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Liu C, Schmitz RA, Pol A, Hogendoorn C, Verhagen D, Peeters SH, van Alen TA, Cremers G, Mesman RA, Op den Camp HJM. Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil. Environ Microbiol 2024; 26:e16602. [PMID: 38454738 DOI: 10.1111/1462-2920.16602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arjan Pol
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Daniël Verhagen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Mesman
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
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Awala SI, Kim Y, Gwak JH, Seo C, Lee S, Kang M, Rhee SK. Methylococcus mesophilus sp. nov., the first non-thermotolerant methanotroph of the genus Methylococcus, from a rice field. Int J Syst Evol Microbiol 2023; 73. [PMID: 37824181 DOI: 10.1099/ijsem.0.006077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Strain 16-5T, a mesophilic methanotroph of the genus Methylococcus, was isolated from rice field soil sampled in Chungcheong Province, Republic of Korea. Strain 16-5T had both particulate and soluble methane monooxygenases and could only grow on methane and methanol as electron donors. Strain 16-5 T cells are Gram-negative, white to light tan in color, non-motile, non-flagellated, diplococcoid to cocci, and have the typical type I intracytoplasmic membrane system. Strain 16-5T grew at 18-38 °C (optimum, 27 °C) and at pH 5.0-8.0 (optimum, pH 6.5-7.0). C16 : 1 ω7c (38.8%), C16 : 1 ω5c (18.8%), C16 : 1 ω6c (16.8%) and C16 : 0 (16.9%) were the major fatty acids, and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid were the major polar lipids. The main respiratory quinone was methylene-ubiquinone-8. Strain 16-5T displayed the highest 16S rRNA gene sequence similarities to other taxonomically recognized members of the genus Methylococcus, i.e. Methylococcus capsulatus TexasT (98.62%) and Methylococcus geothermalis IM1T (98.49 %), which were its closest relatives. It did, however, differ from all other taxonomically described Methylococcus species due to some phenotypic differences, most notably its inability to grow at temperatures above 38 °C, where other Methylococcus species thrive. Its 4.34 Mbp-sized genome has a DNA G+C content of 62.47 mol%, and multiple genome-based properties such as average nucleotide identity and digital DNA-DNA hybridization value distanced it from its closest relatives. Based on the data presented above, this strain represents the first non-thermotolerant species of the genus Methylococcus. The name Methylococcus mesophilus sp. nov. is proposed, and 16-5T (=JCM 35359T=KCTC 82050T) is the type strain.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seungki Lee
- National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Minseo Kang
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics. BIOLOGY 2023; 12:biology12050723. [PMID: 37237535 DOI: 10.3390/biology12050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Wongfaed N, O-Thong S, Sittijunda S, Reungsang A. Taxonomic and enzymatic basis of the cellulolytic microbial consortium KKU-MC1 and its application in enhancing biomethane production. Sci Rep 2023; 13:2968. [PMID: 36804594 PMCID: PMC9941523 DOI: 10.1038/s41598-023-29895-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Lignocellulosic biomass is a promising substrate for biogas production. However, its recalcitrant structure limits conversion efficiency. This study aims to design a microbial consortium (MC) capable of producing the cellulolytic enzyme and exploring the taxonomic and genetic aspects of lignocellulose degradation. A diverse range of lignocellulolytic bacteria and degrading enzymes from various habitats were enriched for a known KKU-MC1. The KKU-MC1 was found to be abundant in Bacteroidetes (51%), Proteobacteria (29%), Firmicutes (10%), and other phyla (8% unknown, 0.4% unclassified, 0.6% archaea, and the remaining 1% other bacteria with low predominance). Carbohydrate-active enzyme (CAZyme) annotation revealed that the genera Bacteroides, Ruminiclostridium, Enterococcus, and Parabacteroides encoded a diverse set of cellulose and hemicellulose degradation enzymes. Furthermore, the gene families associated with lignin deconstruction were more abundant in the Pseudomonas genera. Subsequently, the effects of MC on methane production from various biomasses were studied in two ways: bioaugmentation and pre-hydrolysis. Methane yield (MY) of pre-hydrolysis cassava bagasse (CB), Napier grass (NG), and sugarcane bagasse (SB) with KKU-MC1 for 5 days improved by 38-56% compared to non-prehydrolysis substrates, while MY of prehydrolysed filter cake (FC) for 15 days improved by 56% compared to raw FC. The MY of CB, NG, and SB (at 4% initial volatile solid concentration (IVC)) with KKU-MC1 augmentation improved by 29-42% compared to the non-augmentation treatment. FC (1% IVC) had 17% higher MY than the non-augmentation treatment. These findings demonstrated that KKU-MC1 released the cellulolytic enzyme capable of decomposing various lignocellulosic biomasses, resulting in increased biogas production.
