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Ethica SN, Zilda DS, Oedjijono O, Muhtadi M, Patantis G, Darmawati S, Dewi SS, Sabdono A, Uria AR. Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp. J Genet Eng Biotechnol 2023; 21:18. [PMID: 36786886 PMCID: PMC9928984 DOI: 10.1186/s43141-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Marine bacteria have recently attracted increasing attention to be harnessed for the production of valuable enzymes, vitamins, and bioactive compounds. Bacteria associated with the surfaces of marine macroalgae, called epibionts, are particularly interesting from ecological and biotechnological points of view, as they often exhibit antimicrobial activities to compete with pathogenic bacteria for nutrients and spaces. In search for biotechnologically potential genes from marine bacteria, we sequenced and analysed the genome of the epibiont HI03-3b, a polysaccharide-degrading bacterium associated with the surface of the Indonesian brown algae Hydroclathrus sp. RESULTS The algal epibiont HI03-3b has a genome of approximately 4,860,704 bp in size with 42.02 mol% G + C content, consisting of 5655 open reading frames (ORFs), 4409 genes coding for proteins (CDSs), 94 genes for tRNAs, and 32 genes for rRNAs. The genome sequence of HI03-3b was most closely related to that of Cytobacillus firmus NCTC10335 with the average amino acid identity (AAI) of 95.0 %, average nucleotide identity (ANI) of 94.1 %, and a recommended DNA-DNA hybridization (DDH) of 57.60 %. These scores are lower than the most frequently used standard for species demarcation (95% ANI cutoff) and the new species threshold (DDH > 70.0% for the same bacterial species). Some differences in genome features and gene composition were observed between HI03-3b and NCTC10335, such as genes encoding carbohydrate active enzymes. These suggest that HI03-3b is unique and likely a novel species within Cytobacillus genus, and we therefore proposed its name as Cytobacillus wakatobiense HI03-3b. Genome sequence analyses indicated the presence of genes involved not only in polysaccharide and protein degradation but also in vitamin and secondary metabolite biosynthesis. Some of them encode enzymes and compounds with biotechnological interest, such as protease, chitinase, subtilisin, pullulanase, and bacillolysin, which are often associated with antimicrobial or antibiofilm activities. This antimicrobial potential is supported by our finding that the extracellular protein fraction of this epibiont inhibited the growth of the bacterial pathogen Staphylococcus aureus. CONCLUSION The epibiont Cytobacillus HI03-3b harbours genes for polysaccharide and protein degradation as well as for natural product biosynthesis, suggesting its potential ecological roles in outcompeting other bacteria during biofilm formation as well as in protecting its algal host from predation. Due to the presence of genes for vitamin biosynthesis, it might also provide the algal host with vitamins for growth and development. Some of these metabolic genes are biotechnologically important, as they could become a platform for bioengineering to generate various seaweed-derived substances sustainably, such as antibiofilm agents and vitamins, which are beneficial for human health.
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Affiliation(s)
- Stalis Norma Ethica
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Dewi Seswita Zilda
- Research Center for Deep Sea, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Jl. Pasir Putih Raya, Pademangan, North Jakarta City, Jakarta 14430 Indonesia
| | - Oedjijono Oedjijono
- grid.444191.d0000 0000 9134 0078Faculty of Biology, Universitas Jenderal Soedirman, Purwokerto, 53122 Indonesia
| | - Muhtadi Muhtadi
- grid.444490.90000 0000 8731 0765Faculty of Pharmacy, Universitas Muhammadiyah Surakarta (UMS), Sukoharjo, 57162 Indonesia
| | - Gintung Patantis
- Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Kodek Bay, North Lombok, West Nusa Tenggara 83352 Indonesia
| | - Sri Darmawati
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Sri Sinto Dewi
- grid.444265.50000 0004 0386 6520Diploma Study Program of Medical Laboratory Technology, Faculty of Nursing and Health Sciences, Universitas Muhammadiyah Semarang, Semarang, 50273 Indonesia
| | - Agus Sabdono
- grid.412032.60000 0001 0744 0787Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, 50272 Indonesia
| | - Agustinus Robert Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6 Kita-ku, Sapporo, 060-0812, Japan. .,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita 12 Nishi 6, Sapporo, 060-0812, Japan.
