1
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Sweeney D, Chase AB, Bogdanov A, Jensen PR. MAR4 Streptomyces: A Unique Resource for Natural Product Discovery. JOURNAL OF NATURAL PRODUCTS 2024; 87:439-452. [PMID: 38353658 PMCID: PMC10897937 DOI: 10.1021/acs.jnatprod.3c01007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Marine-derived Streptomyces have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus Streptomyces has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.
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Affiliation(s)
- Douglas Sweeney
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexander B. Chase
- Department
of Earth Sciences, Southern Methodist University, Dallas, Texas 75275, United States
| | - Alexander Bogdanov
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul R. Jensen
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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2
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Fan L, Xu B, Chen S, Liu Y, Li F, Xie W, Prabhu A, Zou D, Wan R, Li H, Liu H, Liu Y, Kao SJ, Chen J, Zhu Y, Rinke C, Li M, Zhu M, Zhang C. Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth. PNAS NEXUS 2024; 3:pgae057. [PMID: 38380056 PMCID: PMC10877094 DOI: 10.1093/pnasnexus/pgae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024]
Abstract
Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.
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Affiliation(s)
- Lu Fan
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Bu Xu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI 96822, USA
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519082, China
| | - Apoorva Prabhu
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Ru Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Haodong Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yuhang Liu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310012, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai 200062, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Maoyan Zhu
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
- Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- State Key Laboratory of Satellite Ocean Environment Dynamics, Hangzhou, Zhejiang 310012, China
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3
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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4
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Broman E, Izabel-Shen D, Rodríguez-Gijón A, Bonaglia S, Garcia SL, Nascimento FJA. Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem. MICROBIOME 2022; 10:126. [PMID: 35965333 PMCID: PMC9377124 DOI: 10.1186/s40168-022-01321-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Francisco J. A. Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
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5
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Becerril-Espinosa A, Hernández-Herrera RM, Meza-Canales ID, Perez-Ramirez R, Rodríguez-Zaragoza FA, Méndez-Morán L, Sánchez-Hernández CV, Palmeros-Suárez PA, Palacios OA, Choix FJ, Juárez-Carrillo E, Lara-González MA, Hurtado-Oliva MÁ, Ocampo-Alvarez H. Habitat-adapted heterologous symbiont Salinispora arenicola promotes growth and alleviates salt stress in tomato crop plants. FRONTIERS IN PLANT SCIENCE 2022; 13:920881. [PMID: 36003821 PMCID: PMC9393590 DOI: 10.3389/fpls.2022.920881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
To ensure food security given the current scenario of climate change and the accompanying ecological repercussions, it is essential to search for new technologies and tools for agricultural production. Microorganism-based biostimulants are recognized as sustainable alternatives to traditional agrochemicals to enhance and protect agricultural production. Marine actinobacteria are a well-known source of novel compounds for biotechnological uses. In addition, former studies have suggested that coral symbiont actinobacteria may support co-symbiotic photosynthetic growth and tolerance and increase the probability of corals surviving abiotic stress. We have previously shown that this activity may also hold in terrestrial plants, at least for the actinobacteria Salinispora arenicola during induced heterologous symbiosis with a wild Solanaceae plant Nicotiana attenuata under in vitro conditions. Here, we further explore the heterologous symbiotic association, germination, growth promotion, and stress relieving activity of S. arenicola in tomato plants under agricultural conditions and dig into the possible associated mechanisms. Tomato plants were grown under normal and saline conditions, and germination, bacteria-root system interactions, plant growth, photosynthetic performance, and the expression of salt stress response genes were analyzed. We found an endophytic interaction between S. arenicola and tomato plants, which promotes germination and shoot and root growth under saline or non-saline conditions. Accordingly, photosynthetic and respective photoprotective performance was enhanced in line with the induced increase in photosynthetic pigments. This was further supported by the overexpression of thermal energy dissipation, which fine-tunes energy use efficiency and may prevent the formation of reactive oxygen species in the chloroplast. Furthermore, gene expression analyses suggested that a selective transport channel gene, SlHKT1,2, induced by S. arenicola may assist in relieving salt stress in tomato plants. The fine regulation of photosynthetic and photoprotective responses, as well as the inhibition of the formation of ROS molecules, seems to be related to the induced down-regulation of other salt stress response genes, such as SlDR1A-related genes or SlAOX1b. Our results demonstrate that the marine microbial symbiont S. arenicola establishes heterologous symbiosis in crop plants, promotes growth, and confers saline stress tolerance. Thus, these results open opportunities to further explore the vast array of marine microbes to enhance crop tolerance and food production under the current climate change scenario.