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Affiliation(s)
- Nantharat Wongfaed
- grid.9786.00000 0004 0470 0856Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Sompong O-Thong
- grid.440406.20000 0004 0634 2087International College, Thaksin University, Songkhla, 90000 Thailand
| | - Sureewan Sittijunda
- grid.10223.320000 0004 1937 0490Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom, 73170 Thailand
| | - Alissara Reungsang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Academy of Science, Royal Society of Thailand, Bangkok, 10300, Thailand.
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Uchimiya M, Hay AG, LeBlanc J. Chemical and microbial characterization of sugarcane mill mud for soil applications. PLoS One 2022; 17:e0272013. [PMID: 35972931 PMCID: PMC9380943 DOI: 10.1371/journal.pone.0272013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
Sugarcane mill mud/filter cake is an activated sludge-like byproduct from the clarifier of a raw sugar production factory, where cane juice is heated to ≈90°C for 1–2 hr, after the removal of bagasse. Mill mud is enriched with organic carbon, nitrogen, and nutrient minerals; no prior report utilized 16S rRNA gene sequencing to characterize the microbial composition. Mill mud could be applied to agricultural fields as biofertilizer to replace or supplement chemical fertilizers, and as bio-stimulant to replenish microorganisms and organic carbon depleted by erosion and post-harvest field burning. However, mill mud has historically caused waste management challenges in the United States. This study reports on the chemical and microbial (16S rRNA) characteristics for mill muds of diverse origin and ages. Chemical signature (high phosphorus) distinguished mill mud from bagasse (high carbon to nitrogen (C/N) ratio) and soil (high pH) samples of diverse geographical/environmental origins. Bacterial alpha diversity of all sample types (mill mud, bagasse, and soil) was inversely correlated with C/N. Firmicutes dominated the microbial composition of fresh byproducts (mill mud and bagasse) as-produced within the operating factory. Upon aging and environmental exposure, the microbial community of the byproducts diversified to resemble that of soils, and became dominated by varying proportions of other phyla such as Acidobacteria, Chloroflexi, and Planctomyces. In summary, chemical properties allowed grouping of sample types (mill mud, bagasse, and soil-like), and microbial diversity analyses visualized aging caused by outdoor exposures including soil amendment and composting. Results suggest that a transient turnover of microbiome by amendments shifts towards more resilient population governed by the chemistry of bulk soil.