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Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations. mSystems 2022; 7:e0147721. [PMID: 35695431 PMCID: PMC9239043 DOI: 10.1128/msystems.01477-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Some marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.” IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.
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Choi E, Huh A, Oh C, Oh JI, Kang HY, Hwang J. Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642. J Microbiol 2022; 60:192-206. [PMID: 35102526 DOI: 10.1007/s12275-022-1619-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 01/02/2023]
Abstract
Toxin-antitoxin (TA) systems are growth-controlling genetic elements consisting of an intracellular toxin protein and its cognate antitoxin. TA systems have been spread among microbial genomes through horizontal gene transfer and are now prevalent in most bacterial and archaeal genomes. Under normal growth conditions, antitoxins tightly counteract the activity of the toxins. Upon stresses, antitoxins are inactivated, releasing activated toxins, which induce growth arrest or cell death. In this study, among nine functional TA modules in Bosea sp. PAMC 26642 living in Arctic lichen, we investigated the functionality of BoHigBA2. BohigBA2 is located close to a genomic island and adjacent to flagellar gene clusters. The expression of BohigB2 induced the inhibition of E. coli growth at 37°C, which was more manifest at 18°C, and this growth defect was reversed when BohigA2 was co-expressed, suggesting that this BoHigBA2 module might be an active TA module in Bosea sp. PAMC 26642. Live/dead staining and viable count analyses revealed that the BoHigB2 toxin had a bactericidal effect, causing cell death. Furthermore, we demonstrated that BoHigB2 possessed mRNA-specific ribonuclease activity on various mRNAs and cleaved only mRNAs being translated, which might impede overall translation and consequently lead to cell death. Our study provides the insight to understand the cold adaptation of Bosea sp. PAMC 26642 living in the Arctic.
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Affiliation(s)
- Eunsil Choi
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Ahhyun Huh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Changmin Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Ho Young Kang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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Sjöqvist C, Delgado LF, Alneberg J, Andersson AF. Ecologically coherent population structure of uncultivated bacterioplankton. THE ISME JOURNAL 2021; 15:3034-3049. [PMID: 33953362 PMCID: PMC8443644 DOI: 10.1038/s41396-021-00985-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.
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Affiliation(s)
- Conny Sjöqvist
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden ,grid.13797.3b0000 0001 2235 8415Åbo Akademi University, Faculty of Science and Engineering, Environmental and Marine Biology, Åbo, Finland
| | - Luis Fernando Delgado
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Johannes Alneberg
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Anders F. Andersson
- grid.5037.10000000121581746KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
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Parizad S, Bera S. The effect of organic farming on water reusability, sustainable ecosystem, and food toxicity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021:10.1007/s11356-021-15258-7. [PMID: 34235694 DOI: 10.1007/s11356-021-15258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/28/2021] [Indexed: 05/12/2023]
Abstract
Water is a fundamental necessity for people's well-being and the ecosystem's sustainability; however, its toxicity due to agrochemicals usage for food production leads to the deterioration of water quality. The poor water quality diminishes its reusability, thus limiting efficient water usage. Organic farming is one of the best ways that does not only reduce the deterioration of water quality but also decrease food toxicity. In organic farming, the crop is grown with no/less chemical usage. Besides, organic farming maintains biodiversity and reduces the anthropogenic footprint on soil, air, water, wildlife, and especially on the farming communities. Fields that are organically managed continuously for years have fewer pest populations and were attributed to increased biodiversity and abundance of multi-trophic interactions as well as to changes in plant metabolites. Fewer insect pests (pathogen vectors), in turn, would result in fewer crop diseases and increase crop production. This review highlights that organic farming may play a critical role in the reduction of pests and pathogens, which eventually would reduce the need for chemical reagents to protect crops, improving yield quality and water reusability.
