1
|
Doménech-Pascual A, Carrasco-Barea L, Gich F, Boadella J, Freixinos Campillo Z, Gómez Cerezo R, Butturini A, Romaní AM. Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream. Environ Microbiol 2024; 26:e16661. [PMID: 38849711 DOI: 10.1111/1462-2920.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.
Collapse
Affiliation(s)
| | - Lorena Carrasco-Barea
- Plant Physiology Unit, Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Frederic Gich
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Judit Boadella
- GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | | | - Rosa Gómez Cerezo
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Andrea Butturini
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Anna M Romaní
- GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| |
Collapse
|
2
|
Multidrug-resistant epi-endophytic bacterial community in Posidonia oceanica of Mahdia coast as biomonitoring factor for antibiotic contamination. Arch Microbiol 2022; 204:229. [PMID: 35353264 DOI: 10.1007/s00203-022-02842-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/12/2022] [Accepted: 03/13/2022] [Indexed: 11/02/2022]
Abstract
Faced with the significant disturbances, mainly of anthropogenic origin, which affect the Mediterranean coastal ecosystem, Posidonia oceanica (L.) Delile has often been used to assess the state of health of this environment. The present study aims to determine the multidrug resistance patterns among isolated and identified epi-endophytic bacterial strains in P. oceanica seagrass collected from Mahdia coastal seawater (Tunisia). To investigate the bacterial community structure and diversity from coastal seawater samples from Mahdia, total DNA extraction and 16S rRNA gene amplification were performed and analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed that some bands were specific to a given site, while other bands were found to be common to more than one sample. In the other hand, bacterial strains were isolated from 1 mL of leaves and epiphytes suspension of P. oceanica seagrass in marine agar. Forty-three isolates were obtained, seven of them were selected and identified on the basis of 16S rRNA gene sequence analysis. These isolates belonged to the genus Bacillus, exhibiting 98-100% of identity with known sequences. Susceptibility patterns of these strains were studied toward commonly used antibiotics in Tunisia. All identified isolates were resistant to Aztreonam (72.1%), Ceftazidime (60.5%), Amoxicillin (56%) and Rifampicin (51.2%). S5-L13 strain had presented the highest multidrug resistance with a MAR index of 0.67.
Collapse
|
3
|
Proenca AM, Oliveira MM, Neves PFR, Giongo A, de Oliveira RR, Ott CT, Marconatto L, de Barros Neto HMC, Ketzer JMM, Medina-Silva R. Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates. Arch Microbiol 2022; 204:205. [PMID: 35266047 DOI: 10.1007/s00203-022-02814-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.
Collapse
Affiliation(s)
- Audrey Menegaz Proenca
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Maiara Monteiro Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Paula Fernanda Ribas Neves
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Adriana Giongo
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Rafael Rodrigues de Oliveira
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Carolina Telles Ott
- Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Letícia Marconatto
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | | | | | - Renata Medina-Silva
- Geobiology Research Group, Institute of Petroleum and Natural Resources, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil. .,Immunology and Microbiology Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, PUCRS, Porto Alegre, Brazil.
| |
Collapse
|
4
|
Nas F, Aissaoui N, Mahjoubi M, Mosbah A, Arab M, Abdelwahed S, Khrouf R, Masmoudi AS, Cherif A, Klouche-Khelil N. A comparative GC-MS analysis of bioactive secondary metabolites produced by halotolerant Bacillus spp. isolated from the Great Sebkha of Oran. Int Microbiol 2021; 24:455-470. [PMID: 34100180 DOI: 10.1007/s10123-021-00185-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
The reemergence of infectious diseases and resistant pathogens represents a serious problem for human life. Hence, the screening for new or alternative antimicrobial compounds is still urgent. Unusual ecosystems such as saline habitats are considered promising environments for the purposes of isolating bacterial strains able to produce potent natural products. The aim of this study is the identification of bioactive compounds biosynthesized by three halotolerant strains isolated from the Sebkha of Oran (Algeria) using gas chromatography coupled to mass spectrometry. Primary screening investigation of antimicrobial activities were performed against reference bacterial and fungal strains and revealed a broad-spectrum activity. Secondary metabolite extraction was carried out using ethyl acetate and chloroform. Crude extracts were tested for bioactivity using the disc diffusion method and subjected to GC-MS analysis. The extracts showed an important inhibitory effect against all tested strains. Fifty-six compounds were identified; they include tert-butyl phenol compounds, fatty acid methyl esters due to the methylation procedure, hydrocarbons, aldehydes, benzoquinones, pyrrols, and terpenes. Literature reports such compounds to have wide biological and pharmaceutical applications. The molecular identification of the three isolates was achieved using the 16S-23S rRNA gene intergenic spacer region (ITS) and 16S rRNA sequencing. Partial 16S rRNA gene sequencing showed very high similarity with many species of Bacillus. This study provided insights on the potential of halotolerant Bacillus as drug research target for bioactive metabolites. The findings suggest that the Great Sebkha of Oran is a valuable source of strains exhibiting variety of beneficial attributes that can be utilized in the development of biological antibiotics.
