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Pudova DS, Toymentseva AA, Gogoleva NE, Shagimardanova EI, Mardanova AM, Sharipova MR. Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases. Genes (Basel) 2022; 13:genes13030409. [PMID: 35327964 PMCID: PMC8950961 DOI: 10.3390/genes13030409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.
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Meena B, Anburajan L, Nitharsan K, Vinithkumar NV, Dharani G. Taxonomic Composition and Biological Activity of Bacterial Communities Associated with Marine Ascidians from Andaman Islands, India. Appl Biochem Biotechnol 2021; 193:2932-2963. [PMID: 34028666 DOI: 10.1007/s12010-021-03577-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
Marine invertebrates, particularly ascidians, constitute an important source of potential active and biofunctional natural products. The microbial diversity associated with ascidians is little recognized, although these microorganisms play a vital role in marine ecosystems. The objective of this study was to investigate bacterial population diversity in four ascidian samples: Phallusia nigra, Phallusia fumigata, Eudistoma viride, and Rhopalaea macrothorax, collected from the North Bay, Andaman and Nicobar Islands. Microbial strains identified up to the species level revealed 236 distinct species/ribotypes out of 298 bacterial strains. Of 298 ascidian-associated bacteria, 72 isolates belong to the class Gammaproteobacteria and the genus Endozoicomonas. The results from this investigation will contribute a broaden knowledge of microbial diversity associated to marine ascidians, and as a promising source for the discovery of new natural products.
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Affiliation(s)
- Balakrishnan Meena
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair, Andaman and Nicobar Islands, 744103, India.
| | - Lawrance Anburajan
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair, Andaman and Nicobar Islands, 744103, India.
| | - Kirubakaran Nitharsan
- Department of Marine Biotechnology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - Nambali Valsalan Vinithkumar
- Atal Centre for Ocean Science and Technology for Islands, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Port Blair, Andaman and Nicobar Islands, 744103, India
| | - Gopal Dharani
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences, Government of India, Chennai, Tamil Nadu, 600100, India
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Choi W, Kim SS. Outbreaks, Germination, and Inactivation of Bacillus cereus in Food Products: A Review. J Food Prot 2020; 83:1480-1487. [PMID: 32822494 DOI: 10.4315/0362-028x.jfp-19-429] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022]
Abstract
ABSTRACT Bacillus cereus has been reported as a foodborne pathogen worldwide. Although food processing technologies to inactivate the pathogen have been developed for decades, foodborne outbreaks related to B. cereus have occurred. In the present review, foodborne outbreaks, germination, inactivation, and detection of B. cereus are discussed, along with inactivation mechanisms. B. cereus outbreaks from 2003 to 2016 are reported based on food commodity, number of cases, and consequent illnesses. Germination before sporicidal treatments is highlighted as an effective way to inactivate B. cereus, because the resistance of the pathogen increases significantly following sporulation. Several germinants used for B. cereus are listed, and their efficacies are compared. Finally, recently used interventions with sporicidal mechanisms are identified, and rapid detection methods that have been developed are discussed. Combining two or more interventions, known as the hurdle technology concept, is suggested to maximize the sporicidal effect. Further study is needed to ensure food safety and to understand germination mechanisms and sporicidal resistance of B. cereus. HIGHLIGHTS
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Affiliation(s)
- Won Choi
- Department of Landscape Architecture and Rural Systems Engineering and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Soon Kim
- Department of Food Engineering, Dankook University, Cheonan, Chungnam 31116, Republic of Korea
