacterial DNA in a reasonable time frame for diagnostic purposes. However, purification of bacterial DNA from specimens remains a rate‐limiting step in the workflow. To further accelerate the process of sample preparation, we adopted a direct PCR strategy that amplifies 16S rRNA genes from bacterial cell suspensions without DNA purification. Our results indicate that differences in cell wall morphology significantly affect direct PCR efficiency and sequencing data. Notably, mechanical cell disruption preceding direct PCR was indispensable for obtaining an accurate representation of the specimen bacterial composition. Furthermore, 16S rRNA gene analysis of mock polymicrobial samples indicated that primer sequence optimization is required to avoid preferential detection of particular taxa and to cover a broad range of bacterial species. This study establishes a relatively simple workflow for rapid bacterial identification via MinION™ sequencing, which reduces the turnaround time from sample to result, and provides a reliable method that may be applicable to clinical settings.
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Affiliation(s)
- Shinichi Kai
- Department of Anesthesia Kyoto University Hospital Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science Institute of Biomedical Science Kansai Medical University Hirakata Japan
| | - So Nakagawa
- Department of Molecular Life Science Tokai University School of Medicine Isehara Japan
| | - Kirill Kryukov
- Department of Molecular Life Science Tokai University School of Medicine Isehara Japan
| | | | - Hiromasa Tanaka
- Department of Human Stress Response Science Institute of Biomedical Science Kansai Medical University Hirakata Japan
| | - Teppei Iwai
- Department of Human Stress Response Science Institute of Biomedical Science Kansai Medical University Hirakata Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science Tokai University School of Medicine Isehara Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science Institute of Biomedical Science Kansai Medical University Hirakata Japan
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111
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Versluis D, de J. Bello González T, Zoetendal EG, van Passel MWJ, Smidt H. High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria. PLoS One 2019; 14:e0210970. [PMID: 30653573 PMCID: PMC6336267 DOI: 10.1371/journal.pone.0210970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/05/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of bacterial pathogens that are resistant to clinical antibiotics poses an increasing risk to human health. An important reservoir from which bacterial pathogens can acquire resistance is the human gut microbiota. However, thus far, a substantial fraction of the gut microbiota remains uncultivated and has been little-studied with respect to its resistance reservoir-function. Here, we aimed to isolate yet uncultivated resistant gut bacteria by a targeted approach. Therefore, faecal samples from 20 intensive care patients who had received the prophylactic antibiotic treatment selective digestive decontamination (SDD), i.e. tobramycin, polymyxin E, amphotericin B and cefotaxime, were inoculated anaerobically on porous aluminium oxide chips placed on top of poor and rich agar media, including media supplemented with the SDD antibiotics. Biomass growing on the chips was analysed by 16S rRNA gene amplicon sequencing, showing large inter-individual differences in bacterial cultivability, and enrichment of a range of taxonomically diverse operational taxonomic units (OTUs). Furthermore, growth of Ruminococcaceae (2 OTUs), Enterobacteriaceae (6 OTUs) and Lachnospiraceae (4 OTUs) was significantly inhibited by the SDD antibiotics. Strains belonging to 16 OTUs were candidates for cultivation to pure culture as they shared ≤95% sequence identity with the closest type strain and had a relative abundance of ≥2%. Six of these OTUs were detected on media containing SDD antibiotics, and as such were prime candidates to be studied regarding antibiotic resistance. One of these six OTUs was obtained in pure culture using targeted isolation. This novel strain was resistant to the antibiotics metrodinazole and imipenem. It was initially classified as member of the Ruminococcaceae, though later it was found to share 99% nucleotide identity with the recently published Sellimonas intestinalis BR72T. In conclusion, we show that high-throughput cultivation-based screening of microbial communities can guide targeted isolation of bacteria that serve as reservoirs of antibiotic resistance.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
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112
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Haloi S, Medhi T. Optimization and characterization of a glycolipid produced by Achromobacter
sp. to use in petroleum industries. J Basic Microbiol 2019; 59:238-248. [DOI: 10.1002/jobm.201800298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/24/2018] [Accepted: 11/10/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Saurav Haloi
- Applied Biochemistry Lab; Department of Molecular Biology and Biotechnology; Tezpur University; Napaam, Sonitpur Assam India
| | - Tapas Medhi
- Applied Biochemistry Lab; Department of Molecular Biology and Biotechnology; Tezpur University; Napaam, Sonitpur Assam India
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113
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Zhou X, Li B, Guo Z, Wang Z, Luo J, Lu C. Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China. Front Microbiol 2018; 9:3122. [PMID: 30619196 PMCID: PMC6305492 DOI: 10.3389/fmicb.2018.03122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.
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Affiliation(s)
- Xue Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Bolun Li
- School of Geographic Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhiyuan Wang
- Center for Eco-Environmental Research, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
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114
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Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, Hallsworth JE. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. FEMS Microbiol Rev 2018; 42:672-693. [PMID: 29893835 DOI: 10.1093/femsre/fuy026] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/08/2018] [Indexed: 11/12/2022] Open
Abstract
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.
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Affiliation(s)
- Callum J D Lee
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Callum J O'Kane
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Rocco L Mancinelli
- BAER Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA
| | - Geoffrey McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de Valencia (CSIC-UV), Valencia, 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 9190401, Israel
| | - Mike L Dyall-Smith
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
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115
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Wang T, Liang C, Sun Y, Gao W, Luo X, Gao Q, Li R, Fu S, Xu H, He T, Yuan H. Strategical isolation of efficient chicken feather-degrading bacterial strains from tea plantation soil sample. Int Microbiol 2018; 22:227-237. [PMID: 30810985 DOI: 10.1007/s10123-018-00042-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 11/28/2022]
Abstract
Chicken feather waste is generally insufficiently utilized despite its high content of protein, constituting an environmental issue. Biodegradation of the waste with enabling microbes provides an advantageous option among the available solutions. In this study, an efficient whole feather-degrading strain was strategically isolated from a soil sample taken from a local tea plantation that has little or nothing to do with feathers. The strain was identified as Bacillus thuringiensis (designated as FDB-10) according to the cloned complete 16S rRNA sequence. The FDB-10 could efficiently degrade briefly heat-treated whole feather (102 °C, 5 min; up to 90% of a maximum concentration of 30 g/L) in a salt medium supplemented with 0.1 g/L yeast extract within 24 h (37 °C, 150 rpm). Addition of carbon sources (glycerol, glucose, starch, Tween 20, Tween 80, 1.25 g/L as glycerol) to the fermentation medium could improve the degradation. However, significant inhibition could be observed when the added carbon source reached the amount usually adopted in the investigation of carbon source preference (1%). Nitrogen source (NH4Cl, (NH4)2SO4, peptone) adversely influenced the performance of the strain. When the molar concentrations of NH4+ were equal for the two salt, the inhibitory effect on degradation of whole feathers was similar. Entirely different from other reported feather-degrading strains showing a preference to melanin-free feather substrates, the strain isolated in this study could degrade melanin-containing feather equally efficiently, and higher protease activity could be detected in the digest mix. As a plus, the strain could degrade feathers in rice wash produced in daily cooking, indicating its potential use in the simultaneous treatment of rice cooker wastewater produced by a rice processing plant. All these results imply that the FDB-10 is a strain with great potential in the biodegradation of feather waste.