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Affiliation(s)
- Minori Uchimiya
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, Louisiana, United States of America
- * E-mail: (MU); (AGH)
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MU); (AGH)
| | - Jeffrey LeBlanc
- Higginbotham Farm, Washington, Louisiana, United States of America
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Banu JR, Kumar G, Chattopadhyay I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 2021; 11:429. [PMID: 34603908 DOI: 10.1007/s13205-021-02962-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
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Affiliation(s)
- J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
| | - Gopalakrishnan Kumar
- Faculty of Science and Technology, Institute of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Forus, Box 8600, 4036 Stavanger, Norway
| | - Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
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7
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2021; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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Boonyapakron K, Chitnumsub P, Kanokratana P, Champreda V. Enhancement of catalytic performance of a metagenome-derived thermophilic oligosaccharide-specific xylanase by binding module removal and random mutagenesis. J Biosci Bioeng 2020; 131:13-19. [PMID: 33067124 DOI: 10.1016/j.jbiosc.2020.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Xylo-oligosaccharide (XO) is a promising pre-biotic with applications in food, feed and healthcare products. XO can be produced by enzymatic digestion of xylan with xylanase. In this study, we aimed to improve the biochemical properties relevant to catalysis and kinetics of X11, a thermophilic glycosyl hydrolase (GH) family 11 endo-β-1,4-xylanase derived from a metagenomic library isolated from sugarcane bagasse, under high-temperature conditions preferred for XO synthesis. Removal of a carbohydrate-binding module (X11C) resulted in 6.5 fold greater catalytic efficiency. X11C was further improved by a Pro71Thr mutation in the X11P variant obtained from a random mutagenesis library, which exhibited 15.9 fold greater catalytic efficiency compared with wild-type X11 under the enzyme's optimal conditions of 80°C and pH 6.0. Homology modeling suggested that the improved performance of X11P could be attributed to formation of an extra H-bond between Thr71 and Ser75, which stabilizes the key catalytic residue Glu180 at the active pocket and β-sheet layers and agrees with the respective increase in melting temperature (Tm) where X11P >X11C >X11 as determined by differential scanning fluorimetry. The X11P variant was tested for hydrolysis of beechwood xylan, which showed X6 as the major product followed by X3 and X4 XOs. The highest yield of 5.5 g total XOs product/mg enzyme was observed for X11P, equivalent to 3.7 fold higher than that of wild-type with XO production of >800 mg/g xylan. The X11P enzyme could be developed as a thermophilic biocatalyst for XO synthesis in biorefineries.
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Affiliation(s)
- Katewadee Boonyapakron
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
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9
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Awala SI, Bellosillo LA, Gwak JH, Nguyen NL, Kim SJ, Lee BH, Rhee SK. Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea. Int J Syst Evol Microbiol 2020; 70:5520-5530. [PMID: 32910751 DOI: 10.1099/ijsem.0.004442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid methanotroph, strain IM1T, was isolated from hot spring soil. Cells of strain IM1T were catalase-negative, oxidase-positive and displayed a characteristic intracytoplasmic membrane arrangement of type I methanotrophs. The strain possessed genes encoding both membrane-bound and soluble methane monooxygenases and grew only on methane or methanol. The strain was capable of growth at temperatures between 15 and 48 °C (optimum, 30-45 °C) and pH values between pH 4.8 and 8.2 (optimum, pH 6.2-7.0). Based on phylogenetic analysis of 16S rRNA gene and PmoA sequences, strain IM1T was demonstrated to be affiliated to the genus Methylococcus. The 16S rRNA gene sequence of this strain was most closely related to the sequences of an uncultured bacterium clone FD09 (100 %) and a partially described cultured Methylococcus sp. GDS2.4 (99.78 %). The most closely related taxonomically described strains were Methylococcus capsulatus TexasT (97.92 %), Methylococcus capsulatus Bath (97.86 %) and Methyloterricola oryzae 73aT (94.21 %). Strain IM1T shared average nucleotide identity values of 85.93 and 85.62 % with Methylococcus capsulatus strains TexasT and Bath, respectively. The digital DNA-DNA hybridization value with the closest type strain was 29.90 %. The DNA G+C content of strain IM1T was 63.3 mol% and the major cellular fatty acids were C16 : 0 (39.0 %), C16 : 1 ω7c (24.0 %), C16 : 1 ω6c (13.6 %) and C16 : 1 ω5c (12.0 %). The major ubiquinone was methylene-ubiquinone-8. On the basis of phenotypic, genetic and phylogenetic data, strain IM1T represents a novel species of the genus Methylococcus for which the name Methylococcus geothermalis sp. nov. is proposed, with strain IM1T (=JCM 33941T=KCTC 72677T) as the type strain.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Lorraine Araza Bellosillo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ngoc-Loi Nguyen