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Alemán-Vega M, Sánchez-Lozano I, Hernández-Guerrero CJ, Hellio C, Quintana ET. Exploring Antifouling Activity of Biosurfactants Producing Marine Bacteria Isolated from Gulf of California. Int J Mol Sci 2020; 21:E6068. [PMID: 32842499 PMCID: PMC7504147 DOI: 10.3390/ijms21176068] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022] Open
Abstract
Biofouling causes major problems and economic losses to marine and shipping industries. In the search for new antifouling agents, marine bacteria with biosurfactants production capability can be an excellent option, due to the amphipathic surface-active characteristic that confers antimicrobial and antibiofilm activities. The aim of this study was to evaluate the antifouling activity of biosurfactants producing marine bacteria from the Gulf of California. The cell free culture supernatant (CFCS) of Bacillus niabensis (S-69), Ralstonia sp. (S-74) (isolated from marine sediment) and of B. niabensis (My-30) (bacteria associated to the sponge Mycale ramulosa) were screened for production of biosurfactants (using hemolysis and drop collapse test, oil displacement and emulsifying activity). The toxicity and antifouling activity were evaluated against biofoulers (bacteria forming biofilm and macrofoulers) both in laboratory and field assays. The results indicate that all bacteria were biosurfactant producers, but the higher capability was shown by B. niabensis (My-30) with high emulsifying properties (E24) of 71%. The CFCS showed moderate toxicity but were considered non-toxic against Artemia franciscana at low concentrations. In the antifouling assay, the CFCS of both strains of B. niabensis showed the best results for the reduction of the biofilm formation (up 50%) against all Gram-positive bacteria and most Gram-negative bacteria with low concentrations. In the field assay, the CFCS of B. niabensis (My-30) led to the reduction of 30% of biofouling compared to the control. The results indicate that the biosurfactant produced by B. niabensis (My-30) has promising antifouling activity.
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Affiliation(s)
- Monserrat Alemán-Vega
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N. Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico; (M.A.-V.); (I.S.-L.)
| | - Ilse Sánchez-Lozano
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N. Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico; (M.A.-V.); (I.S.-L.)
| | - Claudia J. Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N. Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico; (M.A.-V.); (I.S.-L.)
| | - Claire Hellio
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Institut Universitaire Européen de la Mer, F-29280 Plouzané, France
| | - Erika T. Quintana
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de Mexico, Mexico;
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Genome Sequencing and Analysis of Bacillus pumilus ICVB403 Isolated from Acartia tonsa Copepod Eggs Revealed Surfactin and Bacteriocin Production: Insights on Anti-Staphylococcus Activity. Probiotics Antimicrob Proteins 2020; 11:990-998. [PMID: 30229513 DOI: 10.1007/s12602-018-9461-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Here we show that Bacillus pumilus ICVB403 recently isolated from copepod eggs is able to produce, after 48-72 h of growth in Landy medium, extracellular inhibitory compounds, which are active against Staphylococcus aureus ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 43300, MRSA-S1, Staphylococcus epidermidis 11EMB, Staphylococcus warneri 27EMB, and Staphylococcus hominis 13EMB. Moreover, these extracellular inhibitory compound(s) were able to potentiate erythromycin against the aforementioned staphylococci. The minimum inhibitory concentration (MIC) of erythromycin was reduced from 32 μg/mL to 8 μg/mL for MRSA ATCC 43300 and MRSA SA-1 strains, and from 32-64 μg/mL to 4 μg/mL for S. epidermidis 11EMB and S. hominis 13EMB strains.The genome sequencing and analysis of B. pumilus ICVB403 unveiled 3.666.195 nucleotides contained in 22 contigs with a G + C ratio of 42.0%, 3.826 coding sequences, and 73 RNAs. In silico analysis guided identification of two putative genes coding for synthesis of surfactin A, a lipopeptide with 7 amino acids, and for a circular bacteriocin belonging to the circularin A/uberolysin family, respectively.