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Affiliation(s)
- Shirin Parizad
- Department of Research and Development (Plant Probiotics), Nature Biotechnology Company (Biorun), Karaj, Iran.
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E. Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol 2019; 10:2916. [PMID: 31956321 PMCID: PMC6951406 DOI: 10.3389/fmicb.2019.02916] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.
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Affiliation(s)
- Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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Smyrli M, Triga A, Dourala N, Varvarigos P, Pavlidis M, Quoc VH, Katharios P. Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea. Microorganisms 2019; 7:microorganisms7110504. [PMID: 31671797 PMCID: PMC6921072 DOI: 10.3390/microorganisms7110504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.
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Affiliation(s)
- Maria Smyrli
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nancy Dourala
- Fish Pathology Department, Selonda Aquaculture, 15125 Athens, Greece.
| | | | - Michael Pavlidis
- Department of Biology, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500 Crete, Greece.
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Abstract
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations. Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.
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Ramos-Barbero MD, Martin-Cuadrado AB, Viver T, Santos F, Martinez-Garcia M, Antón J. Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly. Syst Appl Microbiol 2018; 42:30-40. [PMID: 30528276 DOI: 10.1016/j.syapm.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
Abstract
Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the "great metagenomics anomaly" and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.
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Affiliation(s)
| | - Ana-B Martin-Cuadrado
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain; Multidisciplinary Institute of Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain.
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Sharma V, Mobeen F, Prakash T. Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. Genes (Basel) 2018; 9:genes9100477. [PMID: 30275399 PMCID: PMC6210967 DOI: 10.3390/genes9100477] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 09/10/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005, India.
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González-Torres P, Gabaldón T. Genome Variation in the Model Halophilic Bacterium Salinibacter ruber. Front Microbiol 2018; 9:1499. [PMID: 30072959 PMCID: PMC6060240 DOI: 10.3389/fmicb.2018.01499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023] Open
Abstract
The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate “Neutral” and “Constant Diversity” models of bacterial evolution.
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Affiliation(s)
- Pedro González-Torres
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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12
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Kazou M, Alexandraki V, Blom J, Pot B, Tsakalidou E, Papadimitriou K. Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. Front Microbiol 2018; 9:1244. [PMID: 29942291 PMCID: PMC6004923 DOI: 10.3389/fmicb.2018.01244] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/23/2018] [Indexed: 02/05/2023] Open
Abstract
Lactobacillus acidipiscis belongs to the Lactobacillus salivarius clade and it is found in a variety of fermented foods. Strain ACA-DC 1533 was isolated from traditional Greek Kopanisti cheese and among the available L. acidipiscis genomes it is the only one with a fully sequenced chromosome. L. acidipiscis strains exhibited a high degree of conservation at the genome level. Investigation of the distribution of prophages and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) among the three strains suggests the potential existence of lineages within the species. Based on the presence/absence patterns of these genomic traits, strain ACA-DC 1533 seems to be more related to strain JCM 10692T than strain KCTC 13900. Interestingly, strains ACA-DC 1533 and JCM 10692T which lack CRISPRs, carry two similar prophages. In contrast, strain KCTC 13900 seems to have acquired immunity to these prophages according to the sequences of spacers in its CRISPRs. Nonetheless, strain KCTC 13900 has a prophage that is absent from strains ACA-DC 1533 and JCM 10692T. Furthermore, comparative genomic analysis was performed among L. acidipiscis ACA-DC 1533, L. salivarius UCC118 and Lactobacillus ruminis ATCC 27782. The chromosomes of the three species lack long-range synteny. Important differences were also determined in the number of glycobiome related proteins, proteolytic enzymes, transporters, insertion sequences and regulatory proteins. Moreover, no obvious genomic traits supporting a probiotic potential of L. acidipiscis ACA-DC 1533 were detected when compared to the probiotic L. salivarius UCC118. However, the existence of more than one glycine-betaine transporter within the genome of ACA-DC 1533 may explain the ability of L. acidipiscis to grow in fermented foods containing high salt concentrations. Finally, in silico analysis of the L. acidipiscis ACA-DC 1533 genome revealed pathways that could underpin the production of major volatile compounds during the catabolism of amino acids that may contribute to the typical piquant flavors of Kopanisti cheese.
