1
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Heckler C, Vale MG, Canales HDS, Stradiotto GC, Giordano ALPL, Schreiber AZ, Sant'Ana AS. Spore-forming bacteria in gelatin: Characterization, identification by 16S rRNA and MALDI-TOF mass spectrometry (MS), and presence of heat resistance and virulence genes. Int J Food Microbiol 2024; 422:110813. [PMID: 38970997 DOI: 10.1016/j.ijfoodmicro.2024.110813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
Gelatin, a versatile protein derived from collagen, is widely used in the food, pharmaceutical and medical sectors. However, bacterial contamination by spore-forming bacteria during gelatin processing represents a significant concern for product safety and quality. In this study, an investigation was carried out to explore the heat and chemical resistance, as well as the identification and characterization of spore-forming bacteria isolated from gelatin processing. The methodologies involved chemical resistance tests with drastic pH in microplates and thermal resistance tests in capillary tubes of various isolates obtained at different processing stages. In addition, phenotypic and genotypic analyses were carried out to characterize the most resistant isolates of spore-forming bacteria. The findings of this study revealed the presence of several species, including Bacillus cereus, Bacillus licheniformis, Bacillus sonorensis, Bacillus subtilis, Geobacillus stearothermophilus, and Clostridium sporogenes, with some isolates exhibiting remarkable chemical and heat resistances. In addition, a significant proportion of the most resistant isolates showed gelatinase activity (n = 19/21; 90.5 %) and the presence of heat resistance (n = 5/21; 23.8 %), and virulence genes (n = 11/21; 52.4 %). The results of this study suggest that interventions should be done in quality control practices and that process parameter adjustments and effective contamination reduction strategies should be implemented through gelatin processing.
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Affiliation(s)
- Caroline Heckler
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Matheus G Vale
- Department of Integrated Systems, Faculty of Mechanical Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Héctor D S Canales
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Graziele C Stradiotto
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Ana Luisa P L Giordano
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Angelica Z Schreiber
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
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2
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Özer H, Wasser D, Sandner L, Soppa J. Intermolecular Gene Conversion for the Equalization of Genome Copies in the Polyploid Haloarchaeon Haloferax volcanii: Identification of Important Proteins. Genes (Basel) 2024; 15:861. [PMID: 39062640 PMCID: PMC11276520 DOI: 10.3390/genes15070861] [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: 05/10/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The model haloarchaeon Haloferax volcanii is polyploid with about 20 copies of its major chromosome. Recently it has been described that highly efficient intermolecular gene conversion operates in H. volcanii to equalize the chromosomal copies. In the current study, 24 genes were selected that encode proteins with orthologs involved in gene conversion or homologous recombination in archaea, bacteria, or eukaryotes. Single gene deletion strains of 22 genes and a control gene were constructed in two parent strains for a gene conversion assay; only radA and radB were shown to be essential. Protoplast fusions were used to generate strains that were heterozygous for the gene HVO_2528, encoding an enzyme for carotinoid biosynthesis. It was revealed that a lack of six of the proteins did not influence the efficiency of gene conversion, while sixteen mutants had severe gene conversion defects. Notably, lack of paralogous proteins of gene families had very different effects, e.g., mutant Δrad25b had no phenotype, while mutants Δrad25a, Δrad25c, and Δrad25d were highly compromised. Generation of a quadruple rad25 and a triple sph deletion strain also indicated that the paralogs have different functions, in contrast to sph2 and sph4, which cannot be deleted simultaneously. There was no correlation between the severity of the phenotypes and the respective transcript levels under non-stressed conditions, indicating that gene expression has to be induced at the onset of gene conversion. Phylogenetic trees of the protein families Rad3/25, MutL/S, and Sph/SMC/Rad50 were generated to unravel the history of the paralogous proteins of H. volcanii. Taken together, unselected intermolecular gene conversion in H. volcanii involves at least 16 different proteins, the molecular roles of which can be studied in detail in future projects.
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Affiliation(s)
| | | | | | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60439 Frankfurt, Germany; (H.Ö.); (D.W.); (L.S.)
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3
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Gaisser KD, Skloss SN, Brettner LM, Paleologu L, Roco CM, Rosenberg AB, Hirano M, DePaolo RW, Seelig G, Kuchina A. High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding. Nat Protoc 2024:10.1038/s41596-024-01007-w. [PMID: 38886529 DOI: 10.1038/s41596-024-01007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. The standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.
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Affiliation(s)
| | | | - Leandra M Brettner
- Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Luana Paleologu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - R William DePaolo
- Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Gastroenterology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Anna Kuchina
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA.
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
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4
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Leunda-Esnaola A, Bunin E, Arrufat P, Pearman PB, Kaberdin VR. Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species. Sci Rep 2024; 14:9908. [PMID: 38688963 PMCID: PMC11061105 DOI: 10.1038/s41598-024-60505-9] [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: 07/14/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.
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Affiliation(s)
- Amaia Leunda-Esnaola
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Evgeni Bunin
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
- CBET Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - Pablo Arrufat
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Peter B Pearman
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
- BC3 Basque Center for Climate Change, Scientific Campus of the University of the Basque Country, 48940, Leioa, Spain.
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
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5
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Bartoš O, Chmel M, Swierczková I. The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification. Sci Rep 2024; 14:9067. [PMID: 38643216 PMCID: PMC11032355 DOI: 10.1038/s41598-024-59667-3] [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: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 04/22/2024] Open
Abstract
The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.