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Savoca S, Lo Giudice A, Papale M, Mangano S, Caruso C, Spanò N, Michaud L, Rizzo C. Antarctic sponges from the Terra Nova Bay (Ross Sea) host a diversified bacterial community. Sci Rep 2019; 9:16135. [PMID: 31695084 PMCID: PMC6834628 DOI: 10.1038/s41598-019-52491-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/04/2019] [Indexed: 11/23/2022] Open
Abstract
Sponges represent important habitats for a community of associated (micro)organisms. Even if sponges dominate vast areas of the Antarctic shelves, few investigations have been performed on Antarctic sponge-associated bacteria. Using a culture-dependent approach, the composition of the bacterial communities associated with 14 Antarctic sponge species from different sites within the Terra Nova Bay (Ross Sea) area was analyzed. Overall, isolates were mainly affiliated to Gammaproteobacteria, followed by Actinobacteria and CF group of Bacteroidetes, being the genera Pseudoalteromonas, Arthrobacter and Gillisia predominant, respectively. Alphaproteobacteria and Firmicutes were less represented. Cluster analyses highlighted similarities/differences among the sponge-associated bacterial communities, also in relation to the sampling site. The gammaproteobacterial Pseudoalteromonas sp. SER45, Psychrobacter sp. SER48, and Shewanella sp. SER50, and the actinobacterial Arthrobacter sp. SER44 phylotypes occurred in association with almost all the analyzed sponge species. However, except for SER50, these phylotypes were retrieved also in seawater, indicating that they may be transient within the sponge body. The differences encountered within the bacterial communities may depend on the different sites of origin, highlighting the importance of the habitat in structuring the composition of the associated bacterial assemblages. Our data support the hypothesis of specific ecological interactions between bacteria and Porifera.
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Affiliation(s)
- Serena Savoca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Angelina Lo Giudice
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche (CNR-ISP), Spianata San Raineri 86, 98122, Messina, Italy.
| | - Maria Papale
- Istituto di Scienze Polari, Consiglio Nazionale delle Ricerche (CNR-ISP), Spianata San Raineri 86, 98122, Messina, Italy
| | - Santina Mangano
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Consolazione Caruso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Nunziacarla Spanò
- Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali, A.O.U. Policlinico "G. Martino", Torre Biologica, Via Consolare Valeria, 98125, Messina, Italy
| | | | - Carmen Rizzo
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Universitàdi Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
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8
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Hernández-González IL, Moreno-Hagelsieb G, Olmedo-Álvarez G. Environmentally-driven gene content convergence and the Bacillus phylogeny. BMC Evol Biol 2018; 18:148. [PMID: 30285626 PMCID: PMC6171248 DOI: 10.1186/s12862-018-1261-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 09/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria. Results The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins. Conclusion Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level. Electronic supplementary material The online version of this article (10.1186/s12862-018-1261-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael L Hernández-González
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, N2L 3C5, Ontario, Canada.
| | - Gabriela Olmedo-Álvarez
- Department of Genetic Engineering, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte, Carr. Irapuato-Leon, Irapuato, 36824, Guanajuato, Mexico.
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Misra S, Dixit VK, Khan MH, Kumar Mishra S, Dviwedi G, Yadav S, Lehri A, Singh Chauhan P. Exploitation of agro-climatic environment for selection of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase producing salt tolerant indigenous plant growth promoting rhizobacteria. Microbiol Res 2017; 205:25-34. [DOI: 10.1016/j.micres.2017.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/27/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
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Saleh MY, Sarhan MS, Mourad EF, Hamza MA, Abbas MT, Othman AA, Youssef HH, Morsi AT, Youssef GH, El-Tahan M, Amer WA, Fayez M, Ruppel S, Hegazi NA. A novel plant-based-sea water culture media for in vitro cultivation and in situ recovery of the halophyte microbiome. J Adv Res 2017; 8:577-590. [PMID: 28794903 PMCID: PMC5540709 DOI: 10.1016/j.jare.2017.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/29/2022] Open
Abstract
The plant-based-sea water culture medium is introduced to in vitro cultivation and in situ recovery of the microbiome of halophytes. The ice plant (Mesembryanthemum crystallinum) was used, in the form of juice and/or dehydrated plant powder packed in teabags, to supplement the natural sea water. The resulting culture medium enjoys the combinations of plant materials as rich source of nutrients and sea water exercising the required salt stress. As such without any supplements, the culture medium was sufficient and efficient to support very good in vitro growth of halotolerant bacteria. It was also capable to recover their in situ culturable populations in the phyllosphere, ecto-rhizosphere and endo-rhizosphere of halophytes prevailing in Lake Mariout, Egypt. When related to the total bacterial numbers measured for Suaeda pruinosa roots by quantitative-PCR, the proposed culture medium increased culturability (15.3-19.5%) compared to the conventional chemically-synthetic culture medium supplemented with (11.2%) or without (3.8%) NaCl. Based on 16S rRNA gene sequencing, representative isolates of halotolerant bacteria prevailed on such culture medium were closely related to Bacillus spp., Halomonas spp., and Kocuria spp. Seed germination tests on 25-50% sea water agar indicated positive interaction of such bacterial isolates with the germination and seedlings' growth of barley seeds.
