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Cohen ZR, Ding D, Zhou L, DasGupta S, Haas S, Sinclair KP, Todd ZR, Black RA, Szostak JW, Catling DC. Natural soda lakes provide compatible conditions for RNA and membrane function that could have enabled the origin of life. PNAS NEXUS 2024; 3:pgae084. [PMID: 38505692 PMCID: PMC10949909 DOI: 10.1093/pnasnexus/pgae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
The origin of life likely occurred within environments that concentrated cellular precursors and enabled their co-assembly into cells. Soda lakes (those dominated by Na+ ions and carbonate species) can concentrate precursors of RNA and membranes, such as phosphate, cyanide, and fatty acids. Subsequent assembly of RNA and membranes into cells is a long-standing problem because RNA function requires divalent cations, e.g. Mg2+, but Mg2+ disrupts fatty acid membranes. The low solubility of Mg-containing carbonates limits soda lakes to moderate Mg2+ concentrations (∼1 mM), so we investigated whether both RNAs and membranes function within these lakes. We collected water from Last Chance Lake and Goodenough Lake in Canada. Because we sampled after seasonal evaporation, the lake water contained ∼1 M Na+ and ∼1 mM Mg2+ near pH 10. In the laboratory, nonenzymatic, RNA-templated polymerization of 2-aminoimidazole-activated ribonucleotides occurred at comparable rates in lake water and standard laboratory conditions (50 mM MgCl2, pH 8). Additionally, we found that a ligase ribozyme that uses oligonucleotide substrates activated with 2-aminoimidazole was active in lake water after adjusting pH from ∼10 to 9. We also observed that decanoic acid and decanol assembled into vesicles in a dilute solution that resembled lake water after seasonal rains, and that those vesicles retained encapsulated solutes despite salt-induced flocculation when the external solution was replaced with dry-season lake water. By identifying compatible conditions for nonenzymatic and ribozyme-catalyzed RNA assembly, and for encapsulation by membranes, our results suggest that soda lakes could have enabled cellular life to emerge on Earth, and perhaps elsewhere.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lijun Zhou
- Department of Biochemistry and Biophysics and Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saurja DasGupta
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sebastian Haas
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kimberly P Sinclair
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - Zoe R Todd
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Chemistry and Department of Astronomy, University of Wisconsin, Madison, WI 53706, USA
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - David C Catling
- Astrobiology Program, University of Washington, Seattle, WA 98195, USA
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
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Hernández-Soto LM, Martínez-Abarca F, Ramírez-Saad H, López-Pérez M, Aguirre-Garrido JF. Genome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas. BMC Genomics 2023; 24:696. [PMID: 37986038 PMCID: PMC10662389 DOI: 10.1186/s12864-023-09800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches. RESULTS The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates. CONCLUSIONS The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.
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Affiliation(s)
- Luis Mario Hernández-Soto
- Doctorado en Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Francisco Martínez-Abarca
- Estructura, Dinámica y Función de Genomas de Rizobacterias, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín-CSIC, Granada, Spain
| | - Hugo Ramírez-Saad
- Departamento Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de Mexico, México
| | - Marcos López-Pérez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana-Lerma, Estado de México, Lerma, México.
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Wang M, Zhang X, Shu Z, Wang Z, Tao Y, Lv C, Zhu D, Shen G. Bacterial and archaeal communities within the alkaline soda Langaco Lake in the Qinghai-Tibet Plateau. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Langaco Lake (LGL) is a soda lake located at an altitude of 4548 m in the Qinghai-Tibet Plateau in China. LGL exhibits unique hydrochemical characteristics among soda lakes, but little is known about the microbial diversity of LGL and the microbial interactions with environmental factors.
Methods
The water samples were filtered using chemical-grade cellulose acetate membrane (pore size of 0.45 μm), and the hydrochemical characteristics were analyzed. Community DNA was extracted, and then high-throughput sequencing of 16S rRNA genes was conducted to evaluate the composition of the microbial community.
Results
The high-throughput sequencing of 16S rRNA genes revealed that the bacterial diversity in LGL consisted of 327 genera in 24 phyla (4871 operational taxonomic units (OTUs); Shannon index values of 5.20–6.07), with a significantly higher diversity than that of the Archaea (eight phyla and 29 genera comprising 1008 OTUs; Shannon index values of 2.98–3.30). The bacterial communities were dominated by Proteobacteria (relative abundances of 42.79–53.70%), followed by Bacteroidetes (11.13–15.18%), Planctomycetes (4.20–12.82%), Acidobacteria (5.91–9.50%), Actinobacteria (2.60–5.80%), and Verrucomicrobia (2.11–4.08%). Furthermore, the archaeal communities were dominated by Crenarchaeota (35.97–58.29%), Euryarchaeota (33.02–39.89%), and Woesearchaeota (6.50–21.57%). The dominant bacterial genus was Thiobacillus (8.92–16.78%), and its abundances were most strongly correlated with the total phosphorus (TP) content, pH value, CO32− concentration, and temperature. The most abundant archaeal genus was Methanoregula (21.40–28.29%), and its abundances were the most highly correlated with the total organic carbon (TOC) content, total salinity (TS), and K+ and Na+ concentrations.