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Affiliation(s)
- Tianwen Wang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China.
| | - Chen Liang
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Yan Sun
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Wanru Gao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Xinqi Luo
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Qian Gao
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Rong Li
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Shuang Fu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Hongjv Xu
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Ting He
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Hongyu Yuan
- College of Life Sciences, and Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China.
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116
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Genderjahn S, Alawi M, Mangelsdorf K, Horn F, Wagner D. Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments. Front Microbiol 2018; 9:2082. [PMID: 30294305 PMCID: PMC6158459 DOI: 10.3389/fmicb.2018.02082] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/14/2018] [Indexed: 01/22/2023] Open
Abstract
More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.
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Affiliation(s)
- Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany.,Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany
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117
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Sheng Y, Wang G, Zhao D, Hao C, Liu C, Cui L, Zhang G. Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China. GROUND WATER 2018; 56:719-731. [PMID: 29121391 DOI: 10.1111/gwat.12615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai-Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi-arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat-based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial-lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath.
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Affiliation(s)
- Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Dan Zhao
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Chunbo Hao
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Chenglong Liu
- Institute of Geology, China Earthquake Administration, Beijing, 100029, China
| | - Linfeng Cui
- State Key Laboratory of Biogeology and Environmental Geology & Key Laboratory of Groundwater Circulation and Evolution, China University of Geosciences, Beijing, 100083, China
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Ge Zhang
- Xi'an Center of Geological Survey, China Geological Survey, Xi'an, 710054, China
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118
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Zhou L, Bai C, Cai J, Hu Y, Shao K, Gao G, Jeppesen E, Tang X. Bio-cord plays a similar role as submerged macrophytes in harboring bacterial assemblages in an eco-ditch. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:26550-26561. [PMID: 29992414 DOI: 10.1007/s11356-018-2697-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
Artificial carriers are widely used to enhance the formation of biofilm and improve pollutants' removal efficiency in agricultural wastewater treatment ditches (eco-ditches), yet comprehensive insight into their bacterial community is scarce. In this study, bacterial diversities in four different habitats-the water column, surface sediments, submerged macrophytes (Myriophyllum verticillatum L.), and the artificial carriers (bio-cord)-were compared in a Chinese eco-ditch. Comparable richness and evenness of bacterial communities were observed on M. verticillatum and bio-cord, both being higher than for free-living bacteria in the water column but lower than for bacteria in the surface sediment. The highest similarity of bacterial community composition and structure also occurred between M. verticillatum and the bio-cord, dominated by α- and γ-proteobacteria, Verrucomicrobia, and Bacteroidetes. Firmicutes and Planctomycetes, respectively, were the exclusive abundant phyla in M. verticillatum and the bio-cord, probably indicating the unique interaction between M. verticillatum and their epiphytic bacteria. Some abundant genera, such as Roseomonas, Pseudomonas, and Rhodopirellula, which were exclusively observed in M. verticillatum or the bio-cord, have been reported to have the same capacity to remove nitrogen and organic matter in wastewater treatment systems. In conclusion, in the studied eco-ditch, the bio-cord was found to play a similar role as submerged macrophytes in harboring bacterial assemblages, and we therefore propose that bio-cord may be a good alternative or supplement to enhance wastewater treatment in agricultural ditches.
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Affiliation(s)
- Lei Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengrong Bai
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Cai
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China
| | - Erik Jeppesen
- Department of Bioscience and Arctic Research Centre, Aarhus University, DK-8600, Silkeborg, Denmark
- Sino-Danish Centre for Education and Research, Beijing, 100190, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, People's Republic of China.
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119
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Lunestad BT, Grevskott DH, Roiha IS, Svanevik CS. Microbiota of lutefisk, a Nordic traditional cod dish with a high pH. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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120
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Sirisena KA, Ramirez S, Steele A, Glamoclija M. Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA. MICROBIAL ECOLOGY 2018; 76:404-418. [PMID: 29380029 DOI: 10.1007/s00248-018-1142-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
Lake Lucero is a gypsum-rich, hypersaline, ephemeral playa located on the southern part of the Alkali Flat at the White Sands National Monument (WSNM), New Mexico, USA. This modern playa setting provides a dynamic extreme environment that changes from a freshwater lake to a hypersaline dry desert during the year. We investigated the microbial diversity (bacteria, archaea, and microbial eukaryotes) of the Lake Lucero sediments using 16S- and 18S-based amplicon sequencing approach and explored the diversity patterns in different geochemical microenvironments. Our results indicated that similar microbial communities, in particular bacterial communities colonized, were remarkably consistent across our depth profiles. Therefore, these communities show a first-order relevance on the environmental conditions (moisture content, oxygen content, and mineral composition). We found that Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were the major bacterial phyla, while Cyanobacteria were present in relatively low abundances and appeared only at the surface. Genus level assessment reflected that Truepera, Delftia, and Pseudomonas were the predominant bacterial genera across all samples. Euryarchaeota was the major archaeal phylum in all the samples, while Candidatus Halobonum and Candidatus Nitrososphaera were the main genera. Diatoms were the dominant eukaryotic group in surface samples and Fungi, Ciliophora, Metazoa, and Nematodes were the other major groups. As expected, metabolic inference indicated that aerobic microbial communities were near surface colonizers, with anaerobic communities dominating with increasing depth. We demonstrated that these microbial communities could be used to characterize unique geochemical microenvironments enabling us to extrapolate these results into other terrestrial and possibly extraterrestrial environments with comparable geochemical characteristics.
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Affiliation(s)
- Kosala Ayantha Sirisena
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA.
