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Saikh SR, Mushtaque MA, Pramanick A, Prasad JK, Roy D, Saha S, Das SK. Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India. Heliyon 2024; 10:e26370. [PMID: 38420377 PMCID: PMC10901028 DOI: 10.1016/j.heliyon.2024.e26370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.
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Affiliation(s)
- Shahina Raushan Saikh
- Department of Physical Sciences, Bose Institute, Kolkata, India
- Department of Life Science & Bio-technology, Jadavpur University, Kolkata, India
| | | | | | | | - Dibakar Roy
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, India
| | - Sanat Kumar Das
- Department of Physical Sciences, Bose Institute, Kolkata, India
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2
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McGregor GB, Sendall BC, Niiyama Y, Tuji A, Willis A. Chrysosporum ovalisporum is synonymous with the true-branching cyanobacterium Umezakia natans (Nostocales/Aphanizomenonaceae). JOURNAL OF PHYCOLOGY 2023; 59:326-341. [PMID: 36680435 DOI: 10.1111/jpy.13317] [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: 08/11/2022] [Revised: 12/11/2022] [Accepted: 12/18/2022] [Indexed: 05/28/2023]
Abstract
True branching is a facultative characteristic only known from two cyanobacteria in the Aphanizomenonaceae, Umezakia natans and Dolichospermum brachiatum. In both cases, its expression has been associated with environmental stress, and its practical use as a diacritical feature has been previously evaluated. In this study, we undertook further evaluation of the phylogeny of Umezakia natans and its relationship to Chrysosporum ovalisporum as a previous study suggested the two were potentially congeneric. We used combined morphological, phylogenetic, and phylogenomic approaches to determine their relatedness using new strains available from a broad geographic range. Phylogenetic analysis based on 16S rRNA gene sequences showed that Australian C. ovalisporum and Japanese U. natans strains clustered together with accessions of C. ovalisporum originating from Australia, Israel, and Spain, with high p-distance similarity values (99.5%-99.9%). Additionally, differences between the two species in the 16S-23S ITS region was low (0%-2.5%). The average nucleotide identity of the U. natans and C. ovalisporum strains was also high (ANI of > 99.5 and AF > 0.9) and supported a genus-level separation from Chrysosporum bergii (83 ANI between clusters). Furthermore, in culture, strains of both species grown in vitamin-free media showed facultative true branching, a feature not previously known in C. ovalisporum. Collectively, the results support unification of C. ovalisporum and U. natans according to the principle of priority as Umezakia ovalisporum.
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Affiliation(s)
- Glenn B McGregor
- Queensland Department of Environment and Science, Brisbane, Australia
| | - Barbara C Sendall
- Queensland Department of Health, Forensic and Scientific Services, Coopers Plains, Australia
| | - Yuko Niiyama
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
| | - Akihiro Tuji
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
| | - Anusuya Willis
- Australian National Algae Culture Collection, National Collections and Marine Infrastructure, CSIRO, Hobart, Tasmania, Australia
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3
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Guo G, Li Z, Chen L, Ling Q, Zan F, Isawi H, Hao T, Ma J, Wang Z, Chen G, Lu H. Advances in elemental sulfur-driven bioprocesses for wastewater treatment: From metabolic study to application. WATER RESEARCH 2022; 213:118143. [PMID: 35149365 DOI: 10.1016/j.watres.2022.118143] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/17/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Elemental sulfur (S0) is known to be an abundant, non-toxic material with a wide range of redox states (-2 to +6) and may serve as an excellent electron carrier in wastewater treatment. In turn, S0-driven bioprocesses, which employ S0 as electron donor or acceptor, have recently established themselves as cost-effective therefore attractive solutions for wastewater treatment. Numerous related processes have, to date, been developed from laboratory experiments into full-scale applications, including S0-driven autotrophic denitrification for nitrate removal and S0-reducing organic removal. Compared to the conventional activated sludge process, these bioprocesses require only a small amount of organic matter and produce very little sludge. There have been great efforts to characterize chemical and biogenic S0 and related functional microorganisms in order to identify the biochemical pathways, upgrade the bioprocesses, and assess the impact of the operating factors on process performance, ultimately aiming to better understand and to optimize the processes. This paper is therefore a comprehensive overview of emerging S0-driven biotechnologies, including the development of S0-driven autotrophic denitrification and S0-based sulfidogenesis, as well as the associated microbiology and biochemistry. Also reviewed here are the physicochemical characteristics of S0 and the effects that environmental factors such as pH, influent sulfur/nitrate ratio, temperature, S0 particle size and reactor configurations have on the process. Research gaps, challenges of process applications and potential areas for future research are further proposed and discussed.