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, 34132 Daejeon, Republic of Korea
| | - Byoung-Hee Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
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Hogendoorn C, Pol A, Picone N, Cremers G, van Alen TA, Gagliano AL, Jetten MSM, D'Alessandro W, Quatrini P, Op den Camp HJM. Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy. Front Microbiol 2020; 11:951. [PMID: 32508778 PMCID: PMC7248562 DOI: 10.3389/fmicb.2020.00951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 02/04/2023] Open
Abstract
Volcanic and geothermal areas are hot and often acidic environments that emit geothermal gasses, including H2, CO and CO2. Geothermal gasses mix with air, creating conditions where thermoacidophilic aerobic H2- and CO-oxidizing microorganisms could thrive. Here, we describe the isolation of two Kyrpidia spormannii strains, which can grow autotrophically by oxidizing H2 and CO with oxygen. These strains, FAVT5 and COOX1, were isolated from the geothermal soils of the Favara Grande on Pantelleria Island, Italy. Extended physiology studies were performed with K. spormannii FAVT5, and showed that this strain grows optimally at 55°C and pH 5.0. The highest growth rate is obtained using H2 as energy source (μmax 0.19 ± 0.02 h–1, doubling time 3.6 h). K. spormannii FAVT5 can additionally grow on a variety of organic substrates, including some alcohols, volatile fatty acids and amino acids. The genome of each strain encodes for two O2-tolerant hydrogenases belonging to [NiFe] group 2a hydrogenases and transcriptome studies using K. spormannii FAVT5 showed that both hydrogenases are expressed under H2 limiting conditions. So far no Firmicutes except K. spormannii FAVT5 have been reported to exhibit a high affinity for H2, with a Ks of 327 ± 24 nM. The genomes of each strain encode for one putative CO dehydrogenase, belonging to Form II aerobic CO dehydrogenases. The genomic potential and physiological properties of these Kyrpidia strains seem to be quite well adapted to thrive in the harsh environmental volcanic conditions.
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Affiliation(s)
- Carmen Hogendoorn
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A van Alen
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | | | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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11
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Gebbie L, Dam TT, Ainscough R, Palfreyman R, Cao L, Harrison M, O'Hara I, Speight R. A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. BMC Biotechnol 2020; 20:12. [PMID: 32111201 PMCID: PMC7049217 DOI: 10.1186/s12896-020-00609-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. RESULTS Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. CONCLUSIONS A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.
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Affiliation(s)
- Leigh Gebbie
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Tuan Tu Dam
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Rebecca Ainscough
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robin Palfreyman
- Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Li Cao
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Mark Harrison
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Ian O'Hara
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia
| | - Robert Speight
- Queensland University of Technology, 2 George St, Brisbane, QLD, 4000, Australia.
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A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley. Microorganisms 2020; 8:microorganisms8020250. [PMID: 32069978 PMCID: PMC7074724 DOI: 10.3390/microorganisms8020250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 11/23/2022] Open
Abstract
Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M.capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy.
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Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure. Antonie van Leeuwenhoek 2016; 109:1217-33. [DOI: 10.1007/s10482-016-0723-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
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Islam T, Torsvik V, Larsen Ø, Bodrossy L, Øvreås L, Birkeland NK. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps. Front Microbiol 2016; 7:851. [PMID: 27379029 PMCID: PMC4908921 DOI: 10.3389/fmicb.2016.00851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.