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Affiliation(s)
- Oldřich Bartoš
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic.
| | - Martin Chmel
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108, Prague, Czech Republic
| | - Iva Swierczková
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic
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6
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Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proc Natl Acad Sci U S A 2024; 121:e2318008121. [PMID: 38306478 PMCID: PMC10861870 DOI: 10.1073/pnas.2318008121] [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: 10/16/2023] [Accepted: 12/02/2023] [Indexed: 02/04/2024] Open
Abstract
Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "raiA motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.
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Affiliation(s)
- Lucas W. Soares
- Department of Microbial Pathogenesis, Yale University, New Haven, CT06536
| | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Chrishan M. Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
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7
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [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: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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8
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Anda M, Yamanouchi S, Cosentino S, Sakamoto M, Ohkuma M, Takashima M, Toyoda A, Iwasaki W. Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nat Commun 2023; 14:7232. [PMID: 37963895 PMCID: PMC10645730 DOI: 10.1038/s41467-023-42681-w] [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: 02/13/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.
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Affiliation(s)
- Mizue Anda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Salvatore Cosentino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masako Takashima
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Institute for Quantitative Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
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9
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Lee PW, Chen L, Hsieh K, Traylor A, Wang TH. Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria. Anal Chem 2023; 95:15522-15530. [PMID: 37812586 DOI: 10.1021/acs.analchem.3c01654] [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] [Indexed: 10/11/2023]
Abstract
Digital PCR combined with high resolution melt (HRM) is an emerging method for identifying pathogenic bacteria with single cell resolution via species-specific digital melt curves. Currently, the development of such digital PCR-HRM assays entails first identifying PCR primers to target hypervariable gene regions within the target bacteria panel, next performing bulk-based PCR-HRM to examine whether the resulting species-specific melt curves possess sufficient interspecies variability (i.e., variability between bacterial species), and then digitizing the bulk-based PCR-HRM assays with melt curves that have high interspecies variability via microfluidics. In this work, we first report our discovery that the current development workflow can be inadequate because a bulk-based PCR-HRM assay that produces melt curves with high interspecies variability can, in fact, lead to a digital PCR-HRM assay that produces digital melt curves with unwanted intraspecies variability (i.e., variability within the same bacterial species), consequently hampering bacteria identification accuracy. Our subsequent investigation reveals that such intraspecies variability in digital melt curves can arise from PCR primers that target nonidentical gene copies or amplify nonspecifically. We then show that computational in silico HRM opens a window to inspect both interspecies and intraspecies variabilities and thus provides the missing link between bulk-based PCR-HRM and digital PCR-HRM. Through this new development workflow, we report a new digital PCR-HRM assay with improved bacteria identification accuracy. More broadly, this work can serve as the foundation for enhancing the development of future digital PCR-HRM assays toward identifying causative pathogens and combating infectious diseases.
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Affiliation(s)
- Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Amelia Traylor
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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10
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van den Elzen A, Helena-Bueno K, Brown CR, Chan LI, Melnikov S. Ribosomal proteins can hold a more accurate record of bacterial thermal adaptation compared to rRNA. Nucleic Acids Res 2023; 51:8048-8059. [PMID: 37395434 PMCID: PMC10450194 DOI: 10.1093/nar/gkad560] [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: 09/09/2022] [Revised: 05/29/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023] Open
Abstract
Ribosomal genes are widely used as 'molecular clocks' to infer evolutionary relationships between species. However, their utility as 'molecular thermometers' for estimating optimal growth temperature of microorganisms remains uncertain. Previously, some estimations were made using the nucleotide composition of ribosomal RNA (rRNA), but the universal application of this approach was hindered by numerous outliers. In this study, we aimed to address this problem by identifying additional indicators of thermal adaptation within the sequences of ribosomal proteins. By comparing sequences from 2021 bacteria with known optimal growth temperature, we identified novel indicators among the metal-binding residues of ribosomal proteins. We found that these residues serve as conserved adaptive features for bacteria thriving above 40°C, but not at lower temperatures. Furthermore, the presence of these metal-binding residues exhibited a stronger correlation with the optimal growth temperature of bacteria compared to the commonly used correlation with the 16S rRNA GC content. And an even more accurate correlation was observed between the optimal growth temperature and the YVIWREL amino acid content within ribosomal proteins. Overall, our work suggests that ribosomal proteins contain a more accurate record of bacterial thermal adaptation compared to rRNA. This finding may simplify the analysis of unculturable and extinct species.
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Affiliation(s)
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lewis I Chan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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11
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Fan J, El Sayyed H, Pambos OJ, Stracy M, Kyropoulos J, Kapanidis AN. RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons. Nucleic Acids Res 2023; 51:8085-8101. [PMID: 37351576 PMCID: PMC10450203 DOI: 10.1093/nar/gkad511] [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: 02/02/2022] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Bacterial transcription by RNA polymerase (RNAP) is spatially organized. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich medium, with several studies linking RNAP clustering and transcription of rRNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons (Δrrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting five or six of the seven chromosomal rrn operons. Spatial analysis in Δrrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at cell endcaps, where the remaining rrn operons reside. These results support a model where RNAPs in Δrrn strains relocate to copies of the remaining rrn operons. In rich medium, Δrrn strains redistribute RNAP to minimize growth defects due to rrn deletions, with very high RNAP densities on rrn genes leading to genomic instability. Our study links RNAP clusters and rrn transcription, and offers insight into how bacteria maintain growth in the presence of only 1-2 rrn operons.