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Affiliation(s)
- Gang Guo
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhaoling Li
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Lei Chen
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Qingshan Ling
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Heba Isawi
- Desert Research Center, Water Resources and Desert Soils Division, Egyptian Desalination Research Center of Excellence (EDRC), Cairo, Egypt
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
| | - Jie Ma
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zongping Wang
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Guanghao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.
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4
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Gupta S, Plugge CM, Klok JBM, Muyzer G. Comparative analysis of microbial communities from different full-scale haloalkaline biodesulfurization systems. Appl Microbiol Biotechnol 2022; 106:1759-1776. [PMID: 35147744 PMCID: PMC8882115 DOI: 10.1007/s00253-022-11771-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/17/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Abstract
Abstract In biodesulfurization (BD) at haloalkaline and dO2-limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten reactors sampled in 2018 indicated the presence of 444 bacterial Amplicon Sequence Variants (ASVs). A core microbiome represented by 30 ASVs was found in all ten reactors, with Thioalkalivibrio sulfidiphilus as the most dominant species. The majority of these ASVs are phylogenetically related to bacteria previously identified in haloalkaline BD processes and in natural haloalkaline ecosystems. The source and composition of the feed gas had a great impact on the microbial community composition followed by alkalinity, sulfate, and thiosulfate concentrations. The halophilic SOB of the genus Guyparkeria (formerly known as Halothiobacillus) and heterotrophic SOB of the genus Halomonas were identified as potential indicator organisms of sulfate and thiosulfate accumulation in the BD process. Key points • Biodesulfurization (BD) reactors share a core microbiome • The source and composition of the feed gas affects the microbial composition in the BD reactors • Guyparkeria and Halomonas indicate high concentrations of sulfate and thiosulfate in the BD process Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11771-y.
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Affiliation(s)
- Suyash Gupta
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes B M Klok
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Paqell B.V, Utrecht, The Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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5
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Johansen JR, González-Resendiz L, Escobar-Sánchez V, Segal-Kischinevzky C, Martínez-Yerena J, Hernández-Sánchez J, Hernández-Pérez G, León-Tejera H. When will taxonomic saturation be achieved? A case study in Nunduva and Kyrtuthrix (Rivulariaceae, Cyanobacteria). JOURNAL OF PHYCOLOGY 2021; 57:1699-1720. [PMID: 34289115 DOI: 10.1111/jpy.13201] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
A number of heterocytous, mat-forming, tapering cyanobacteria in Rivulariaceae have recently been observed in both the Atlantic and Pacific coasts in the rocky intertidal and supratidal zones. These belong to the genera Nunduva, Kyrtuthrix, and Phyllonema and have been the subject of several recent studies. Herein, two new species of Nunduva (N. komarkovae and N. sanagustinensis) and two new species of Kyrtuthrix (K. munecosensis and K. totonaca) are characterized and described from the coasts of Mexico. Genetic separation based on the 16S-23S ITS region was pronounced (>10% in all comparisons). Morphological differences between all existing species in these two genera were also observed, but the group is morphologically complex, and these taxa are considered pseudocryptic. Nunduva and Kyrtuthrix remain morphologically and phylogenetically separate even with the addition of new species. However, how long will this remain the case? Many new genera and species of cyanobacteria have recently been described. Will the taxonomy of cyanobacteria eventually become saturated? Will we start to see multiple populations for the same cryptic species, or will future taxonomists collapse multiple species into fewer species, or multiple genera into single genera. The description of even more Nunduva and Kyrtuthrix species causes us to pause and evaluate the future of cyanobacterial taxonomy. These same questions are faced by algal taxonomists studying other phyla, and the resolution may ultimately be similar.