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Affiliation(s)
- Amayaly Becerril-Espinosa
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico
| | - Rosalba M. Hernández-Herrera
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ivan D. Meza-Canales
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
- Instituto Transdisciplinar de Investigación y Servicios, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Mexico
| | - Rodrigo Perez-Ramirez
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Fabián A. Rodríguez-Zaragoza
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Lucila Méndez-Morán
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Carla V. Sánchez-Hernández
- Departamento de Producción Agrícola, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Paola A. Palmeros-Suárez
- Departamento de Producción Agrícola, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Oskar A. Palacios
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Francisco J. Choix
- Consejo Nacional de Ciencia y Tecnología, Mexico City, Mexico
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Eduardo Juárez-Carrillo
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Martha A. Lara-González
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | | | - Héctor Ocampo-Alvarez
- Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
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6
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Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005207] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkaliphilic actinobacterium, designated VN6-2T, was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2T exhibited a 16S rRNA gene sequence similarity of 93.9 % to
Salinactinospora qingdaonensis
CXB832T, 93.7 % to
Murinocardiopsis flavida
14-Be-013T, and 93.7 % to
Lipingzhangella halophila
14-Be-013T. Genome sequencing revealed a genome size of 5.9 Mb and an in silico G+C content of 69.3 mol%. Both of the phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core gene sequences revealed that strain VN6-2T formed a distinct monophyletic clade within the family
Nocardiopsaceae
. Chemotaxonomic assessment of strain VN6-2T showed that the major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0, and the predominant respiratory quinones were MK-9, MK-9(H2) and MK-9(H4). Whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid, and ribose and xylose as the diagnostic sugars. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, aminophospholipids, glycolipid and phospholipid. Based on the results of this polyphasic study, a novel genus, Spiractinospora gen. nov., is proposed within the family
Nocardiopsaceae
and the type species Spiractinospora alimapuensis gen. nov., sp. nov. The type strain is VN6-2T (CECT 30026T, CCUG 66258T). On the basis of the phylogenetic results herein, we also propose that Nocardiopsis arvandica and Nocardiopsis litoralis are later heterotypic synonyms of
Nocardiopsis sinuspersici
and
Nocardiopsis kunsanensis
, respectively, for which emended descriptions are given.
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7
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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8
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Albuquerque P, Ribeiro I, Correia S, Mucha AP, Tamagnini P, Braga-Henriques A, Carvalho MDF, Mendes MV. Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. Mar Drugs 2021; 19:md19110621. [PMID: 34822492 PMCID: PMC8622039 DOI: 10.3390/md19110621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.
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Affiliation(s)
- Pedro Albuquerque
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Inês Ribeiro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sofia Correia
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
| | - Ana Paula Mucha
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Paula Tamagnini
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Andreia Braga-Henriques
- OOM—Oceanic Observatory of Madeira & MARE—Marine and Environmental Sciences Centre, ARDITI—Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Caminho da Penteada, 9020-105 Funchal, Portugal;
- Regional Directorate for Fisheries, Regional Secretariat for the Sea and Fisheries, Government of the Azores, Rua Cônsul Dabney—Colónia Alemã, 9900-014 Horta, Portugal
| | - Maria de Fátima Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marta V. Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Correspondence:
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9
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A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean. mBio 2021; 12:e0130621. [PMID: 34154421 PMCID: PMC8262872 DOI: 10.1128/mbio.01306-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria inhabiting polar oceans, particularly the Arctic Ocean, are less studied than those at lower latitudes. Discovering bacterial adaptations to Arctic Ocean conditions is essential for understanding responses to the accelerated environmental changes occurring in the North. The Methylophilaceae are emerging as a model for investigating the genomic basis of habitat adaptation, because related lineages are widely distributed across both freshwater and marine ecosystems. Here, we investigated Methylophilaceae diversity in the salinity-stratified surface waters of the Canada Basin, Arctic Ocean. In addition to a diversity of marine OM43 lineages, we report on the genomic characteristics and evolution of a previously undescribed Methylophilaceae clade (BS01) common to polar surface waters yet related to freshwater sediment Methylotenera species. BS01 is restricted to the lower-salinity surface waters, while OM43 is found throughout the halocline. An acidic proteome supports a marine lifestyle for BS01, but gene content shows increased metabolic versatility compared to OM43 and evidence for ongoing genome-streamlining. Phylogenetic reconstruction shows that BS01 colonized the pelagic ocean independently of OM43 via convergent evolution. Salinity adaptation and differences in one-carbon and nitrogen metabolism may play a role in niche differentiation between BS01 and OM43. In particular, urea utilization by BS01 is predicted to provide an ecological advantage over OM43 given the limited amount of inorganic nitrogen in the Canada Basin. These observations provide further evidence that the Arctic Ocean is inhabited by distinct bacterial groups and that at least one group (BS01) evolved via a freshwater to marine environmental transition.
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10
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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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11
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Vidal LMR, Gonçalves ARP, Venas TM, Garcia GD, Tschoeke DA, Thompson FL, Thompson CC. Genome sequence of Vibrio fluvialis 362.3 isolated from coral Mussismilia braziliensis reveals genes related to marine environment adaptation. Arch Microbiol 2021; 203:3683-3686. [PMID: 33829291 DOI: 10.1007/s00203-021-02279-6] [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: 04/08/2020] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
Vibrio fluvialis is a halophilic bacterium frequently found in estuarine and coastal waters environments. The strain 362.3 was isolated from Mussismilia braziliensis coral of Abrolhos Bank. In this study, to gain insights into the marine adaptation in V. fluvialis, we sequenced the genome of 362.3 strain, which comprised 4,607,294 bp with a G + C content of 50.2%. In silico analysis showed that V. fluvialis 362.2 encodes genes related to chitin catabolic pathway, iron metabolism, osmotic stress and membrane transport.