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Affiliation(s)
- Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
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12
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Fishman FJ, Lennon JT. Macroevolutionary constraints on global microbial diversity. Ecol Evol 2023; 13:e10403. [PMID: 37560179 PMCID: PMC10408003 DOI: 10.1002/ece3.10403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Biologists have long sought to quantify the number of species on Earth. Often missing from these efforts is the contribution of microorganisms, the smallest but most abundant form of life on the planet. Despite recent large‐scale sampling efforts, estimates of global microbial diversity span many orders of magnitude. It is important to consider how speciation and extinction over the last 4 billion years constrain inventories of biodiversity. We parameterized macroevolutionary models based on birth–death processes that assume constant and universal speciation and extinction rates. The models reveal that richness beyond 1012 species is feasible and in agreement with empirical predictions. Additional simulations suggest that mass extinction events do not place hard limits on modern‐day microbial diversity. Together, our study provides independent support for a massive global‐scale microbiome while shedding light on the upper limits of life on Earth.
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Affiliation(s)
- Ford J. Fishman
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | - Jay T. Lennon
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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13
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Bromfield ESP, Cloutier S, Hynes MF. Ensifer canadensis sp. nov. strain T173 T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae. Front Microbiol 2023; 14:1195755. [PMID: 37389331 PMCID: PMC10306167 DOI: 10.3389/fmicb.2023.1195755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/09/2023] [Indexed: 07/01/2023] Open
Abstract
A bacterial strain, designated T173T, was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173T was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173T. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173T in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04T as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173T compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173T has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173T. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173T. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173T (= LMG 32374T = HAMBI 3766T) as the species type strain.
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Affiliation(s)
- Eden S. P. Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael F. Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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14
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Wolf-Baca M, Siedlecka A. Seasonal and spatial variations of antibiotic resistance genes and bacterial biodiversity in biofilms covering the equipment at successive stages of drinking water purification. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131660. [PMID: 37210784 DOI: 10.1016/j.jhazmat.2023.131660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/21/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
The presence of ARGs (antibiotic resistance genes) in the aquatic environment is a serious threat to public health especially in environmental biofilms as natural reservoirs of ARGs in water treatment plants (WTP). It has been shown that the treatment technology and source of water have a significant impact on the abundance and type of genes determining antibiotic resistance. The following indicator genes were proposed that should absolutely be controlled in environmental biofilms: intl1, sul2, sul1, tetA, blaOXA, and blaTEM. In both studied WTPs, the highest number of copies was determined for the intI1 gene. Among the tested ARGs, the highest values were obtained for genes sul1 and tetA. The qPCR analysis also revealed that the amounts of determined ARGs decreased in the following order: sulphonamides>carbapenems >tetracyclines > β-lactams >macrolides. The dominant bacterial types in all analysed samples were Proteobacteria and Bacteroidetes. Both ARGs and bacterial biodiversity was determined rather by sampling site (spatial variation) than seasonality. The obtained results show that biofilms are reservoirs of ARGs. This may affect the microbiological quality of water entering the water system. It is therefore necessary to include their analysis in the classical studies of water quality.
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Affiliation(s)
- Mirela Wolf-Baca
- Department of Environmental Protection Engineering, Faculty of Environmental Engineering, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Agata Siedlecka
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
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15
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Wick RR, Judd LM, Holt KE. Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLoS Comput Biol 2023; 19:e1010905. [PMID: 36862631 PMCID: PMC9980784 DOI: 10.1371/journal.pcbi.1010905] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism's genome-each replicon sequence is complete and contains no errors. While this has been difficult to achieve in the past, improvements in long-read sequencing, assemblers, and polishers have brought perfect assemblies within reach. Here, we describe our recommended approach for assembling a bacterial genome to perfection using a combination of Oxford Nanopore Technologies long reads and Illumina short reads: Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, followed by other short-read polishing tools and manual curation. We also discuss potential pitfalls one might encounter when assembling challenging genomes, and we provide an online tutorial with sample data (github.com/rrwick/perfect-bacterial-genome-tutorial).
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Affiliation(s)
- Ryan R. Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Louise M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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16
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Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
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Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
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17
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Ohkusu K. Enterococcus faecium 129 BIO 3B is classified as Enterococcus lactis 129 BIO 3B. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 42:180-185. [PMID: 37404571 PMCID: PMC10315194 DOI: 10.12938/bmfh.2022-088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 07/06/2023]
Abstract
Enterococcus faecium 129 BIO 3B is a lactic acid bacterium that has been safely used as a probiotic product for over 100 years. Recently, concerns about its safety have arisen because some species of E. faecium belong to the vancomycin-resistant enterococci. The groups of E. faecium with less pathogenic potential have been split into a separate species (Enterococcus lactis). In this study, I investigated the phylogenetic classification and safety of E. faecium 129 BIO 3B as well as E. faecium 129 BIO 3B-R, which is naturally resistant to ampicillin. Mass spectrometry and basic local alignment search tool analysis using specific gene regions failed to differentiate 3B and 3B-R into E. faecium or E. lactis. However, multilocus sequence typing successfully identified 3B and 3B-R as the same sequence types as E. lactis. Overall genome relatedness indices showed that 3B and 3B-R have high degrees of homology with E. lactis. Gene amplification was confirmed for 3B and 3B-R with E. lactis species-specific primers. The minimum inhibitory concentration of ampicillin was confirmed to be 2 µg/mL for 3B, which is within the safety standard for E. faecium set by the European Food Safety Authority. Based on the above results, E. faecium 129 BIO 3B and E. faecium 129 BIO 3B-R were classified as E. lactis. The absence of pathogenic genes except for fms21 in this study demonstrates that these bacteria are safe for use as probiotics.