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, USA.
- Department of Zoology, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
| | - Steven Ramirez
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - Andrew Steele
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, USA
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
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121
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Benaiges-Fernandez R, Urmeneta J. Use of specific PCR primers for the study of sulfate-reducing bacteria diversity in microbial mats of Ebro Delta, Spain. Int Microbiol 2018; 21:231-235. [PMID: 30810897 DOI: 10.1007/s10123-018-0020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 11/27/2022]
Abstract
Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Sulfate-reducing bacteria (SRB) play a key role in sulfur and nutrient recycling in these ecosystems. In this work, specific primers for 16S rRNA encoding gene, previously described, were used to study the diversity of SRB in microbial mats of the Ebro Delta. We confirm that this method is reliable to identify the diversity of SRB in these ecosystems. However, some mismatches in obtained sequences had been observed in our system and must be taken under consideration. Various genera of SRB in Ebro Delta microbial mats were identified, such as Desulfonema, Desulfatitalea, Desulfosalsimonas, Desulfoccocus, and Desulfovibrio. The diversity observed in our samples is very similar to previously reported in other microbial mats communities.
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Affiliation(s)
- Robert Benaiges-Fernandez
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
- Institute of Environmental Assessment and Water Research (IDAEA, CSIC), 08034, Barcelona, Catalonia, Spain
| | - Jordi Urmeneta
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain.
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain.
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122
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Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles 2018. [PMID: 29687212 DOI: 10.1007/s00792-018-1027-6/figures/3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Pablo Cabrera
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Viviana Urtuvia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil, 2147, Valparaiso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile.
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
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Oueriaghli N, Castro DJ, Llamas I, Béjar V, Martínez-Checa F. Study of Bacterial Community Composition and Correlation of Environmental Variables in Rambla Salada, a Hypersaline Environment in South-Eastern Spain. Front Microbiol 2018; 9:1377. [PMID: 29977233 PMCID: PMC6021518 DOI: 10.3389/fmicb.2018.01377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 06/06/2018] [Indexed: 12/03/2022] Open
Abstract
We studied the bacterial community in Rambla Salada in three different sampling sites and in three different seasons and the effect of salinity, oxygen, and pH. All sites samples had high diversity and richness (Rr > 30). The diversity indexes and the analysis of dendrograms obtained by DGGE fingerprint after applying Pearson's and Dice's coefficient showed a strong influence of sampling season. The Pareto-Lorenz (PL) curves and Fo analysis indicated that the microbial communities were balanced and despite the changing environmental conditions, they can preserve their functionality. The main phyla detected by DGGE were Bacteroidetes (39.73%), Proteobacteria (28.43%), Firmicutes (8.23%), and Cyanobacteria (5.14%). The majority of the sequences corresponding to uncultured bacteria belonged to Bacteroidetes phylum. Within Proteobacteria, the main genera detected were Halothiobacillus and Roseovarius. The environmental factors which influenced the community in a higher degree were the salinity and oxygen. The bacteria belonging to Bacteroidetes and Proteobacteria were positively influenced by salinity. Nevertheless, bacteria related to Alpha- and Betaproteobacteria classes and phylum Firmicutes showed a positive correlation with oxygen and pH but negative with salinity. The phylum Cyanobacteria were less influenced by the environmental variables. The bacterial community composition of Rambla Salada was also studied by dilution-to-extinction technique. Using this method, 354 microorganisms were isolated. The 16S sequences of 61 isolates showed that the diversity was very different to those obtained by DGGE and with those obtained previously by using classic culture techniques. The taxa identified by dilution-to-extinction were Proteobacteria (81.92%), Firmicutes (11.30%), Actinobacteria (4.52%), and Bacteroidetes (2.26%) phyla with Gammaproteobacteria as predominant class (65.7%). The main genera were: Marinobacter (38.85%), Halomonas (20.2%), and Bacillus (11.2%). Nine of the 61 identified bacteria showed less than 97% sequence identity with validly described species and may well represent new taxa. The number of bacteria in different samples, locations, and seasons were calculated by CARD-FISH, ranging from 54.3 to 78.9% of the total prokaryotic population. In conclusion, the dilution-to-extinction technique could be a complementary method to classical culture based method, but neither gets to cultivate the major taxa detected by DGGE. The bacterial community was influenced significantly by the physico-chemical parameters (specially the salinity and oxygen), the location and the season of sampling.
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Affiliation(s)
- Nahid Oueriaghli
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David J. Castro
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Inmaculada Llamas
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Victoria Béjar
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Fernando Martínez-Checa
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
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Rezaei Somee M, Shavandi M, Dastgheib SMM, Amoozegar MA. Bioremediation of oil-based drill cuttings by a halophilic consortium isolated from oil-contaminated saline soil. 3 Biotech 2018; 8:229. [PMID: 29719771 PMCID: PMC5924431 DOI: 10.1007/s13205-018-1261-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 04/24/2018] [Indexed: 10/17/2022] Open
Abstract
Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter, and Halomonas. DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter, and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus, and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.
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Affiliation(s)
- Maryam Rezaei Somee
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - Mahmoud Shavandi
- Biotechnology Research Center, Research Institute of Petroleum Industry, Tehran, Iran
| | | | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
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125
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Mandakovic D, Maldonado J, Pulgar R, Cabrera P, Gaete A, Urtuvia V, Seeger M, Cambiazo V, González M. Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert. Extremophiles 2018; 22:665-673. [PMID: 29687212 DOI: 10.1007/s00792-018-1027-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Pablo Cabrera
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Viviana Urtuvia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil, 2147, Valparaiso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Center for Nanotechnology, Systems Biology and Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España, 1680, Valparaiso, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
- Fondap Center for Genome Regulation (CGR), Avenida Blanco Encalada, 2085, Santiago, Chile.
- Laboratorio de Genómica Aplicada, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.
