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Adjeroud M, Kecha M, Escuder-Rodríguez JJ, Becerra M, González-Siso MI. AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer. Appl Microbiol Biotechnol 2024; 108:114. [PMID: 38204131 PMCID: PMC10781878 DOI: 10.1007/s00253-023-12844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/12/2024]
Abstract
A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.
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Affiliation(s)
- Moussa Adjeroud
- Laboratoire de Mycologie, Département de Biologie Appliquée, de Biotechnologie Et de L'Activité Microbienne (LaMyBAM), Faculté Des Sciences de La Nature Et de La Vie, Université Des Frères Mentouri Constantine 1, 25000, Constantine, Algeria
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté Des Sciences de La Nature Et de La Vie, Département de Microbiologie, Université de Bejaia, Campus Targa Ouzemmour, 6000, Bejaia, Algeria
| | - Juan-José Escuder-Rodríguez
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain
| | - Manuel Becerra
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
| | - María-Isabel González-Siso
- University of A Coruña, Grupo EXPRELA, Facultade de Ciencias, Centro Interdisciplinar de Química e Bioloxía (CICA), A Coruña, Spain.
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Ninck S, Klaus T, Kochetkova TV, Esser SP, Sewald L, Kaschani F, Bräsen C, Probst AJ, Kublanov IV, Siebers B, Kaiser M. Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. ENVIRONMENTAL MICROBIOME 2024; 19:36. [PMID: 38831353 PMCID: PMC11145796 DOI: 10.1186/s40793-024-00577-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/06/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging. RESULTS Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. CONCLUSIONS By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.
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Affiliation(s)
- Sabrina Ninck
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
| | - Thomas Klaus
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Sarah P Esser
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Leonard Sewald
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Centre One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany
- Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
- Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60-Let Oktyabrya 7-2, Moscow, 117312, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 5, 45117, Essen, Germany.
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
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Choudhary G, Kumari S, Anu K, Devi S. Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach. Braz J Microbiol 2024; 55:1465-1476. [PMID: 38662153 PMCID: PMC11153388 DOI: 10.1007/s42770-024-01346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Anu K, Kumari S, Choudhary G, Devi S. Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India. Braz J Microbiol 2024; 55:1545-1555. [PMID: 38421596 PMCID: PMC11153464 DOI: 10.1007/s42770-024-01284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.
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Affiliation(s)
- Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Sousa J, Santos-Pereira C, Gomes JS, Costa ÂMA, Santos AO, Franco-Duarte R, Linhares JMM, Sousa SF, Silvério SC, Rodrigues LR. Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library. Appl Microbiol Biotechnol 2024; 108:329. [PMID: 38727750 PMCID: PMC11087322 DOI: 10.1007/s00253-024-13169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.
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Affiliation(s)
- Joana Sousa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cátia Santos-Pereira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana S Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ângela M A Costa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andréia O Santos
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S - Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - João M M Linhares
- Physics Center of Minho and Porto Universities (CF-UM-UP), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sérgio F Sousa
- LAQV/REQUIMTE BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sara C Silvério
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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6
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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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7
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Huanca-Juarez J, Nascimento-Silva EA, Silva NH, Silva-Rocha R, Guazzaroni ME. Identification and functional analysis of novel protein-encoding sequences related to stress-resistance. Front Microbiol 2023; 14:1268315. [PMID: 37840709 PMCID: PMC10568318 DOI: 10.3389/fmicb.2023.1268315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.
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Affiliation(s)
- Joshelin Huanca-Juarez
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Edson Alexandre Nascimento-Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Ninna Hirata Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
| | | | - María-Eugenia Guazzaroni
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
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Lema NK, Gemeda MT, Woldesemayat AA. Recent Advances in Metagenomic Approaches, Applications, and Challenge. Curr Microbiol 2023; 80:347. [PMID: 37733134 DOI: 10.1007/s00284-023-03451-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/20/2023] [Indexed: 09/22/2023]
Abstract
Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.
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Affiliation(s)
- Niguse K Lema
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Department of Biotechnology, Arba Minch University, Arba Minch, Ethiopia
| | - Mesfin T Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna A Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Biotechnology and Bioprocess Center of Excellence, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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10
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Ishaq K, Shah AH, Fariq A, Rasheed S, Jannat S. Diversity of culturable thermophilic bacteria from Tata Pani hotspring of Kotli Azad Jammu and Kashmir. Biodivers Data J 2023; 11:e99224. [PMID: 38327337 PMCID: PMC10848829 DOI: 10.3897/bdj.11.e99224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Hot water springs are unique areas populated by mesophiles, thermotolerant and hyperthermophiles. They are the source of diversity of thermophiles, mainly belonging to archaea and bacteria domains. The diversity of thermophiles gives an outline of the huge biological potential that can be exploited for industrial applications.To this end, this study was aimed to isolate and characterise the unexplored thermophilic microorganisms from hot water spring in Tatapani, Tehsil & District Kotli AJK, Pakistan. Around 10 bacterial isolates were identified using morphological, biochemical, physiological and molecular attributes. Sequencing of the 16S rDNA gene of the isolates followed by BLAST search revealed that the strain MBT008 has 100% similarity with Anoxybacilluskamchatkensis. MBT012 showed 99.57% similarity with A.mongoliensis, MBT014 was affiliated with A.tengchongensis with 99.43% similarity, MBT009 showed 99.83% homology with A.gonensis and MBT018, 98.70% similarity with A.karvacharensis. The presence of all this microbial diversity in one common source is of immense importance related to envioronmental and industrial aspects in general and extraction of thermostable enzymes from these thermophiles specifically opens new horizons in the field of industrial biotechnology. These thermophiles are revealing new capabilities and are being manipulated by biotechnologists in utilizing them in different unique ways.