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Affiliation(s)
- Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, 6-1-1 Shinjuku-ku, Shinjuku, Tokyo 160-8402, Japan
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18
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Greco M, Morard R, Darling K, Kucera M. Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 2023; 11:e15255. [PMID: 37123000 PMCID: PMC10143585 DOI: 10.7717/peerj.15255] [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: 10/24/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
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Affiliation(s)
- Mattia Greco
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Institut de Ciències del Mar (ICM), Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Raphaël Morard
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kate Darling
- School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Michal Kucera
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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19
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Lorenzi JN, Thibessard A, Lioy VS, Boccard F, Leblond P, Pernodet JL, Bury-Moné S. Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome. Nucleic Acids Res 2022; 50:11654-11669. [PMID: 36408918 PMCID: PMC9723626 DOI: 10.1093/nar/gkac1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genetic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons are structural boundaries of a central functional compartment prone to transcription in Streptomyces.
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Affiliation(s)
- Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | | | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
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20
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El Hamss H, Maruthi MN, Ally HM, Omongo CA, Wang HL, van Brunschot S, Colvin J, Delatte H. Spatio-temporal changes in endosymbiont diversity and composition in the African cassava whitefly, Bemisia tabaci SSA1. Front Microbiol 2022; 13:986226. [DOI: 10.3389/fmicb.2022.986226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Sap-sucking insects, including whiteflies, are amongst the most devastating and widely distributed organisms on the planet. They are often highly invasive and endosymbiont communities within these insects help them adapt to new or changing environments. Bemisia tabaci (Gennadius; Hemiptera: Aleyrodidae) whitefly species are vectors of more than 500 known plant-viruses and harbour highly diverse endosymbionts communities. To date, however, whitefly–endosymbiont interactions, community structure and their spatio-temporal changes are still poorly understood. In this study, we investigated the spatio-temporal changes in the composition and diversity of bacterial endosymbionts in the agricultural crop pest whitefly species, Bemisia tabaci sub-Saharan Africa 1-subgroup 1 and 2 (SSA1-SG1 and SSA1-SG2). 16S rRNA amplicon sequencing analysis was carried out to characterise endosymbiont compositionsin field-collected SSA1 (SSA1-SG1 and SSA1-SG2) populations infesting cassava in Uganda in 1997 and 2017. We detected Portiera, Arsenophonus, Wolbachia, Hamiltonella and Hemipteriphilus, with Arsenophonus and Wolbachia infections being predominant. Hemipteriphilus and Hamiltonella frequencies were very low and were detected in seven and two samples, respectively. Bacterial diversity based on three independent parameters including Simpson index, number of haplotypes and Bray–Curtis dissimilarity matrix was significantly higher in 1997 than in 2017. This period also coincided with the advent of super-abundant cassava-whitefly populations on cassava crops in Uganda. We discuss how endosymbionts may influence the biology and behaviour of whiteflies leading to population explosions.
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21
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Lin JN, Lai CH, Lin SY, Lee CC, Lee NY, Liu PY, Yang CH, Huang YH. Effect of Intragenomic Sequence Heterogeneity among Multiple 16S rRNA Genes on Species Identification of Elizabethkingia. Microbiol Spectr 2022; 10:e0133822. [PMID: 36036645 PMCID: PMC9604143 DOI: 10.1128/spectrum.01338-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/15/2022] [Indexed: 12/30/2022] Open
Abstract
Accurate identification of Elizabethkingia species mostly requires the use of molecular techniques, and 16S rRNA gene sequencing is generally considered the method of choice. In this study, we evaluated the effect of intraspecific diversity among the multiple copies of the 16S rRNA gene on the accuracy of species identification in the genus Elizabethkingia. Sequences of 16S rRNA genes obtained from the 32 complete whole-genome sequences of Elizabethkingia deposited in GenBank and from 218 clinical isolates collected from 5 hospitals in Taiwan were analyzed. Four or five copies of 16S rRNA were identified in the Elizabethkingia species with complete genome sequences. The dissimilarity among the copies of the16S rRNA gene was <1% in all Elizabethkingia strains. E. meningoseptica demonstrated a significantly higher rate of nucleotide variations in the 16S rRNA than did E. anophelis (P = 0.011). Nucleotide alterations occurred more frequently in regions V2 and V6 than in other hypervariable regions (P < 0.001). E. meningoseptica, E. anophelis, and E. argenteiflava strains were clustered distinctly in the phylogenetic tree inferred from 16S rRNA genes, and the intragenomic variation of gene sequences had no profound effect on the classification of taxa. However, E. miricola, E. bruuniana, E. ursingii, and E. occulta were grouped closely in the phylogenetic analysis, and the variation among the multiple copies of the 16S rRNA in one E. ursingii strain affected species classification. Other marker genes may be required to supplement the species classification of closely related taxa in the genus Elizabethkingia. IMPORTANCE Incorrect identification of bacterial species would influence the epidemiology and clinical analysis of patients infected with Elizabethkingia. The results of the present study suggest that 16S rRNA gene sequencing should not be considered the gold standard for the accurate identification of Elizabethkingia species.
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Affiliation(s)
- Jiun-Nong Lin
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
- Department of Critical Care Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Shang-Yi Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Chi Lee
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, Meiho University, Pingtung, Taiwan
| | - Yi-Han Huang
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
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22
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Rusch DB, Huang J, Hemmerich C, Hahn MW. High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS. ISME COMMUNICATIONS 2022; 2:99. [PMID: 37938727 PMCID: PMC9723582 DOI: 10.1038/s43705-022-00183-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2023]
Abstract
Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities at the subspecies designation. Using rolling-circle amplification, this methodology produces long-read sequences from a circular construct containing the complete 16S ribosomal gene and the neighboring internally transcribed spacer (ITS). These long reads can be used to generate a high-fidelity circular consensus sequence. Generally, the ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism and the assessment of their relative stoichiometry, as well as the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to an artificial microbial community that was also sequenced using the Illumina platform, to assess its accuracy in quantifying the relative abundance and identity of each species.