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Affiliation(s)
- Mohamed Y. Saleh
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohamed S. Sarhan
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Elhussein F. Mourad
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mervat A. Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohamed T. Abbas
- Microbiology Department, Faculty of Agriculture and Natural Resources, Aswan University, P.O. Box 81528, Aswan, Egypt
| | - Amal A. Othman
- Hydrobiology Laboratory, Inland Water and Lake Division, National Institute of Oceanography and Fisheries (NIOF), 11516 Cairo, Egypt
| | - Hanan H. Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ahmed T. Morsi
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Gehan H. Youssef
- Soils, Water and Environment Research Institute, Agricultural Research Center, 12112 Giza, Egypt
| | - Mahmoud El-Tahan
- Institute of Feed Research, Agricultural Research Center, 12112 Giza, Egypt
| | - Wafaa A. Amer
- Department of Botany and Microbiology, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Grossbeeren, Germany
| | - Nabil A. Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
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Markande AR, Nerurkar AS. Microcosm-based interaction studies between members of two ecophysiological groups of bioemulsifier producer and a hydrocarbon degrader from the Indian intertidal zone. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14462-14471. [PMID: 27068903 DOI: 10.1007/s11356-016-6625-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
Isolates were obtained from intertidal zone site samples from all five western and one eastern coastal states of India and were screened. These ecophysiological groups of aerobic, mesophilic, heterotrophic, sporulating, and bioemulsifier-producing bacteria were from Planococcaceae and Bacillaceae. This is the first report of bioemulsifier production by Sporosarcina spp., Lysinibacillus spp., B. thuringiensis, and B. flexus. In this group, Solibacillus silvestris AM1 was found to produce the highest emulsification activity (62.5 %EI) and the sample that yielded it was used to isolate the ecophysiological group of non-bioemulsifier-producing, hydrocarbon-degrading bacteria (belonging to Chromatiales and Bacillales). These yielded hitherto unreported degrader, Rheinheimera sp. CO6 which was selected for the interaction studies (in a microcosm) with bioemulsifier-producing S. silvestris AM1. The gas chromatographic study of these microcosm experiments revealed increased degradation of benzene, toluene, and xylene (BTX) and the growth of Rheinheimera sp. CO6 in the presence of bioemulsifier produced by S. silvestris AM1. Enhancement of the growth of S. silvestris AM1 in the presence of Rheinheimera sp. CO6 was observed possibly due to reduced toxicity of BTX suggesting mutualistic association between the two. This study elucidates the presence and interaction between enhancers and degraders in a hydrocarbon-contaminated intertidal zone and contributes to the knowledge during application of the two in remediation processes.
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Affiliation(s)
- A R Markande
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India, 390002.
- C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Gujarat, India, 394 350.
| | - A S Nerurkar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India, 390002
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12
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Yadav AN, Sachan SG, Verma P, Kaushik R, Saxena AK. Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub-glacial lakes of NW Indian Himalayas. J Basic Microbiol 2015; 56:294-307. [PMID: 26933936 DOI: 10.1002/jobm.201500230] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/29/2015] [Indexed: 11/08/2022]
Abstract
The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes.