Collapse
Affiliation(s)
- Fatima Nas
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Faculty of Nature and Life, Earth and Universe Sciences, Department of Biology, Aboubekr Belkaïd University of Tlemcen, Tlemcen, Algeria
| | - Nadia Aissaoui
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Faculty of Nature and Life, Earth and Universe Sciences, Department of Biology, Aboubekr Belkaïd University of Tlemcen, Tlemcen, Algeria
| | - Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabe, 2020, Ariana, Tunisia
| | - Amor Mosbah
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabe, 2020, Ariana, Tunisia
| | - Mounia Arab
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Faculty of Nature and Life, Earth and Universe Sciences, Department of Biology, Aboubekr Belkaïd University of Tlemcen, Tlemcen, Algeria
| | - Soukaina Abdelwahed
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabe, 2020, Ariana, Tunisia
| | - Rim Khrouf
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabe, 2020, Ariana, Tunisia
| | | | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabe, 2020, Ariana, Tunisia
| | - Nihel Klouche-Khelil
- Laboratory of Applied Microbiology in Food, Biomedical and Environment (LAMAABE), Faculty of Nature and Life, Earth and Universe Sciences, Department of Biology, Aboubekr Belkaïd University of Tlemcen, Tlemcen, Algeria. .,Laboratory of Experimental Surgery, Medical Faculty, Dental Surgery Department, Aboubekr Belkaïd University of Tlemcen, Tlemcen, Algeria.
| |
Collapse
|
5
|
Luo Y, Wei X, Yang S, Gao YH, Luo ZH. Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions. Mycology 2020; 11:214-229. [PMID: 33062383 PMCID: PMC7534268 DOI: 10.1080/21501203.2020.1799878] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.
Collapse
Affiliation(s)
- Ye Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Xu Wei
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Yuan-Hao Gao
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, PR China
- Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, PR China
| |
Collapse
|
6
|
Assessment of biotechnological potentials of strains isolated from repasso olive pomace in Tunisia. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
7
|
Bacterial community structure and novel species of magnetotactic bacteria in sediments from a seamount in the Mariana volcanic arc. Sci Rep 2017; 7:17964. [PMID: 29269894 PMCID: PMC5740136 DOI: 10.1038/s41598-017-17445-4] [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: 06/05/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Seamounts are undersea mountains rising abruptly from the sea floor and interacting dynamically with underwater currents. They represent unique biological habitats with various microbial community structures. Certain seamount bacteria form conspicuous extracellular iron oxide structures, including encrusted stalks, flattened bifurcating tubes, and filamentous sheaths. To extend our knowledge of seamount ecosystems, we performed an integrated study on population structure and the occurrence of magnetotactic bacteria (MTB) that synthesize intracellular iron oxide nanocrystals in sediments of a seamount in the Mariana volcanic arc. We found Proteobacteria dominant at 13 of 14 stations, but ranked second in abundance to members of the phylum Firmicutes at the deep-water station located on a steep slope facing the Mariana-Yap Trench. Live MTB dwell in biogenic sediments from all 14 stations ranging in depth from 238 to 2,023 m. Some magnetotactic cocci possess the most complex flagellar apparatus yet reported; 19 flagella are arranged in a 3:4:5:4:3 array within a flagellar bundle. Phylogenetic analysis of 16S rRNA gene sequences identified 16 novel species of MTB specific to this seamount. Together the results obtained indicate that geographic properties of the seamount stations are important in shaping the bacterial community structure and the MTB composition.
Collapse
|
8
|
Hoffmann T, Bleisteiner M, Sappa PK, Steil L, Mäder U, Völker U, Bremer E. Synthesis of the compatible solute proline by Bacillus subtilis: point mutations rendering the osmotically controlled proHJ promoter hyperactive. Environ Microbiol 2017; 19:3700-3720. [PMID: 28752945 DOI: 10.1111/1462-2920.13870] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/09/2017] [Accepted: 07/24/2017] [Indexed: 01/29/2023]
Abstract
The ProJ and ProH enzymes of Bacillus subtilis catalyse together with ProA (ProJ-ProA-ProH), osmostress-adaptive synthesis of the compatible solute proline. The proA-encoded gamma-glutamyl phosphate reductase is also used for anabolic proline synthesis (ProB-ProA-ProI). Transcription of the proHJ operon is osmotically inducible whereas that of the proBA operon is not. Targeted and quantitative proteome analysis revealed that the amount of ProA is not limiting for the interconnected anabolic and osmostress-responsive proline production routes. A key player for enhanced osmostress-adaptive proline production is the osmotically regulated proHJ promoter. We used site-directed mutagenesis to study the salient features of this stress-responsive promoter. Two important features were identified: (i) deviations of the proHJ promoter from the consensus sequence of SigA-type promoters serve to keep transcription low under non-inducing growth conditions, while still allowing a finely tuned induction of transcriptional activity when the external osmolarity is increased and (ii) a suboptimal spacer length for SigA-type promoters of either 16-bp (the natural proHJ promoter), or 18-bp (a synthetic promoter variant) is strictly required to allow regulation of promoter activity in proportion to the external salinity. Collectively, our data suggest that changes in the local DNA structure at the proHJ promoter are important determinants for osmostress-inducibility of transcription.