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Affiliation(s)
- Livia M R Vidal
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Aline R P Gonçalves
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tainá M Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Biomedical Engineer Program - COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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12
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Vairagkar U, Nipanikar-Gokhale P, Mirza Y. Genomic insights into biocontrol potential of edible seaweed-associated Bacillus velezensis MTCC 10456 from Gulf of Mannar. Arch Microbiol 2021; 203:2941-2952. [PMID: 33770230 DOI: 10.1007/s00203-021-02244-3] [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: 05/03/2020] [Revised: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Bacillus velezensis MTCC 10456, is a marine mesophilic heterotrophic bacterium, isolated from edible red seaweed, Laurenciae papillosa, with a potential for plant growth promotion and biocontrol activity. We report the genome sequence analysis of strain MTCC 10456, which has a genome size of 4.19 Mb with an average G + C content of 45.9%, 4077 coding sequences and 94 RNAs. Comparative genome analysis of MTCC 10456 with 76 other land plant-based strains with complete information on the source of their isolation, was carried out. This study provided evidence that multiple gene clusters that contributed to the seaweed colonization, growth promotion, immunity and hyperosmotic stress tolerance are conserved in different B. velezensis strains. A unique methyltransferase gene that can cause global alterations in DNA methylation patterns affecting gene expression and regulation of transcription in MTCC 10456 genome was identified. The genome provides insights into multiple gene clusters encoding antagonistic metabolites, such as non-ribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs), unidentified metabolites and genes for antimicrobial resistance. Overall, findings from this study indicate the application of B. velezensis MTCC 10456 in the aquaculture industry as a biocontrol agent and may also contribute in understanding the ecological adaptations of plant-associated B. velezensis strains in different habitats.
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Affiliation(s)
- Uttara Vairagkar
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India.,Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Padmaja Nipanikar-Gokhale
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India
| | - Yasmin Mirza
- Praj-Matrix-R and D Centre (Division of Praj Industries Limited), 402/403/1098, Urawade, Pirangut, Mulshi, Pune, 412115, India.
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13
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Román-Ponce B, Millán-Aguiñaga N, Guillen-Matus D, Chase AB, Ginigini JGM, Soapi K, Feussner KD, Jensen PR, Trujillo ME. Six novel species of the obligate marine actinobacterium Salinispora, Salinispora cortesiana sp. nov., Salinispora fenicalii sp. nov., Salinispora goodfellowii sp. nov., Salinispora mooreana sp. nov., Salinispora oceanensis sp. nov. and Salinispora vitiensis sp. nov., and emended description of the genus Salinispora. Int J Syst Evol Microbiol 2020; 70:4668-4682. [PMID: 32701422 DOI: 10.1099/ijsem.0.004330] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus Salinispora and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized Salinispora species. Comparative genomic analyses resulted in the delineation of six new species based on average nucleotide identity and digital DNA-DNA hybridization values below 95 and 70 %, respectively. The species status of the six new groups was supported by a core-genome phylogeny reconstructed from 2106 orthologs detected in 118 publicly available Salinispora genomes. Chemotaxonomic and physiological studies were used to complete the phenotypic characterization of the strains. The fatty acid profiles contained the major components iso-C16 : 0, C15 : 0, iso-17 : 0 and anteiso C17 : 0. Galactose and xylose were common in all whole-sugar patterns but differences were found between the six groups of strains. Polar lipid compositions were also unique for each species. Distinguishable physiological and biochemical characteristics were also recorded. The names proposed are Salinispora cortesiana sp. nov., CNY-202T (=DSM 108615T=CECT 9739T); Salinispora fenicalii sp. nov., CNT-569T (=DSM 108614T=CECT 9740T); Salinispora goodfellowii sp. nov., CNY-666T (=DSM 108616T=CECT 9738T); Salinispora mooreana sp. nov., CNT-150T (=DSM 45549T=CECT 9741T); Salinispora oceanensis sp. nov., CNT-138T (=DSM 45547T=CECT 9742T); and Salinispora vitiensis sp. nov., CNT-148T (=DSM 45548T=CECT 9743T).
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Affiliation(s)
- Brenda Román-Ponce
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Natalie Millán-Aguiñaga
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Dulce Guillen-Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Joape G M Ginigini
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Katy Soapi
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Klaus D Feussner
- The University of South Pacific, Faculty of Science, Technology and Environment, Institute of Applied Sciences, Suva, Fiji
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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14
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Ocampo-Alvarez H, Meza-Canales ID, Mateos-Salmón C, Rios-Jara E, Rodríguez-Zaragoza FA, Robles-Murguía C, Muñoz-Urias A, Hernández-Herrera RM, Choix-Ley FJ, Becerril-Espinosa A. Diving Into Reef Ecosystems for Land-Agriculture Solutions: Coral Microbiota Can Alleviate Salt Stress During Germination and Photosynthesis in Terrestrial Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:648. [PMID: 32523601 PMCID: PMC7261865 DOI: 10.3389/fpls.2020.00648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
From their chemical nature to their ecological interactions, coral reef ecosystems have a lot in common with highly productive terrestrial ecosystems. While plants are responsible for primary production in the terrestrial sphere, the photosynthetic endosymbionts of corals are the key producers in reef communities. As in plants, coral microbiota have been suggested to stimulate the growth and physiological performance of the photosynthetic endosymbionts that provide energy sources to the coral. Among them, actinobacteria are some of the most probable candidates. To explore the potential of coral actinobacteria as plant biostimulants, we have analyzed the activity of Salinispora strains isolated from the corals Porites lobata and Porites panamensis, which were identified as Salinispora arenicola by 16S rRNA sequencing. We evaluated the effects of this microorganism on the germination, plant growth, and photosynthetic response of wild tobacco (Nicotiana attenuata) under a saline regime. We identified protective activity of this actinobacteria on seed germination and photosynthetic performance under natural light conditions. Further insights into the possible mechanism showed an endophytic-like symbiosis between N. attenuata roots and S. arenicola and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity by S. arenicola. We discuss these findings in the context of relevant ecological and physiological responses and biotechnological potential. Overall, our results will contribute to the development of novel biotechnologies to cope with plant growth under saline stress. Our study highlights the importance of understanding marine ecological interactions for the development of novel, strategic, and sustainable agricultural solutions.