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Affiliation(s)
- Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, University of South Bohemia, Branišovská 1760, Česke Budějovice, 370 05, Czech Republic
| | - Laura González-Resendiz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana- Cuajimalpa, Av. Vasco de Quiroga 4871, Ciudad de México, C.P. 053000, Mexico
| | - Viviana Escobar-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Claudia Segal-Kischinevzky
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - José Martínez-Yerena
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Joaquín Hernández-Sánchez
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Gabriela Hernández-Pérez
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
| | - Hilda León-Tejera
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Código Postal, Ciudad de México, 04510, Mexico
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6
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Saini MK, Sebastian A, Shirotori Y, Soulier NT, Garcia Costas AM, Drautz-Moses DI, Schuster SC, Albert I, Haruta S, Hanada S, Thiel V, Tank M, Bryant DA. Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species. Front Microbiol 2021; 12:704168. [PMID: 34220789 PMCID: PMC8245765 DOI: 10.3389/fmicb.2021.704168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain B T ) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.
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Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Aswathy Sebastian
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Yoshiki Shirotori
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Nathan T. Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M. Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Istvan Albert
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
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Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes. mSystems 2021; 6:6/2/e01202-20. [PMID: 33906913 PMCID: PMC8092127 DOI: 10.1128/msystems.01202-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2T originated from a soda lake in southeast Siberia that is exposed to strong seasonal temperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B12 biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2T upregulated flagellin expression, whereas ALJ2 downregulated it. IMPORTANCE In addition to their haloalkaline conditions, soda lakes can also harbor a variety of other extreme parameters, to which their microbial communities need to adapt. However, for most of these supplementary stressors, it is not well known yet how haloalkaliphiles adapt and resist. Here, we studied the strategy for adaptation to low temperature in the haloalkaliphilic genus Thioalkalivibrio by using two strains isolated from soda lakes with different temperature regimes. Even though the strains showed a strong difference in growth rate at 10°C, they exhibited similar molecular and physiological adaptation responses. We hypothesize that they take advantage of resistance mechanisms against other stressors commonly found in soda lakes, which are therefore maintained in the bacteria living in the absence of low-temperature pressure. A major difference, however, was detected for their glycine betaine content at 10°C, highlighting the power of this osmolyte to also act as a key compound in cryoprotection. Author Video: An author video summary of this article is available.