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Affiliation(s)
- Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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13
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Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 2018; 6:e4320. [PMID: 29423345 PMCID: PMC5804319 DOI: 10.7717/peerj.4320] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/13/2018] [Indexed: 12/13/2022] Open
Abstract
Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.
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Affiliation(s)
- Tom O. Delmont
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
| | - A. Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, United States of America
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, United States of America
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14
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Torregrosa-Crespo J, González-Torres P, Bautista V, Esclapez JM, Pire C, Camacho M, Bonete MJ, Richardson DJ, Watmough NJ, Martínez-Espinosa RM. Analysis of multiple haloarchaeal genomes suggests that the quinone-dependent respiratory nitric oxide reductase is an important source of nitrous oxide in hypersaline environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:788-796. [PMID: 28925557 DOI: 10.1111/1758-2229.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. While the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors). The study revealed that the only nor gene found in haloarchaea is one that encodes a single subunit quinone dependent Nor homologous to the qNor found in bacteria. This surprising discovery is considered in terms of our emerging understanding of haloarchaeal bioenergetics and NO management.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Pedro González-Torres
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88. 08003 Barcelona, Spain
| | - Vanesa Bautista
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Julia M Esclapez
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Mónica Camacho
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - María José Bonete
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - David J Richardson
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Rosa María Martínez-Espinosa
- Department of Agrochemistry and Biochemistry. Faculty of Science, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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15
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Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki ME, Speich S, Stemmann L, Pedrós-Alió C, Acinas SG. Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Front Microbiol 2017; 8:1317. [PMID: 28790980 PMCID: PMC5525439 DOI: 10.3389/fmicb.2017.01317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 12/03/2022] Open
Abstract
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.
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Affiliation(s)
- Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - José M González
- Department of Microbiology, University of La LagunaLa Laguna, Spain
| | | | - Sabrina Speich
- École Normale Supérieure, Département de Géosciences, Laboratoire de Météorologie Dynamique, UMR 8539 ENS-CNRS- École PolytechniqueParis, France
| | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV) UMR7093, Observatoire OcéanologiqueVillefranche-sur-Mer, France
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Genética i de Microbiologia, Facultat de Biociències, Universitat Autònoma de BarcelonaBellaterra, Spain
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16
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Vannier T, Leconte J, Seeleuthner Y, Mondy S, Pelletier E, Aury JM, de Vargas C, Sieracki M, Iudicone D, Vaulot D, Wincker P, Jaillon O. Survey of the green picoalga Bathycoccus genomes in the global ocean. Sci Rep 2016; 6:37900. [PMID: 27901108 PMCID: PMC5128809 DOI: 10.1038/srep37900] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/03/2016] [Indexed: 01/23/2023] Open
Abstract
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.
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Affiliation(s)
- Thomas Vannier
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Jade Leconte
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Yoann Seeleuthner
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Samuel Mondy
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Eric Pelletier
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Jean-Marc Aury
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michael Sieracki
- National Science Foundation, 4201 Wilson Blvd., Arlington, VA 22230, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Daniel Vaulot
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Olivier Jaillon
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.,CNRS, UMR 8030, CP5706 Evry, France.,Université d'Evry, UMR 8030, CP5706 Evry, France
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17
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Fadeev E, De Pascale F, Vezzi A, Hübner S, Aharonovich D, Sher D. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island. Front Microbiol 2016; 7:248. [PMID: 27014193 PMCID: PMC4781885 DOI: 10.3389/fmicb.2016.00248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/15/2016] [Indexed: 12/20/2022] Open
Abstract
Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de novo methods. In general, the de novo assemblies clearly outperformed the reference-based or hybrid ones, covering >99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (∼4.5 Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to A. macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island (fGI), containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire fGI suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon.