Conclusions
The results of this study provide valuable insights for developing a more comprehensive understanding of microbial diversity in these unique carbonate alkaline environments, as well as a better understanding of the microbial resources on the Qinghai-Tibet Plateau.
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Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081280. [PMID: 36013459 PMCID: PMC9409723 DOI: 10.3390/life12081280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.
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Cotta SR, Pellegrinetti TA, Andreote APD, Costa JS, Sarmento H, Fiore MF. Disentangling the lifestyle of bacterial communities in tropical soda lakes. Sci Rep 2022; 12:7939. [PMID: 35562544 PMCID: PMC9106740 DOI: 10.1038/s41598-022-12046-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial lifestyles may reveal niche-specific signatures and can contribute to detecting the effects of abiotic fluctuations on biogeochemical cycles. Microorganisms make a tradeoff between optimizing nutrient uptake, improving biomass yield, and overcoming environmental changes according to environmental hostility. Soda lakes are natural environments rich in carbonate and bicarbonate water, resulting in elevated pH and salinities that frequently approach saturation. We hypothesized that during the dry period (elevated pH and salinity), microorganisms try to overcome this harshness by allocating energy to the cellular maintenance process. As these environmental conditions improve during the wet period, microorganisms will begin to invest in nutrient uptake. To test this hypothesis, we evaluated four soda lakes in two different seasons by applying metagenomics combined with flow cytometry (estimate heterotrophic bacterial biomass). The natural occurrence of cyanobacterial blooms in some lakes is the main driver of carbon. These primary producers provide organic carbon that supports heterotrophic bacterial growth and, consequently, a high biomass yield. Under harsh conditions (dry season), cyanobacteria invest in nutrient uptake mechanisms, whereas heterotrophic bacteria allocate energy to survive at the expense of biomass yield. Lakes without cyanobacteria blooms invest in nutrient uptake independent of environmental hostility. This study clarifies the microbial tradeoffs in hostile environments and the impact of this choice on carbon and energy flux in tropical alkaline lakes.
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Affiliation(s)
- Simone R Cotta
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Thierry A Pellegrinetti
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Ana Paula D Andreote
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Juliana S Costa
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marli F Fiore
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil.
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Complete Genome Sequence of Halomonas venusta Type Strain DSM 4743, a Moderately Halophilic Marine Bacterium. Microbiol Resour Announc 2021; 10:10/18/e00144-21. [PMID: 33958412 PMCID: PMC8103857 DOI: 10.1128/mra.00144-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the genome sequence of Halomonas venusta strain DSM4743T, a moderately halophilic marine bacterium. This type species genome consists of a 4.3-Mb chromosome, with 3,777 protein-coding genes, 60 tRNA loci, and 6 complete rRNA operons, plus a 6.1-kb plasmid termed p4743-A. Here, we report the genome sequence of Halomonas venusta strain DSM 4743T, a moderately halophilic marine bacterium. This type species genome consists of a 4.3-Mb chromosome, with 3,777 protein-coding genes, 60 tRNA loci, and 6 complete rRNA operons, plus a 6.1-kb plasmid termed p4743-A.
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Simultaneous nitrification/denitrification and desulfurization of wastewater polluted with ammonium, COD and sulfide: effectiveness of a new up-flow vertical hybrid reactor. 3 Biotech 2021; 11:123. [PMID: 33643758 DOI: 10.1007/s13205-021-02671-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Industrial wastewater discharges pose an environmental risk. Here, the effectiveness of an up-flow vertical hybrid system, operating with synthetic and industrial wastewater was investigated, as a new approach to perform nitrification/denitrification and desulfurization within a single reactor. The hybrid reactor is divided in two reaction zones, the oxic and anoxic. The removal of chemical oxygen demand (COD), ammonium, and sulfide was investigated, highlighting changes in microbial diversity. The reactor was evaluated at hydraulic residence time (HRT) of 1.6 days, and its performance throughout 180 days is presented in four stages. In stages I-II, high COD and ammonium removal was obtained with synthetic wastewater. In stage-III, sulfide-rich synthetic wastewater did not alter the system, attaining COD, ammonium, and sulfide removal efficiencies of 81, 99.5, and 99.7%, respectively. In the last stage, a mixture of effluents was fed into the reactor at loading rates of 277 mg COD/L-d, 46.5 mg NH4 +-N /L-d, and 15 mg HS--S /L-d. Sulfide and ammonium removals were 100% and 99.9%, respectively. However, low COD removal was observed, being of 51%, and the system removed 97% in terms of BOD5. The structure and microbial diversity also changed. Sulfide feeding, induced the proliferation of sulfur oxidizers like Thiomiscropira and Thiobacillus. Industrial wastewater enhanced the abundance of Pseudomonas (15.53%) and favored the proliferation of new bacteria of the genus Truepera (2.98%) and Alicyclipilus (7.56%). This is the first study reporting simultaneous nitrification/denitrification and desulfurization to remove ammonium, COD and sulfide from complex industrial wastewater using an up-flow vertical hybrid reactor.