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Affiliation(s)
- Kazima Ishaq
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Asad Hussain Shah
- Senior Research Fellow, Faculty of Biology Medicine and Health The University of Manchester The Michael Smith Building Oxford Road Manchester M13 9PT, Manchester, United KingdomSenior Research Fellow, Faculty of Biology Medicine and Health The University of Manchester The Michael Smith Building Oxford Road Manchester M13 9PTManchesterUnited Kingdom
| | - Anila Fariq
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Sajida Rasheed
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
| | - Sammyia Jannat
- Department of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and Kashmir, Kotli, PakistanDepartment of Biotechnology, Faculty of Basic and Applied Sciences, University of Kotli Azad Jammu and KashmirKotliPakistan
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11
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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12
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Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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13
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Yin X, Gong W, Zhan Z, Wei W, Li M, Jiao J, Chen B, Liu L, Li W, Gao Z. Mining and engineering of valine dehydrogenases from a hot spring sediment metagenome for the synthesis of chiral non-natural L-amino acids. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Kukkar D, Sharma PK, Kim KH. Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass. ENVIRONMENTAL RESEARCH 2022; 215:114369. [PMID: 36165858 DOI: 10.1016/j.envres.2022.114369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.
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Affiliation(s)
- Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India.
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Wangsimni-ro, Seoul - 04763, South Korea.
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15
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Liu Q, Yang J, Wang B, Liu W, Hua Z, Jiang H. Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments. Front Microbiol 2022; 13:1019010. [PMID: 36519167 PMCID: PMC9742235 DOI: 10.3389/fmicb.2022.1019010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/08/2022] [Indexed: 08/23/2023] Open
Abstract
Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L-1. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Wen Liu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Zhengshuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
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16
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Wani AK, Akhtar N, Singh R, Chopra C, Kakade P, Borde M, Al-Khayri JM, Suprasanna P, Zimare SB. Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response. Mol Biol Rep 2022; 49:12165-12179. [PMID: 36169892 DOI: 10.1007/s11033-022-07936-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/19/2022] [Accepted: 09/08/2022] [Indexed: 12/01/2022]
Abstract
Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, 144411, Phagwara, India
| | - Prachi Kakade
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India
| | - Mahesh Borde
- Department of Botany, Savitribai Phule Pune University, 411007, Pune, India
| | - Jameel M Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, 31982, Al- Ahsa, Saudi Arabia
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, 400094, Mumbai, India
| | - Saurabha B Zimare
- Department of Botany, Amdar Shashikant Shinde Mahavidyalay, 415012, Medha, Satara, India. .,Department of Botany, D. P. Bhosale College, Koregaon, , Satara, 415501, Maharashtra, India.
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17
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Zhang Y, Guan F, Xu G, Liu X, Zhang Y, Sun J, Yao B, Huang H, Wu N, Tian J. A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem. BIORESOUR BIOPROCESS 2022; 9:54. [PMID: 38647756 PMCID: PMC10991277 DOI: 10.1186/s40643-022-00543-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/27/2022] [Indexed: 12/27/2022] Open
Abstract
Chitin is abundant in nature and its degradation products are highly valuable for numerous applications. Thermophilic chitinases are increasingly appreciated for their capacity to biodegrade chitin at high temperatures and prolonged enzyme stability. Here, using deep learning approaches, we developed a prediction tool, Preoptem, to screen thermophilic proteins. A novel thermophilic chitinase, Chi304, was mined directly from the marine metagenome. Chi304 showed maximum activity at 85 ℃, its Tm reached 89.65 ± 0.22℃, and exhibited excellent thermal stability at 80 and 90 °C. Chi304 had both endo- and exo-chitinase activities, and the (GlcNAc)2 was the main hydrolysis product of chitin-related substrates. The product yields of colloidal chitin degradation reached 97% within 80 min, and 20% over 4 days of reaction with crude chitin powder. This study thus provides a method to mine the novel thermophilic chitinase for efficient chitin biodegradation.
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Affiliation(s)
- Yan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jilu Sun
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Bin Yao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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18
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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. BIOLOGY 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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19
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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20
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Zatopek KM, Fossa SL, Bilotti K, Caffrey PJ, Chuzel L, Gehring AM, Lohman GJS, Taron CH, Gardner AF. Capillary Electrophoresis-Based Functional Genomics Screening to Discover Novel Archaeal DNA Modifying Enzymes. Appl Environ Microbiol 2022; 88:e0213721. [PMID: 34788065 PMCID: PMC8788744 DOI: 10.1128/aem.02137-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 12/05/2022] Open
Abstract
It has been predicted that 30 to 80% of archaeal genomes remain annotated as hypothetical proteins with no assigned gene function. Further, many archaeal organisms are difficult to grow or are unculturable. To overcome these technical and experimental hurdles, we developed a high-throughput functional genomics screen that utilizes capillary electrophoresis (CE) to identify nucleic acid modifying enzymes based on activity rather than sequence homology. Here, we describe a functional genomics screening workflow to find DNA modifying enzyme activities encoded by the hyperthermophile Thermococcus kodakarensis (T. kodakarensis). Large DNA insert fosmid libraries representing an ∼5-fold average coverage of the T. kodakarensis genome were prepared in Escherichia coli. RNA-seq showed a high fraction (84%) of T. kodakarensis genes were transcribed in E. coli despite differences in promoter structure and translational machinery. Our high-throughput screening workflow used fluorescently labeled DNA substrates directly in heat-treated lysates of fosmid clones with capillary electrophoresis detection of reaction products. Using this method, we identified both a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and a novel AP lyase DNA repair enzyme family (termed 'TK0353') that is found only in a small subset of Thermococcales. The screening methodology described provides a fast and efficient way to explore the T. kodakarensis genome for a variety of nucleic acid modifying activities and may have implications for similar exploration of enzymes and pathways that underlie core cellular processes in other Archaea. IMPORTANCE This study provides a rapid, simple, high-throughput method to discover novel archaeal nucleic acid modifying enzymes by utilizing a fosmid genomic library, next-generation sequencing, and capillary electrophoresis. The method described here provides the details necessary to create 384-well fosmid library plates from Thermococcus kodakarensis genomic DNA, sequence 384-well fosmids plates using Illumina next-generation sequencing, and perform high-throughput functional read-out assays using capillary electrophoresis to identify a variety of nucleic acid modifying activities, including DNA cleavage and ligation. We used this approach to identify a new DNA endonuclease activity for a previously described RNA endonuclease (Nob1) and identify a novel AP lyase enzyme (TK0353) that lacks sequence homology to known nucleic acid modifying enzymes.