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Affiliation(s)
- Tajul Islam
- Department of Biology, University of Bergen Bergen, Norway
| | - Vigdis Torsvik
- Department of Biology, University of Bergen Bergen, Norway
| | - Øivind Larsen
- Department of Biology, University of BergenBergen, Norway; Uni Environment, Uni ResearchBergen, Norway
| | | | - Lise Øvreås
- Department of Biology, University of Bergen Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of BergenBergen, Norway; Centre for Geobiology, University of BergenBergen, Norway
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15
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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16
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Identification of glycosyl hydrolases from a metagenomic library of microflora in sugarcane bagasse collection site and their cooperative action on cellulose degradation. J Biosci Bioeng 2015; 119:384-91. [DOI: 10.1016/j.jbiosc.2014.09.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/12/2014] [Accepted: 09/13/2014] [Indexed: 11/19/2022]
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Mhuantong W, Charoensawan V, Kanokratana P, Tangphatsornruang S, Champreda V. Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:16. [PMID: 25709713 PMCID: PMC4337096 DOI: 10.1186/s13068-015-0200-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 01/08/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND As one of the most abundant agricultural wastes, sugarcane bagasse is largely under-exploited, but it possesses a great potential for the biofuel, fermentation, and cellulosic biorefinery industries. It also provides a unique ecological niche, as the microbes in this lignocellulose-rich environment thrive in relatively high temperatures (50°C) with varying microenvironments of aerobic surface to anoxic interior. The microbial community in bagasse thus presents a good resource for the discovery and characterization of new biomass-degrading enzymes; however, it remains largely unexplored. RESULTS We have constructed a fosmid library of sugarcane bagasse and obtained the largest bagasse metagenome to date. A taxonomic classification of the bagasse metagenome reviews the predominance of Proteobacteria, which are also found in high abundance in other aerobic environments. Based on the functional characterization of biomass-degrading enzymes, we have demonstrated that the bagasse microbial community benefits from a large repertoire of lignocellulolytic enzymes, which allows them to digest different components of lignocelluoses into single molecule sugars. Comparative genomic analyses with other lignocellulolytic and non-lignocellulolytic metagenomes show that microbial communities are taxonomically separable by their aerobic "open" or anoxic "closed" environments. Importantly, a functional analysis of lignocellulose-active genes (based on the CAZy classifications) reveals core enzymes highly conserved within the lignocellulolytic group, regardless of their taxonomic compositions. Cellulases, in particular, are markedly more pronounced compared to the non-lignocellulolytic group. In addition to the core enzymes, the bagasse fosmid library also contains some uniquely enriched glycoside hydrolases, as well as a large repertoire of the newly defined auxiliary activity proteins. CONCLUSIONS Our study demonstrates a conservation and diversification of carbohydrate-active genes among diverse microbial species in different biomass-degrading niches, and signifies the importance of taking a global approach to functionally investigate a microbial community as a whole, as compared to focusing on individual organisms.
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Affiliation(s)
- Wuttichai Mhuantong
- />Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand
| | - Varodom Charoensawan
- />Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
- />Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, 73170 Thailand
| | - Pattanop Kanokratana
- />Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand
| | - Sithichoke Tangphatsornruang
- />Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand
| | - Verawat Champreda
- />Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathumthani, 12120 Thailand
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18
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Wanangkarn A, Liu DC, Swetwiwathana A, Jindaprasert A, Phraephaisarn C, Chumnqoen W, Tan FJ. Lactic acid bacterial population dynamics during fermentation and storage of Thai fermented sausage according to restriction fragment length polymorphism analysis. Int J Food Microbiol 2014; 186:61-7. [PMID: 25005265 DOI: 10.1016/j.ijfoodmicro.2014.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 06/09/2014] [Accepted: 06/14/2014] [Indexed: 11/26/2022]
Abstract
This study applied restriction fragment length polymorphism (RFLP) analysis to identify the lactic acid bacteria (LAB) isolated from "mum" Thai fermented sausages during fermentation and storage. A total of 630 lactic acid bacteria were isolated from the sausages prepared using 2 methods. In Method 1, after stuffing, the sausages were stored at 30 °C for 14 days. In Method 2, after stuffing and storage at 30 °C for 3 days, the sausages were vacuum-packed and stored at 4 °C until Day 28. The sausages were sampled on Days 0, 3, 14, and 28 for analyses. The 16S rDNA was amplified and digested using restriction enzymes. Of the restriction enzymes evaluated, Dde I displayed the highest discrimination capacity. The LAB were classified and 7 species were identified For Methods 1 and 2, during fermentation, the Lactobacillus sakei and Lactobacillus plantarum species were dominant. For Method 2, the proportion of Leuconostoc mesenteroides markedly increased during storage, until L. sakei and Ln. mesenteroides represented the dominant species. The identification of LAB in the sausage samples could facilitate the selection of appropriate microorganisms for candidate starter cultures for future controlled mum production.