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Affiliation(s)
- Héctor Ocampo-Alvarez
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Iván D. Meza-Canales
- Laboratorio de Evolución de Sistemas Ecológicos, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
- Laboratorio de Biología Molecular, Genómica y Proteómica, Instituto Transdisciplinar de Investigación y Servicios, Universidad de Guadalajara, Zapopan, Mexico
| | - Carolina Mateos-Salmón
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Eduardo Rios-Jara
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Fabián A. Rodríguez-Zaragoza
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Celia Robles-Murguía
- Laboratorio de Evolución de Sistemas Ecológicos, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Alejandro Muñoz-Urias
- Laboratorio de Evolución de Sistemas Ecológicos, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | - Rosalba Mireya Hernández-Herrera
- Laboratorio de Investigación en Biotecnología, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
| | | | - Amayaly Becerril-Espinosa
- CONACYT, Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Mexico
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15
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Contribution of mechanosensitive channels to osmoadaptation and ectoine excretion in Halomonas elongata. Extremophiles 2020; 24:421-432. [PMID: 32266565 PMCID: PMC7174268 DOI: 10.1007/s00792-020-01168-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/24/2020] [Indexed: 12/05/2022]
Abstract
For osmoadaptation the halophilic bacterium Halomonas elongata synthesizes as its main compatible solute the aspartate derivative ectoine. H. elongata does not rely entirely on synthesis but can accumulate ectoine by uptake from the surrounding environment with the help of the osmoregulated transporter TeaABC. Disruption of the TeaABC-mediated ectoine uptake creates a strain that is constantly losing ectoine to the medium. However, the efflux mechanism of ectoine in H. elongata is not yet understood. H. elongata possesses four genes encoding mechanosensitive channels all of which belong to the small conductance type (MscS). Analysis by qRT-PCR revealed a reduction in transcription of the mscS genes with increasing salinity. The response of H. elongata to hypo- and hyperosmotic shock never resulted in up-regulation but rather in down-regulation of mscS transcription. Deletion of all four mscS genes created a mutant that was unable to cope with hypoosmotic shock. However, the knockout mutant grew significantly faster than the wildtype at high salinity of 2 M NaCl, and most importantly, still exported 80% of the ectoine compared to the wildtype. We thus conclude that a yet unknown system, which is independent of mechanosensitive channels, is the major export route for ectoine in H. elongata.
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16
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Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW. Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. Front Microbiol 2019; 10:1713. [PMID: 31404169 PMCID: PMC6676996 DOI: 10.3389/fmicb.2019.01713] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 12/28/2022] Open
Abstract
The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.
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Affiliation(s)
| | | | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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17
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Sun W, Liu C, Zhang F, Zhao M, Li Z. Comparative Genomics Provides Insights Into the Marine Adaptation in Sponge-Derived Kocuriaflava S43. Front Microbiol 2018; 9:1257. [PMID: 29937765 PMCID: PMC6002675 DOI: 10.3389/fmicb.2018.01257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Sponge-derived actinomycetes represent a significant component of marine actinomycetes. Members of the genus Kocuria are distributed in various habitats such as soil, rhizosphere, clinical specimens, marine sediments, and sponges, however, to date, little is known about the mechanism of their environmental adaptation. Kocuria flava S43 was isolated from a coastal sponge. Phylogenetic analysis revealed that it was closely related to the terrestrial airborne K. flava HO-9041. In this study, to gain insights into the marine adaptation in K. flava S43 we sequenced the draft genome for K. flava S43 by third generation sequencing (TGS) and compared it with those of K. flava HO-9041 and some other Kocuria relatives. Comparative genomics and phylogenetic analyses revealed that K. flava S43 might adapt to the marine environment mainly by increasing the number of the genes linked to potassium homeostasis, resistance to heavy metals and phosphate metabolism, and acquiring the genes associated with electron transport and the genes encoding ATP-binding cassette (ABC) transporter, aquaporin, and thiol/disulfide interchange protein. Notably, gene acquisition was probably a primary mechanism of environmental adaptation in K. flava S43. Furthermore, this study also indicated that the Kocuria isolates from various marine and hyperosmotic environments possessed common genetic basis for environmental adaptation.