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Affiliation(s)
| | | | | | | | - Léa Chuzel
- New England Biolabs, Inc., Ipswich, Massachusetts, USA
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21
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Rego A, Fernandez-Guerra A, Duarte P, Assmy P, Leão PN, Magalhães C. Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes. Microb Genom 2021; 7. [PMID: 34904945 PMCID: PMC8767328 DOI: 10.1099/mgen.0.000731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- *Correspondence: Pedro N. Leão,
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- *Correspondence: Catarina Magalhães,
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22
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Arbab S, Ullah H, Khan MIU, Khattak MNK, Zhang J, Li K, Hassan IU. Diversity and distribution of thermophilic microorganisms and their applications in biotechnology. J Basic Microbiol 2021; 62:95-108. [PMID: 34878177 DOI: 10.1002/jobm.202100529] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/16/2021] [Accepted: 11/27/2021] [Indexed: 11/07/2022]
Abstract
Hot springs ecosystem is the most ancient continuously inhabited ecosystem on earth which harbors diverse thermophilic bacteria and archaea distributed worldwide. Life in extreme environments is very challenging so there is a great potential biological dark matter and their adaptation to harsh environments eventually producing thermostable enzymes which are very vital for the welfare of mankind. There is an enormous need for a new generation of stable enzymes that can endure harsh conditions in industrial processes and can either substitute or complement conventional chemical processes. Here, we review at the variety and distribution of thermophilic microbes, as well as the different thermostable enzymes that help them survive at high temperatures, such as proteases, amylases, lipases, cellulases, pullulanase, xylanases, and DNA polymerases, as well as their special properties, such as high-temperature stability. We have documented the novel isolated thermophilic and hyperthermophilic microorganisms, as well as the discovery of their enzymes, demonstrating their immense potential in the scientific community and in industry.
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Affiliation(s)
- Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Muhammad I U Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Muhammad N K Khattak
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China.,Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China
| | - Inam Ul Hassan
- Department of Microbiology, Hazara University, Manshera, Pakistan
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23
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Costa ÂMA, Santos AO, Sousa J, Rodrigues JL, Gudiña EJ, Silvério SC, Rodrigues LR. Improved method for the extraction of high-quality DNA from lignocellulosic compost samples for metagenomic studies. Appl Microbiol Biotechnol 2021; 105:8881-8893. [PMID: 34724083 DOI: 10.1007/s00253-021-11647-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022]
Abstract
The world economy is currently moving towards more sustainable approaches. Lignocellulosic biomass has been widely used as a substitute for fossil sources since it is considered a low-cost bio-renewable resource due to its abundance and continuous production. Compost habitats presenting high content of lignocellulosic biomass are considered a promising source of robust lignocellulose-degrading enzymes. Recently, several novel biocatalysts from different environments have been identified using metagenomic techniques. A key point of the metagenomics studies is the extraction and purification of nucleic acids. Nevertheless, the isolation of high molecular weight DNA from soil-like samples, such as compost, with the required quality for metagenomic approaches remains technically challenging, mainly due to the complex composition of the samples and the presence of contaminants like humic substances. In this work, a rapid and cost-effective protocol for metagenomic DNA extraction from compost samples composed of lignocellulosic residues and containing high content of humic substances was developed. The metagenomic DNA was considered as representative of the global environment and presented high quality (> 99% of humic acids effectively removed) and sufficient quantity (10.5-13.8 µg g-1 of compost) for downstream applications, namely functional metagenomic studies. The protocol takes about 4 h of bench work, and it can be performed using standard molecular biology equipment and reagents available in the laboratory. KEY POINTS/HIGHLIGHTS: • Metagenomic DNA was successfully extracted from compost samples rich in humic acids • The improved protocol was established by optimizing the cell lysis method and buffer • Complete removal of humic acids was achieved through the use of activated charcoal • The suitability of the DNA was proven by the construction of a metagenomic library.
