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Abstract
With the advent of metagenomics, a quest began to identify the dynamics of the microbial communities in different ecological niches. Altogether, this has resulted in identification of microorganisms but is limited to only a small number of phylogenetic groups that can be easily cultured. The majority of metagenomic sequencing data remains unassigned to any known microbial group and is regarded as the "microbial dark matter." Our group is now working on integrating culturomics (isolation of pure cultures) and metagenomics from extreme environments, particularly from hot water springs and chemically contaminated soils. Our target is to culture the rare extremophiles with biotechnological significance by designing culture media based on inputs from metagenomics. While culturomics integrated with metagenomics has been extensively employed for updating the microbial catalog from the human gut, there is a need to extend this approach to extreme environmental settings to explore the microbial dark matter.
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Affiliation(s)
- Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Post-Graduate Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhigrid.8195.5, New Delhi, India
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Alves KJ, da Silva MCP, Cotta SR, Ottoni JR, van Elsas JD, de Oliveira VM, Andreote FD. Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods. Braz J Microbiol 2019; 51:217-228. [PMID: 31741310 DOI: 10.1007/s42770-019-00162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 11/25/2022] Open
Abstract
Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.
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Affiliation(s)
- Kelly Jaqueline Alves
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mylenne Calciolari Pinheiro da Silva
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| | - Simone Raposo Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Centenario Avenue, 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Júlia Ronzella Ottoni
- University Center Dinâmica das Cataratas, Castelo Branco Street, 349, Foz do Iguaçu, Paraná, 85852-010, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Valeria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Alexandre Cazellato Avenue, 999, Paulínia, São Paulo, 13140-000, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
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Carrazco-Palafox J, Rivera-Chavira BE, Ramírez-Baca N, Manzanares-Papayanopoulos LI, Nevárez-Moorillón GV. Improved method for qualitative screening of lipolytic bacterial strains. MethodsX 2018; 5:68-74. [PMID: 30622910 PMCID: PMC6318097 DOI: 10.1016/j.mex.2018.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/18/2018] [Indexed: 11/19/2022] Open
Abstract
Esterases and lipases are lipolytic enzymes that catalyse the hydrolysis of triacylglycerols, Determination of lipolysis on agar plates is a simple approach to determine lipase or esterase action, but visual evaluation of lipolysis is frequently difficult in practice. Therefore, the aim of this work was to improve the efficiency of lipolysis visualization in tributyrin agar (mTBA) by adding calcium and/or magnesium ions in the screening of lipolytic microbial strains. Lipolytic activity was evaluated in mTBA using the well diffusion technique, where a clear zone around the inoculated wells indicated lipid hydrolysis. Results suggest that the addition of 2.5 mM calcium and 5.0 mM magnesium was the best combination of ion addition to TBA. Lipolytic activity increased the clearing zone up to 38% more than without the addition of ions and the clear zone was clearly observed. The mTBA plate was used with culture collection microbial strains, as well as with a collection of soil microorganisms, to identify lipase producers. The addition of calcium and magnesium ions can provide an easier screening procedure for selection of lipolytic bacterial strains. •A modified tributyrin agar for screening of lipolytic bacteria was prepared by adding calcium and magnesium ions.•The modified TBA agar was tested with control bacterial strains, and, based on the results, 2.5 mM Ca and 5.0 mM Mg ions were added in the mTBA.•mTBA was validated with environmental bacterial strains for screening of lipolytic activity.
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Affiliation(s)
- Jair Carrazco-Palafox
- Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Circuito No. 1, Campus Universitario II Chihuahua, Chihuahua 31125, Mexico
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
| | - Blanca E. Rivera-Chavira
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
| | - Norma Ramírez-Baca
- Secretaría de Comunicaciones y Obras Públicas, Gobierno del Estado de Chihuahua, Beethoven 4000, Fraccionamiento la Herradura, Chihuahua, Chihuahua 31206, Mexico
| | - Luisa I. Manzanares-Papayanopoulos
- Capítulo Mexicano del Consejo Empresarial Mundial para el Desarrollo Sostenible, Comisión de Estudios del Sector Privado para el Desarrollo Sustentable, Lancaster 15, Col. Juárez, Mexico City, D.F. 06600, Mexico
| | - Guadalupe V. Nevárez-Moorillón
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus Universitario II, Chihuahua, Chihuahua 31125, Mexico
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Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D. The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 2017; 44:212-229. [PMID: 28562180 DOI: 10.1080/1040841x.2017.1332003] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.
