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Straková D, Sánchez-Porro C, de la Haba RR, Ventosa A. Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species. Microorganisms 2024; 12:334. [PMID: 38399738 PMCID: PMC10892550 DOI: 10.3390/microorganisms12020334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12T and S3CR25-11T, that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB' gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12T (= CECT 30620T = CCM 9252T) and S3CR25-11T (= CECT 30621T = CCM 9254T) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12T and S3CR25-11T, respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera.
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Affiliation(s)
| | | | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain; (D.S.); (C.S.-P.); (R.R.d.l.H.)
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Galisteo C, de la Haba RR, Sánchez-Porro C, Ventosa A. A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils. Front Microbiol 2023; 14:1192059. [PMID: 37228371 PMCID: PMC10203224 DOI: 10.3389/fmicb.2023.1192059] [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: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.
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Kumar G, Radha V, Jagadeeshwari U, Sasikala C, Venkata Ramana C. Bacterial communities of sponges from the wetland ecosystem of Little Rann of Kutch, India with particular reference to Planctomycetes. 3 Biotech 2020; 10:478. [PMID: 33094088 PMCID: PMC7568738 DOI: 10.1007/s13205-020-02449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Five sponge specimens belonging to the genera Spongilla and Ciocalypta were collected from Little Rann of Kutch (in Gujarat, India) and analysed for associated microbiomes. Critical analysis was done with respect to members of the phylum Planctomycetes, using two different strategies; 1. Culture-independent metagenomic approach and 2. culture-dependent anaerobic enrichment for anammox-planctomycetes. The 16S rRNA gene (V1-V3 region) amplicon metagenome analysis revealed significant divergence in bacterial diversity, including Planctomycetes among the sponges analysed. Community metagenomics revealed a total of 376 Operational Taxonomic Units (OTUs) belonging to 41 different phyla. OTUs belonging to Proteobacteria was the most abundant (38%) among the sponge analysed. The KEGG annotation predicted a total of 6909 KEGG orthologs (KOs); most of the KOs are associated with membrane transport, xenobiotic degradation, production of secondary metabolites, amino acid metabolism and carbohydrate metabolism. In the culture-dependent study, FISH analysis confirmed the association of anammox-planctomycetes with sponges. Partial 16S rRNA gene sequences of two planctomycetes (JC545, JC543) were cladding with those of uncultured Phycisphaerae class. The other three putative anammox bacteria (JC541, JC542, JC544) formed a different clade with "Candidatus Brocadia anammoxidans". These three putative bacteria believably represent new species/genus related to "Candidatus Brocadia".
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Vaddavalli Radha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Uppadda Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
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Durán-Viseras A, Andrei AS, Ghai R, Sánchez-Porro C, Ventosa A. New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea. Front Microbiol 2019; 10:1928. [PMID: 31507553 PMCID: PMC6719526 DOI: 10.3389/fmicb.2019.01928] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/05/2019] [Indexed: 11/13/2022] Open
Abstract
Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15BT and F9-27T) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525T, Halonotius aquaticus F13-13T and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15BT = CECT 9688T = CCM 8954T) and Halonotius roseus sp. nov. (type strain F9-27T = CECT 9745T = CCM 8956T) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B12) to the halophilic microbial communities at large.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Adrian-Stefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czechia
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Bachran M, Kluge S, Lopez-Fernandez M, Cherkouk A. Microbial Diversity in an Arid, Naturally Saline Environment. MICROBIAL ECOLOGY 2019; 78:494-505. [PMID: 30593603 DOI: 10.1007/s00248-018-1301-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.
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Affiliation(s)
- Madlen Bachran
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Sindy Kluge
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Andrea Cherkouk
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
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Spatial distribution of prokaryotic communities in hypersaline soils. Sci Rep 2019; 9:1769. [PMID: 30741985 PMCID: PMC6370769 DOI: 10.1038/s41598-018-38339-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/20/2018] [Indexed: 11/29/2022] Open
Abstract
Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.
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Vera-Gargallo B, Ventosa A. Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain). Genes (Basel) 2018. [PMID: 29518047 PMCID: PMC5867873 DOI: 10.3390/genes9030152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hypersaline environments encompass aquatic and terrestrial habitats. While only a limited number of studies on the microbial diversity of saline soils have been carried out, hypersaline lakes and marine salterns have been thoroughly investigated, resulting in an aquatic-biased knowledge about life in hypersaline environments. To improve our understanding of the assemblage of microbes thriving in saline soils, we assessed the phylogenetic diversity and metabolic potential of the prokaryotic community of two hypersaline soils (with electrical conductivities of ~24 and 55 dS/m) from the Odiel saltmarshes (Spain) by metagenomics. Comparative analysis of these soil databases with available datasets from salterns ponds allowed further identification of unique and shared traits of microbial communities dwelling in these habitats. Saline soils harbored a more diverse prokaryotic community and, in contrast to their aquatic counterparts, contained sequences related to both known halophiles and groups without known halophilic or halotolerant representatives, which reflects the physical heterogeneity of the soil matrix. Our results suggest that Haloquadratum and certain Balneolaeota members may preferentially thrive in aquatic or terrestrial habitats, respectively, while haloarchaea, nanohaloarchaea and Salinibacter may be similarly adapted to both environments. We reconstructed 4 draft genomes related to Bacteroidetes, Balneolaeota and Halobacteria and appraised their metabolism, osmoadaptation strategies and ecology. This study greatly improves the current understanding of saline soils microbiota.
