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Zhang TT, Liu D, Zhang XY, Wang JC, Du ZJ. Spiribacter salilacus sp. nov., a novel moderately halophilic bacterium isolated from a saline lake in China. Arch Microbiol 2023; 205:166. [PMID: 37014519 DOI: 10.1007/s00203-023-03511-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023]
Abstract
A Gram-staining-negative, non-motile, rod-shaped or curved rod-shaped, moderately halophilic bacterium, designated C176T, was isolated from Yuncheng Salt Lake in Shanxi Province, P.R. China. The optimal temperature, salinity and pH for growth of strain C176T was 37 °C, 6% (w/v) NaCl and 7.5. Phylogenetic analysis using 16S rRNA gene sequences indicated strain C176T has the highest similarity with Spiribacter salinus LMG 27464 T (97.7%), following by the S. halobius E85T (97.6%), S. curvatus DSM 28542 T (97.2%), S. roseus CECT 9117 T (97.0%) and S. vilamensis DSM 21056 T (96.9%). The ANI and dDDH values between strain C176T and S. salinus LMG 27464 T were 69.8 and 17.7%, respectively. The DNA G + C content of genome for strain C176T was 54.1%. Summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0 were detected as its major fatty acids, with content of 38.7 and 28.6% respectively, while Q-8 was the predominant ubiquinone. The major polar lipids of strain C176T contained phospholipid, phosphatidylglycerol and phosphoglycolipid. In accordance with results of polyphasic taxonomy, strain C176T is considered as a novel species of the genus Spiribacter, for which the name Spiribacter salilacus sp. nov. is proposed. The type strain is C176T (= MCCC 1H00417T = KCTC 72692 T).
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Affiliation(s)
- Tong-Tong Zhang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Dun Liu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Xiao-Yu Zhang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong, China
| | - Jia-Cheng Wang
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai, 264209, Shandong, China.
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2
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Gorrasi S, Franzetti A, Ambrosini R, Pittino F, Pasqualetti M, Fenice M. Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy). Molecules 2021; 26:molecules26051338. [PMID: 33801538 PMCID: PMC7958962 DOI: 10.3390/molecules26051338] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).
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Affiliation(s)
- Susanna Gorrasi
- Dipartimento di Ecologia e Biologia, Università degli Studi della Tuscia, Largo Università snc, 01100 Viterbo, Italy; (S.G.); (M.P.)
| | - Andrea Franzetti
- Dipartimento di Scienze dell’Ambiente e della Terra, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (A.F.); (F.P.)
| | - Roberto Ambrosini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy;
| | - Francesca Pittino
- Dipartimento di Scienze dell’Ambiente e della Terra, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (A.F.); (F.P.)
| | - Marcella Pasqualetti
- Dipartimento di Ecologia e Biologia, Università degli Studi della Tuscia, Largo Università snc, 01100 Viterbo, Italy; (S.G.); (M.P.)
- Laboratoro di Ecologia dei Funghi Marini CONISMA, Università degli Studi della Tuscia, Largo Università snc, 01100 Viterbo, Italy
| | - Massimiliano Fenice
- Dipartimento di Ecologia e Biologia, Università degli Studi della Tuscia, Largo Università snc, 01100 Viterbo, Italy; (S.G.); (M.P.)
- Laboratorio di Microbiologia Marina Applicata, CONISMA, Università degli Studi della Tuscia, Largo Università snc, 01100 Viterbo, Italy
- Correspondence: ; Tel.: +39-0761-357318
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3
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Chasanah E, Marraskuranto E, Sugiyono, Pratitis A, Nursid M, Yogiara. Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia. Lett Appl Microbiol 2020; 72:157-166. [PMID: 33012031 DOI: 10.1111/lam.13401] [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: 07/17/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/28/2022]
Abstract
Successive microbes in solar salt ponds are essential since it is well correlated with the quality of salt produced. This research aimed to analyse the microbial diversity of the solar salt ponds in Indonesia, which use high-density polyethylene in the ponds. There are two systems, that is, an integrated open system (In-system) and a closed system (Tt-system). The In-system uses seawater while the Tt-system uses seawater from the saline artesian well. Results showed that the In-system had richer microbes than the Tt-system. Both systems shared similar halophilic microbes profile. Ponds with low salinity (3-4 Be) had very low archaea, that is, 0·2 and 0·7% for the In-system and Tt-system respectively and were dominantly inhabited by phylum Proteobacteria. In the pond with high salinity, that is, 25 Be, both systems were dominated by the phylum Euryarchaeota, family Halobacteriaceae, and genera Halorubrum was dominantly found in In25 ponds and Tt25 ponds. Even though the two systems use the same parent seawater, that is, the Java Sea and share similar microbial composition at the phylum level, we found the dominance identified microbes in both systems were different.
