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Yang S, Lee J, Mahmood M, Min D, Im J. Evaluation and optimization of lysis method for microbial DNA extraction from epiphytic phyllosphere samples. J Microbiol Methods 2023; 206:106677. [PMID: 36716930 DOI: 10.1016/j.mimet.2023.106677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/29/2023]
Abstract
Analysis of microbial communities in the epiphytic phyllosphere can be challenging, especially when applying sequencing-based techniques, owing to the interference of plant-derived biomolecules such as nucleic acids. A review of recent studies on the epiphytic microbiome revealed that both mechanical and enzymatic lysis methods are widely used. Here, we evaluated the effects of the two lysis methods on DNA extraction yield, purity, integrity, and microbial 16S rRNA gene copy number per ng of template genomic DNA under different extraction conditions. Furthermore, the effect on bacterial community composition, diversity, and reproducibility was examined using 16S rRNA gene amplicon sequencing. The enzymatic lysis method yielded one to two orders of magnitude more DNA, but the DNA quality was suboptimal. Conversely, the samples prepared using the mechanical method showed high DNA purity albeit lower yield. Unexpectedly, mechanical lysis showed a higher DNA integrity number (DIN) than enzymatic lysis. The 16S rRNA amplicon sequencing results demonstrated that the samples prepared via mechanical disruption exhibited reproducibly similar microbial community compositions regardless of the extraction conditions. In contrast, the enzymatic lysis method resulted in inconsistent taxonomic compositions under different extraction conditions. This study demonstrates that mechanical DNA disruption is more suitable for epiphytic phyllosphere samples than enzymatic disruption.
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Affiliation(s)
- Seongmin Yang
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Jaejin Lee
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - Maheen Mahmood
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Jeongdae Im
- Department of Civil Engineering, Kansas State University, Manhattan, KS 66506, USA.
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2
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Sar T, Harirchi S, Ramezani M, Bulkan G, Akbas MY, Pandey A, Taherzadeh MJ. Potential utilization of dairy industries by-products and wastes through microbial processes: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152253. [PMID: 34902412 DOI: 10.1016/j.scitotenv.2021.152253] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/18/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
The dairy industry generates excessive amounts of waste and by-products while it gives a wide range of dairy products. Alternative biotechnological uses of these wastes need to be determined to aerobic and anaerobic treatment systems due to their high chemical oxygen demand (COD) levels and rich nutrient (lactose, protein and fat) contents. This work presents a critical review on the fermentation-engineering aspects based on defining the effective use of dairy effluents in the production of various microbial products such as biofuel, enzyme, organic acid, polymer, biomass production, etc. In addition to microbial processes, techno-economic analyses to the integration of some microbial products into the biorefinery and feasibility of the related processes have been presented. Overall, the inclusion of dairy wastes into the designed microbial processes seems also promising for commercial approaches. Especially the digestion of dairy wastes with cow manure and/or different substrates will provide a positive net present value (NPV) and a payback period (PBP) less than 10 years to the plant in terms of biogas production.
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Affiliation(s)
- Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden
| | - Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden; Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Gülru Bulkan
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden
| | - Meltem Yesilcimen Akbas
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze-Kocaeli 41400, Turkey
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
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3
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Chen Z, Yin Y, Cheng SQ, Sun Y, Liu Y. Construction of a caged single-molecule protein with ultra-stability. Chem 2021. [DOI: 10.1016/j.chempr.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Ueda H, Tabata J, Seshime Y, Masaki K, Sameshima-Yamashita Y, Kitamoto H. Cutinase-like biodegradable plastic-degrading enzymes from phylloplane yeasts have cutinase activity. Biosci Biotechnol Biochem 2021; 85:1890-1898. [PMID: 34160605 DOI: 10.1093/bbb/zbab113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022]
Abstract
Phylloplane yeast genera Pseudozyma and Cryptococcus secrete biodegradable plastic (BP)-degrading enzymes, termed cutinase-like enzymes (CLEs). Although CLEs contain highly conserved catalytic sites, the whole protein exhibits ≤30% amino acid sequence homology with cutinase. In this study, we analyzed whether CLEs exhibit cutinase activity. Seventeen Cryptococcus magnus strains, which degrade BP at 15 °C, were isolated from leaves and identified the DNA sequence of the CLE in one of the strains. Cutin was prepared from tomato leaves and treated with CLEs from 3 Cryptococcus species (C. magnus, Cryptococcus flavus, and Cryptococcus laurentii) and Pseudozyma antarctia (PaE). A typical cutin monomer, 10,16-dihydroxyhexadecanoic acid, was detected in extracts of the reaction solution via gas chromatography-mass spectrometry, showing that cutin was indeed degraded by CLEs. In addition to the aforementioned monomer, separation analysis via thin-layer chromatography detected high-molecular-weight products resulting from the breakdown of cutin by PaE, indicating that PaE acts as an endo-type enzyme.