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Affiliation(s)
- Amornrat Wanangkarn
- Department of Agricultural Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Deng-Cheng Liu
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Adisorn Swetwiwathana
- Faculty of Agroindustry, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Aphacha Jindaprasert
- Faculty of Agroindustry, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | | | - Wanwisa Chumnqoen
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Fa-Jui Tan
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan.
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Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MB. Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes. Int J Syst Evol Microbiol 2014; 64:1264-1270. [PMID: 24425740 DOI: 10.1099/ijs.0.057463-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, thermophilic, moderately acidophilic, non-spore-forming bacterium, strain P373(T), was isolated from geothermally heated soil at Waikite, New Zealand. Cells were filamentous rods, 0.2-0.4 µm in diameter and grew in chains up to 80 µm in length. On the basis of 16S rRNA gene sequence similarity, strain P373(T) was shown to belong to the family Chitinophagaceae (class Sphingobacteriia) of the phylum Bacteroidetes, with the most closely related cultivated strain, Chitinophaga pinensis UQM 2034(T), having 87.6 % sequence similarity. Cells stained Gram-negative, and were catalase- and oxidase-positive. The major fatty acids were i-15 : 0 (10.8 %), i-17 : 0 (24.5 %) and i-17 : 0 3-OH (35.2 %). Primary lipids were phosphatidylethanolamine, two unidentified aminolipids and three other unidentified polar lipids. The presence of sulfonolipids (N-acyl-capnines) was observed in the total lipid extract by mass spectrometry. The G+C content of the genomic DNA was 47.3 mol% and the primary respiratory quinone was MK-7. Strain P373(T) grew at 35-63 °C with an optimum temperature of 60 °C, and at pH 5.5-8.7 with an optimum growth pH of 7.3-7.4. NaCl tolerance was up to 5 % (w/v) with an optimum of 0.1-0.25 % (w/v). Cell colonies were non-translucent and pigmented vivid yellow-orange. Cells displayed an oxidative chemoheterotrophic metabolism. The distinct phylogenetic position and the phenotypic characteristics separate strain P373(T) from all other members of the phylum Bacteroidetes and indicate that it represents a novel species in a new genus, for which the name Thermoflavifilum aggregans gen. nov., sp. nov. is proposed. The type strain of the type species is P373(T) ( = ICMP 20041(T) = DSM 27268(T)).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Karen M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - Jean F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | | | | | - Jason L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - Eric G Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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Jiménez DJ, Korenblum E, van Elsas JD. Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion. Appl Microbiol Biotechnol 2013; 98:2789-803. [PMID: 24113822 DOI: 10.1007/s00253-013-5253-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/03/2013] [Accepted: 09/07/2013] [Indexed: 10/26/2022]
Abstract
To develop a targeted metagenomics approach for the analysis of novel multispecies microbial consortia involved in the bioconversion of lignocellulose and furanic compounds, we applied replicated sequential batch aerobic enrichment cultures with either pretreated or untreated wheat straw as the sources of carbon and energy. After each transfer, exponential growth of bacteria was detected using microscopic cell counts, indicating that the substrate was being utilized. In batch, the final bacterial abundances increased from an estimated 5 to 8.7-9.5 log 16S rRNA gene copy numbers/ml. The abundances of fungal propagules showed greater variation, i.e., between 5.4 and 8.0 log ITS1 copies/ml. Denaturing gradient gel electrophoresis analyses showed that the bacterial consortia in both treatments reached approximate structural stability after six transfers. Moreover, the structures of the fungal communities were strongly influenced by substrate treatment. A total of 124 bacterial strains were isolated from the two types of enrichment cultures. The