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Affiliation(s)
- Ajar Nath Yadav
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India.,Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, India
| | | | - Priyanka Verma
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
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Chaabouni I, Barkallah I, Hamdi C, Jouini A, Saidi M, Mahillon J, Cherif A. Metabolic capacities and toxigenic potential as key drivers of Bacillus cereus ubiquity and adaptation. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0941-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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14
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Diversity and phylogenetic profiling of niche-specific Bacilli from extreme environments of India. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0897-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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15
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Phylogenetic diversity of the Bacillus pumilus group and the marine ecotype revealed by multilocus sequence analysis. PLoS One 2013; 8:e80097. [PMID: 24244618 PMCID: PMC3823796 DOI: 10.1371/journal.pone.0080097] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/30/2013] [Indexed: 11/19/2022] Open
Abstract
Bacteria closely related to Bacillus pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus simply by 16S rRNA gene sequence. In this report, 76 marine strains were subjected to phylogenetic analysis based on 7 housekeeping genes to understand the phylogeny and biogeography in comparison with other origins. A phylogenetic tree based on the 7 housekeeping genes concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB was constructed and compared with trees based on the single genes. All these trees exhibited a similar topology structure with small variations. Our 79 strains were divided into 6 groups from A to F; Group A was the largest and contained 49 strains close to B. altitudinis. Additional two large groups were presented by B. safensis and B. pumilus respectively. Among the housekeeping genes, gyrB and pyrE showed comparatively better resolution power and may serve as molecular markers to distinguish these closely related strains. Furthermore, a recombinant phylogenetic tree based on the gyrB gene and containing 73 terrestrial and our isolates was constructed to detect the relationship between marine and other sources. The tree clearly showed that the bacteria of marine origin were clustered together in all the large groups. In contrast, the cluster belonging to B. safensis was mainly composed of bacteria of terrestrial origin. Interestingly, nearly all the marine isolates were at the top of the tree, indicating the possibility of the recent divergence of this bacterial group in marine environments. We conclude that B. altitudinis bacteria are the most widely spread of the B. pumilus group in marine environments. In summary, this report provides the first evidence regarding the systematic evolution of this bacterial group, and knowledge of their phylogenetic diversity will help in the understanding of their ecological role and distribution in marine environments.
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Guesmi A, Ettoumi B, El Hidri D, Essanaa J, Cherif H, Mapelli F, Marasco R, Rolli E, Boudabous A, Cherif A. Uneven distribution of Halobacillus trueperi species in arid natural saline systems of Southern Tunisian Sahara. MICROBIAL ECOLOGY 2013; 66:831-839. [PMID: 23949950 DOI: 10.1007/s00248-013-0274-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 07/28/2013] [Indexed: 06/02/2023]
Abstract
The genetic diversity of a collection of 336 spore-forming isolates recovered from five salt-saturated brines and soils (Chott and Sebkhas) mainly located in the hyper-arid regions of the southern Tunisian Sahara has been assessed. Requirements and abilities for growth at a wide range of salinities\ showed that 44.3 % of the isolates were extremely halotolerant, 23 % were moderate halotolerant, and 32.7 % were strict halophiles, indicating that they are adapted to thrive in these saline ecosystems. A wide genetic diversity was documented based on 16S-23S rRNA internal transcribed spacer fingerprinting profiles (ITS) and 16S rRNA gene sequences that clustered the strains into seven genera: Bacillus, Gracilibacillus, Halobacillus, Oceanobacillus, Paenibacillus, Pontibacillus, and Virgibacillus. Halobacillus trueperi was the most encountered species in all the sites and presented a large intraspecific diversity with a multiplicity of ITS types. The most frequent ITS type included 42 isolates that were chosen for assessing of the intraspecific diversity by BOX-PCR fingerprinting. A high intraspecific microdiversity was documented by 14 BOX-PCR genotypes whose distribution correlated with the strain geographic origin. Interestingly, H. trueperi isolates presented an uneven geographic distribution among sites with the highest frequency of isolation from the coastal sites, suggesting a marine rather than terrestrial origin of the strains. The high frequency and diversity of H. trueperi suggest that it is a major ecosystem-adapted microbial component of the Tunisian Sahara harsh saline systems of marine origin.