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Affiliation(s)
- Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changrong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingzhu Zhao
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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18
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Ahmed V, Verma MK, Gupta S, Mandhan V, Chauhan NS. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front Microbiol 2018; 9:159. [PMID: 29472909 PMCID: PMC5809485 DOI: 10.3389/fmicb.2018.00159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022] Open
Abstract
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
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Affiliation(s)
- Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Manoj K Verma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vibha Mandhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Nar S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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Genomic analyses of five Roseivirga species: Insights into marine adaptation. Mar Genomics 2018; 38:97-101. [PMID: 29306571 DOI: 10.1016/j.margen.2017.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/06/2017] [Accepted: 12/27/2017] [Indexed: 11/21/2022]
Abstract
To date, the genus Roseivirga consists of six species with one subspecies and is one of the least-studied genera among the family Flammeovirgaceae. In order to further explore this genus, the genome sequences of five Roseivirga spp. were compared and described in this study. The Roseivirga genomes have similar sizes in the range of 4.08-4.47Mb with an average of 4.22Mb. Several key proteins related to osmotic stress adaptation were identified in Roseivirga spp. including betaine transporter, choline dehydrogenase, and glutamate synthases. Significant amount of proteins associated with amino acid transport and metabolism were also present in Roseivirga genome. All five Roseivirga spp. were able to grow in medium contained casamino acids (mixture of amino acids) as sole carbon or nitrogen sources. Taken together, these findings suggested the potential role of Roseivirga in decomposing organic nitrogen matter in marine environment.
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20
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Taxonomic and Metabolite Diversity of Actinomycetes Associated with Three Australian Ascidians. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Dereplication of peptidic natural products through database search of mass spectra. Nat Chem Biol 2016; 13:30-37. [PMID: 27820803 PMCID: PMC5409158 DOI: 10.1038/nchembio.2219] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 08/17/2016] [Indexed: 11/08/2022]
Abstract
Peptidic Natural Products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. While recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers utilize dereplication strategies that identify known PNPs and lead to the discovery of new ones even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enabled high-throughput PNP identification and that is compatible with large-scale mass spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts.
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Talukdar M, Das D, Bora C, Bora TC, Deka Boruah HP, Singh AK. Complete genome sequencing and comparative analyses of broad-spectrum antimicrobial-producing Micromonospora sp. HK10. Gene 2016; 594:97-107. [PMID: 27609432 DOI: 10.1016/j.gene.2016.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023]
Abstract
Micromonospora genus produces >700 bioactive compounds of medical relevance. In spite of its ability to produce high number of bioactive compounds, no genome sequence is available with comprehensive secondary metabolite gene clusters analysis for anti-microbial producing Micromonospora strains. Thus, here we contribute the full genome sequence of Micromonospora sp. HK10 strain, which has high antibacterial activity against several important human pathogens like, Mycobacterium abscessus, Mycobacterium smegmatis, Bacillus subtillis, Staphylococcus aureus, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella and Escherichia coli. We have generated whole genome sequence data of Micromonospora sp. HK10 strain using Illumina NexSeq 500 sequencing platform (2×150bp paired end library) and assembled it de novo. The sequencing of HK10 genome enables identification of various genetic clusters associated with known- and probably unknown- antimicrobial compounds, which can pave the way for new antimicrobial scaffolds.
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Affiliation(s)
- Madhumita Talukdar
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Dhrubajyoti Das
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Chiranjeeta Bora
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Tarun Chandra Bora
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Hari Prasanna Deka Boruah
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Anil Kumar Singh
- Department of Biotechnology, CSIR-North East Institute of Science and Technology, Jorhat 785006, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India.
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Dann LM, Rosales S, McKerral J, Paterson JS, Smith RJ, Jeffries TC, Oliver RL, Mitchell JG. Marine and giant viruses as indicators of a marine microbial community in a riverine system. Microbiologyopen 2016; 5:1071-1084. [PMID: 27506856 PMCID: PMC5221468 DOI: 10.1002/mbo3.392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.
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Affiliation(s)
- Lisa M Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Stephanie Rosales
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Jody McKerral
- School of Computer Science, Engineering and Mathematics, Flinders University, Adelaide, Australia
| | - James S Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Renee J Smith
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Rod L Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia
| | - James G Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
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Undabarrena A, Beltrametti F, Claverías FP, González M, Moore ERB, Seeger M, Cámara B. Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile. Front Microbiol 2016; 7:1135. [PMID: 27486455 PMCID: PMC4949237 DOI: 10.3389/fmicb.2016.01135] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/07/2016] [Indexed: 11/13/2022] Open
Abstract
Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although, Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II (73%). Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | | | - Fernanda P. Claverías
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Myriam González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Edward R. B. Moore
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
| | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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25
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An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria. mSystems 2016; 1:mSystems00028-15. [PMID: 27822535 PMCID: PMC5069768 DOI: 10.1128/msystems.00028-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.
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26
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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]
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27
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Maansson M, Vynne NG, Klitgaard A, Nybo JL, Melchiorsen J, Nguyen DD, Sanchez LM, Ziemert N, Dorrestein PC, Andersen MR, Gram L. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria. mSystems 2016. [PMID: 27822535 DOI: 10.1128/msystems.00038-00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.