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Affiliation(s)
- Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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Mangrola AV, Dudhagara PR, Koringa PG, Joshi CG, Patel RK. Metagenomic microbial community profiling of Unnai hot spring by Ion-Torrent based shotgun sequencing. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718010113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bhatt HB, Azmatunnisa Begum M, Chintalapati S, Chintalapati VR, Singh SP. Desertibacillus haloalkaliphilus gen. nov., sp. nov., isolated from a saline desert. Int J Syst Evol Microbiol 2017; 67:4435-4442. [PMID: 28920841 DOI: 10.1099/ijsem.0.002310] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, rod-shaped and endospore-forming bacteria that represent a single species, designated strains KJ1-10-99T and KJ1-10-93, were isolated from a saline desert of Little Rann of Kutch, Gujarat, India. Analysis of 16S rRNA gene sequences revealed that the isolates belonged to the family Bacillaceae and were closely related to each other with 16S rRNA gene sequence similarity of 99.9 %. However, these two isolates formed a novel phylogenetic branch within this family. Both strains were aerobic, catalase and oxidase positive, and could grow optimally at 37 °C and pH 9. Further, strains KJ1-10-99T and KJ1-10-93 grew optimally at a NaCl concentration of 7.5 and 15 % (w/v), respectively. Both strains shared highest sequence similarity with Fermentibacillus polygoni IEB3T (96.90 %) followed by Bacillus nanhaiisediminis NH3T (96.3 %) and Bacillus alkalinitrilicus ANL-iso4T (96.3 %). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17:0, C16 : 0, and iso-C15 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol in both strains. The predominant isoprenoid quinone was MK-7 in both the strains. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP) as the diagnostic diamino acid. The DNA G+C content of strains KJ1-10-99T and KJ1-10-93 were 48.7 and 48.9 mol% respectively. Both strains could be distinguished from closest phylogenetic neighbours based on a number of phenotypic properties. On the basis of polyphasic taxonomic analysis and phylogenetic data, we conclude that the strains KJ1-10-99T (=LMG 29918T=KCTC 33878T) and KJ1-10-93 (=LMG 29919=KCTC 33877) represent a novel species of a new genus in the family Bacillaceae, order Bacillales, for which the name Desertibacillus haloalkaliphilus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Hitarth B Bhatt
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot-360005, Gujarat, India
| | - M Azmatunnisa Begum
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500085, India
| | - Sasikala Chintalapati
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500085, India
| | - Venkata Ramana Chintalapati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot-360005, Gujarat, India
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Bhagat C, Dudhagara P, Tank S. Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS. J Appl Microbiol 2017; 124:316-335. [PMID: 28921830 DOI: 10.1111/jam.13589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/17/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022]
Abstract
Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology.
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Affiliation(s)
- C Bhagat
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - P Dudhagara
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - S Tank
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
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Abdul Majid S, Graw MF, Chatziefthimiou AD, Nguyen H, Richer R, Louge M, Sultan AA, Schloss P, Hay AG. Microbial Characterization of Qatari Barchan Sand Dunes. PLoS One 2016; 11:e0161836. [PMID: 27655399 PMCID: PMC5031452 DOI: 10.1371/journal.pone.0161836] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/13/2016] [Indexed: 01/17/2023] Open
Abstract
This study represents the first characterization of sand microbiota in migrating barchan sand dunes. Bacterial communities were studied through direct counts and cultivation, as well as 16S rRNA gene and metagenomic sequence analysis to gain an understanding of microbial abundance, diversity, and potential metabolic capabilities. Direct on-grain cell counts gave an average of 5.3 ± 0.4 x 105 cells g-1 of sand. Cultured isolates (N = 64) selected for 16S rRNA gene sequencing belonged to the phyla Actinobacteria (58%), Firmicutes (27%) and Proteobacteria (15%). Deep-sequencing of 16S rRNA gene amplicons from 18 dunes demonstrated a high relative abundance of Proteobacteria, particularly enteric bacteria, and a dune-specific-pattern of bacterial community composition that correlated with dune size. Shotgun metagenome sequences of two representative dunes were analyzed and found to have similar relative bacterial abundance, though the relative abundances of eukaryotic, viral and enterobacterial sequences were greater in sand from the dune closer to a camel-pen. Functional analysis revealed patterns similar to those observed in desert soils; however, the increased relative abundance of genes encoding sporulation and dormancy are consistent with the dune microbiome being well-adapted to the exceptionally hyper-arid Qatari desert.