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126
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Yang J, Jiang H, Liu W, Wang B. Benthic Algal Community Structures and Their Response to Geographic Distance and Environmental Variables in the Qinghai-Tibetan Lakes With Different Salinity. Front Microbiol 2018; 9:578. [PMID: 29636745 PMCID: PMC5880929 DOI: 10.3389/fmicb.2018.00578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 03/13/2018] [Indexed: 11/13/2022] Open
Abstract
Uncovering the limiting factors for benthic algal distributions in lakes is of great importance to understanding of their role in global carbon cycling. However, limited is known about the benthic algal community distribution and how they are influenced by geographic distance and environmental variables in alpine lakes. Here, we investigated the benthic algal community compositions in the surface sediments of six lakes on the Qinghai-Tibetan Plateau (QTP), China (salinity ranging from 0.8 to 365.6 g/L; pairwise geographic distance among the studied lakes ranging 8–514 km) employing an integrated approach including Illumina-Miseq sequencing and environmental geochemistry. The results showed that the algal communities of the studied samples were mainly composed of orders of Bacillariales, Ceramiales, Naviculales, Oscillatoriales, Spirulinales, Synechococcales, and Vaucheriales. The benthic algal community compositions in these QTP lakes were significantly (p < 0.05) correlated with many environmental (e.g., dissolved inorganic and organic carbon, illumination intensity, total nitrogen and phosphorus, turbidity and water temperature) and spatial factors, and salinity did not show significant influence on the benthic algal community structures in the studied lakes. Furthermore, geographic distance showed strong, significant correlation (r = 0.578, p < 0.001) with the benthic algal community compositions among the studied lakes, suggesting that spatial factors may play important roles in influencing the benthic algal distribution. These results expand our current knowledge on the influencing factors for the distributions of benthic alga in alpine lakes.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- 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
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127
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Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation. Sci Rep 2018. [PMID: 29540760 PMCID: PMC5851986 DOI: 10.1038/s41598-018-22788-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
While saline soils account for 6.5% of the total land area globally, it comprises about 70% of the area in northwestern China. Microbiota in these saline soils are particularly important because they are critical to maintaining ecosystem services. However, little is known about the microbial diversity and community composition in saline soils. To investigate the distribution patterns and edaphic determinants of bacterial communities in saline soils, we collected soil samples across the hypersaline Ebinur Lake shoreline in northwestern China and assessed soil bacterial communities using bar-coded pyrosequencing. Bacterial communities were diverse, and the dominant phyla (>5% of all sequences) across all soil samples were Gammaproteobacteria, Actinobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes and Betaproteobacteria. These dominant phyla made a significant (P < 0.05) contribution to community structure variations between soils. Halomonas, Smithella, Pseudomonas and Comamonas were the indicator taxa across the salinity gradient. Bacterial community composition showed significant (P < 0.05) correlations with salt content and soil pH. Indeed, bacterial phylotype richness and phylogenetic diversity were also higher in soils with middle-level salt rates, and were significantly (P < 0.05) correlated with salt content and soil pH. Overall, our results show that both salinity and pH are the determinants of bacterial communities in saline soils in northwest China.
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128
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Miao J, Zhang N, Liu H, Wang H, Zhong Z, Zhu J. Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing. Arch Microbiol 2018; 200:685-694. [DOI: 10.1007/s00203-018-1478-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/29/2017] [Accepted: 01/12/2018] [Indexed: 10/18/2022]
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An ISMap02-like insertion sequence in Mycobacterium spp. interferes with specific detection of Mycobacterium avium subsp. paratuberculosis. Vet Microbiol 2018. [PMID: 29519503 DOI: 10.1016/j.vetmic.2018.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease or paratuberculosis (PTB), which is a chronic debilitating disease in ruminants, that is characterized by incurable enteritis and persistent diarrhea. ISMap02 is one of the major targets of PCR because it is present in multicopies (six copies) and known to be specific to MAP. However, in the present study, non-MAP mycobacteria were shown to be positive by ISMap02 targeting PCR. Two bacterial isolates (Sample ID: BO-038 and BO-042) were cultured from bovine fecal samples that produced positive results in three of two ISMap02 targeting PCR analyses with negative results in IS900 real-time PCR. Species identification using 16S rRNA gene sequencing and hsp65 gene partial sequencing revealed that strains BO-038 and BO-042 were M. virginiense and M. nonchromogenicum, respectively, which both belong to the M. terrae complex (MTC). Moreover, the two isolates shared a novel insertion sequence (IS) with high similarity to some parts of nucleotide sequences of ISMap02, and IS was presumed to be identical to that present in M. heraklionense. Both the novel IS and ISMap02 were characterized as IS1182 family members, and several sequences similar to ISMap02 were identified by BLAST analysis. In addition, the DDE transposase of the novel IS showed great similarity in the N-terminal portion with the IS5/1182 DDE transposase of other mycobacteria. These results suggest that ISMap02 has a conserved region with similarity to other ISs, and that the diagnostic value of the primer sets targeting that region should be re-addressed.
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130
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Nag S, Pramanik A, Chattopadhyay D, Bhattacharyya M. Green-fabrication of gold nanomaterials using Staphylococcus warneri from Sundarbans estuary: an effective recyclable nanocatalyst for degrading nitro aromatic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:2331-2349. [PMID: 29124636 DOI: 10.1007/s11356-017-0617-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Microbial synthesis of gold nanoparticles (GNPs) has attracted considerable attention in recent times due to their exceptional capability for the bioremediation of industrial wastes and also for the treatment of wastewater. A bacterial strain Staphylococcus warneri, isolated from the estuarine mangroves of Sundarbans region produced highly stable GNPs by reducing hydrogen auric chloride (HAucl4) salt using intracellular protein extract. The nanoparticles were characterized utilizing ultraviolet-visible spectrophotometry, transmission electron microscopy, scanning electron microscopy, atomic force microscopy, X-ray diffraction, and surface enhanced Raman scattering. Highly dispersed, spherically shaped GNPs varied around 15-25 nm in size and were highly crystalline with face-centered cubic structures. Recyclable catalytic activity of as-synthesized GNPs was evidenced by complete degradation of nitro aromatic pollutants like 2-nitroaniline, 4-nitroaniline, 2-nitrophenol and 4-nitrophenol. Our GNPs show excellent and efficient catalytic activity with significantly high rate constant (10-1 order) and high turnover frequency (103 order) in recyclable manner up to three times. To our knowledge, this is the first report of Staphylococcus warneri in the production of gold nanoparticles. This green technology for bioremediation of toxic nitro aromatic pollutants is safe and economically beneficial to challenge the development and sustainability issue.
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Affiliation(s)
- Sudip Nag
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Arnab Pramanik
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Dhrubajyoti Chattopadhyay
- Amity University, Major Arterial Road, Action Area II, Rajarhat, Newtown, Kolkata, West Bengal, 700156, India
| | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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131
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Mora-Ruiz MDR, Cifuentes A, Font-Verdera F, Pérez-Fernández C, Farias ME, González B, Orfila A, Rosselló-Móra R. Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments. Syst Appl Microbiol 2017; 41:139-150. [PMID: 29352612 DOI: 10.1016/j.syapm.2017.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 01/21/2023]
Abstract
Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to "species") using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms.