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Affiliation(s)
- Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA.
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Matthew W Hahn
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
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23
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Azevedo AS, Fernandes RM, Faria AR, Silvestre OF, Nieder JB, Lou C, Wengel J, Almeida C, Azevedo NF. Spectral imaging and nucleic acid mimics fluorescence in situ hybridization (SI-NAM-FISH) for multiplex detection of clinical pathogens. Front Microbiol 2022; 13:976639. [PMID: 36246234 PMCID: PMC9557775 DOI: 10.3389/fmicb.2022.976639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The application of nucleic acid mimics (NAMs), such as locked nucleic acid (LNA) and 2′-O-methyl-RNA (2’OMe), has improved the performance of fluorescence in situ hybridization (FISH) methods for the detection/location of clinical pathogens since they provide design versatility and thermodynamic control. However, an important limitation of FISH techniques is the low number of distinguishable targets. The use of filters in fluorescence image acquisition limits the number of fluorochromes that can be simultaneously differentiated. Recent advances in fluorescence spectral image acquisition have allowed the unambiguous identification of several microorganisms in a single sample. In this work, we aimed to combine NAM-FISH and spectral image analysis to develop and validate a new FISH variant, the spectral imaging-NAM-FISH (SI-NAM-FISH), that allows a multiplexed, robust and rapid detection of clinical pathogens. In the first stage, to implement/validate the method, we have selected seven fluorochromes with distinct spectral properties and seven bacterial species (Pseudomonas aeruginosa, Citrobacter freundii, Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter calcoaceticus). As a strong variation in fluorescence intensities is found between species and between fluorochromes, seven versions of a EUB LNA/2’OMe probe, each conjugated to one of seven fluorochromes, were used to rank species/fluorochromes by FISH and then optimize species/fluorochrome pairing. Then, final validation tests were performed using mixed populations to evaluate the potential of the technique for separating/quantifying the different targets. Overall, validation tests with different proportions of bacteria labeled with the respective fluorochrome have shown the ability of the method to correctly distinguish the species.
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Affiliation(s)
- Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
- *Correspondence: Andreia S. Azevedo,
| | - Ricardo M. Fernandes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Ana R. Faria
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Oscar F. Silvestre
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Jana B. Nieder
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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24
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González-Tortuero E, Anthon C, Havgaard JH, Geissler AS, Breüner A, Hjort C, Gorodkin J, Seemann SE. The Bacillaceae-1 RNA motif comprises two distinct classes. Gene 2022; 841:146756. [PMID: 35905857 DOI: 10.1016/j.gene.2022.146756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.
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Affiliation(s)
- Enrique González-Tortuero
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jakob H Havgaard
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adrian S Geissler
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Stefan E Seemann
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
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25
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Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022; 10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82]. RESULTS At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%). CONCLUSIONS Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.
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Affiliation(s)
- Hayley B. Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Brett Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Carson Moore
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Elizabeth Lawson
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | | | - Brook T. Russell
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
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26
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Park EH, Kim YS, Cha CJ. Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea. Int J Syst Evol Microbiol 2022; 72. [PMID: 35316175 DOI: 10.1099/ijsem.0.005287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).
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Affiliation(s)
- Eun-Hee Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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27
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Mori JF, Kanaly RA. Natural Chromosome-Chromid Fusion across rRNA Operons in a Burkholderiaceae Bacterium. Microbiol Spectr 2022; 10:e0222521. [PMID: 34985328 PMCID: PMC8729776 DOI: 10.1128/spectrum.02225-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 12/31/2022] Open
Abstract
Chromids (secondary chromosomes) in bacterial genomes that are present in addition to the main chromosome appear to be evolutionarily conserved in some specific bacterial groups. In rare cases among these groups, a small number of strains from Rhizobiales and Vibrionales were shown to possess a naturally fused single chromosome that was reported to have been generated through intragenomic homologous recombination between repeated sequences on the chromosome and chromid. Similar examples have never been reported in the family Burkholderiaceae, a well-documented group that conserves chromids. Here, an in-depth genomic characterization was performed on a Burkholderiaceae bacterium that was isolated from a soil bacterial consortium maintained on diesel fuel and mutagenic benzo[a]pyrene. This organism, Cupriavidus necator strain KK10, was revealed to carry a single chromosome with unexpectedly large size (>6.6 Mb), and results of comparative genomics with the genome of C. necator N-1T indicated that the single chromosome of KK10 was generated through fusion of the prototypical chromosome and chromid at the rRNA operons. This fusion hypothetically occurred through homologous recombination with a crossover between repeated rRNA operons on the chromosome and chromid. Some metabolic functions that were likely expressed from genes on the prototypical chromid region were indicated to be retained. If this phenomenon-the bacterial chromosome-chromid fusion across the rRNA operons through homologous recombination-occurs universally in prokaryotes, the multiple rRNA operons in bacterial genomes may not only contribute to the robustness of ribosome function, but also provide more opportunities for genomic rearrangements through frequent recombination. IMPORTANCE A bacterial chromosome that was naturally fused with the secondary chromosome, or "chromid," and presented as an unexpectedly large single replicon was discovered in the genome of Cupriavidus necator strain KK10, a biotechnologically useful member of the family Burkholderiaceae. Although Burkholderiaceae is a well-documented group that conserves chromids in their genomes, this chromosomal fusion event has not been previously reported for this family. This fusion has hypothetically occurred through intragenomic homologous recombination between repeated rRNA operons and, if so, provides novel insight into the potential of multiple rRNA operons in bacterial genomes to lead to chromosome-chromid fusion. The harsh conditions under which strain KK10 was maintained-a genotoxic hydrocarbon-enriched milieu-may have provided this genotype with a niche in which to survive.