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Lee J, Mahandra H, Hein GA, Ramsay J, Ghahreman A. Toward Sustainable Solution for Biooxidation of Waste and Refractory Materials Using Neutrophilic and Alkaliphilic Microorganisms—A Review. ACS APPLIED BIO MATERIALS 2021; 4:2274-2292. [DOI: 10.1021/acsabm.0c01582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jung Lee
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Harshit Mahandra
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Guillermo Alvial Hein
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Juliana Ramsay
- Department of Chemical Engineering, Queen’s University, 19 Division Street, Kingston, Ontario K7L 3N6, Canada
| | - Ahmad Ghahreman
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
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Freitas L, Appolinario L, Calegario G, Campeão M, Tschoeke D, Garcia G, Venancio IM, Cosenza CAN, Leomil L, Bernardes M, Albuquerque AL, Thompson C, Thompson F. Glacial-interglacial transitions in microbiomes recorded in deep-sea sediments from the western equatorial Atlantic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140904. [PMID: 32763595 DOI: 10.1016/j.scitotenv.2020.140904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
In the late Quaternary, glacial-interglacial transitions are marked by major environmental changes. Glacial periods in the western equatorial Atlantic (WEA) are characterized by high continental terrigenous input, which increases the proportion of terrestrial organic matter (e.g. lignin, alkanes), nutrients (e.g. iron and sulphur), and lower primary productivity. On the other hand, interglacials are characterized by lower continental contribution and maxima in primary productivity. Microbes can serve as biosensors of past conditions, but scarce information is available on deep-sea sediments in the WEA. The hypothesis put forward in this study is that past changes in climate conditions modulated the taxonomic/functional composition of microbes from deep sediment layers. To address this hypothesis, we collected samples from a marine sediment core located in the WEA, which covered the last 130 kyr. This region is influenced by the presence of the Amazon River plume, which outputs dissolved and particulate nutrients in vast oceanic regions, as well as the Parnaiba river plume. Core GL-1248 was analysed by shotgun metagenomics and geochemical analyses (alkane, lignin, perylene, sulphur). Two clusters (glacial and interglacial-deglacial) were found based on taxonomic and functional profiles of metagenomes. The interglacial period had a higher abundance of genes belonging to several sub-systems (e.g. DNA, RNA metabolism, cell division, chemotaxis, and respiration) that are consistent with a past environment with enhanced primary productivity. On the other hand, the abundance of Alcanivorax, Marinobacter, Kangiella and aromatic compounds that may serve as energy sources for these bacteria were higher in the glacial. The glacial period was enriched in genes for the metabolism of aromatic compounds, lipids, isoprenoids, iron, and Sulphur, consistent with enhanced fluvial input during the last glacial period. In contrast, interglacials have increased contents of more labile materials originating from phytoplankton (e.g. Prochlorococcus). This study provides new insights into the microbiome as climatic archives at geological timescales.
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Affiliation(s)
- Lucas Freitas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Luciana Appolinario
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Gabriela Calegario
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Mariana Campeão
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Diogo Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil
| | - Igor Martins Venancio
- Center for Weather Forecasting and Climate Studies (CPTEC), National Institute for Space Research (INPE), Cachoeira Paulista, Brazil; Gradutate Program on Geoscience (Geochemistry), Federal Fluminense University, Niterói, Brazil
| | | | | | - Marcelo Bernardes
- Gradutate Program on Geoscience (Geochemistry), Federal Fluminense University, Niterói, Brazil
| | - Ana Luiza Albuquerque
- Gradutate Program on Geoscience (Geochemistry), Federal Fluminense University, Niterói, Brazil.
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil.
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, UFRJ, Rio de Janeiro, Brazil.
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10
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Kiragosyan K, Picard M, Timmers PHA, Sorokin DY, Klok JBM, Roman P, Janssen AJH. Effect of methanethiol on process performance, selectivity and diversity of sulfur-oxidizing bacteria in a dual bioreactor gas biodesulfurization system. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:123002. [PMID: 32506049 DOI: 10.1016/j.jhazmat.2020.123002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
This study provides important new insights on how to achieve high sulfur selectivities and stable gas biodesulfurization process operation in the presence of both methanethiol and H2S in the feed gas. On the basis of previous research, we hypothesized that a dual bioreactor lineup (with an added anaerobic bioreactor) would favor sulfur-oxidizing bacteria (SOB) that yield a higher sulfur selectivity. Therefore, the focus of the present study was to enrich thiol-resistant SOB that can withstand methanethiol, the most prevalent and toxic thiol in sulfur-containing industrial off gases. In addition, the effect of process conditions on the SOB population dynamics was investigated. The results confirmed that thiol-resistant SOB became dominant with a concomitant increase of the sulfur selectivity from 75 mol% to 90 mol% at a loading rate of 2 mM S methanethiol day-1. The abundant SOB in the inoculum - Thioalkalivibrio sulfidiphilus - was first outcompeted by Alkalilimnicola ehrlichii after which Thioalkalibacter halophilus eventually became the most abundant species. Furthermore, we found that the actual electron donor in our lab-scale biodesulfurization system was polysulfide, and not the primarily supplied sulfide.