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Affiliation(s)
- M Del R Mora-Ruiz
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain.
| | - A Cifuentes
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - F Font-Verdera
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - C Pérez-Fernández
- Environmental Microbiology Laboratory, Puerto Rico University, Rio Piedras campus, Puerto Rico
| | - M E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - B González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez - Center of Applied Ecology and Sustainability, Santiago, Chile
| | - A Orfila
- Marine Technology and Operational Oceanography Department, IMEDEA (CSIC-UIB), Esporles, Spain
| | - R Rosselló-Móra
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
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Viršek MK, Lovšin MN, Koren Š, Kržan A, Peterlin M. Microplastics as a vector for the transport of the bacterial fish pathogen species Aeromonas salmonicida. MARINE POLLUTION BULLETIN 2017; 125:301-309. [PMID: 28889914 DOI: 10.1016/j.marpolbul.2017.08.024] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/12/2017] [Accepted: 08/12/2017] [Indexed: 05/20/2023]
Abstract
Microplastics is widespread in the marine environment where it can cause numerous negative effects. It can provide space for the growth of organisms and serves as a vector for the long distance transfer of marine microorganisms. In this study, we examined the sea surface concentrations of microplastics in the North Adriatic and characterized bacterial communities living on the microplastics. DNA from microplastics particles was isolated by three different methods, followed by PCR amplification of 16S rDNA, clone libraries preparation and phylogenetic analysis. 28 bacterial species were identified on the microplastics particles including Aeromonas spp. and hydrocarbon-degrading bacterial species. Based on the 16S rDNA sequences the pathogenic fish bacteria Aeromonas salmonicida was identified for the first time on microplastics. Because A. salmonicida is responsible for illnesses in fish, it is crucial to get answers if and how microplastics pollution is responsible for spreading of diseases.
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Affiliation(s)
- Manca Kovač Viršek
- Institute for Water of the Republic of Slovenia, Sector for Marine Waters, Dunajska c. 156, 1000 Ljubljana, Slovenia.
| | - Marija Nika Lovšin
- University of Nova Gorica, School of Environmental Sciences, Vipavska 13, 5000 Nova Gorica, Slovenia
| | - Špela Koren
- Institute for Water of the Republic of Slovenia, Sector for Marine Waters, Dunajska c. 156, 1000 Ljubljana, Slovenia
| | - Andrej Kržan
- National Institute of Chemistry, Department for Polymer Chemistry and Technology, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Monika Peterlin
- Institute for Water of the Republic of Slovenia, Sector for Marine Waters, Dunajska c. 156, 1000 Ljubljana, Slovenia
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133
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Cheng Z, Xiao L, Wang H, Yang H, Li J, Huang T, Xu Y, Ma N. Bacterial and Archaeal Lipids Recovered from Subsurface Evaporites of Dalangtan Playa on the Tibetan Plateau and Their Astrobiological Implications. ASTROBIOLOGY 2017; 17:1112-1122. [PMID: 28926282 DOI: 10.1089/ast.2016.1526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals. Bacterial fatty acids and archaeal acyclic diether and tetraether membrane lipids were detected, and they varied throughout the sections in concentration and abundance. Bacterial and archaeal biomolecules indicate a dominance of Gram-positive bacteria and halophilic archaea in this hypersaline ecosystem that is similar to those in other hypersaline environments. Furthermore, the abundance of bacterial lipids decreases with the increase of salinity, whereas archaeal lipids showed a reverse trend. The detection of microbial lipids in hypersaline environments would indicate, for example on Mars, a high potential for the detection of microbial biomarkers in evaporites over geological timescales. Key Words: Dalangtan playa-The Qaidam Basin-Subsurface evaporites-Lipid biomarkers-Mars. Astrobiology 17, 1112-1122.
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Affiliation(s)
- Ziye Cheng
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
| | - Long Xiao
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
- 2 Macau University of Science and Technology , Macau, China
| | - Hongmei Wang
- 3 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan, China
| | - Huan Yang
- 3 State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences , Wuhan, China
| | - Jingjing Li
- 4 State Key Laboratory of Lake Sciences and Environment, Nanjing Institute of Geography and Limnology , Chinese Academy of Sciences, Nanjing, China
| | - Ting Huang
- 1 State Key Laboratory of Geological Processes and Mineral Resources, Planetary Science Institute, School of Earth Sciences, China University of Geosciences , Wuhan, China
| | - Yi Xu
- 2 Macau University of Science and Technology , Macau, China
| | - Nina Ma
- 5 Key Laboratory of Saline Lake Resources and Environments, Chinese Academy of Geological Sciences , Beijing, China
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134
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Xie K, Deng Y, Zhang S, Zhang W, Liu J, Xie Y, Zhang X, Huang H. Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils. Sci Rep 2017; 7:13332. [PMID: 29042583 PMCID: PMC5645410 DOI: 10.1038/s41598-017-13608-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/26/2017] [Indexed: 02/01/2023] Open
Abstract
Salinity effects on microbial communities in saline soils is still unclear, and little is known about subsurface soil microbial communities especially in saline or hypersaline ecosystems. Here we presented the survey of the prokaryotic community in saline soils along a salinity gradient (17.3-148.3 dS/m) in surface (0-10 cm) and subsurface (15-30 cm) saline soils of Qarhan Salt Lake, China. Moreover, we compared them with three paired nonsaline normal soils. Using the high-throughput sequencing technology and several statistical methods, we observed no significant community difference between surface soils and subsurface soils. For environmental factors, we found that TOC was the primary driver of the prokaryotic community distribution in surface saline soils, so was pH in subsurface saline soils. Salinity had more effects on the prokaryotic community in subsurface saline soils than in surface saline soils and played a less important role in saline soils than in saline waters or saline sediments. Our research provided references for the prokaryotic community distribution along a salinity gradient in both surface and subsurface saline soils of arid playa areas.
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Affiliation(s)
- Kehui Xie
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Yong Deng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Shaocun Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Wenhao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jianrong Liu
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China
| | - Yulong Xie
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China
| | - Xuze Zhang
- School of Chemistry and Chemical Engineering, Qinghai University for Nationalities, Xining, 810007, People's Republic of China.