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Affiliation(s)
- Jiro F. Mori
- Graduate School of Nanobiosicences, Yokohama City University, Yokohama, Japan
| | - Robert A. Kanaly
- Graduate School of Nanobiosicences, Yokohama City University, Yokohama, Japan
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28
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Shneider M, Ignatov A, Miroshnikov K. Curtobacterium spp. and Curtobacterium flaccumfaciens: Phylogeny, Genomics-Based Taxonomy, Pathogenicity, and Diagnostics. Curr Issues Mol Biol 2022; 44:889-927. [PMID: 35723345 PMCID: PMC8929003 DOI: 10.3390/cimb44020060] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
The genus of Curtobacterium, belonging to the Microbacteriaceae family of the Actinomycetales order, includes economically significant pathogenic bacteria of soybeans and other agricultural crops. Thorough phylogenetic and full-genome analysis using the latest genomic data has demonstrated a complex and contradictory taxonomic picture within the group of organisms classified as the Curtobacterium species. Based on these data, it is possible to delineate about 50 new species and to reclassify a substantial part of the Curtobacterium strains. It is suggested that 53 strains, including most of the Curtobacterium flaccumfaciens pathovars, can compose a monophyletic group classified as C. flaccumfaciens. A genomic analysis using the most recent inventory of bacterial chromosomal and plasmid genomes deposited to GenBank confirmed the possible role of Microbacteriaceae plasmids in pathogenicity and demonstrated the existence of a group of related plasmids carrying virulence factors and possessing a gene distantly related to DNA polymerase found in bacteriophages and archaeal and eukaryotic viruses. A PCR diagnostic assay specific to the genus Curtobacterium was developed and tested. The presented results assist in the understanding of the evolutionary relations within the genus and can lay the foundation for further taxonomic updates.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str., 49, 127434 Moscow, Russia;
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Moscow Institute of Physics and Technology, Federal University, Institutskiy per., 9, 141701 Dolgoprudny, Moscow Oblast, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia;
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia; (A.L.); (A.T.); (M.S.)
- Correspondence: (P.E.); (K.M.)
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29
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Nittami T, Batinovic S. Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking. Lett Appl Microbiol 2021; 75:759-775. [PMID: 34919734 DOI: 10.1111/lam.13634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/30/2023]
Abstract
Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, 'Ca. Kouleothrix', is used here as an example of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.
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Affiliation(s)
- T Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, Yokohama, Japan
| | - S Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, Vic., Australia
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30
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Siqueira JF, Rôças IN. A critical analysis of research methods and experimental models to study the root canal microbiome. Int Endod J 2021; 55 Suppl 1:46-71. [PMID: 34714548 DOI: 10.1111/iej.13656] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
| | - Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
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31
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Kapustina Ž, Medžiūnė J, Alzbutas G, Rokaitis I, Matjošaitis K, Mackevičius G, Žeimytė S, Karpus L, Lubys A. High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. Microb Genom 2021; 7. [PMID: 34473015 PMCID: PMC8715429 DOI: 10.1099/mgen.0.000624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1-V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing.
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Affiliation(s)
- Žana Kapustina
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius 10257, Lithuania
| | - Justina Medžiūnė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania.,Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, Vilnius 03225, Lithuania
| | - Gediminas Alzbutas
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | | | - Karolis Matjošaitis
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Gytis Mackevičius
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Simona Žeimytė
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
| | - Laurynas Karpus
- Biomatter Designs, Žirmūnų str. 139A, Vilnius 09120, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, V. A. Graičiūno str. 8, Vilnius 02241, Lithuania
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32
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Wu K, Cheng ZH, Williams E, Turner NT, Ran D, Li H, Zhou X, Guo H, Sung W, Liu DF, Lynch M, Long H. Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. Genome Biol Evol 2021; 13:evab148. [PMID: 34180992 PMCID: PMC8350357 DOI: 10.1093/gbe/evab148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.
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Affiliation(s)
- Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhou-Hua Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dapeng Ran
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Haichao Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Huilin Guo
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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33
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Schwob G, Segovia NI, González-Wevar C, Cabrol L, Orlando J, Poulin E. Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean. Front Microbiol 2021; 12:703792. [PMID: 34335536 PMCID: PMC8317501 DOI: 10.3389/fmicb.2021.703792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.
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Affiliation(s)
- Guillaume Schwob
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Nicolás I. Segovia
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Universidad Católica del Norte, Coquimbo, Chile
| | - Claudio González-Wevar
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Facultad de Ciencias, Centro Fondap IDEAL, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Léa Cabrol
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Julieta Orlando
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
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Wasser D, Borst A, Hammelmann M, Ludt K, Soppa J. Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid Haloarchaeon Haloferax volcanii. Front Microbiol 2021; 12:680854. [PMID: 34177864 PMCID: PMC8223754 DOI: 10.3389/fmicb.2021.680854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
Gene conversion is defined as the non-reciprocal transfer of genetic information from one site to a homologous, but not identical site of the genome. In prokaryotes, gene conversion can increase the variance of sequences, like in antigenic variation, but can also lead to a homogenization of sequences, like in the concerted evolution of multigene families. In contrast to these intramolecular mechanisms, the intermolecular gene conversion in polyploid prokaryotes, which leads to the equalization of the multiple genome copies, has hardly been studied. We have previously shown the intermolecular gene conversion in halophilic and methanogenic archaea is so efficient that it can be studied without selecting for conversion events. Here, we have established an approach to characterize unselected intermolecular gene conversion in Haloferax volcanii making use of two genes that encode enzymes involved in carotenoid biosynthesis. Heterozygous strains were generated by protoplast fusion, and gene conversion was quantified by phenotype analysis or/and PCR. It was verified that unselected gene conversion is extremely efficient and it was shown that gene conversion tracts are much longer than in antigenic variation or concerted evolution in bacteria. Two sites were nearly always co-converted when they were 600 bp apart, and more than 30% co-conversion even occurred when two sites were 5 kbp apart. The gene conversion frequency was independent from the extent of genome differences, and even a one nucleotide difference triggered conversion.