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Affiliation(s)
- Hirokazu Ueda
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Japan
| | - Jun Tabata
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Japan
| | - Yasuyo Seshime
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Japan
| | | | - Yuka Sameshima-Yamashita
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Japan
| | - Hiroko Kitamoto
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Japan
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5
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Simultaneous hydrolysis of cheese whey and lactulose production catalyzed by β-galactosidase from Kluyveromyces lactis NRRL Y1564. Bioprocess Biosyst Eng 2020; 43:711-722. [DOI: 10.1007/s00449-019-02270-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/10/2019] [Indexed: 12/20/2022]
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6
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Oliveira D, Puri R, Fenelon MA, O'Mahony JA. Delactosed permeate as a dairy processing co‐product with major potential value: a review. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.14064] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Diana Oliveira
- School of Food and Nutritional Sciences University College Cork Room 234, Food Science Building Cork Ireland
- Dairy Processing Technology Centre University College Cork Room 234, Food Science Building Cork Ireland
| | - Ritika Puri
- School of Food and Nutritional Sciences University College Cork Room 234, Food Science Building Cork Ireland
- Dairy Processing Technology Centre University College Cork Room 234, Food Science Building Cork Ireland
| | - Mark A. Fenelon
- Food Chemistry and Technology Department Teagasc Food Research Centre Moorepark, Fermoy, Co. Cork P61 C996 Ireland
| | - James A. O'Mahony
- School of Food and Nutritional Sciences University College Cork Room 234, Food Science Building Cork Ireland
- Dairy Processing Technology Centre University College Cork Room 234, Food Science Building Cork Ireland
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Misson M, Jin B, Zhang H. Recirculating Spiral Bioreactor for Galactooligosaccharide Production Using Polymer Nanofiber-β-galactosidase Assembly. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b03156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mailin Misson
- Bioprocess
Engineering Research Group, Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Bo Jin
- School
of Chemical Engineering, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Hu Zhang
- School
of Chemical Engineering, The University of Adelaide, Adelaide, SA 5000, Australia
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Application of Chitinous Materials in Production and Purification of a Poly(l-lactic acid) Depolymerase from Pseudomonas tamsuii TKU015. Polymers (Basel) 2016; 8:polym8030098. [PMID: 30979189 PMCID: PMC6432605 DOI: 10.3390/polym8030098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 12/02/2022] Open
Abstract
The management of fishery residues and plastics is considered to be a vital strategy for conserving resources and maintaining the quality of the environment. Poly(l-lactic acid) (PLA) is a commercially promising, renewable, and biodegradable plastic. In this study, a PLA depolymerase was produced in a squid pen powder (SPP) and recycled plastic waste (PLA powder)-containing medium by Pseudomonas tamsuii TKU015, a bacterial strain isolated from Taiwanese soil. This PLA depolymerase had a molecular weight of 58 kDa and was purified to homogeneity from the supernatant of a TKU015 culture. The optimum pH of TKU015 PLA depolymerase is 10, and the optimal temperature of the enzyme is 60 °C. In addition to PLA, TKU015 PLA depolymerase degraded fibrinogen and tributyrin, but did not hydrolyze casein, triolein, and poly(β-hydroxybutyrate). Taken together, these data demonstrate that P. tamsuii TKU015 produces a PLA depolymerase to utilize SPP and polylactide as carbon/nitrogen sources.
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Misson M, Dai S, Jin B, Chen BH, Zhang H. Manipulation of nanofiber-based β-galactosidase nanoenvironment for enhancement of galacto-oligosaccharide production. J Biotechnol 2016; 222:56-64. [PMID: 26876609 DOI: 10.1016/j.jbiotec.2016.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 02/05/2016] [Accepted: 02/08/2016] [Indexed: 12/23/2022]
Abstract
The nanoenvironment of nanobiocatalysts, such as local hydrophobicity, pH and charge density, plays a significant role in optimizing the enzymatic selectivity and specificity. In this study, Kluyveromyces lactis β-galactosidase (Gal) was assembled onto polystyrene nanofibers (PSNFs) to form PSNF-Gal nanobiocatalysts. We proposed that local hydrophobicity on the nanofiber surface could expel water molecules so that the transgalactosylation would be preferable over hydrolysis during the bioconversion of lactose, thus improve the galacto-oligosaccharides (GOS) yield. PSNFs were fabricated by electro-spinning and the operational parameters were optimized to obtain the nanofibers with uniform size and ordered alignment. The resulting nanofibers were functionalized for enzyme immobilization through a chemical oxidation method. The functionalized PSNF improved the enzyme adsorption capacity up to 3100 mg/g nanofiber as well as enhanced the enzyme stability with 80% of its original activity. Importantly, the functionalized PSNF-Gal significantly improved the GOS yield and the production rate was up to 110 g/l/h in comparison with 37 g/l/h by free β-galactosidase. Our research findings demonstrate that the localized nanoenvironment of the PSNF-Gal nanobiocatalysts favour transgalactosylation over hydrolysis in lactose bioconversion.