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Affiliation(s)
- Sara Abdul Majid
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Michael F. Graw
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | | | - Hanh Nguyen
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Renee Richer
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Michel Louge
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, United States of America
| | - Ali A. Sultan
- Department of Research, Weill Cornell Medical Qatar, Qatar Foundation, Doha, Qatar
| | - Patrick Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
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Dudhagara P, Bhavsar S, Bhagat C, Ghelani A, Bhatt S, Patel R. Web Resources for Metagenomics Studies. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:296-303. [PMID: 26602607 PMCID: PMC4678780 DOI: 10.1016/j.gpb.2015.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 10/26/2022]
Abstract
The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
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Affiliation(s)
- Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India.
| | - Sunil Bhavsar
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Chintan Bhagat
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Anjana Ghelani
- Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001, India
| | - Shreyas Bhatt
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India
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Mangrola A, Dudhagara P, Koringa P, Joshi CG, Parmar M, Patel R. Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach. GENOMICS DATA 2015; 4:153-5. [PMID: 26484204 PMCID: PMC4535658 DOI: 10.1016/j.gdata.2015.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/12/2015] [Indexed: 01/22/2023]
Abstract
Here, we report metagenome from the Tuwa hot spring, India using shotgun sequencing approach. Metagenome consisted of 541,379 sequences with 98.7 Mbps size with 46% G + C content. Metagenomic sequence reads were deposited into the EMBL database under accession number ERP009321. Community analysis presented 99.1% sequences belong to bacteria, 0.3% of eukaryotic origin, 0.2% virus derived and 0.05% from archea. Unclassified and unidentified sequences were 0.4% and 0.07% respectively. A total of 22 bacterial phyla include 90 families and 201 species were observed in the hot spring metagenome. Firmicutes (97.0%), Proteobacteria (1.3%) and Actinobacteria (0.4%) were reported as dominant bacterial phyla. In functional analysis using Cluster of Orthologous Group (COG), 21.5% drops in the poorly characterized group. Using subsystem based annotation, 4.0% genes were assigned for stress responses and 3% genes were fit into the metabolism of aromatic compounds. The hot spring metagenome is very rich with novel sequences affiliated to unclassified and unidentified lineages, suggesting the potential source for novel microbial species and their products.
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Affiliation(s)
- Amitsinh Mangrola
- Department of Biochemistry, Shri Alpesh N. Patel Post Graduate Institute, Anand, India
| | - Pravin Dudhagara
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, India
| | - Prakash Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Mansi Parmar
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
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Shotgun metagenomic sequencing based microbial diversity assessment of Lasundra hot spring, India. GENOMICS DATA 2015; 4:73-5. [PMID: 26484181 PMCID: PMC4536006 DOI: 10.1016/j.gdata.2015.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/16/2015] [Indexed: 11/24/2022]
Abstract
This is the first report on the metagenomic approach for unveiling the microbial diversity of Lasundra hot spring, Gujarat State, India. High-throughput sequencing of community DNA was performed on an Ion Torrent PGM platform. Metagenome consisted of 606,867 sequences represent 98,567,305 bps size with an average length of 162 bps and 46% G + C content. Metagenome sequence information is available at EBI under EBI Metagenomic database with accession no. ERP009313. MG-RAST assisted community analysis revealed that 99.21% sequences were bacterial origin, 0.43% was fit to eukaryotes and 0.11% belongs to archaea. A total of 29 bacterial, 20 eukaryotic and 4 archaeal phyla were detected. Abundant genera were Bacillus (86.7%), Geobacillus (2.4%), Paenibacillus (1.0%), Clostridium (0.7%) and Listeria (0.5%), that represent 91.52% in metagenome. In functional analysis, Cluster of Orthologous Group (COG) based annotation revealed that 45.4% was metabolism connected and 19.6% falls in poorly characterized group. Subsystem based annotation approach suggests that the 14.0% was carbohydrates, 7.0% was protein metabolism and 3.0% genes for various stress responses together with the versatile presence of commercially useful traits.
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Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India. GENOMICS DATA 2015; 4:54-6. [PMID: 26484176 PMCID: PMC4536058 DOI: 10.1016/j.gdata.2015.03.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 11/20/2022]
Abstract
A taxonomic description of bacteria was deduced from 5.78 Mb metagenomic sequence retrieved from Tulsi Shyam hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome contained 10,893 16S rDNA sequences that were analyzed by MG-RAST server to generate the comprehensive profile of bacteria. Metagenomic data are available at EBI under EBI Metagenomics database with accession no. ERP009559. Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome. Most abundant phyla were Firmicutes (65.38%), Proteobacteria (21.21%) and unclassified bacteria (10.69%). Whereas, Peptostreptococcaceae (37.33%), Clostridiaceae (23.36%), and Enterobacteriaceae (16.37%) were highest reported families in metagenome. Ubiquitous species were Clostridium bifermentans (17.47%), Clostridium lituseburense (13.93%) and uncultured bacterium (10.15%). Our data provide new information on hot spring bacteria and shed light on their abundance, diversity, distribution and coexisting organisms.
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