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Affiliation(s)
- Daniel Wasser
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Mathias Hammelmann
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Katharina Ludt
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt, Germany
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Quiñones B, Yambao JC, De Guzman VS, Lee BG, Medin DL. Genomic analysis of high copy-number sequences for the targeted detection of Listeria species using a flow-through surveillance system. Arch Microbiol 2021; 203:3667-3682. [PMID: 34076739 PMCID: PMC8289798 DOI: 10.1007/s00203-021-02388-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/14/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022]
Abstract
The bacterial foodborne pathogen Listeria monocytogenes has been implicated in fresh produce outbreaks with a significant economic impact. Given that L. monocytogenes is widespread in the environment, food production facilities constantly monitor for the presence of Listeria species. To develop a surveillance platform for food processing facilities, this study conducted a comparative genomic analysis for the identification of conserved high copy sequences in the ribosomal RNA of Listeria species. Simulated folding was performed to assess RNA accessibility in the identified genomic regions targeted for detection, and the developed singleplex assay accurately detected cell amounts lower than 5 cells, while no signals were detected for non-targeted bacteria. The singleplex assay was subsequently tested with a flow-through system, consisting of a DNA aptamer-capture step, followed by sample concentration and mechanical lysis for the detection of Listeria species. Validation experiments indicated the continuous flow-through system accurately detected Listeria species at low cell concentrations.
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Affiliation(s)
- Beatriz Quiñones
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, 94710, USA.
| | - Jaszemyn C Yambao
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, 94710, USA
| | | | - Bertram G Lee
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, 94710, USA
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Rees TAV, Raven JA. The maximum growth rate hypothesis is correct for eukaryotic photosynthetic organisms, but not cyanobacteria. THE NEW PHYTOLOGIST 2021; 230:601-611. [PMID: 33449358 PMCID: PMC8048539 DOI: 10.1111/nph.17190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/23/2020] [Indexed: 05/12/2023]
Abstract
The (maximum) growth rate (µmax ) hypothesis predicts that cellular and tissue phosphorus (P) concentrations should increase with increasing growth rate, and RNA should also increase as most of the P is required to make ribosomes. Using published data, we show that though there is a strong positive relationship between the µmax of all photosynthetic organisms and their P content (% dry weight), leading to a relatively constant P productivity, the relationship with RNA content is more complex. In eukaryotes there is a strong positive relationship between µmax and RNA content expressed as % dry weight, and RNA constitutes a relatively constant 25% of total P. In prokaryotes the rRNA operon copy number is the important determinant of the amount of RNA present in the cell. The amount of phospholipid expressed as % dry weight increases with increasing µmax in microalgae. The relative proportions of each of the five major P-containing constituents is remarkably constant, except that the proportion of RNA is greater and phospholipids smaller in prokaryotic than eukaryotic photosynthetic organisms. The effect of temperature differences between studies was minor. The evidence for and against P-containing constituents other than RNA being involved with ribosome synthesis and functioning is discussed.
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Affiliation(s)
- T. A. V. Rees
- Leigh Marine LaboratoryInstitute of Marine ScienceUniversity of AucklandAuckland1142New Zealand
| | - John A. Raven
- Division of Plant ScienceUniversity of Dundee at the James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- Climate Change ClusterFaculty of ScienceUniversity of TechnologySydney, UltimoNSW2007Australia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
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Weitekamp CA, Kvasnicka A, Keely SP, Brinkman NE, Howey XM, Gaballah S, Phelps D, Catron T, Zurlinden T, Wheaton E, Tal T. Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish. Anim Microbiome 2021; 3:12. [PMID: 33499997 PMCID: PMC7818562 DOI: 10.1186/s42523-020-00069-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Background Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivity. The mechanism through which bacteria interact with host cells to trigger normal neurobehavioral development in larval zebrafish is not well understood. Here, we monoassociated zebrafish with either one of six different zebrafish-associated bacteria, mixtures of these host-associates, or with an environmental bacterial isolate. Results As predicted, the axenic cohort was hyperactive. Monoassociation with three different host-associated bacterial species, as well as with the mixtures, resulted in control-like locomotor behavior. Monoassociation with one host-associate and the environmental isolate resulted in the hyperactive phenotype characteristic of axenic larvae, while monoassociation with two other host-associated bacteria partially blocked this phenotype. Furthermore, we found an inverse relationship between the total concentration of bacteria per larvae and locomotor behavior. Lastly, in the axenic and associated cohorts, but not in the larvae with complex communities, we detected unexpected bacteria, some of which may be present as facultative predators. Conclusions These data support a growing body of evidence that individual species of bacteria can have different effects on host behavior, potentially related to their success at intestinal colonization. Specific to the zebrafish model, our results suggest that differences in the composition of microbes in fish facilities could affect the results of behavioral assays within pharmacological and toxicological studies. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00069-x.