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Affiliation(s)
- Mailin Misson
- School of Chemical Engineering, University of Adelaide, Adelaide SA 5000, Australia; Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Sheng Dai
- School of Chemical Engineering, University of Adelaide, Adelaide SA 5000, Australia
| | - Bo Jin
- School of Chemical Engineering, University of Adelaide, Adelaide SA 5000, Australia
| | - Bing H Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hu Zhang
- School of Chemical Engineering, University of Adelaide, Adelaide SA 5000, Australia.
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Simultaneous bioethanol distillery wastewater treatment and xylanase production by the phyllosphere yeast Pseudozyma antarctica GB-4(0). AMB Express 2015; 5:121. [PMID: 26069206 PMCID: PMC4463951 DOI: 10.1186/s13568-015-0121-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/19/2015] [Indexed: 11/25/2022] Open
Abstract
Bioethanol production using lignocellulosic biomass generates lignocellulosic bioethanol distillery wastewater (LBDW) that contains a large amount of xylose, making it a potential inexpensive source of xylose for biomaterials production. The main goal of this study was the production of useful enzymes from LBDW during treatment of this wastewater. In this study, we found that xylose strongly induced two yeast strains, Pseudozyma antarctica T-34 and GB-4(0), to produce novel xylanases, PaXynT and PaXynG, respectively. The nucleotide sequence of PaXynT [accession No. DF196774 (GAC73192.1)], obtained from the genome database of strain T-34 using its N-terminal amino acid sequence, was 91% identical to that of PaXynG (accession No. AB901085), and the deduced amino acid sequence is 98% identical. The specific activities of the purified PaXynT and PaXynG were about 52 U/mg. The optimal pH and temperature for both enzymes’ activities were 5.2 and 50°C, respectively. They hydrolyzed xylan to xylose and neither had β-xylosidase (EC 3.2.1.37) activity, indicating that they are endo-β-xylanases (EC 3.2.1.8). With these results, we expect that PaXyns can be employed in saccharizing lignocellulosic biomass materials for the production of useful products just like other endoxylanases. After 72 h of LBDW fed-batch cultivation using a jar-fermentor, strain GB-4(0) produced 17.3 U/ml (corresponding to about 0.3 g/l) of PaXynG and removed 63% of dissolved organic carbon and 87% of dissolved total phosphorus from LBDW. These results demonstrate the potential of P. antarctica for xylanase production during LBDW treatment.
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Watanabe T, Suzuki K, Shinozaki Y, Yarimizu T, Yoshida S, Sameshima-Yamashita Y, Koitabashi M, Kitamoto HK. A UV-induced mutant of Cryptococcus flavus GB-1 with increased production of a biodegradable plastic-degrading enzyme. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Nasanit R, Tangwong-O-Thai A, Tantirungkij M, Limtong S. The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method. Fungal Biol 2015; 119:1145-1157. [PMID: 26615738 DOI: 10.1016/j.funbio.2015.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 11/27/2022]
Abstract
The diversity of epiphytic yeasts from sugarcane (Saccharum officinarum Linn.) phyllospheres in Thailand was investigated by culture-independent method based on the analysis of the D1/D2 domains of the large subunit rRNA gene sequences. Forty-five samples of sugarcane leaf were collected randomly from ten provinces in Thailand. A total of 1342 clones were obtained from 45 clone libraries. 426 clones (31.7 %) were closely related to yeast strains in the GenBank database, and they were clustered into 31 operational taxonomic units (OTUs) with a similarity threshold of 99 %. All OTU sequences were classified in phylum Basidiomycota which were closely related to 11 yeast species in seven genera including Cryptococcus flavus, Hannaella coprosmaensis, Rhodotorula taiwanensis, Jaminaea angkoreiensis, Malassezia restricta, Pseudozyma antarctica, Pseudozyma aphidis, Pseudozyma hubeiensis, Pseudozyma prolifica, Pseudozyma shanxiensis, and Sporobolomyces vermiculatus. The most predominant yeasts detected belonged to Ustilaginales with 89.4 % relative frequency and the prevalent yeast genus was Pseudozyma. However, the majority were unable to be identified as known yeast species and these sequences may represent the sequences of new yeast taxa. In addition, The OTU that closely related to P. prolifica was commonly detected in sugarcane phyllosphere.
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Affiliation(s)
- Rujikan Nasanit
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom 73000, Thailand
| | - Apirat Tangwong-O-Thai
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom 73000, Thailand
| | - Manee Tantirungkij
- Central Laboratory and Greenhouse Complex, Faculty of Agriculture at Kamphaeng Sean, Kasetsart University, Kamphaeng Sean Campus, Nakhon Pathom 73140, Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Jatujak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand.
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