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China.
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135
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Versluis D, McPherson K, van Passel MWJ, Smidt H, Sipkema D. Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:454-468. [PMID: 28695385 PMCID: PMC5599449 DOI: 10.1007/s10126-017-9766-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/14/2017] [Indexed: 06/07/2023]
Abstract
Sponges often harbour a dense and diverse microbial community. Presently, a large discrepancy exists between the cultivable bacterial fraction from sponges and the community in its natural environment. Here, we aimed to acquire additional insights into cultivability of (previously uncultured) bacteria from three sponge species, namely Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis, by studying bacterial growth on five media in the form of 60 communities scraped from plates without antibiotics, as well as in the form of individual isolates that were grown on these media supplemented with antibiotics. We applied (double-)barcoded 16S ribosomal RNA (rRNA) gene amplicon sequencing for species identification. We show that previously uncultured bacteria can be cultivated using conventional plating and that application of antibiotics in the media can serve to capture a greater bacterial diversity. Moreover, we present criteria to address an important caveat of the plate scraping method whereby bacteria may be detected that did not actually grow. Fourteen out of 27 cultivated novel taxa (<95% identity of the 16S rRNA gene amplicon to reported species) belong to Actinobacteria, which indicates the presence of a large untapped reservoir of bioactive compounds. Three Flavobacteriaceae spp. were isolated that potentially constitute two new genera and one new species.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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Asakawa Y, Takesue N, Asano S, Shimotsu S, Iijima K, Suzuki K, Motoyama Y, Aizawa M. Lactobacillus curtus sp. nov., isolated from beer in Finland. Int J Syst Evol Microbiol 2017; 67:3899-3906. [DOI: 10.1099/ijsem.0.002220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuki Asakawa
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Nobuchika Takesue
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Shizuka Asano
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Satoshi Shimotsu
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Kazumaru Iijima
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Koji Suzuki
- Quality Control Center, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Yasuo Motoyama
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
| | - Masayuki Aizawa
- Research Laboratories for Alcohol Beverages, Asahi Breweries, Ltd, 1-21, Midori 1-chome, Moriya-shi, Ibaraki, 302-0106, Japan
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137
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Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria). GENOME ANNOUNCEMENTS 2017; 5:5/39/e01090-17. [PMID: 28963227 PMCID: PMC5624773 DOI: 10.1128/genomea.01090-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Pseudomonas sp. strain DrBHI1. The total assembly length is 5,649,751 bp in 146 contigs. This strain was isolated from zebrafish (Danio rerio) feces.
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138
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Han R, Zhang X, Liu J, Long Q, Chen L, Liu D, Zhu D. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895-908. [PMID: 28850799 DOI: 10.1139/cjm-2016-0773] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl-, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
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Affiliation(s)
- Rui Han
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.,b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Xin Zhang
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Jing Liu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Qifu Long
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Laisheng Chen
- b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Deli Liu
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Derui Zhu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
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139
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Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017; 67:3645-3654. [PMID: 28840805 DOI: 10.1099/ijsem.0.002189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
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Affiliation(s)
- Joana G Vicente
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Steve Rothwell
- Vitacress Ltd, Lower Link Farm, St. Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Eric B Holub
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
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140
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Wang B, Liu W, Liu X, Franks AE, Teng Y, Luo Y. Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 590-591:297-303. [PMID: 28274604 DOI: 10.1016/j.scitotenv.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
Microcosms for enrichment of DDT degrading microorganisms were monitored using culture-dependent and -independent methods. Culture dependent methods isolated several strains with DDT degradation potential, Pseudomonas species being the most frequent. One isolate, Streptomyces sp. strain D3, had a degradation rate of 77% with 20mgL-1 of DDT after 7days incubation, D3 also had degradation rates of 75% and 30% for PCB77 (3,3',4,4'-tetrachloro biphenyl) and PCNB (pentachloronitrobenzene) respectively. Culture-independent high-throughput sequencing identified a different subset of the microbial community within the enrichment microcosms to the culture dependent method. Pseudomonas, the most frequently isolated strain, only represented the 12th most abundant operational taxonomic unit in the sequencing dataset (relative abundance 0.9%). The most frequently observed bacterial genus in the culture-independent analysis did not correspond with those recovered by culture-dependent methods. These results suggested that deep sequencing followed by a targeted isolation approach might provide an advantageous route to bioremediation studies.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaoyan Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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141
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Tsuji K, Asayama T, Shiraki N, Inoue S, Okuda E, Hayashi C, Nishida K, Hasegawa H, Harada E. Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria. PLANT, CELL & ENVIRONMENT 2017; 40:1163-1173. [PMID: 28098343 DOI: 10.1111/pce.12910] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/24/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Many aquatic plants act as biosorbents, removing and recovering metals from the environment. To assess the biosorbent activity of Egeria densa, a submerged freshwater macrophyte, plants were collected monthly from a circular drainage area in Lake Biwa basin and the Mn concentrations of the plants were analysed. Mn concentrations in these plants were generally above those of terrestrial hyperaccumulators, and were markedly higher in spring and summer than in autumn. Mn concentrations were much lower in plants incubated in hydroponic medium at various pH levels with and without Mn supplementation than in field-collected plants. The precipitation of Mn oxides on the leaves was determined by variable pressure scanning electron microscopy-energy dispersive X-ray analysis and Leucoberbelin blue staining. Several strains of epiphytic bacteria were isolated from the field-collected E. densa plants, with many of these strains, including those of the genera Acidovorax, Comamonas, Pseudomonas and Rhizobium, found to have Mn-oxidizing activity. High Mn concentrations in E. densa were mediated by the production of biogenic Mn oxide in biofilms on leaf surfaces. These findings provide new insights into plant epidermal bacterial flora that affect metal accumulation in plants and suggest that these aquatic plants may have use in Mn phytomining.