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Affiliation(s)
- Ângela M A Costa
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
| | - Andréia O Santos
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
| | - Joana Sousa
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
| | - Joana L Rodrigues
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
| | - Eduardo J Gudiña
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal.
| | - Ligia R Rodrigues
- CEB - Centre of Biological Engineering, Universidade Do Minho, 4710-057, Braga, Portugal
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24
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Kotsyurbenko OR, Cordova JA, Belov AA, Cheptsov VS, Kölbl D, Khrunyk YY, Kryuchkova MO, Milojevic T, Mogul R, Sasaki S, Słowik GP, Snytnikov V, Vorobyova EA. Exobiology of the Venusian Clouds: New Insights into Habitability through Terrestrial Models and Methods of Detection. ASTROBIOLOGY 2021; 21:1186-1205. [PMID: 34255549 PMCID: PMC9545807 DOI: 10.1089/ast.2020.2296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 04/16/2021] [Indexed: 06/13/2023]
Abstract
The search for life beyond Earth has focused on Mars and the icy moons Europa and Enceladus, all of which are considered a safe haven for life due to evidence of current or past water. The surface of Venus, on the other hand, has extreme conditions that make it a nonhabitable environment to life as we know it. This is in contrast, however, to its cloud layer, which, while still an extreme environment, may prove to be a safe haven for some extreme forms of life similar to extremophiles on Earth. We consider the venusian clouds a habitable environment based on the presence of (1) a solvent for biochemical reactions, (2) appropriate physicochemical conditions, (3) available energy, and (4) biologically relevant elements. The diversity of extreme microbial ecosystems on Earth has allowed us to identify terrestrial chemolithoautotrophic microorganisms that may be analogs to putative venusian organisms. Here, we hypothesize and describe biological processes that may be performed by such organisms in the venusian clouds. To detect putative venusian organisms, we describe potential biosignature detection methods, which include metal-microbial interactions and optical methods. Finally, we describe currently available technology that can potentially be used for modeling and simulation experiments.
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Affiliation(s)
- Oleg R. Kotsyurbenko
- Yugra State University, The Institute of Oil and Gas, School of Ecology, Khanty-Mansiysk, Russian Federation
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
| | - Jaime A. Cordova
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Andrey A. Belov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Vladimir S. Cheptsov
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
- Space Research Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | - Denise Kölbl
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuliya Y. Khrunyk
- Department of Heat Treatment and Physics of Metal, Ural Federal University, Ekaterinburg, Russian Federation
- M.N. Mikheev Institute of Metal Physics of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
| | - Margarita O. Kryuchkova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
| | - Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, California, USA
| | - Satoshi Sasaki
- School of Biosciences and Biotechnology/School of Health Sciences, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Grzegorz P. Słowik
- Institute of Materials and Biomedical Engineering, Faculty of Mechanical Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Valery Snytnikov
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Elena A. Vorobyova
- Network of Researchers on the Chemical Evolution of Life, Leeds, UK
- Moscow State University, Faculty of Soil Science, Moscow, Russian Federation
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25
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Franco-Frías E, Mercado-Guajardo V, Merino-Mascorro A, Pérez-Garza J, Heredia N, León JS, Jaykus LA, Dávila-Aviña J, García S. Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment. MICROBIAL ECOLOGY 2021; 82:613-622. [PMID: 33570667 DOI: 10.1007/s00248-021-01709-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.
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Affiliation(s)
- Eduardo Franco-Frías
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Victor Mercado-Guajardo
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Angel Merino-Mascorro
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Janeth Pérez-Garza
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Norma Heredia
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Juan S León
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, NC, USA
| | - Jorge Dávila-Aviña
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México
| | - Santos García
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Apdo. Postal 124-F, San Nicolás, N.L., 66451, México.
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26
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Wang X, Pecoraro L. Diversity and Co-Occurrence Patterns of Fungal and Bacterial Communities from Alkaline Sediments and Water of Julong High-Altitude Hot Springs at Tianchi Volcano, Northeast China. BIOLOGY 2021; 10:894. [PMID: 34571771 PMCID: PMC8464750 DOI: 10.3390/biology10090894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/28/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022]
Abstract
The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure and networks in sediments and water from the Julong hot springs using a combination of culture-based methods and metabarcoding. A total of 65 fungal and 21 bacterial strains were isolated. Fungal genera Trichoderma and Cladosporium were dominant in sediments, while the most abundant fungi in hot spring water were Aspergillus and Alternaria. Bacterial communities in sediments and water were dominated by the genera Chryseobacterium and Pseudomonas, respectively. Metabarcoding analysis revealed significant differences in the microorganism communities from the two hot springs. Results suggested a strong influence of pH on the analyzed microbial diversity, at least when the environmental conditions became clearly alkaline. Our analyses indicated that mutualistic interactions may play an essential role in shaping stable microbial networks in the studied hot springs. The much more complicated bacterial than fungal networks described in our study may suggest that the more flexible trophic strategies of bacteria are beneficial for their survival and fitness under extreme conditions.
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Affiliation(s)
- Xiao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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27
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Rivera-Urbalejo AP, Vázquez D, Fernández Vázquez JL, Rosete Enríquez M, Cesa-Luna C, Morales-García YE, Muñoz Rojas J, Quintero Hernández V. APORTES Y DIFICULTADES DE LA METAGENÓMICA DE SUELOS Y SU IMPACTO EN LA AGRICULTURA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.85760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.
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Abstract
In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities present in three thermal waters of the Galician region in Spain and two samples of the northern region in Portugal. These collected water samples were analyzed for physicochemical characterization and the respective hydrogenome of the waters using next generation sequencing together with 16S rRNA gene sequencing. The sequencing showed a high diversity of microorganisms in all analyzed waters; however, there is a clear bacterial predominance of Proteobacteria phylum, followed by Firmicutes, Deinococcus-Thermus, Aquificae and Nitrospira. The main physicochemical parameters responsible for the clustering within the Spanish waters were sulfur compounds (SO32− and S2−), CO32− and neutral pH, and in the Portuguese waters were Mg, Ca and Sr, nitrogen compounds (NO3− and NH4+), Na, Rb, conductivity and dry residue. This work will allow for a better understanding of the microbial community’s composition and how these microorganisms interfere in the physicochemical constitution of these waters often associated with medicinal properties. Furthermore, the hydrogenome may be used as an auxiliary tool in the practice of medical hydrology, increasing the likelihood of safe use of these unique water types.