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Affiliation(s)
- Eduard Fadeev
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Fabio De Pascale
- Department of Biology and CRIBI Biotechnology Centre, University of Padua Padova, Italy
| | - Alessandro Vezzi
- Department of Biology and CRIBI Biotechnology Centre, University of Padua Padova, Italy
| | - Sariel Hübner
- Department of Botany and Biodiversity Research Centre, University of British ColumbiaVancouver, Canada; The Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
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18
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Dias L, Caetano T, Pinheiro M, Mendo S. The lanthipeptides of Bacillus methylotrophicus and their association with genomic islands. Syst Appl Microbiol 2015; 38:525-33. [PMID: 26559891 DOI: 10.1016/j.syapm.2015.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/25/2022]
Abstract
Bacillus methylotrophicus strains are known for their potential as plant-growth promoters and as microbial pesticides that effectively control plant diseases caused by bacteria and fungi. Over the past few years, a wide diversity of their secondary metabolites has been extensively characterized. Among these are the RiPPs lanthipeptides, which are an important and growing group of notable compounds. The increasing interest in B. methylotrophicus species, accompanied by the development of high throughput sequencing techniques, has resulted in a substantial number of full genomes being available. Here, an in silico analysis was performed on these genomes in order to survey the presence of lanthipeptide biosynthetic clusters. It was found that the pan genome of B. methylotrophicus only encoded the biosynthesis of mersacidin and amylolysin, which are lanthipeptides with antibacterial activity. However, the amylolysin gene cluster identified was comprised of more genetic elements than those previously described, and it had certain features of two-peptide lantibiotics. Additionally, it was also established that the association of lanthipeptides with genomic islands (GIs) was not confined to mersacidin. This was also found for the amylolysin cluster as well as other class I and class II lanthipeptides, supporting the idea that their production is probably related to functional adaptation.
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Affiliation(s)
- L Dias
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - T Caetano
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Pinheiro
- School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom
| | - S Mendo
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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19
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Bentkowski P, Van Oosterhout C, Mock T. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments. Genome Biol Evol 2015; 7:2344-51. [PMID: 26242601 PMCID: PMC4558865 DOI: 10.1093/gbe/evv148] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt.
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Affiliation(s)
- Piotr Bentkowski
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom Present address: Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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20
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Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil. Microbiology (Reading) 2015; 161:1018-1033. [DOI: 10.1099/mic.0.000068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2015] [Indexed: 12/28/2022] Open
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21
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Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark. Curr Opin Microbiol 2015; 25:33-9. [PMID: 25863027 DOI: 10.1016/j.mib.2015.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/07/2015] [Accepted: 03/16/2015] [Indexed: 11/24/2022]
Abstract
Prokaryotes are extremely abundant in the ocean where they drive biogeochemical cycles. The recent development and application of -omics techniques has provided an astonishing amount of information revealing the existence of a vast diversity of functional genes and a large heterogeneity within each gene. The big challenge for microbial ecologists is now to understand the ecological relevance of this variability for ecosystem functioning, a question that remains largely understudied. This brief review highlights some of the latest advances in the study of the diversity of biogeochemically relevant functional genes in the sunlit ocean.
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22
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Crowley SP, O'Gara F, O'Sullivan O, Cotter PD, Dobson ADW. Marine Pseudovibrio sp. as a novel source of antimicrobials. Mar Drugs 2014; 12:5916-29. [PMID: 25501794 PMCID: PMC4278209 DOI: 10.3390/md12125916] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance among pathogenic microorganisms is becoming ever more common. Unfortunately, the development of new antibiotics which may combat resistance has decreased. Recently, however the oceans and the marine animals that reside there have received increased attention as a potential source for natural product discovery. Many marine eukaryotes interact and form close associations with microorganisms that inhabit their surfaces, many of which can inhibit the attachment, growth or survival of competitor species. It is the bioactive compounds responsible for the inhibition that is of interest to researchers on the hunt for novel bioactives. The genus Pseudovibrio has been repeatedly identified from the bacterial communities isolated from marine surfaces. In addition, antimicrobial activity assays have demonstrated significant antimicrobial producing capabilities throughout the genus. This review will describe the potency, spectrum and possible novelty of the compounds produced by these bacteria, while highlighting the capacity for this genus to produce natural antimicrobial compounds which could be employed to control undesirable bacteria in the healthcare and food production sectors.