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Affiliation(s)
- Johanna Gutleben
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Maryam Chaib De Mares
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Jan Dirk van Elsas
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Hauke Smidt
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Jörg Overmann
- c Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen , Braunschweig , Germany
| | - Detmer Sipkema
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
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Kimura N, Kamagata Y. A Thermostable Bilirubin-Oxidizing Enzyme from Activated Sludge Isolated by a Metagenomic Approach. Microbes Environ 2016; 31:435-441. [PMID: 27885197 PMCID: PMC5158116 DOI: 10.1264/jsme2.me16106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus. Purified BopA exhibited maximum activity at pH 7.5 with bilirubin as its substrate and was found to be active over a markedly broad pH range from 6 to 11. It also showed notable thermostability; its activity remained intact even after a heat treatment at 90°C for 60 min. This enzyme is a thermostable-bilirubin oxidase that exhibits markedly higher thermostability than that previously reported for laccases.
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Affiliation(s)
- Nobutada Kimura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Yamada C, Sawano K, Iwase N, Matsuoka M, Arakawa T, Nishida S, Fushinobu S. Isolation and characterization of a thermostable lipase from Bacillus thermoamylovorans NB501. J GEN APPL MICROBIOL 2016; 62:313-319. [PMID: 27885194 DOI: 10.2323/jgam.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Two thermophilic bacterial strains, Bacillus thermoamylovorans NB501 and NB502, were isolated from a high-temperature aerobic fermentation reactor system that processes tofu refuse (okara) in the presence of used soybean oil. We cloned a lipase gene from strain NB501, which secretes a thermophilic lipase. The biochemical characteristics of the recombinant enzyme (Lip501r) were elucidated. Lip501r is monomeric in solution with an apparent molecular mass of 38 kDa on SDS-PAGE. The optimal pH and apparent optimal temperature of Lip501r were 8 and 60°C, respectively. Supplementation of 5 mM Ca2+ enhanced the thermostability, and the enzyme retained 56% of its activity for 30 min at 50°C. Lip501r was active on a wide range of substrates with different lengths of p-nitrophenyl (pNP) esters, and showed a remarkably higher activity with pNP-myristate. The Km and Vmax values for pNP-butyrate in the presence of 5 mM CaCl2 were 1.8 mM and 220 units/mg, respectively. The possible industrial use of the thermophilic lipase in modifying edible oil was explored by examining the degradation of soybean oil. A TLC analysis of the degraded products indicated that Lip501r is an 1,3-position specific lipase. A homology modeling study revealed that helix α6 in the lid domain of NB501 lipase was shorter than that of lipases from the Geobacillus group.
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Kamagata Y. Keys to Cultivating Uncultured Microbes: Elaborate Enrichment Strategies and Resuscitation of Dormant Cells. Microbes Environ 2016; 30:289-90. [PMID: 26699453 PMCID: PMC4676551 DOI: 10.1264/jsme2.me3004rh] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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Affiliation(s)
- Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology,
2–24–16 Nakacho, Koganei, Tokyo, 184–8588,
Japan
- Senior Editor, Microbes and Environments, E-mail:
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Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes. Appl Environ Microbiol 2015; 82:528-37. [PMID: 26546427 DOI: 10.1128/aem.02838-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/01/2015] [Indexed: 01/31/2023] Open
Abstract
The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications.
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Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y. Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments. Front Microbiol 2015; 6:386. [PMID: 25999927 PMCID: PMC4419728 DOI: 10.3389/fmicb.2015.00386] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/15/2015] [Indexed: 11/13/2022] Open
Abstract
Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8-98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides.
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Affiliation(s)
- Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Azusa Oikawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Kiyofumi Suzuki
- Methane Hydrate Research & Development Division, Japan Oil, Gas and Metals National Corporation Chiba, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry and MARUM, University of Bremen Bremen, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
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