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Affiliation(s)
- E Chasanah
- Research Center for Marine and Fisheries Product Processing and Biotechnology, Jakarta, Indonesia
| | - E Marraskuranto
- Research Center for Marine and Fisheries Product Processing and Biotechnology, Jakarta, Indonesia
| | - Sugiyono
- Research Center for Marine and Fisheries Product Processing and Biotechnology, Jakarta, Indonesia
| | - A Pratitis
- Research Center for Marine and Fisheries Product Processing and Biotechnology, Jakarta, Indonesia
| | - M Nursid
- Research Center for Marine and Fisheries Product Processing and Biotechnology, Jakarta, Indonesia
| | - Yogiara
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Banten, Indonesia
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4
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Mani K, Taib N, Hugoni M, Bronner G, Bragança JM, Debroas D. Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India. Front Microbiol 2020; 11:1891. [PMID: 33013726 PMCID: PMC7461921 DOI: 10.3389/fmicb.2020.01891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/20/2020] [Indexed: 11/26/2022] Open
Abstract
The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na+) and chloride (Cl–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.
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Affiliation(s)
- Kabilan Mani
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India.,Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Najwa Taib
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Gisele Bronner
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Judith M Bragança
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India
| | - Didier Debroas
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
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León MJ, Galisteo C, Ventosa A, Sánchez-Porro C. Spiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov. Int J Syst Evol Microbiol 2020; 70:2873-2878. [DOI: 10.1099/ijsem.0.004113] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A comparative taxonomic study of
Spiribacter
and
Halopeptonella
species was carried out using a phylogenomic approach based on comparison of the core genome, orthologous average nucleotide identity (OrthoANIu), Genome-to-Genome Distance Calculator (GGDC) and average amino acid identity (AAI). Phylogenomic analysis based on 976 core translated gene sequences obtained from their genomes showed that
Spiribacter aquaticus
SP30T,
S. curvatus
UAH-SP71T,
S. roseus
SSL50T,
S. salinus
M19-40T and
Halopeptonella vilamensis
DSM 21056T formed a robust cluster, clearly separated from the remaining species of closely related taxa. AAI between
H. vilamensis
DSM 21056T and the species of the genus
Spiribacter
was ≥73.1 %, confirming that all these species belong to the same single genus. On the other hand,
S. roseus
SSL50T and
S. aquaticus
SP30T showed percentages of OrthoANIu and digital DNA–DNA hybridization of 98.4 % and 85.3 %, respectively, while these values among those strains and the type strains of the other species of
Spiribacter
and
H. vilamensis
DSM 21056T were ≤80.8 and 67.8 %, respectively. Overall, these data show that
S. roseus
SSL50T and
S. aquaticus
SP30T constitute a single species and thus that
S. aquaticus
SP30T should be considered as a later, heterotypic synonym of
S. roseus
SSL50T based on the rules for priority of names. We propose an emended description of
S. roseus
, including the features of
S. aquaticus
. We also propose the reclassification of
H. vilamensis
as Spiribacter vilamensis comb. nov.
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Affiliation(s)
- María José León
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Galisteo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Viver T, Orellana LH, Díaz S, Urdiain M, Ramos‐Barbero MD, González‐Pastor JE, Oren A, Hatt JK, Amann R, Antón J, Konstantinidis KT, Rosselló‐Móra R. Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities. Environ Microbiol 2019; 21:4300-4315. [DOI: 10.1111/1462-2920.14790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Luis H. Orellana
- School of Civil and Environmental Engineering Georgia Institute of Technology Atlanta GA USA
| | - Sara Díaz
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | | | - José E. González‐Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología Consejo Superior de Investigaciones Científicas – Instituto Nacional de Técnica Aeroespacial Madrid Spain
| | - Aharon Oren
- Department of Plant and Environmental Sciences The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Jerusalem 9190401 Israel
| | - Janet K. Hatt
- School of Civil and Environmental Engineering Georgia Institute of Technology Atlanta GA USA
| | - Rudolf Amann
- Department of Molecular Ecology Max‐Planck‐Institut für Marine Mikrobiologie Bremen D‐28359 Germany
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology University of Alicante Alicante Spain
| | | | - Ramon Rosselló‐Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
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7
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Gómez-Villegas P, Vigara J, León R. Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain). Mar Drugs 2018; 16:md16090332. [PMID: 30213145 PMCID: PMC6164061 DOI: 10.3390/md16090332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 12/11/2022] Open
Abstract
The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.
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Affiliation(s)
- Patricia Gómez-Villegas
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Javier Vigara
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Rosa León
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
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León MJ, Hoffmann T, Sánchez-Porro C, Heider J, Ventosa A, Bremer E. Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics. Front Microbiol 2018; 9:108. [PMID: 29497403 PMCID: PMC5818414 DOI: 10.3389/fmicb.2018.00108] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.
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Affiliation(s)
- María J León
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps University of Marburg, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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