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Affiliation(s)
- Amel Guesmi
- Laboratoire MBA, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Campus Universitaire, 2092, Tunis, Tunisia
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Genetic and biochemical diversity of Paenibacillus larvae isolated from Tunisian infected honey bee broods. BIOMED RESEARCH INTERNATIONAL 2013; 2013:479893. [PMID: 24073406 PMCID: PMC3774041 DOI: 10.1155/2013/479893] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/27/2013] [Indexed: 01/08/2023]
Abstract
Paenibacillus larvae is the causative agent of American foulbrood (AFB), a virulent disease of honeybee (Apis mellifera) larvae. In Tunisia, AFB has been detected in many beekeeping areas, where it causes important economic losses, but nothing is known about the diversity of the causing agent. Seventy-five isolates of P. larvae, identified by biochemical tests and 16S rRNA gene sequencing, were obtained from fifteen contaminated broods showing typical AFB symptoms, collected in different locations in the northern part of the country. Using BOX-PCR, a distinct profile of P. larvae with respect to related Paenibacillus species was detected which may be useful for its identification. Some P. larvae-specific bands represented novel potential molecular markers for the species. BOX-PCR fingerprints indicated a relatively high intraspecific diversity among the isolates not described previously with several molecular polymorphisms identifying six genotypes on polyacrylamide gel. Polymorphisms were also detected in several biochemical characters (indol production, nitrate reduction, and methyl red and oxidase tests). Contrary to the relatively high intraspecies molecular and phenotypic diversity, the in vivo virulence of three selected P. larvae genotypes did not differ significantly, suggesting that the genotypic/phenotypic differences are neutral or related to ecological aspects other than virulence.
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Ettoumi B, Guesmi A, Brusetti L, Borin S, Najjari A, Boudabous A, Cherif A. Microdiversity of deep-sea Bacillales isolated from Tyrrhenian sea sediments as revealed by ARISA, 16S rRNA gene sequencing and BOX-PCR fingerprinting. Microbes Environ 2013; 28:361-9. [PMID: 24005887 PMCID: PMC4070960 DOI: 10.1264/jsme2.me13013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
With respect to their terrestrial relatives, marine Bacillales have not been sufficiently investigated. In this report, the diversity of deep-sea Bacillales, isolated from seamount and non-seamount stations at 3,425 to 3,580 m depth in the Tyrrhenian Sea, was investigated using PCR fingerprinting and 16S rRNA sequence analysis. The isolate collection (n=120) was de-replicated by automated ribosomal intergenic spacer analysis (ARISA), and phylogenetic diversity was analyzed by 16S rRNA gene sequencing of representatives of each ARISA haplotype (n=37). Phylogenetic analysis of isolates showed their affiliation to six different genera of low G+C% content Gram-positive Bacillales: Bacillus, Staphylococcus, Exiguobacterium, Paenibacillus, Lysinibacillus and Terribacillus. Bacillus was the dominant genus represented by the species B. licheniformis, B. pumilus, B. subtilis, B. amyloliquefaciens and B. firmus, typically isolated from marine sediments. The most abundant species in the collection was B. licheniformis (n=85), which showed seven distinct ARISA haplotypes with haplotype H8 being the most dominant since it was identified by 63 isolates. The application of BOX-PCR fingerprinting to the B. licheniformis sub-collection allowed their separation into five distinct BOX genotypes, suggesting a high level of intraspecies diversity among marine B. licheniformis strains. This species also exhibited distinct strain distribution between seamount and non-seamount stations and was shown to be highly prevalent in non-seamount stations. This study revealed the great microdiversity of marine Bacillales and contributes to understanding the biogeographic distribution of marine bacteria in deep-sea sediments.
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Affiliation(s)
- Besma Ettoumi
- LR Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar
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Deciphering the diversity of culturable thermotolerant bacteria from Manikaran hot springs. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0709-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Basu S, Deobagkar DD, Matondkar SGP, Furtado I. Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea. MICROBIAL ECOLOGY 2013; 65:934-954. [PMID: 23280496 DOI: 10.1007/s00248-012-0148-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ≈ 2-3-fold higher in comparison to non-bloom waters and ranged from 3.20 × 10(5) to 6.84 × 10(5) cfu ml(-1). An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia-Pseudomonas-Psychrobacter-Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50-41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial associates of Noctiluca are likely to play a critical role in the biogeochemical ramifications of these unique seasonally emerging tropical open-water blooms of the Northern Arabian Sea.