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Affiliation(s)
- Susan P Crowley
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Fergal O'Gara
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Paul D Cotter
- Teagasc, Moorepark Food Research Centre, Fermoy Co. Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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23
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Mounier J, Camus A, Mitteau I, Vaysse PJ, Goulas P, Grimaud R, Sivadon P. The marine bacteriumMarinobacter hydrocarbonoclasticusSP17 degrades a wide range of lipids and hydrocarbons through the formation of oleolytic biofilms with distinct gene expression profiles. FEMS Microbiol Ecol 2014; 90:816-31. [DOI: 10.1111/1574-6941.12439] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/05/2014] [Accepted: 10/06/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Julie Mounier
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Arantxa Camus
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Isabelle Mitteau
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Pierre-Joseph Vaysse
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Philippe Goulas
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Régis Grimaud
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
| | - Pierre Sivadon
- UMR UPPA-CNRS 5254 IPREM; Université de Pau et des Pays de l'Adour, Equipe Environnement et Microbiologie; Pau Cedex France
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24
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Xie J, Zhou F, Xu G, Mai G, Hu J, Wang G, Li F. Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization. Mol Biol Rep 2014; 41:5883-9. [PMID: 25108673 DOI: 10.1007/s11033-014-3463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 06/13/2014] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis) is one of the most widely spread human pathogenic bacteria, and it frequently exchanges pathogenesis genes among its strains or with other pathogenic microbes. The purpose of this study was to screen the pathogenicity islands (PAIs) in M. tuberculosis using the genomic barcode visualization technique and to characterize the functions of the detected PAIs. By visually screening the barcode image of the M. tuberculosis chromosomes, three candidate PAIs were detected as MPI-1, MPI-2 and MPI-3, among which MPI-2 and MPI-3 were known to harbor pathogenesis genes, and MPI-1 represents a novel candidate. Based on the functional annotations of Pfam domains and GO categories, both MPI-2 and MPI-3 carry genes encoding PE/PPE family proteins, MPI-2 encodes the type VII secretion system, and MPI-3 encodes genes for mycolic acid synthesis in the cell wall. Some of these genes were already widely used in early diagnosis or treatment of M. tuberculosis. The novel candidate PAI MPI-1 encodes CRISPR-C as family proteins, which are known to be associated with persistent infection of M. tuberculosis. Our data represents a molecular basis and protocol for comprehensive annotating the pathogenic systems of M. tuberculosis, and will also facilitate the development of diagnosis and vaccination techniques of M. tuberculosis.
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Affiliation(s)
- Jiao Xie
- Norman Bethune Medical College of Jilin University, Changchun, 130021, Jilin, China
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25
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Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One 2013; 8:e78237. [PMID: 24250794 PMCID: PMC3826726 DOI: 10.1371/journal.pone.0078237] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. PRINCIPAL FINDINGS Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. SIGNIFICANCE For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.
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Affiliation(s)
- Lillian G. Acuña
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Juan Pablo Cárdenas
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Paulo C. Covarrubias
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | | | | | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingenieria, Universidad de Talca, Talca, Chile
| | | | - Jorge Valdés
- Center for Systems Biotechnology, Fraunhofer Chile, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Douglas E. Rawlings
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - David S. Holmes
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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26
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Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME JOURNAL 2013; 7:1026-37. [PMID: 23303374 DOI: 10.1038/ismej.2012.169] [Citation(s) in RCA: 408] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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27
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Affiliation(s)
- Ramon Massana
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar (CSIC); Barcelona; Catalonia; Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar (CSIC); Barcelona; Catalonia; Spain
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