most abundant strains were affiliated with the genera Raoultella/Klebsiella, Kluyvera, Citrobacter, Enterobacter, Pseudomonas, Acinetobacter, Flavobacterium and Arthrobacter. Totals of 43 and 11 strains obtained from the untreated and pretreated substrates, respectively, showed (hemi)cellulolytic activity (CMC-ase and xylanase), whereas 96 strains were capable of growth in 7.5 mM 5-hydroxymethylfurfural. About 50 % of the latter showed extracellular oxidoreductase activity as detected by a novel iodide oxidation method. Also, (hemi)cellulolytic fungal strains related to Coniochaeta, Plectosphaerella and Penicillium were isolated. One Trichosporon strain was isolated from pretreated wheat straw. The two novel bacterial-fungal consortia are starting points for lignocellulose degradation applications.
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Affiliation(s)
- Diego Javier Jiménez
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Nijenborgh 7, 9747AG, Groningen, The Netherlands,
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Kanokratana P, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Eurwilaichitr L, Pootanakit K, Champreda V. Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site. MICROBIAL ECOLOGY 2013; 66:322-34. [PMID: 23504022 DOI: 10.1007/s00248-013-0209-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 03/05/2013] [Indexed: 05/05/2023]
Abstract
Industrial bagasse collection sites at sugar mills are an important resource for biomass-based industries and represent a unique ecological niche in lignocellulose degradation. In this study, microbial community structures at regions with varying microenvironmental conditions contained within a bagasse collection site were explored using tagged 16S rRNA gene pyrosequencing. Overall, remarkable differences in microbial community structures were found in aerobic surface and oxygen-limited interior regions of the pile. A variety of Alphaproteobacteria and Gammaproteobacteria represented the majority of bacteria in the aerobic upper-pile regions with the predominance of acetic acid bacteria towards the outer surface. Diverse Proteobacteria, Bacteroidetes, and Acidobacteria represented the predominant phyla at the exterior soil-contact pile base with an increasing abundance of anaerobic Spirochaetes with the increasing depth, where it shared similar community structures to that in the open-field soil from decomposed bagasse. Using complementary shotgun pyrosequencing, a variety of genes encoding various glycosyl hydrolases targeting cellulose and hemicellulose degradation were identified in the oxygen-limited interior pile base. Most were relevant to orders Clostridiales, Bacteroidales, Sphingobacteriales, and Cytophagales, suggesting their role in lignocellulose degradation in this region, as evidenced by the decrease in cellulose and respective increase in lignin fractions of the biomass. Partial carbon flux in the anoxic region was metabolized through mixed methanogenesis pathways as suggested by the annotated functional genes in methane synthesis. This study gives insights into native microbial community structures and functions in this unique lignocellulose degrading environment and provides the basis for controlling microbial processes important for utilization of bagasse in bio-industries.
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Affiliation(s)
- Pattanop Kanokratana
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
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22
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Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol 2013; 15:2573-87. [DOI: 10.1111/1462-2920.12159] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/29/2013] [Accepted: 05/15/2013] [Indexed: 12/01/2022]
Affiliation(s)
| | | | - Vatalie Stavila
- Biological and Materials Sciences Center; Sandia National Laboratories; Livermore; CA; 94551; USA
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Trujillo-Cabrera Y, Ponce-Mendoza A, Vásquez-Murrieta MS, Rivera-Orduña FN, Wang ET. Diverse cellulolytic bacteria isolated from the high humus, alkaline-saline chinampa soils. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0533-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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