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Affiliation(s)
- Kousuke Tsuji
- Graduate School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Takuma Asayama
- Graduate School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Nozomi Shiraki
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Shota Inoue
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Erina Okuda
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Chizuru Hayashi
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Kazuma Nishida
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Hiroshi Hasegawa
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
| | - Emiko Harada
- School of Environmental Science, The University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga, 522-8533, Japan
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142
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Introducing a Novel Media to Improve the Recovery of Culturable Bacteria from the Fish Parasite Anisakis spp. larvae (Nematoda: Anisakidae). Curr Microbiol 2017. [PMID: 28623453 DOI: 10.1007/s00284-017-1281-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This paper describes a cultivation method to increase the recovery of bacteria from the marine muscle-invading parasitic nematode larvae of Anisakis spp. These larvae hold a high and complex population of accumulated bacteria, originating from seawater, crustaceans, fish, and marine mammals, all involved in the lifecycle of Anisakis. Two in-house agars based on fish juice prepared by either mechanical or enzymatic degradation of the fish tissue, were made. The Anisakis larvae were homogenised prior to cultivation on the in-house fish juice agars and the bacterial numbers and diversity were compared to those obtained applying the commercially available Marine Agar and Iron Agar Lyngby. Bacterial colonies of unique appearance were subcultured and identified by 16S rRNA gene sequencing. Totally three of twenty identified taxa were found on the in-house fish juice agars only. Fish juice agar prepared enzymatically would be the best supplementary agar, as this agar gave significantly higher heterotrophic plate counts, compared to mechanical preparation. The enzymatically prepared fish juice gave more suitable agar quality, was more resource efficient, and had apparently increased nutrient density and availability.
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143
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Shift in microbial group during remediation by enhanced natural attenuation (RENA) of a crude oil-impacted soil: a case study of Ikarama Community, Bayelsa, Nigeria. 3 Biotech 2017; 7:152. [PMID: 28597163 DOI: 10.1007/s13205-017-0782-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/15/2017] [Indexed: 10/19/2022] Open
Abstract
Acute and chronic pollution of environments with crude oil does not bode well for biota living within the vicinity of polluted environments. This is due to environmental and public health concerns on the negative impact of crude oil pollution on living organisms. Enhancing microbial activities by adding nutrients and other amendments had proved effective in pollutant removal during bioremediation. This study was carried out to determine how microbial group respond during remediation by enhanced natural attenuation (RENA) during a field-scale bioremediation. Crude oil-polluted soil samples were collected (before, during, and after remediation) from a site undergoing remediation by enhanced natural attenuation (RENA) at Ikarama Community, Bayelsa State, Nigeria, and were analyzed for total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH), and a shift in microbial community. The gas chromatography-flame ionization detector (GC-FID) results showed that the pollutant concentrations (TPH and PAH) reduced by 98 and 85%, respectively, after the remediation. Culturable hydrocarbon utilizing bacteria (CHUB) was highest (8.3 × 104 cfu/g) for sample collected during the remediation studies, whilst sample collected after remediation had low CHUB (6.1 × 104 cfu/g) compared to that collected before remediation (7.7 × 104 cfu/g). Analysis of 16S rRNA of the isolated CHUB showed they belonged to eight bacterial genera namely: Achromobacter, Alcaligenes, Azospirillus, Bacillus, Lysinibacillus, Ochrobactrum, Proteus, and Pusillimonas, with Alcaligenes as the dominant genus. In this study, it was observed that the bacterial community shifted from mixed group (Gram-positive and -negative) before and during the remediation, to only the latter group after the remediation studies. The betaproteobacteria groups were the dominant isolated bacterial phylotype. This study showed that RENA is an effective method of reducing pollutant concentration in crude oil-polluted sites, and could be applied to other polluted sites in the Niger Delta region of Nigeria to mitigate the devastating effects of crude oil pollution.
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144
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Ashraf A, Imran M, Yaqub T, Tayyab M, Shehzad W, Thomson PC. A novel multiplex PCR assay for simultaneous detection of nine clinically significant bacterial pathogens associated with bovine mastitis. Mol Cell Probes 2017; 33:57-64. [DOI: 10.1016/j.mcp.2017.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/18/2017] [Accepted: 03/19/2017] [Indexed: 02/08/2023]
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145
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Chemical Structure of the Lipid A component of Pseudomonas sp. strain PAMC 28618 from Thawing Permafrost in Relation to Pathogenicity. Sci Rep 2017; 7:2168. [PMID: 28526845 PMCID: PMC5438365 DOI: 10.1038/s41598-017-02145-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/07/2017] [Indexed: 12/02/2022] Open
Abstract
Climate change causes permafrost thawing, and we are confronted with the unpredictable risk of newly discovered permafrost microbes that have disease-causing capabilities. Here, we first characterized the detailed chemical structure of the lipid A moiety from a Pseudomonas species that was isolated from thawing arctic permafrost using MALDI-based mass spectrometric approaches (i.e., MALDI-TOF MS and MALDI-QIT-TOF MSn). The MALDI multi-stage mass spectrometry (MS) analysis of lipid A extracted from the Pseudomonas sp. strain PAMC 28618 demonstrated that the hexaacyl lipid A ([M−H]− at m/z 1616.5) contains a glucosamine (GlcN) disaccharide backbone, two phosphates, four main acyl chains and two branched acyl chains. Moreover, the lipid A molecule–based structural activity relationship with other terrestrial Gram-negative bacteria indicated that strain PAMC 28618 has an identical lipid A structure with the mesophilic Pseudomonas cichorii which can cause rot disease in endive (Cichorium endivia) and that their bacterial toxicities were equivalent. Therefore, the overall lipid A validation process provides a general strategy for characterizing bacteria that have been isolated from arctic permafrost and analyzing their respective pathogenicities.
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146
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Brown T, Otero C, Grajales A, Rodriguez E, Rodriguez-Lanetty M. Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank. PeerJ 2017; 5:e3235. [PMID: 28533949 PMCID: PMC5436572 DOI: 10.7717/peerj.3235] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/27/2017] [Indexed: 02/01/2023] Open
Abstract
Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.
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Affiliation(s)
- Tanya Brown
- Biological Sciences, Florida International University, Miami, FL, USA
| | - Christopher Otero
- Biological Sciences, Florida International University, Miami, FL, USA
| | - Alejandro Grajales
- Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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147
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Fang H, Chen Y, Huang L, He G. Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment. Sci Rep 2017; 7:1299. [PMID: 28465599 PMCID: PMC5431010 DOI: 10.1038/s41598-017-01446-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
Microorganisms are ubiquitous in aqueous environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, a rotating reactor was designed to study the effects of substrata and flow conditions on sediment bacterial communities using 16S rRNA gene sequencing, assaying three groups of size-fractionated sediments and three different levels of applied shear stress. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of the microbial communities, with more anaerobic bacteria and opportunistic pathogens being detected under static water conditions, while more aerobic bacteria were detected under dynamic water flow conditions. Most of the top 10 genera were present in all the samples; however, there were significant differences in the species abundance. Paludibacter and Comamonadaceae_unclassified were the most abundant genera under static and dynamic conditions, respectively. Under static water conditions, the medium-grained sediment had the highest microbial diversity, followed by the fine and coarse sediments. Under dynamic water flow conditions, a higher flow velocity corresponded to a greater microbial diversity. Overall, there was no significant difference in the community richness or diversity between the static and dynamic water flow conditions. This study is beneficial for further understanding the heterogeneities of microbial communities in natural aquatic ecosystems.