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Affiliation(s)
- Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaj G Vynne
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jane L Nybo
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jette Melchiorsen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Don D Nguyen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Laura M Sanchez
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany; Collaborative Mass Spectrometry Innovation Center, University of California at San Diego, La Jolla, California, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Pieter C Dorrestein
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA; Collaborative Mass Spectrometry Innovation Center, University of California at San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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28
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Gómez-Lunar Z, Hernández-González I, Rodríguez-Torres MD, Souza V, Olmedo-Álvarez G. Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation. Front Microbiol 2016; 7:58. [PMID: 26903955 PMCID: PMC4744853 DOI: 10.3389/fmicb.2016.00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/13/2016] [Indexed: 11/27/2022] Open
Abstract
Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that revealed that in addition to gene gain and loss, regulation adjustment of gene expression also has contributed to the intraspecific diversity of B. coahuilensis.
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Affiliation(s)
- Zulema Gómez-Lunar
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - Ismael Hernández-González
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - María-Dolores Rodríguez-Torres
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
| | - Valeria Souza
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México México City, Mexico
| | - Gabriela Olmedo-Álvarez
- Laboratorio de Biología Molecular y Ecología Microbiana, Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, Mexico
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Mehrshad M, Amoozegar MA, Ghai R, Shahzadeh Fazeli SA, Rodriguez-Valera F. Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea. Appl Environ Microbiol 2016; 82:1599-1612. [PMID: 26729711 PMCID: PMC4771326 DOI: 10.1128/aem.03381-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
We present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts of Actinobacteria and Alphaproteobacteria, while Gammaproteobacteria and Betaproteobacteria were present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes from Actinobacteria, Thaumarchaea, and Alphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of the Alphaproteobacteria) or freshwater (a member of the Actinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon " Candidatus Nitrosopelagicus" or the actinobacterium "Candidatus Actinomarina," were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.
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Affiliation(s)
- Maliheh Mehrshad
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Rohit Ghai
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Seyed Abolhassan Shahzadeh Fazeli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
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Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation. Antonie van Leeuwenhoek 2015; 108:1075-90. [DOI: 10.1007/s10482-015-0561-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/18/2015] [Indexed: 12/22/2022]
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31
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Salt Stress Induced Changes in the Exoproteome of the Halotolerant Bacterium Tistlia consotensis Deciphered by Proteogenomics. PLoS One 2015; 10:e0135065. [PMID: 26287734 PMCID: PMC4545795 DOI: 10.1371/journal.pone.0135065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
The ability of bacteria to adapt to external osmotic changes is fundamental for their survival. Halotolerant microorganisms, such as Tistlia consotensis, have to cope with continuous fluctuations in the salinity of their natural environments which require effective adaptation strategies against salt stress. Changes of extracellular protein profiles from Tistlia consotensis in conditions of low and high salinities were monitored by proteogenomics using a bacterial draft genome. At low salinity, we detected greater amounts of the HpnM protein which is involved in the biosynthesis of hopanoids. This may represent a novel, and previously unreported, strategy by halotolerant microorganisms to prevent the entry of water into the cell under conditions of low salinity. At high salinity, proteins associated with osmosensing, exclusion of Na+ and transport of compatible solutes, such as glycine betaine or proline are abundant. We also found that, probably in response to the high salt concentration, T. consotensis activated the synthesis of flagella and triggered a chemotactic response neither of which were observed at the salt concentration which is optimal for growth. Our study demonstrates that the exoproteome is an appropriate indicator of adaptive response of T. consotensis to changes in salinity because it allowed the identification of key proteins within its osmoadaptive mechanism that had not previously been detected in its cell proteome.
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Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738-51. [PMID: 25730728 PMCID: PMC4414829 DOI: 10.1039/c4np00167b] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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LC-MS-based metabolomics study of marine bacterial secondary metabolite and antibiotic production in Salinispora arenicola. Mar Drugs 2015; 13:249-66. [PMID: 25574739 PMCID: PMC4306935 DOI: 10.3390/md13010249] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023] Open
Abstract
An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A "chemical profile" link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time.
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34
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Booth IR, Miller S, Müller A, Lehtovirta-Morley L. The evolution of bacterial mechanosensitive channels. Cell Calcium 2014; 57:140-50. [PMID: 25591932 DOI: 10.1016/j.ceca.2014.12.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/17/2023]
Abstract
Mechanosensitive channels are ubiquitous and highly studied. However, the evolution of the bacterial channels remains enigmatic. It can be argued that mechanosensitivity might be a feature of all membrane proteins with some becoming progressively less sensitive to membrane tension over the course of evolution. Bacteria and archaea exhibit two main classes of channels, MscS and MscL. Present day channels suggest that the evolution of MscL may be highly constrained, whereas MscS has undergone elaboration via gene fusion (and potentially gene fission) events to generate a diversity of channel structures. Some of these channel variants are constrained to a small number of genera or species. Some are only found in higher organisms. Only exceptionally have these diverse channels been investigated in any detail. In this review we consider both the processes that might have led to the evolved complexity but also some of the methods exploiting the explosion of genome sequences to understand (and/or track) their distribution. The role of MscS-related channels in calcium-mediated cell biology events is considered.
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Affiliation(s)
- Ian R Booth
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
| | - Samantha Miller
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Axel Müller
- Division of Chemistry and Chemical Engineering, Broad Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
| | - Laura Lehtovirta-Morley
- Institute of Biological and Environmental Sciences, Cruikshank Building, University of Aberdeen, St Machar Drive, Aberdeen AB24 3UU, UK.