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Affiliation(s)
- Karine Kiragosyan
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
| | - Magali Picard
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Eurofins Agroscience Services Chem SAS 75, chemin de Sommières 30310, Vergèze, France
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Dimitry Y Sorokin
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Prospect 60-let Oktyabrya 7/2, Moscow, Russian Federation; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Johannes B M Klok
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands; Paqell B.V., Reactorweg 301, 3542 AD, Utrecht, the Netherlands
| | - Pawel Roman
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Albert J H Janssen
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands; Shell, Oostduinlaan 2, 2596 JM, the Hague, the Netherlands
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11
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Florentino AP, Costa RB, Hu Y, O'Flaherty V, Lens PNL. Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery. Front Bioeng Biotechnol 2020; 8:550253. [PMID: 33195115 PMCID: PMC7644789 DOI: 10.3389/fbioe.2020.550253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/25/2020] [Indexed: 12/19/2022] Open
Abstract
This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S0, SO 3 2 - , SO 4 2 - , and S2 O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S0- and S2 O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S0-reducing cultures. In S2 O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S0-reducing cultures were not affected by oleate concentrations up to 5 mM, while S2 O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S0-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S2 O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.
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Affiliation(s)
- Anna Patrícya Florentino
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Rachel Biancalana Costa
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, Brazil
| | - Yuansheng Hu
- Department of Civil Engineering, School of Engineering, College of Science and Engineering, National University of Ireland Galway, Galway, Ireland
| | - Vincent O'Flaherty
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Piet N L Lens
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
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12
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A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions. WATER 2020. [DOI: 10.3390/w12051385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new halo-alkaline sulfur-oxidising bacterial strain was isolated from brackish estuary sediments contaminated by total petroleum hydrocarbon. The isolate was classified as a new strain of Thioalkalivibrio sulfidiphilus sp., showing a higher capability of adaptation to pH and a higher optimal sodium concentration for growth, when compared to Thioalkalivibrio sulfidiphilus sp. HL-EbGr7, type strain of the species. The strain was capable to grow in saline concentrations up to 1.5 M Na+ and pH up to 10. The genome of the new isolate was sequenced and annotated. The comparison with the genome of Thioalkalivibrio sulfidiphilus sp. HL-EbGr7 showed a duplication of an operon encoding for a putative primary sodium extruding pump and the presence of a sodium/proton antiporter with optimal efficiency at halo-alkaline conditions. The new strain was able to oxidize sulfide at halo-alkaline conditions at the rate of 1 mmol/mg-N/h, suitable for industrial applications dedicated to the recovery of alkaline scrubber for H2S emission absorption and abatement.
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13
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Kiragosyan K, Picard M, Sorokin DY, Dijkstra J, Klok JBM, Roman P, Janssen AJH. Effect of dimethyl disulfide on the sulfur formation and microbial community composition during the biological H 2S removal from sour gas streams. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121916. [PMID: 31884361 DOI: 10.1016/j.jhazmat.2019.121916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/06/2019] [Accepted: 12/15/2019] [Indexed: 06/10/2023]
Abstract
Removal of organic and inorganic sulfur compounds from sour gases is required because of their toxicity and atmospheric pollution. The most common are hydrogen sulfide (H2S) and methanethiol (MT). Under oxygen-limiting conditions about 92 mol% of sulfide is oxidized to sulfur by haloalkaliphilic sulfur-oxidizing bacteria (SOB), whilst the remainder is oxidized either biologically to sulfate or chemically to thiosulfate. MT is spontaneously oxidized to dimethyl disulfide (DMDS), which was found to inhibit the oxidation of sulfide to sulfate. Hence, we assessed the effect of DMDS on product formation in a lab-scale biodesulfurization setup. DMDS was quantified using a newly, in-house developed analytical method. Subsequently, a chemical reaction mechanism was proposed for the formation of methanethiol and dimethyl trisulfide from the reaction between sulfide and DMDS. Addition of DMDS resulted in significant inhibition of sulfate formation, leading to 96 mol% of sulfur formation. In addition, a reduction in the dominating haloalkaliphilic SOB species, Thioalkalivibrio sulfidiphilus, was observed in favor of Thioalkaibacter halophilus as a more DMDS-tolerant with the 50 % inhibition coefficient at 2.37 mM DMDS.