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Taxogenomics of the Genus Cyclobacterium: Cyclobacterium xiamenense and Cyclobacterium halophilum as Synonyms and Description of Cyclobacterium plantarum sp. nov. Microorganisms 2020; 8:microorganisms8040610. [PMID: 32340290 PMCID: PMC7232363 DOI: 10.3390/microorganisms8040610] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 11/17/2022] Open
Abstract
The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA–DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to this genus and constitute a coherent phylogenomic group, but with species forming two separate branches. In addition, the genome-based analyses revealed that Cyclobacterium xiamenense and Cyclobacterium halophilum are members of the same species. Besides, we carried out a taxonomic characterization of the new strain GBPx2T, isolated from the halophytic plant Salicornia sp. Analysis of its 16S rRNA gene sequence showed the highest sequence similarity (97.5%) to Cyclobacterium lianum HY9T. Percentages of GGDC and OrthoANI between strain GBPx2T and species of the genus Cyclobacterium were lower than the threshold value for species delineation. The DNA G+C content was 43.0 mol%. The polar lipids included phosphatidylethanolamine as well as one unidentified phospholipid and four unidentified lipids, and its major cellular fatty acids were iso-C15:0 and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The only quinone present was menaquinone 7. Based on a combination of phenotypic, chemotaxonomic, and phylogenomic features, the GBPx2T strain represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium plantarum sp. nov. is proposed. The type strain of Cyclobacterium plantarum is GBPx2T (= IBRC-M 10634T = LMG 28551T).
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Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample. Int Microbiol 2020; 23:467-474. [PMID: 31933014 DOI: 10.1007/s10123-020-00119-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/03/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
Abstract
Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.
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10
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Hugoni M, Escalas A, Bernard C, Nicolas S, Jézéquel D, Vazzoler F, Sarazin G, Leboulanger C, Bouvy M, Got P, Ader M, Troussellier M, Agogué H. Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Mol Ecol 2018; 27:4775-4786. [DOI: 10.1111/mec.14901] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Mylène Hugoni
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Arthur Escalas
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Cécile Bernard
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Sébastien Nicolas
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Fanny Vazzoler
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | | | - Marc Bouvy
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Patrice Got
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Magali Ader
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Marc Troussellier
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Hélène Agogué
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
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Li W, Yang J, Zhang D, Li B, Wang E, Yuan H. Concentration and Community of Airborne Bacteria in Response to Cyclical Haze Events During the Fall and Midwinter in Beijing, China. Front Microbiol 2018; 9:1741. [PMID: 30108578 PMCID: PMC6079307 DOI: 10.3389/fmicb.2018.01741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/12/2018] [Indexed: 02/01/2023] Open
Abstract
Since 2013, severe haze events frequently have occurred in Beijing between October and March, which have created a significant public health threat. Although variations in the chemical composition of these haze events have been studied widely, information pertaining to airborne bacteria in such haze events remains limited. In this study, we characterized the concentration, community structure, and composition of the airborne bacteria in response to nine haze events that occurred between October 1, 2015, and January 5, 2016. We also analyzed the correlations of airborne bacteria (concentration, community structure, and composition) with pollution levels and meteorological factors. The results indicated that airborne bacterial concentration showed a positive cyclical correlation with the haze events, but the bacterial concentration plateaued at the yellow pollution level. In addition, we found particulate matter (PM10) and relative humidity to be key factors that significantly affected the airborne bacterial concentration and community structure. Moreover, Halomonas and Shewanella were enriched on haze days for all nine of the haze events. Finally, the correlations between haze pollution and airborne bacteria in midwinter were weaker than those in fall and early winter, indicating an obvious staged distinction among the effects of haze on airborne bacteria. Our study illuminated the dynamic variation of bioaerosols corresponding to the cyclical haze events and revealed the interactions among air pollution, climate factors (mainly relative humidity), and airborne bacteria. These results imply that different strategies should be applied to deal with the potential threat of airborne bacteria during haze events in different seasons.
