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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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2
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Odelgard A, Hägglund E, Guy L, Andersson SGE. Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota. Genome Biol Evol 2024; 16:evae068. [PMID: 38547507 PMCID: PMC11032199 DOI: 10.1093/gbe/evae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/22/2024] Open
Abstract
The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
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Affiliation(s)
- Anna Odelgard
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emil Hägglund
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Rekadwad BN, Shouche YS, Jangid K. Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis. Arch Microbiol 2023; 205:366. [PMID: 37917352 DOI: 10.1007/s00203-023-03694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India.
- Microbe AI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India.
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India
- Gut Microbiology Research Division, SKAN Research Trust, Bangalore, 560034, Karnataka, India
| | - Kamlesh Jangid
- Bioenergy Group, DST-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, Maharashtra, India
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Mat Rani NNI, Alzubaidi ZM, Butt AM, Mohammad Faizal NDF, Sekar M, Azhari H, Mohd Amin MCI. Outer membrane vesicles as biomimetic vaccine carriers against infections and cancers. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1784. [PMID: 35194964 DOI: 10.1002/wnan.1784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
In the last decade, nanoparticle-based therapeutic modalities have emerged as promising treatment options for cancer and infectious diseases. To improve prognosis, chemotherapeutic and antimicrobial drugs must be delivered selectively to the target sites. Researchers have increasingly focused their efforts on improving drug delivery, with a particular emphasis on cancer and infectious diseases. When drugs are administered systemically, they become diluted and can diffuse to all tissues but only until the immune system intervenes and quickly removes them from circulation. To enhance and prolong the systemic circulation of drugs, nanocarriers have been explored and used; however, nanocarriers have a major drawback in that they can trigger immune responses. Numerous nanocarriers for optimal drug delivery have been developed using innovative and effective biointerface technologies. Autologous cell-derived drug carriers, such as outer membrane vesicles (OMVs), have demonstrated improved bioavailability and reduced toxicity. Thus, this study investigates the use of biomimetic OMVs as biomimetic vaccine carriers against infections and cancers to improve our understanding in the field of nanotechnology. In addition, discussion on the advantages, disadvantages, and future prospects of OMVs will also be explored. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Nur Najihah Izzati Mat Rani
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
- Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak, Malaysia
| | - Zahraa M Alzubaidi
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Adeel Masood Butt
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nur Dini Fatini Mohammad Faizal
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak, Malaysia
| | - Hanisah Azhari
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
| | - Mohd Cairul Iqbal Mohd Amin
- Centre for Drug Delivery Technology, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, Malaysia
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Grodnitskaya ID, Kuznetsova GV, Pashkeeva OE, Antonov GI. Features of the Formation of Microbiomes in Two Types of Soils under Pine Provenance Trials of Pinus sibirica Du Tour and Pinus koraiensis Siebold et Zucc. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021030067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Serra V, Gammuto L, Nitla V, Castelli M, Lanzoni O, Sassera D, Bandi C, Sandeep BV, Verni F, Modeo L, Petroni G. Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov. Sci Rep 2020; 10:20311. [PMID: 33219271 PMCID: PMC7679464 DOI: 10.1038/s41598-020-76348-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023] Open
Abstract
Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.
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Affiliation(s)
- Valentina Serra
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Leandro Gammuto
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Venkatamahesh Nitla
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Michele Castelli
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Olivia Lanzoni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology "Lazzaro Spallanzani", Pavia University, Pavia, Italy
| | - Claudio Bandi
- Department of Biosciences, Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, Milan, Italy
| | | | - Franco Verni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy
| | - Letizia Modeo
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Volta 4/6, 56126, Pisa, Italy.
- CIME, Centro Interdipartimentale di Microscopia Elettronica, Università di Pisa, Pisa, Italy.
- CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Pisa, India.
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Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities. J Microbiol 2020; 58:377-386. [PMID: 32281049 DOI: 10.1007/s12275-020-9365-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 12/16/2022]
Abstract
The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the "microscomics" approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect "minimicrobes" Candidate Phyla Radiation (CPR) for the first time in human stool samples. This "microscomics" approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.
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Mahajan M, Yee B, Hägglund E, Guy L, Fuerst JA, Andersson SGE. Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures. Mol Biol Evol 2019; 37:1020-1040. [DOI: 10.1093/molbev/msz287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have resequenced the 9.2-Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10-Mb genome of G. massiliana Soil9, the 7.9-Mb genome of CJuql4, and the 6.7-Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multidomain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, leucine-rich repeat, tetratricopeptide repeat and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length, and protein domain composition patterns.
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Affiliation(s)
- Mayank Mahajan
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Benjamin Yee
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Emil Hägglund
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
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Marinho MC, Lage OM, Catita J, Antunes SC. Adequacy of planctomycetes as supplementary food source for Daphnia magna. Antonie van Leeuwenhoek 2017; 111:825-840. [PMID: 29222603 DOI: 10.1007/s10482-017-0997-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Abstract
The nutritional quality of daphnids diet can influence their growth, reproduction and survival. In aquatic ecosystems, bacteria can contribute significantly to Daphnia diet by supporting, for instances, their high needs for phosphorus. The laboratory feeding of the model organisms Daphnia spp. is algal based, but should be improved to allow their better performance. The aim of this study was to evaluate the potential of two planctomycetes, Gemmata obscuriglobus and Rhodopirellula rubra, from exponential and stationary growth phases as alternative or supplementary food source for Daphnia magna. The actinobacterium Arthrobacter sp. was used for comparison. The feeding with only bacteria showed the inefficacy of both planctomycetes and actinobacteria as the only food source. However, when used in supplement to Raphidocelis subcapitata, a decrease in the age of first reproduction, a significant increase in reproductive output, in somatic growth and in rate of population increase was found for the highest cell densities of bacteria tested. The typical pink coloration of these bacteria present in daphnids body and eggs confirmed bacterial absorption and metabolization of their pigment. Planctomycetes yielded better results than the actinobacteria Arthrobacter but G. obscuriglobus that possesses sterols did not induce a better performance comparatively to R. rubra. No relation could be established between the feeding treatments that allowed improvement of Daphnia performance and the different kind of Daphnia' Fatty Acid Methyl Esters. The use of sonication to separate planctomycetal cells before feeding the daphnids proved to be efficient. We confirmed that R. subcapitata supplemented by bacteria allows a better growth performance of D. magna.
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Affiliation(s)
- M C Marinho
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - O M Lage
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal. .,Centro Interdisciplinar de Investigação Marinha e A8 Ambiental (CIIMAR/CIMAR), Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - José Catita
- Paralab, SA, Valbom, Portugal.,CEBIMED - Faculty of Health Sciences, University Fernando Pessoa, Porto, Portugal
| | - S C Antunes
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Centro Interdisciplinar de Investigação Marinha e A8 Ambiental (CIIMAR/CIMAR), Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
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Pinos S, Pontarotti P, Raoult D, Merhej V. Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. BMC Evol Biol 2017; 17:75. [PMID: 28274202 PMCID: PMC5343374 DOI: 10.1186/s12862-017-0921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. RESULTS Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. CONCLUSIONS The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
| | - Didier Raoult
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Vicky Merhej
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
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Staley JT, Fuerst JA. Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis. Res Microbiol 2017; 168:395-412. [PMID: 28111289 DOI: 10.1016/j.resmic.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 12/23/2022]
Abstract
The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.
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Affiliation(s)
- James T Staley
- Department of Microbiology and Astrobiology Program, University of Washington, Seattle 98195, USA
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4072, Australia.
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