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Affiliation(s)
- Karine Kiragosyan
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands; Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
| | - Magali Picard
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands; Eurofins Agroscience Services Chem SAS 75, chemin de Sommières 30310, Vergèze, France
| | - Dimitry Y Sorokin
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands; Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Prospect 60-let Oktyabrya 7/2, Moscow, Russian Federation; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jelmer Dijkstra
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Johannes B M Klok
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands; Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands; Paqell B.V., Reactorweg 301, 3542 AD Utrecht, The Netherlands
| | - Pawel Roman
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Albert J H Janssen
- Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands; Shell, Oostduinlaan 2, 2596 JM the Hague, The Netherlands
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14
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Bacterial Intracellular Sulphur Globules. BACTERIAL ORGANELLES AND ORGANELLE-LIKE INCLUSIONS 2020. [DOI: 10.1007/978-3-030-60173-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Florentino AP, Costa RB, Hu Y, O'Flaherty V, Lens PNL. Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery. Front Bioeng Biotechnol 2020. [PMID: 33195115 DOI: 10.3389/fbioe.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S0, SO 3 2 - , SO 4 2 - , and S2 O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S0- and S2 O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S0-reducing cultures. In S2 O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S0-reducing cultures were not affected by oleate concentrations up to 5 mM, while S2 O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S0-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S2 O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.
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Affiliation(s)
- Anna Patrícya Florentino
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Rachel Biancalana Costa
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, Brazil
| | - Yuansheng Hu
- Department of Civil Engineering, School of Engineering, College of Science and Engineering, National University of Ireland Galway, Galway, Ireland
| | - Vincent O'Flaherty
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Piet N L Lens
- Department of Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
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16
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Zorz JK, Sharp C, Kleiner M, Gordon PMK, Pon RT, Dong X, Strous M. A shared core microbiome in soda lakes separated by large distances. Nat Commun 2019; 10:4230. [PMID: 31530813 PMCID: PMC6748926 DOI: 10.1038/s41467-019-12195-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/16/2019] [Indexed: 11/25/2022] Open
Abstract
In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.
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Affiliation(s)
- Jackie K Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Christine Sharp
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paul M K Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, T2N 2T9, Canada
| | - Richard T Pon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, T2N 2T9, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
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17
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Kiragosyan K, van Veelen P, Gupta S, Tomaszewska-Porada A, Roman P, Timmers PHA. Development of quantitative PCR for the detection of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus in gas biodesulfurization processes. AMB Express 2019; 9:99. [PMID: 31278455 PMCID: PMC6611852 DOI: 10.1186/s13568-019-0826-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/29/2019] [Indexed: 12/14/2022] Open
Abstract
Chemolithoautotrophic sulfur-oxidizing bacteria (SOB) are crucial key players in biotechnological processes to remove hydrogen sulfide from sour gas streams. Several different haloalkaliphilic SOB have been detected and isolated from lab- and full-scale facilities, which all performed differently considering end product yields (sulfur and sulfate) and conversion rates. Understanding and regulating bacterial community dynamics in biodesulfurization processes will enable optimization of the process operation. We developed quantitative PCR (qPCR) assays to quantify haloalkaliphilic sulfur-oxidizing gammaproteobacterial species Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus, and Thioalkalibacter halophilus that dominate bacterial communities of biodesulfurization lab- and full-scale installations at haloalkaline conditions. The specificity and PCR efficiency of novel primer sets were evaluated using pure cultures of these target species. We further validated the qPCR assays by quantification of target organisms in five globally distributed full-scale biodesulfurization installations. The qPCR assays perform a sensitive and accurate quantification of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus, thus providing rapid and valuable insights into process performance and SOB growth dynamics in gas biodesulfurization systems.