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Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style? PLoS One 2014; 9:e108522. [PMID: 25268993 PMCID: PMC4182475 DOI: 10.1371/journal.pone.0108522] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 12/03/2022] Open
Abstract
Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.
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Affiliation(s)
- Martha E. Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - Rodrigo Bacigalupe
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Petar Pujic
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, Kurokawa, Imizu, Toyama, Japan
| | - Patricia Benito
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Claudine Médigue
- Genoscope, CNRS-UMR 8030, Atelier de Génomique Comparative, Evry, France
| | - Philippe Normand
- Université Lyon 1, Université de Lyon, CNRS-UMR5557 Ecologie Microbienne, Villeurbanne, France
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Overy DP, Bayman P, Kerr RG, Bills GF. An assessment of natural product discovery from marine ( sensu strictu) and marine-derived fungi. Mycology 2014; 5:145-167. [PMID: 25379338 PMCID: PMC4205923 DOI: 10.1080/21501203.2014.931308] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/30/2014] [Indexed: 11/21/2022] Open
Abstract
The natural products community has been investigating secondary metabolites from marine fungi for several decades, but when one attempts to search for validated reports of new natural products from marine fungi, one encounters a literature saturated with reports from ‘marine-derived’ fungi. Of the 1000+ metabolites that have been characterized to date, only approximately 80 of these have been isolated from species from exclusively marine lineages. These metabolites are summarized here along with the lifestyle and habitats of their producing organisms. Furthermore, we address some of the reasons for the apparent disconnect between the stated objectives of discovering new chemistry from marine organisms and the apparent neglect of the truly exceptional obligate marine fungi. We also offer suggestions on how to reinvigorate enthusiasm for marine natural products discovery from fungi from exclusive marine lineages and highlight the need for critically assessing the role of apparently terrestrial fungi in the marine environment.
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Affiliation(s)
- David P Overy
- Department of Chemistry, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Nautilus Biosciences Canada, Duffy Research Center, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3
| | - Paul Bayman
- Department of Biology, University of Puerto Rico-Río Piedras , P. O. Box 23360, San Juan 00931 , Puerto Rico
| | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Nautilus Biosciences Canada, Duffy Research Center, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center , 1881 East Rd., Houston , TX 77054 , USA
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Ian E, Malko DB, Sekurova ON, Bredholt H, Rückert C, Borisova ME, Albersmeier A, Kalinowski J, Gelfand MS, Zotchev SB. Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: insights into marine adaptation and secondary metabolite biosynthesis potential. PLoS One 2014; 9:e96719. [PMID: 24819608 PMCID: PMC4018334 DOI: 10.1371/journal.pone.0096719] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/10/2014] [Indexed: 11/23/2022] Open
Abstract
A total of 74 actinomycete isolates were cultivated from two marine sponges, Geodia barretti and Phakellia ventilabrum collected at the same spot at the bottom of the Trondheim fjord (Norway). Phylogenetic analyses of sponge-associated actinomycetes based on the 16S rRNA gene sequences demonstrated the presence of species belonging to the genera Streptomyces, Nocardiopsis, Rhodococcus, Pseudonocardia and Micromonospora. Most isolates required sea water for growth, suggesting them being adapted to the marine environment. Phylogenetic analysis of Streptomyces spp. revealed two isolates that originated from different sponges and had 99.7% identity in their 16S rRNA gene sequences, indicating that they represent very closely related strains. Sequencing, annotation, and analyses of the genomes of these Streptomyces isolates demonstrated that they are sister organisms closely related to terrestrial Streptomyces albus J1074. Unlike S. albus J1074, the two sponge streptomycetes grew and differentiated faster on the medium containing sea water. Comparative genomics revealed several genes presumably responsible for partial marine adaptation of these isolates. Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor, or acquired from other actinomycetes. Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts.
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Affiliation(s)
- Elena Ian
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dmitry B. Malko
- N.I. Vavilov Institute of General Genetics, Department of Computational Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga N. Sekurova
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Harald Bredholt
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Rückert
- Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany
| | - Marina E. Borisova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Andreas Albersmeier
- Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Institut fuer Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universitaet Bielefeld, Bielefeld, Germany
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - Sergey B. Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
- * E-mail:
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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Ng YK, Hodson MP, Hewavitharana AK, Bose U, Shaw PN, Fuerst JA. Effects of salinity on antibiotic production in sponge-derived Salinispora actinobacteria. J Appl Microbiol 2014; 117:109-25. [PMID: 24684523 DOI: 10.1111/jam.12507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/02/2014] [Accepted: 03/14/2014] [Indexed: 11/28/2022]
Abstract
AIMS To investigate the effects of growth conditions related to marine habitat on antibiotic production in sponge-derived Salinispora actinobacteria. METHODS AND RESULTS Media with varying salt concentration were used to investigate the effects of salinity in relation to Salinispora growth and rifamycin production. The chemotypic profiles of the model strain Salinispora arenicola M413 was then assessed using metabolomic fingerprints from high-pressure liquid chromatography with diode array detection (HPLC-DAD) and multivariate data analysis, before extending this approach to two other strains of S. arenicola. Fingerprint data were generated from extracts of S. arenicola broth cultures grown in media of varying salt (NaCl) concentrations. These fingerprints were then compared using multivariate analysis methods such as principal components analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA). From the analysis, a low-sodium growth condition (1% NaCl) was found to delay the onset of growth of the model S. arenicola M413 strain when compared to growth in media with either 3% artificial sea salt or 3% NaCl. However, low-sodium growth conditions also increased cell mass yield and contributed to at least a significant twofold increase in rifamycin yield when compared to growth in 3% artificial sea salt and 3% NaCl. CONCLUSIONS The integration of HPLC-DAD and multivariate analysis proved to be an effective method of assessing chemotypic variations in Salinispora grown in different salt conditions, with clear differences between strain-related chemotypes apparent due to varying salt concentrations. SIGNIFICANCE AND IMPACT OF THE STUDY The observed variation in S. arenicola chemotypic profiles further suggests diversity in secondary metabolites in this actinomycete in response to changes in the salinity of its environment.