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29
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Strategies for Natural Products Discovery from Uncultured Microorganisms. Molecules 2021; 26:molecules26102977. [PMID: 34067778 PMCID: PMC8156983 DOI: 10.3390/molecules26102977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Microorganisms are highly regarded as a prominent source of natural products that have significant importance in many fields such as medicine, farming, environmental safety, and material production. Due to this, only tiny amounts of microorganisms can be cultivated under standard laboratory conditions, and the bulk of microorganisms in the ecosystems are still unidentified, which restricts our knowledge of uncultured microbial metabolism. However, they could hypothetically provide a large collection of innovative natural products. Culture-independent metagenomics study has the ability to address core questions in the potential of NP production by cloning and analysis of microbial DNA derived directly from environmental samples. Latest advancements in next generation sequencing and genetic engineering tools for genome assembly have broadened the scope of metagenomics to offer perspectives into the life of uncultured microorganisms. In this review, we cover the methods of metagenomic library construction, and heterologous expression for the exploration and development of the environmental metabolome and focus on the function-based metagenomics, sequencing-based metagenomics, and single-cell metagenomics of uncultured microorganisms.
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Analysis of Soil Fungal and Bacterial Communities in Tianchi Volcano Crater, Northeast China. Life (Basel) 2021; 11:life11040280. [PMID: 33810555 PMCID: PMC8066613 DOI: 10.3390/life11040280] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/26/2022] Open
Abstract
High-altitude volcanoes, typical examples of extreme environments, are considered of particular interest in biology as a possible source of novel and exclusive microorganisms. We analyzed the crater soil microbial diversity of Tianchi Volcano, northeast China, by combining molecular and morphological analyses of culturable microbes, and metabarcoding based on Illumina sequencing, in order to increase our understanding of high-altitude volcanic microbial community structure. One-hundred and seventeen fungal strains belonging to 51 species and 31 genera of Ascomycota, Basidiomycota and Mucoromycota were isolated. Penicillium, Trichoderma, Cladosporium, Didymella, Alternaria and Fusarium dominated the culturable fungal community. A considerable number of isolated microbes, including filamentous fungi, such as Aureobasidium pullulans and Epicoccum nigrum, yeasts (Leucosporidium creatinivorum), and bacteria (Chryseobacterium lactis and Rhodococcus spp.), typical of high-altitude, cold, and geothermal extreme environments, provided new insights in the ecological characterization of the investigated environment, and may represent a precious source for the isolation of new bioactive compounds. A total of 1254 fungal and 2988 bacterial operational taxonomic units were generated from metabarcoding. Data analyses suggested that the fungal community could be more sensitive to environmental and geographical change compared to the bacterial community, whose network was characterized by more complicated and closer associations.
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31
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Choure K, Parsai S, Kotoky R, Srivastava A, Tilwari A, Rai PK, Sharma A, Pandey P. Comparative Metagenomic Analysis of Two Alkaline Hot Springs of Madhya Pradesh, India and Deciphering the Extremophiles for Industrial Enzymes. Front Genet 2021; 12:643423. [PMID: 33763123 PMCID: PMC7982539 DOI: 10.3389/fgene.2021.643423] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 11/25/2022] Open
Abstract
Hot springs are considered to be a unique environment with extremophiles, that are sources of industrially important enzymes, and other biotechnological products. The objective of this study was to undertake, analyze, and characterize the microbiome of two major hot springs located in the state of Madhya Pradesh explicitly, Chhoti Anhoni (Hotspring 1), and Badi Anhoni (Hotspring 2) to find out the inhabitant microbial population, and their functional characteristics. The taxonomic analysis of the microbiome of the hot springs revealed the phylum Proteobacteria was the most abundant taxa in both the hot-springs, however, its abundance in hot-spring 1 (~88%) was more than the hot-spring 2 (~52%). The phylum Bacteroides (~10–22%) was found to be the second most abundant group in the hot-springs followed by Spirocheates (~2–11%), Firmicutes (~6–8%), Chloroflexi (1–5%), etc. The functional analysis of the microbiome revealed different features related to several functions including metabolism of organics and degradation of xenobiotic compounds. The functional analysis showed that most of the attributes of the microbiome was related to metabolism, followed by cellular processes and environmental information processing functions. The functional annotation of the microbiomes at KEGG level 3 annotated the sequences into 279 active features that showed variation in abundance between the hot spring samples, where hot-spring 1 was functionally more diverse. Interestingly, the abundance of functional genes from methanogenic bacteria, was higher in the hot-spring 2, which may be related to the relatively higher pH and temperature than Hotspring 1. The study showed the presence of different unassigned bacterial taxa with high abundance which indicates the potential of novel genera or phylotypes. Culturable isolates (28) were bio-prospected for industrially important enzymes including amylase, protease, lipase, gelatinase, pectinase, cellulase, lecithinase, and xylanase. Seven isolates (25%) had shown positive results for all the enzyme activities whereas 23 isolates (82%) produced Protease, 27 isolates (96%) produced lipase, 27 isolates produced amylase, 26 isolates (92%) produced cellulase, 19 isolates (67%) produced pectinase, 19 isolates (67%) could produce lecithinase, and 13 isolates (46%) produced gelatinase. The seven isolates, positive for all the enzymes were analyzed further for quantitative analysis and identified through molecular characterization.