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Affiliation(s)
- Karine Kiragosyan
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands.
- Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.
| | - Pieter van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
| | - Suyash Gupta
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Agnieszka Tomaszewska-Porada
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
| | - Pawel Roman
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
- Laboratory of Microbiology, Wageningen University, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
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18
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Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G. Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. Front Microbiol 2019; 10:1514. [PMID: 31333619 PMCID: PMC6620896 DOI: 10.3389/fmicb.2019.01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2T, and Thioalkalivibrio thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lucia Cavalca
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Milena Colombo
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - J Merijn Schuurmans
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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19
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Berben T, Overmars L, Sorokin DY, Muyzer G. Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 2019; 10:160. [PMID: 30837958 PMCID: PMC6382920 DOI: 10.3389/fmicb.2019.00160] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.
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Affiliation(s)
- Tom Berben
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lex Overmars
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute for Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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20
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Ni G, Harnawan P, Seidel L, Ter Heijne A, Sleutels T, Buisman CJN, Dopson M. Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell. JOURNAL OF HAZARDOUS MATERIALS 2019; 363:197-204. [PMID: 30308358 DOI: 10.1016/j.jhazmat.2018.09.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfide treatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfide removal rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m2 compared to 210 mA/m2 while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioalkalivibrio, Thioalkalimicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.
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Affiliation(s)
- Gaofeng Ni
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands; Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Pebrianto Harnawan
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands
| | - Laura Seidel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Annemiek Ter Heijne
- Sub-Department of Environmental Technology, Wageningen University, Bornse Weilanden 9, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands
| | - Cees J N Buisman
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands; Sub-Department of Environmental Technology, Wageningen University, Bornse Weilanden 9, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave. Microorganisms 2019; 7:microorganisms7020029. [PMID: 30678083 PMCID: PMC6406701 DOI: 10.3390/microorganisms7020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 11/16/2022] Open
Abstract
The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.
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González JM, Hernández L, Manzano I, Pedrós-Alió C. Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate. ISME JOURNAL 2019; 13:1183-1197. [PMID: 30643200 DOI: 10.1038/s41396-019-0347-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/22/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.
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Affiliation(s)
- José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain.
| | - Laura Hernández
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Iris Manzano
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Vavourakis CD, Andrei AS, Mehrshad M, Ghai R, Sorokin DY, Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. MICROBIOME 2018; 6:168. [PMID: 30231921 PMCID: PMC6146748 DOI: 10.1186/s40168-018-0548-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/03/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. RESULTS We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. CONCLUSIONS Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.
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Affiliation(s)
- Charlotte D. Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
| | - Adrian-Stefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic
| | - Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, 60 let Oktyabrya pr-t, 7, bld. 2, Moscow, Russian Federation 117312
- Environmental Biotechnology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Postbus 94248, 1090 GE Amsterdam, the Netherlands
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Namsaraev ZB. Microbial Communities of the Central Asian Lakes as Indicators of Climatic and Ecological Changes in the Region. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Zaitseva SV, Abidueva EY, Radnagurueva AA, Bazarov SM, Buryukhaev SP. Structure of Microbial Communities of the Sediments of Alkaline Transbaikalia Lakes with Different Salinity. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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26
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Walter JM, Coutinho FH, Dutilh BE, Swings J, Thompson FL, Thompson CC. Ecogenomics and Taxonomy of Cyanobacteria Phylum. Front Microbiol 2017; 8:2132. [PMID: 29184540 PMCID: PMC5694629 DOI: 10.3389/fmicb.2017.02132] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/18/2017] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.
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Affiliation(s)
- Juline M Walter
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Felipe H Coutinho
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Bas E Dutilh
- Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Jean Swings
- Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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