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Affiliation(s)
- Y K Ng
- School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
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Booth IR. Bacterial mechanosensitive channels: progress towards an understanding of their roles in cell physiology. Curr Opin Microbiol 2014; 18:16-22. [PMID: 24607989 PMCID: PMC4005912 DOI: 10.1016/j.mib.2014.01.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 12/24/2022]
Abstract
Multiple mechanosensitive channels are found in most bacteria and archaea. Channels are required to prevent loss of structural integrity during transitions from high to low osmolarity. Channel diversity feeds into the detailed response of cells to hypo-osmotic stress. There is growing evidence that organisms have evolved MS channels that reflect their niche. Structural diversity may reflect roles additional to the observed function of protection of structural integrity.
Bacterial mechanosensitive channels sense the changes in lateral tension in the bilayer of the cytoplasmic membrane generated by rapid water flow into the cell. Two major structural families are found widely distributed across bacteria and archaea: MscL and MscS. Our understanding of the mechanisms of gating has advanced rapidly through genetic analysis, structural biology and electrophysiology. It is only recently that the analysis of the physiological roles of the channels has kept pace with mechanistic studies. Recent advances have increased our understanding of the role of the channels in preventing structural perturbation during osmotic transitions and its relationship to water flow across the membrane. It is to these recent developments that this review is dedicated.
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Affiliation(s)
- Ian R Booth
- School of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom; Visiting Associate in Chemistry, California Institute of Technology, Pasadena, CA 91125, United States.
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Flowers JJ, He S, Malfatti S, del Rio TG, Tringe SG, Hugenholtz P, McMahon KD. Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME JOURNAL 2013; 7:2301-14. [PMID: 23887171 DOI: 10.1038/ismej.2013.117] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/14/2013] [Accepted: 06/11/2013] [Indexed: 11/09/2022]
Abstract
Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80-90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.
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Affiliation(s)
- Jason J Flowers
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin at Madison, Madison, WI, USA
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Lin Z, Torres JP, Ammon MA, Marett L, Teichert RW, Reilly CA, Kwan JC, Hughen RW, Flores M, Tianero MD, Peraud O, Cox JE, Light AR, Villaraza AJL, Haygood MG, Concepcion GP, Olivera BM, Schmidt EW. A bacterial source for mollusk pyrone polyketides. ACTA ACUST UNITED AC 2013; 20:73-81. [PMID: 23352141 DOI: 10.1016/j.chembiol.2012.10.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/11/2012] [Accepted: 10/24/2012] [Indexed: 12/29/2022]
Abstract
In the oceans, secondary metabolites often protect otherwise poorly defended invertebrates, such as shell-less mollusks, from predation. The origins of these metabolites are largely unknown, but many of them are thought to be made by symbiotic bacteria. In contrast, mollusks with thick shells and toxic venoms are thought to lack these secondary metabolites because of reduced defensive needs. Here, we show that heavily defended cone snails also occasionally contain abundant secondary metabolites, γ-pyrones known as nocapyrones, which are synthesized by symbiotic bacteria. The bacteria, Nocardiopsis alba CR167, are related to widespread actinomycetes that we propose to be casual symbionts of invertebrates on land and in the sea. The natural roles of nocapyrones are unknown, but they are active in neurological assays, revealing that mollusks with external shells are an overlooked source of secondary metabolite diversity.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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Genetic complementation of the obligate marine actinobacterium Salinispora tropica with the large mechanosensitive channel gene mscL rescues cells from osmotic downshock. Appl Environ Microbiol 2012; 78:4175-82. [PMID: 22492446 DOI: 10.1128/aem.00577-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine actinomycetes in the genus Salinispora fail to grow when seawater is replaced with deionized (DI) water in complex growth media. While bioinformatic analyses have led to the identification of a number of candidate marine adaptation genes, there is currently no experimental evidence to support the genetic basis for the osmotic requirements associated with this taxon. One hypothesis is that the lineage-specific loss of mscL is responsible for the failure of strains to grow in media prepared with DI water. The mscL gene encodes a conserved transmembrane protein that reduces turgor pressure under conditions of acute osmotic downshock. In the present study, the mscL gene from a Micromonospora strain capable of growth on media prepared with DI water was transformed into S. tropica strain CNB-440. The single-copy, chromosomal genetic complementation yielded a recombinant Salinispora mscL(+) strain that demonstrated an increased capacity to survive osmotic downshock. The enhanced survival of the S. tropica transformant provides experimental evidence that the loss of mscL is associated with the failure of Salinispora spp. to grow in low-osmotic-strength media.
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