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Affiliation(s)
- Hongwei Fang
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
| | - Yishan Chen
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
| | - Lei Huang
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China.
| | - Guojian He
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
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148
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Moghaieb REA, Abdelhadi AA, El-Sadawy HA, Allam NAT, Baiome BA, Soliman MH. Molecular identification and genetic diversity among Photorhabdus and Xenorhabdus isolates. 3 Biotech 2017; 7:6. [PMID: 28391470 PMCID: PMC5385175 DOI: 10.1007/s13205-016-0594-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/23/2016] [Indexed: 11/30/2022] Open
Abstract
Five bacterial strains were isolated from the hemocoel of the greater wax moth larvae (Galleria mellonella) infected with the entomopathogenic nematodes: Heterorhabditis bacteriophora HP88, Heterorhabditis indicus RM1 and Heterorhabditis sp (S1), Steinernema abbasi and Steinernema sp. (S II). Strains were identified as Photorhabdus luminescens HRM1, P. luminescens HS1, P. luminescens HP88, Xenorhabdus indica and X. nematophila ATTC19061 using 16S rDNA sequence analysis. To reveal the genetic diversity among these strains, three molecular markers (RAPD, ISSR and SRAP) were employed. RAPD analysis showed 73.8 and 54.5 polymorphism percentages for the Photorhabdus and Xenorhabdus strains, respectively. ISSR analysis resulted in 70.1 and 75.2 polymorphism percentages among the Photorhabdus and Xenorhabdus strains, respectively. The SRAP analysis indicated that 75.6 and 61.2% genetic polymorphism was detected among Photorhabdus and Xenorhabdus strains, respectively. The cluster analysis grouped the three Photorhabdus strains together in one cluster and the two Xenorhabdus strains together in another cluster indicating the phylogenetic relationships among them. The genotype-specific markers detected from the three molecular markers (RAPD, ISSR and SRAP) were sufficient to distinguish between the different bacterial strains tested and can be used in the future IBM program that could be built on the use of these strains.
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Affiliation(s)
- Reda E A Moghaieb
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt
- College of Biotechnology, University of Modern Science, UAE, 232816, Dubai, United Arab Emirates
| | - Abdelhadi A Abdelhadi
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt
| | - Hanan A El-Sadawy
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Nesreen A T Allam
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Baiome Abdelmaguid Baiome
- Parasitology and Animal Diseases Department, National Research Centre, Elbuhoth St., Dokki, Giza, 12311, Egypt
| | - Mohamed H Soliman
- Department of Genetics and Genetic Engineering Research Center (GERC), Faculty of Agriculture Cairo University, Giza, 12613, Egypt.
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149
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Liu Y, Lai Q, Du J, Shao Z. Genetic diversity and population structure of the Bacillus cereus group bacteria from diverse marine environments. Sci Rep 2017; 7:689. [PMID: 28386130 PMCID: PMC5429728 DOI: 10.1038/s41598-017-00817-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/20/2017] [Indexed: 11/25/2022] Open
Abstract
The phylogenetic diversity of marine bacteria belonged to the Bacillus cereus group has not been well investigated. Here, we present the genetic diversity and population structure of 71 bacteria from diverse marine environments, using a multilocus sequence typing (MLST) approach and the analyses of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) based on some representative genomic sequences. The MLST analysis demonstrated that these isolates were highly diverse and a wide distribution in marine environments and some of them showed niche specificity to some extent. They were assigned to 27 sequence types (STs) with 23 novel STs. Phylogenetic analysis of 82 bacteria containing 11 type strains based on MLST discriminated them as 20 clusters including 10 new ones. Both the dDDH and ANI results supported the proposition that each of 20 clusters represented one independent species, including 10 putative novel species. Values of 98.3% of MLST similarity and 96.2% of ANI were proposed as the standard for the species definition of this group. In summary, the first insight into the phylogenetic diversity of the group bacteria from marine environments will contribute to better understanding of their ecological role and evolution in contrast with terrestrial environments.
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Affiliation(s)
- Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China.
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150
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Yabe S, Sakai Y, Abe K, Yokota A. Diversity of Ktedonobacteria with Actinomycetes-Like Morphology in Terrestrial Environments. Microbes Environ 2017; 32:61-70. [PMID: 28321007 PMCID: PMC5371077 DOI: 10.1264/jsme2.me16144] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria with an actinomycetes-like morphology have recently been discovered, and the class Ktedonobacteria was created for these bacteria in the phylum Chloroflexi. They may prove to be a valuable resource with the potential to produce unprecedented secondary metabolites. However, our understanding of their diversity, richness, habitat, and ecological significance is very limited. We herein developed a 16S rRNA gene-targeted, Ktedonobacteria-specific primer and analyzed ktedonobacterial amplicons. We investigated abundance, diversity, and community structure in forest and garden soils, sand, bark, geothermal sediment, and compost. Forest soils had the highest diversity among the samples tested (1181-2934 operational taxonomic units [OTUs]; Chao 1 estimate, 2503-5613; Shannon index, 4.21-6.42). A phylogenetic analysis of representative OTUs revealed at least eight groups within unclassified Ktedonobacterales, expanding the known diversity of this order. Ktedonobacterial communities markedly varied among our samples. The common mesic environments (soil, sand, and bark) were dominated by diverse phylotypes within the eight groups. In contrast, compost and geothermal sediment samples were dominated by known ktedonobacterial families (Thermosporotrichaceae and Thermogemmatisporaceae, respectively). The relative abundance of Ktedonobacteria in the communities, based on universal primers, was ≤0.8%, but was 12.9% in the geothermal sediment. These results suggest that unknown diverse Ktedonobacteria inhabit common environments including forests, gardens, and sand at low abundances, as well as extreme environments such as geothermal areas.
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Affiliation(s)
- Shuhei Yabe
- Graduate School of Agricultural Sciences, Tohoku University
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