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Affiliation(s)
- Kamlesh Choure
- Department of Biotechnology, AKS University, Satna, India
| | | | - Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, India
| | | | - Anita Tilwari
- Centre of Excellence in Biotechnology, Madhya Pradesh Council of Science and Technology, Bhopal, India
| | | | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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32
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Kryukova MV, Petrovskaya LE, Novototskaya-Vlasova KA, Kryukova EA, Yakimov SA, Nikolaeva AY, Boyko KM, Dolgikh DA, Kirpichnikov MP. Effect of Cysteine Residue Substitution in the GCSAG Motif of the PMGL2 Esterase Active Site on the Enzyme Properties. BIOCHEMISTRY (MOSCOW) 2021; 85:709-716. [PMID: 32586234 DOI: 10.1134/s0006297920060085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gene coding for PMGL2 esterase, which belongs to the family of mammalian hormone-sensitive lipases (HSLs), was discovered by screening a metagenomic DNA library from a permafrost soil. The active site of PMGL2 contains conserved GXSXG motif which includes Cys173 residue next to the catalytic Ser174. In order to clarify the functional role of the cysteine residue in the GCSAG motif, we constructed a number of PMGL2 mutants with Cys173 substitutions and studied their properties. The specific activity of the C173D mutant exceeded the specific activity of the wild-type enzyme (wtPMGL2) by 60%, while the C173T/C202S mutant displayed reduced catalytic activity. The activity of the C173D mutant with p-nitrophenyl octanoate was 15% higher, while the activity of the C173T/C202S mutant was 17% lower compared to wtPMGL2. The C173D mutant was also characterized by a high activity at low temperatures (20-35°C) and significant loss of thermal stability. The kcat value for this protein was 56% higher than for the wild-type enzyme. The catalytic constants of the C173S mutant were close to those of wtPMGL2; this enzyme also demonstrated the highest thermal stability among the studied mutants. The obtained results demonstrate that substitutions of amino acid residues adjacent to the catalytic serine residue in the GXSXG motif can have a significant effect on the properties of PMGL2 esterase.
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Affiliation(s)
- M V Kryukova
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Novototskaya-Vlasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - E A Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S A Yakimov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A Y Nikolaeva
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - K M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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Akanbi TO, Ji D, Agyei D. Revisiting the scope and applications of food enzymes from extremophiles. J Food Biochem 2020; 44:e13475. [PMID: 32996180 DOI: 10.1111/jfbc.13475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/27/2022]
Abstract
Microorganisms from extreme environments tend to undergo various adaptations due to environmental conditions such as extreme pH, temperature, salinity, heavy metals, and solvents. Thus, they produce enzymes with unique properties and high specificity, making them useful industrially, particularly in the food industries. Despite these enzymes' remarkable properties, only a few instances can be reported for actual exploitation in the food industry. This review's objectives are to highlight the properties of these enzymes and their prospects in the food industry. First, an introduction to extremophilic organisms is presented, followed by the categories and application of food enzymes from extremophiles. Then, the unique structural features of extremozymes are shown. This review also covers the prospective applications of extremozymes in the food industry in a broader sense, including degradation of toxins, deconstruction of polymers into monomers, and catalysis of multistep processes. Finally, the challenges in bioprocessing of extremozymes and applications in food are presented. PRACTICAL APPLICATIONS: Enzymes are important players in food processing and preservation. Extremozymes, by their nature, are ideal for a broad range of food processing applications, particularly those that require process conditions of extreme pH, temperature, and salinity. As the global food industry grows, so too will grow the need to research and develop food products that are diverse, safe, healthy, and nutritious. There is also the need to produce food in a sustainable way that generates less waste or maximizes waste valorization. We anticipate that extremozymes can meet some of the research and development needs of the food industry.
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Affiliation(s)
- Taiwo O Akanbi
- Faculty of Science, School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Dawei Ji
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
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Krüger A, Schäfers C, Busch P, Antranikian G. Digitalization in microbiology - Paving the path to sustainable circular bioeconomy. N Biotechnol 2020; 59:88-96. [PMID: 32750680 DOI: 10.1016/j.nbt.2020.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022]
Abstract
The transition to a sustainable bio-based circular economy requires cutting edge technologies that ensure economic growth with environmentally responsible action. This transition will only be feasible when the opportunities of digitalization are also exploited. Digital methods and big data handling have already found their way into life sciences and generally offer huge potential in various research areas. While computational analyses of microbial metagenome data have become state of the art, the true potential of bioinformatics remains mostly untapped so far. In this article we present challenges and opportunities of digitalization including multi-omics approaches in discovering and exploiting the microbial diversity of the planet with the aim to identify robust biocatalysts for application in sustainable bioprocesses as part of the transition from a fossil-based to a bio-based circular economy. This will contribute to solving global challenges, including utilization of natural resources, food supply, health, energy and the environment.
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Affiliation(s)
- Anna Krüger
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Christian Schäfers
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Philip Busch
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg, Germany.
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A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy). Microorganisms 2020; 8:microorganisms8060936. [PMID: 32580393 PMCID: PMC7356649 DOI: 10.3390/microorganisms8060936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023] Open
Abstract
Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.