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Affiliation(s)
- Subhajit Basu
- Department of Microbiology, Goa University, Taleigao Plateau, Goa, 403206, India
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Van-Thuoc D, Huu-Phong T, Thi-Binh N, Thi-Tho N, Minh-Lam D, Quillaguamán J. Polyester production by halophilic and halotolerant bacterial strains obtained from mangrove soil samples located in Northern Vietnam. Microbiologyopen 2012; 1:395-406. [PMID: 23233461 PMCID: PMC3535385 DOI: 10.1002/mbo3.44] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 11/24/2022] Open
Abstract
This research article reports halophilic and halotolerant bacteria isolated from mangrove forests located in Northern Vietnam. Several of these bacteria were able to synthesize polyhydroxyalkanoates (PHAs). PHAs are polyesters stored by microorganisms under the presence of considerable amounts of a carbon source and deficiency of other essential nutrient such as nitrogen or phosphorous. Mangrove forests in Northern Vietnam are saline coastal habitats that have not been microbiologically studied. Mangrove ecosystems are, in general, rich in organic matter, but deficient in nutrients such as nitrogen and phosphorus. We have found about 100 microorganisms that have adapted to mangrove forests by accumulating PHAs. The production of polyesters might therefore be an integral part of the carbon cycle in mangrove forests. Three of the strains (ND153, ND97, and QN194) isolated from the Vietnamese forests were identified as Bacillus species, while other five strains (QN187, ND199, ND218, ND240, and QN271) were phylogenetically close related to the α-proteobacterium Yangia pacifica. These strains were found to accumulate PHAs in noticeable amounts. Polymer inclusions and chemical structure were studied by transmission electron microscopy and proton nuclear magnetic resonance (NMR) spectroscopy analyses, respectively. Strains ND153, ND97, QN194, QN187, ND240, and QN271 synthesized poly(3-hydroxybutyrate) (PHB) from glucose, whereas strains ND199 and ND218 synthesized poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) from this carbohydrate. With the exception of strain QN194, the strains accumulated PHBV when a combination of glucose and propionate was included in the culture medium. The polymer yields and cell growth reached by one Bacillus isolate, strain ND153, and one Gram-negative bacterium, strain QN271, were high and worth to be researched further. For experiments performed in shake flasks, strain ND153 reached a maximum PHBV yield of 71 wt% and a cell dry weight (CDW) of 3.6 g/L while strain QN271 attained a maximum PHB yield of 48 wt% and a CDW of 5.1 g/L. Both strain ND153 and strain QN271 may only represent a case in point that exemplifies of the potential that mangrove forests possess for the discovery of novel halophilic and halotolerant microorganisms able to synthesize different types of biopolyesters.
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Affiliation(s)
- Doan Van-Thuoc
- Department of Microbiology and Biotechnology, Faculty of Biology, Hanoi National University of Education136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Tran Huu-Phong
- Department of Microbiology and Biotechnology, Faculty of Biology, Hanoi National University of Education136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Nguyen Thi-Binh
- Department of Microbiology and Biotechnology, Faculty of Biology, Hanoi National University of Education136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Nguyen Thi-Tho
- Department of Microbiology and Biotechnology, Faculty of Biology, Hanoi National University of Education136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Duong Minh-Lam
- Department of Microbiology and Biotechnology, Faculty of Biology, Hanoi National University of Education136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Jorge Quillaguamán
- Center of Biotechnology, Faculty of Sciences and Technology, Universidad Mayor de San SimónCochabamba, Bolivia
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Phelan RW, O'Halloran JA, Kennedy J, Morrissey JP, Dobson ADW, O'Gara F, Barbosa TM. Diversity and bioactive potential of endospore-forming bacteria cultured from the marine sponge Haliclona simulans. J Appl Microbiol 2011; 112:65-78. [PMID: 21985154 DOI: 10.1111/j.1365-2672.2011.05173.