Collapse
Affiliation(s)
- Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Monika Bleisteiner
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Praveen Kumar Sappa
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerweinstr. 6, Marburg D-35043, Germany
| |
Collapse
|
9
|
Fernandes JP, Mucha AP, Francisco T, Gomes CR, Almeida CMR. Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics. MARINE POLLUTION BULLETIN 2017; 119:176-183. [PMID: 28363429 DOI: 10.1016/j.marpolbul.2017.03.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/17/2017] [Accepted: 03/25/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. CAPSULE The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation.
Collapse
Affiliation(s)
- Joana P Fernandes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Ana P Mucha
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Telmo Francisco
- Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Carlos Rocha Gomes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - C Marisa R Almeida
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| |
Collapse
|
10
|
Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
Collapse
Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
11
|
Ettoumi B, Chouchane H, Guesmi A, Mahjoubi M, Brusetti L, Neifar M, Borin S, Daffonchio D, Cherif A. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea. Microbiol Res 2016; 186-187:71-80. [DOI: 10.1016/j.micres.2016.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 03/31/2016] [Indexed: 11/26/2022]
|
12
|
More RP, Purohit HJ. The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. J Comput Biol 2016; 23:651-61. [PMID: 27104769 DOI: 10.1089/cmb.2016.0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classification of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a regular expression that is specific to each particular taxon. Our main goal was to identify discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We applied combined composite vector and multiple sequence alignment approaches to generate gene-specific signatures. Further, we mapped all the patterns into the different hypervariable regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as V3-V4 for targeted taxa. We also examined the evolution in discriminating patterns of signatures across taxonomic levels. We assessed the comparative classification accuracy of signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity close to 0.99. We developed signature-based software DNA Barcode Identification (DNA BarID) for taxonomic classification that is available at website http://www.neeri.res.in/DNA_BarID.htm . This pattern-based study provides a deeper understanding of taxon-specific discriminating patterns in 16S rRNA gene with respect to taxonomic classification.
Collapse
Affiliation(s)
- Ravi P More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
| | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
| |
Collapse
|
13
|
Molecular Phylogenetics: Concepts for a Newcomer. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:185-196. [DOI: 10.1007/10_2016_49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
14
|
Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E. Abiotic stress protection by ecologically abundant dimethylsulfoniopropionate and its natural and synthetic derivatives: insights from Bacillus subtilis. Environ Microbiol 2014; 17:2362-78. [PMID: 25384455 DOI: 10.1111/1462-2920.12698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/28/2014] [Indexed: 12/01/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant osmolyte and anti-stress compound produced primarily in marine ecosystems. After its release into the environment, microorganisms can exploit DMSP as a source of sulfur and carbon, or accumulate it as an osmoprotectant. However, import systems for this ecophysiologically important compatible solute, and its stress-protective properties for microorganisms that do not produce it are insufficiently understood. Here we address these questions using a well-characterized set of Bacillus subtilis mutants to chemically profile the influence of DMSP import on stress resistance, the osmostress-adaptive proline pool and on osmotically controlled gene expression. We included in this study the naturally occurring selenium analogue of DMSP, dimethylseleniopropionate (DMSeP), as well as a set of synthetic DMSP derivatives. We found that DMSP is not a nutrient for B. subtilis, but it serves as an excellent stress protectant against challenges conferred by sustained high salinity or lasting extremes in both low and high growth temperatures. DMSeP and synthetic DMSP derivatives retain part of these stress protective attributes, but DMSP is clearly the more effective stress protectant. We identified the promiscuous and widely distributed ABC transporter OpuC as a high-affinity uptake system not only for DMSP, but also for its natural and synthetic derivatives.
Collapse
Affiliation(s)
- Sebastian Broy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Chiliang Chen
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Gabriele Nau-Wagner
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Mohamed Jebbar
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,Laboratory of Microbiology of Extreme Environments, UMR 6197 (CNRS - Ifremer - UBO), European Institute of Marine Studies, University of West Brittany (Brest), Technopole Brest-Iroise, F-29280, Plouzané, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitäts Str. 1, D-40225, Düsseldorf, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany.,Kekule-Institute for Organic Chemistry and Biochemistry, Friedrich Wilhelms-University Bonn, Gerhard-Domagk-Str. 1, D-53121, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| |
Collapse
|
15
|
Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
| |
Collapse
|