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Lamprecht-Grandío M, Cortesão M, Mirete S, de la Cámara MB, de Figueras CG, Pérez-Pantoja D, White JJ, Farías ME, Rosselló-Móra R, González-Pastor JE. Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments. Front Microbiol 2020; 11:453. [PMID: 32292392 PMCID: PMC7135895 DOI: 10.3389/fmicb.2020.00453] [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: 08/22/2019] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory. Thus, a functional metagenomic approach was used and for this, small-insert libraries were constructed with DNA isolated from microorganisms of high-altitude Andean hypersaline lakes in Argentina (Diamante and Ojo Seco lakes, 4,589 and 3,200 m, respectively) and from the Es Trenc solar saltern in Spain. The libraries were hosted in a UV radiation-sensitive strain of Escherichia coli (recA mutant) and they were exposed to UVB. The resistant colonies were analyzed and as a result, four clones were identified with environmental DNA fragments containing five genes that conferred resistance to UV radiation in E. coli. One gene encoded a RecA-like protein, complementing the mutation in recA that makes the E. coli host strain more sensitive to UV radiation. Two other genes from the same DNA fragment encoded a TATA-box binding protein and an unknown protein, both responsible for UV resistance. Interestingly, two other genes from different and remote environments, the Ojo Seco Andean lake and the Es Trenc saltern, encoded two hypothetical proteins that can be considered homologous based on their significant amino acid similarity (49%). All of these genes also conferred resistance to 4-nitroquinoline 1-oxide (4-NQO), a compound that mimics the effect of UV radiation on DNA, and also to perchlorate, a powerful oxidant that can induce DNA damage. Furthermore, the hypothetical protein from the Es Trenc salterns was localized as discrete foci possibly associated with damaged sites in the DNA in cells treated with 4-NQO, so it could be involved in the repair of damaged DNA. In summary, novel genes involved in resistance to UV radiation, 4-NQO and perchlorate have been identified in this work and two of them encoding hypothetical proteins that could be involved in DNA damage repair activities not previously described.
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Affiliation(s)
| | - Marta Cortesão
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Salvador Mirete
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | | | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Joseph John White
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), Centro Científico Tecnológico, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122782. [PMID: 30544637 PMCID: PMC6313336 DOI: 10.3390/ijerph15122782] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 01/10/2023]
Abstract
Contamination of the environment by petroleum products is a growing concern worldwide, and strategies to remove these contaminants have been evaluated. One of these strategies is biodegradation, which consists of the use of microorganisms. Biodegradation is significantly improved by increasing the temperature of the medium, thus, the use of thermophiles, microbes that thrive in high-temperature environments, will render this process more efficient. For instance, various thermophilic enzymes have been used in industrial biotechnology because of their unique catalytic properties. Biodegradation has been extensively studied in the context of mesophilic microbes, and the mechanisms of biodegradation of aliphatic and aromatic petroleum hydrocarbons have been elucidated. However, in comparison, little work has been carried out on the biodegradation of petroleum hydrocarbons by thermophiles. In this paper, a detailed review of the degradation of petroleum hydrocarbons (both aliphatic and aromatic) by thermophiles was carried out. This work has identified the characteristics of thermophiles, and unraveled specific catabolic pathways of petroleum products that are only found with thermophiles. Gaps that limit our understanding of the activity of these microbes have also been highlighted, and, finally, different strategies that can be used to improve the efficiency of degradation of petroleum hydrocarbons by thermophiles were proposed.
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Kaushal G, Kumar J, Sangwan RS, Singh SP. Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes. Int J Biol Macromol 2018; 119:882-895. [DOI: 10.1016/j.ijbiomac.2018.07.196] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
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Napp AP, Pereira JES, Oliveira JS, Silva-Portela RCB, Agnez-Lima LF, Peralba MCR, Bento FM, Passaglia LMP, Thompson CE, Vainstein MH. Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste. CHEMOSPHERE 2018; 209:7-16. [PMID: 29908430 DOI: 10.1016/j.chemosphere.2018.06.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/24/2018] [Accepted: 06/10/2018] [Indexed: 06/08/2023]
Abstract
The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.
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Affiliation(s)
- Amanda P Napp
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
| | - José Evandro S Pereira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
| | - Jorge S Oliveira
- INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1000-029, Portugal; Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Rita C B Silva-Portela
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Lucymara F Agnez-Lima
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Maria C R Peralba
- Departamento de Química Inorgânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil.
| | - Fátima M Bento
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 90050-170, Brazil.
| | - Luciane M P Passaglia
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil.
| | - Claudia E Thompson
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil; Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
| | - Marilene H Vainstein
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
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Chuzel L, Ganatra MB, Rapp E, Henrissat B, Taron CH. Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156). J Biol Chem 2018; 293:18138-18150. [PMID: 30249617 PMCID: PMC6254351 DOI: 10.1074/jbc.ra118.003302] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.
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Affiliation(s)
- Léa Chuzel
- From New England Biolabs, Ipswich, Massachusetts 01938,; the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | | | - Erdmann Rapp
- the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany,; glyXera GmbH, 39120 Magdeburg, Germany
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France,; the Institut National de la Recherche Agronomique (INRA), Unité Sous Contrat (USC) 1408, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France, and; the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Wu L, Ali DC, Liu P, Peng C, Zhai J, Wang Y, Ye B. Degradation of phenol via ortho-pathway by Kocuria sp. strain TIBETAN4 isolated from the soils around Qinghai Lake in China. PLoS One 2018; 13:e0199572. [PMID: 29949643 PMCID: PMC6021097 DOI: 10.1371/journal.pone.0199572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/09/2018] [Indexed: 01/17/2023] Open
Abstract
Based on the feature of high-altitude permafrost topography and the diverse microbial ecological communities of the Qinghai-Tibetan Plateau, soil samples from thirteen different collection points around Qinghai lake were collected to screen for extremophilic strains with the ability to degrade phenol, and one bacterial strain recorded as TIBETAN4 that showed effective biodegradation of phenol was isolated and identified. TIBETAN4 was closely related to Kocuria based on its observed morphological, molecular and biochemical characteristics. TIBETAN4 grew well in the LB medium at pH 7–9 and 0–4% NaCl showing alkalophilicity and halophilism. The isolate could also tolerate up to 12.5 mM phenol and could degrade 5 mM phenol within 3 days. It maintained a high phenol degradation rate at pH 7–9 and 0–3% NaCl in MSM with 5 mM phenol added as the sole carbon source. Moreover, TIBETAN4 could maintain efficient phenol degradation activity in MSM supplemented with both phenol and glucose and complex water environments, including co-culture Penicillium strains or selection of non-sterilized natural lake water as a culture. It was found that TIBETAN4 showed enzymatic activity of phenol hydroxylase and catechol 1,2-dioxygenase after induction by phenol and the corresponding genes of the two enzymes were detected in the genome of the isolate, while catechol 2,3-dioxygenase or its gene was not, which means there could be a degradation pathway of phenol through the ortho-pathway. The Q-PCR results showed that the transcripts of both the phenol hydroxylase gene and catechol 1,2-dioxygenase gene were up-regulated under the stimulation of phenol, demonstrating again that the strain degraded phenol via ortho-degradation pathway.