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Despite the frequent isolation of endospore-formers from marine sponges, little is known about the diversity and characterization of individual isolates. The main aims of this study were to isolate and characterize the spore-forming bacteria from the marine sponge Haliclona simulans and to examine their potential as a source for bioactive compounds. METHODS AND RESULTS A bank of presumptive aerobic spore-forming bacteria was isolated from the marine sponge H. simulans. These represented c. 1% of the total culturable bacterial population. A subgroup of thirty isolates was characterized using morphological, phenotypical and phylogenetic analysis. A large diversity of endospore-forming bacteria was present, with the thirty isolates being distributed through a variety of Bacillus and Paenibacillus species. These included ubiquitous species, such as B. subtilis, B. pumilus, B. licheniformis and B. cereus group, as well as species that are typically associated with marine habitats, such as B. aquimaris, B. algicola and B. hwajinpoensis. Two strains carried the aiiA gene that encodes a lactonase known to be able to disrupt quorum-sensing mechanisms, and various isolates demonstrated protease activity and antimicrobial activity against different pathogenic indicator strains, including Clostridium perfringens, Bacillus cereus and Listeria monocytogenes. CONCLUSIONS The marine sponge H. simulans harbours a diverse collection of endospore-forming bacteria, which produce proteases and antibiotics. This diversity appears to be overlooked by culture-dependent and culture-independent methods that do not specifically target sporeformers. SIGNIFICANCE AND IMPACT OF STUDY Marine sponges are an as yet largely untapped and poorly understood source of endospore-forming bacterial diversity with potential biotechnological, biopharmaceutical and probiotic applications. These results also indicate the importance of combining different methodologies for the comprehensive characterization of complex microbial populations such as those found in marine sponges.
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Affiliation(s)
- R W Phelan
- Department of Microbiology, University College Cork, Cork, Ireland
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Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b, isolated from the Indian ocean. J Bacteriol 2010; 193:1276-7. [PMID: 21183663 DOI: 10.1128/jb.01351-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis is an aerobic spore-forming Gram-positive bacterium that is a model organism and of great industrial significance as the source of diverse novel functional molecules. Here we present, to our knowledge, the first genome sequence of Bacillus subtilis strain gtP20b isolated from the marine environment. A subset of candidate genes and gene clusters were identified, which are potentially involved in production of diverse functional molecules, like novel ribosomal and nonribosomal antimicrobial peptides. The genome sequence described in this paper is due to its high strain specificity of great importance for basic as well as applied researches on marine organisms.
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Yadav S, Kaushik R, Saxena AK, Arora DK. Diversity and phylogeny of plant growth-promoting bacilli from moderately acidic soil. J Basic Microbiol 2010; 51:98-106. [DOI: 10.1002/jobm.201000098] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 06/21/2010] [Indexed: 11/10/2022]
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25
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Menezes CBA, Bonugli-Santos RC, Miqueletto PB, Passarini MRZ, Silva CHD, Justo MR, Leal RR, Fantinatti-Garboggini F, Oliveira VM, Berlinck RGS, Sette LD. Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil. Microbiol Res 2010; 165:466-82. [PMID: 19879115 DOI: 10.1016/j.micres.2009.09.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/24/2009] [Accepted: 09/27/2009] [Indexed: 02/07/2023]
Abstract
Little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. The aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. Data derived from ARDRA and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. Microbial strains identified up to the genus level revealed 144 distinct ribotypes out of 256 fungal strains and 158 distinct ribotypes out of 181 bacterial strains. Filamentous fungi were distributed among 24 different genera belonging to Ascomycota, Zygomycota and Basidiomycota, some of which had never been reported in the literature as marine invertebrate-inhabiting fungi (Pestalotiopsis, Xylaria, Botrysphaeria and Cunnninghamella). Bacterial isolates were affiliated to 41 different genera, being Bacillus, Ruegeria, Micrococcus, Pseudovibrio and Staphylococcus the most abundant ones. Results revealed an unexpected high microbial diversity associated to the macroorganisms which have been collected and suggested the selection of certain microbial taxonomic groups according to the host. The combined data gathered from this investigation contribute to broaden the knowledge of microbial diversity associated to marine macroorganisms, including as a promising source for the discovery of new natural products.
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Affiliation(s)
- Cláudia B A Menezes
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches. Syst Appl Microbiol 2010; 33:222-31. [PMID: 20413241 DOI: 10.1016/j.syapm.2010.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/21/2022]
Abstract
Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.
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