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Affiliation(s)
- Weilin Li
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Daizhou Zhang
- Faculty of Environmental & Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, Japan
| | - Baozhen Li
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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Oueriaghli N, Castro DJ, Llamas I, Béjar V, Martínez-Checa F. Study of Bacterial Community Composition and Correlation of Environmental Variables in Rambla Salada, a Hypersaline Environment in South-Eastern Spain. Front Microbiol 2018; 9:1377. [PMID: 29977233 PMCID: PMC6021518 DOI: 10.3389/fmicb.2018.01377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 06/06/2018] [Indexed: 12/03/2022] Open
Abstract
We studied the bacterial community in Rambla Salada in three different sampling sites and in three different seasons and the effect of salinity, oxygen, and pH. All sites samples had high diversity and richness (Rr > 30). The diversity indexes and the analysis of dendrograms obtained by DGGE fingerprint after applying Pearson's and Dice's coefficient showed a strong influence of sampling season. The Pareto-Lorenz (PL) curves and Fo analysis indicated that the microbial communities were balanced and despite the changing environmental conditions, they can preserve their functionality. The main phyla detected by DGGE were Bacteroidetes (39.73%), Proteobacteria (28.43%), Firmicutes (8.23%), and Cyanobacteria (5.14%). The majority of the sequences corresponding to uncultured bacteria belonged to Bacteroidetes phylum. Within Proteobacteria, the main genera detected were Halothiobacillus and Roseovarius. The environmental factors which influenced the community in a higher degree were the salinity and oxygen. The bacteria belonging to Bacteroidetes and Proteobacteria were positively influenced by salinity. Nevertheless, bacteria related to Alpha- and Betaproteobacteria classes and phylum Firmicutes showed a positive correlation with oxygen and pH but negative with salinity. The phylum Cyanobacteria were less influenced by the environmental variables. The bacterial community composition of Rambla Salada was also studied by dilution-to-extinction technique. Using this method, 354 microorganisms were isolated. The 16S sequences of 61 isolates showed that the diversity was very different to those obtained by DGGE and with those obtained previously by using classic culture techniques. The taxa identified by dilution-to-extinction were Proteobacteria (81.92%), Firmicutes (11.30%), Actinobacteria (4.52%), and Bacteroidetes (2.26%) phyla with Gammaproteobacteria as predominant class (65.7%). The main genera were: Marinobacter (38.85%), Halomonas (20.2%), and Bacillus (11.2%). Nine of the 61 identified bacteria showed less than 97% sequence identity with validly described species and may well represent new taxa. The number of bacteria in different samples, locations, and seasons were calculated by CARD-FISH, ranging from 54.3 to 78.9% of the total prokaryotic population. In conclusion, the dilution-to-extinction technique could be a complementary method to classical culture based method, but neither gets to cultivate the major taxa detected by DGGE. The bacterial community was influenced significantly by the physico-chemical parameters (specially the salinity and oxygen), the location and the season of sampling.
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Affiliation(s)
- Nahid Oueriaghli
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David J. Castro
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Inmaculada Llamas
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Victoria Béjar
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Fernando Martínez-Checa
- Microbial Exopolysacharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
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Changes in the soil bacterial community along a pedogenic gradient. Sci Rep 2017; 7:14593. [PMID: 29109410 PMCID: PMC5674076 DOI: 10.1038/s41598-017-15133-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/20/2017] [Indexed: 11/08/2022] Open
Abstract
Current research on the influence of environmental and physicochemical factors in shaping the soil bacterial structure has seldom been approached from a pedological perspective. We studied the bacterial communities of eight soils selected along a pedogenic gradient at the local scale in a Mediterranean calcareous mountain (Sierra de María, SE Spain). The results showed that the relative abundance of Acidobacteria, Canditate division WPS-1, and Armatimonadetes decreased whereas that of Actinobacteria, Bacteroidetes, and Proteobacteria increased from the less-developed soils (Leptosol) to more-developed soils (Luvisol). This bacterial distribution pattern was also positively correlated with soil-quality parameters such as organic C, water-stable aggregates, porosity, moisture, and acidity. In addition, at a lower taxonomic level, the abundance of Acidobacteria Gp4, Armatimonadetes_gp4, Solirubrobacter, Microvirga, Terrimonas, and Nocardioides paralleled soil development and quality. Therefore, our work indicates that the composition of bacterial populations changes with pedogenesis, which could be considered a factor influencing the communities according to the environmental and physicochemical conditions during the soil formation.
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