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Affiliation(s)
- Leyang Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Daniel C. Ali
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Peng Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Cheng Peng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Jingxin Zhai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
| | - Ying Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- * E-mail: (YW); (BY)
| | - Boping Ye
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People’s Republic of China
- * E-mail: (YW); (BY)
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43
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Marques CR. Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation. Front Microbiol 2018; 9:1191. [PMID: 29910794 PMCID: PMC5992296 DOI: 10.3389/fmicb.2018.01191] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022] Open
Abstract
Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.
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Affiliation(s)
- Catarina R Marques
- Departamento de Biologia and Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
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44
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Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, Chan KG. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. Microbiologyopen 2018; 7:e00615. [PMID: 29602271 PMCID: PMC6291792 DOI: 10.1002/mbo3.615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
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Affiliation(s)
- Li Sin Lee
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Geok Yuan Annie Tan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia.,Jiangsu University, Zhenjiang, China
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Strahsburger E, Zapata F, Pedroso I, Fuentes D, Tapia P, Ponce R, Valdes J. Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile. Braz J Microbiol 2018; 49:7-9. [PMID: 28757098 PMCID: PMC5790568 DOI: 10.1016/j.bjm.2017.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/14/2017] [Accepted: 03/10/2017] [Indexed: 11/24/2022] Open
Abstract
In this report, we present a draft genome of 2,886,173bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.
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Affiliation(s)
- Erwin Strahsburger
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile.
| | - Felipe Zapata
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Derie Fuentes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Paz Tapia
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile
| | - Raul Ponce
- Universidad Arturo Prat, Faculty of Renewable Naturals Resources, Molecular Biotechnology Laboratory, Iquique, Chile
| | - Jorge Valdes
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Bio-Computing and Applied Genetics Division, Santiago, Chile.
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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Amin A, Ahmed I, Salam N, Kim BY, Singh D, Zhi XY, Xiao M, Li WJ. Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan. MICROBIAL ECOLOGY 2017; 74:116-127. [PMID: 28105510 DOI: 10.1007/s00248-017-0930-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.
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Affiliation(s)
- Arshia Amin
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan
- Department of Microbiology, Quaid-e-Azam University, Islamabad, 45320, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan.
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Byung-Yong Kim
- Chun Lab Inc., Seoul National University, Seoul, 151-742, Republic of South Korea
| | - Dharmesh Singh
- Environmental Genomics Division, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, 440024, India
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
- State Key Laboratory of Biocontrol and Guandong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Isolation and characterization of a novel endo-β-1,4-glucanase from a metagenomic library of the black-goat rumen. Braz J Microbiol 2017; 48:801-808. [PMID: 28689814 PMCID: PMC5628298 DOI: 10.1016/j.bjm.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 02/06/2017] [Accepted: 03/01/2017] [Indexed: 11/21/2022] Open
Abstract
The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1 kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30–50 °C at a pH of 6–7. The thermostability was retained and the pH was stable in the range of 30–50 °C at a pH of 5–7.
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Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A, Sharma VK. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Front Microbiol 2017; 7:2123. [PMID: 28105025 PMCID: PMC5214690 DOI: 10.3389/fmicb.2016.02123] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022] Open
Abstract
Extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. India harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. The aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central India namely, Badi Anhoni, Chhoti Anhoni, and Tattapani at two geographically distinct regions (Anhoni and Tattapani), to uncover the resident microbial community and their metabolic traits. Samples were collected from seven distinct sites of the three hot spring locations with temperature ranging from 43.5 to 98°C. The 16S rRNA gene amplicon sequencing of V3 hypervariable region and shotgun metagenome sequencing uncovered a unique taxonomic and metabolic diversity of the resident thermophilic microbial community in these hot springs. Genes associated with hydrocarbon degradation pathways, such as benzoate, xylene, toluene, and benzene were observed to be abundant in the Anhoni hot springs (43.5–55°C), dominated by Pseudomonas stutzeri and Acidovorax sp., suggesting the presence of chemoorganotrophic thermophilic community with the ability to utilize complex hydrocarbons as a source of energy. A high abundance of genes belonging to methane metabolism pathway was observed at Chhoti Anhoni hot spring, where methane is reported to constitute >80% of all the emitted gases, which was marked by the high abundance of Methylococcus capsulatus. The Tattapani hot spring, with a high-temperature range (61.5–98°C), displayed a lower microbial diversity and was primarily dominated by a nitrate-reducing archaeal species Pyrobaculum aerophilum. A higher abundance of cell metabolism pathways essential for the microbial survival in extreme conditions was observed at Tattapani. Taken together, the results of this study reveal a novel consortium of microbes, genes, and pathways associated with the hot spring environment.
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Affiliation(s)
- Rituja Saxena
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Darshan B Dhakan
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Parul Mittal
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Prashant Waiker
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Anirban Chowdhury
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Arundhuti Ghatak
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Bhopal, India
| | - Vineet K Sharma
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, India
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