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Affiliation(s)
| | - Allison Kvasnicka
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Scott P Keely
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Nichole E Brinkman
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Xia Meng Howey
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Shaza Gaballah
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Drake Phelps
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Tara Catron
- Oak Ridge Institute for Science and Education, RTP, NC, USA.,, Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Todd Zurlinden
- , Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA
| | - Emily Wheaton
- Center for Environmental Measurement and Modeling, US EPA, Cincinnati, OH, USA
| | - Tamara Tal
- , Center for Computational Toxicology and Exposure, US EPA, RTP, NC, USA. .,Bioanalytical Ecotoxicology Department, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany. .,Present Address: Bioanalytical Ecotoxicology Department, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
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Chua KO, See-Too WS, Yong HS, Song SL, Yin WF, Chan KG. Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae). Plasmid 2021; 114:102559. [PMID: 33476637 DOI: 10.1016/j.plasmid.2021.102559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022]
Abstract
The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.
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Affiliation(s)
- Kah-Ooi Chua
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia; China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
| | - Wai-Fong Yin
- Guangdong Provincial Key Laboratory of Marine Biology, & Institute of Marine Sciences, Shantou University, Shantou 515063, China
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; International Genome Centre, Jiangsu University, Zhenjiang, China.
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Paulsen SS, Isbrandt T, Kirkegaard M, Buijs Y, Strube ML, Sonnenschein EC, Larsen TO, Gram L. Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov. Sci Rep 2020; 10:21630. [PMID: 33303891 PMCID: PMC7730127 DOI: 10.1038/s41598-020-78439-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 11/25/2020] [Indexed: 01/23/2023] Open
Abstract
Novel antimicrobials are urgently needed due to the rapid spread of antibiotic resistant bacteria. In a genome-wide analysis of Pseudoalteromonas strains, one strain (S4498) was noticed due to its potent antibiotic activity. It did not produce the yellow antimicrobial pigment bromoalterochromide, which was produced by several related type strains with which it shared less than 95% average nucleotide identity. Also, it produced a sweet-smelling volatile not observed from other strains. Mining the genome of strain S4498 using the secondary metabolite prediction tool antiSMASH led to eight biosynthetic gene clusters with no homology to known compounds, and synteny analyses revealed that the yellow pigment bromoalterochromide was likely lost during evolution. Metabolome profiling of strain S4498 using HPLC-HRMS analyses revealed marked differences to the type strains. In particular, a series of quinolones known as pseudanes were identified and verified by NMR. The characteristic odor of the strain was linked to the pseudanes. The highly halogenated compound tetrabromopyrrole was detected as the major antibacterial component by bioassay-guided fractionation. Taken together, the polyphasic analysis demonstrates that strain S4498 belongs to a novel species within the genus Pseudoalteromonas, and we propose the name Pseudoalteromonas galatheae sp. nov. (type strain S4498T = NCIMB 15250T = LMG 31599T).
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Affiliation(s)
- Sara Skøtt Paulsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Thomas Isbrandt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Markus Kirkegaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Yannick Buijs
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kgs. Lyngby, Denmark.
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Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon. BIOLOGY 2020; 9:biology9120440. [PMID: 33287185 PMCID: PMC7761764 DOI: 10.3390/biology9120440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 11/18/2022]
Abstract
Simple Summary Exploring the genomic changes that organisms have undergone to adapt to their specific environment is one of the most important processes in ecology and evolutionary biology. Here, we found that almost all rRNA operon-unlinked bacteria are symbiotic bacteria, which could be evidence of specific selective pressures in symbionts like genome reduction. This is meaningful and suggests that not only does the copy number variation of the rRNA operon sensitively respond to the bacterial lifestyle, but structural modification can also strongly reflect adaptation to the surrounding environmental conditions. Abstract Ribosomal RNA is an indispensable molecule in living organisms that plays an essential role in protein synthesis. Especially in bacteria, 16S, 23S, and 5S rRNAs are usually co-transcribed as operons. Despite the positive effects of rRNA co-transcription on growth and reproduction rate, a recent study revealed that bacteria with unlinked rRNA operons are more widespread than expected. However, it is still unclear why the rRNA operon is broken. Here, we explored rRNA operon linkage status in 15,898 bacterial genomes and investigated whether they have common features or lifestyles; 574 genomes were found to have unlinked rRNA operons and tended to be phylogenetically conserved. Most of them were symbionts and showed enhanced symbiotic genomic features such as reduced genome size and high adenine–thymine (AT) content. In an eggNOG-mapper analysis, they were also found to have significantly fewer genes than rRNA operon-linked bacteria in the “transcription” and “energy production and conversion in metabolism” categories. These genomes also tend to decrease RNases related to the synthesis of ribosomes and tRNA processing. Based on these results, the disruption of the rRNA operon seems to be one of the tendencies associated with the characteristics of bacteria requiring a low dynamic range.
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But SY, Dedysh SN, Popov VO, Pimenov NV, Khmelenina VN. Construction of a Type-I Metanotroph with Reduced Capacity for Glycogen and Sucrose Accumulation. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kim M, Cha IT, Lee KE, Lee EY, Park SJ. Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea. Microorganisms 2020; 8:microorganisms8091412. [PMID: 32937826 PMCID: PMC7564069 DOI: 10.3390/microorganisms8091412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 11/16/2022] Open
Abstract
Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea;
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (I.-T.C.); (K.-E.L.)
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (I.-T.C.); (K.-E.L.)
| | - Eun-Young Lee
- Exhibition & Education Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, Korea;
- Correspondence: ; Tel.: +82-64-753-3524; Fax: +82-64-756-3541
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Emrizal R, Nor Muhammad NA. Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer. PeerJ 2020; 8:e9019. [PMID: 32617187 PMCID: PMC7323717 DOI: 10.7717/peerj.9019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 03/28/2020] [Indexed: 12/20/2022] Open
Abstract
Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.
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Affiliation(s)
- Reeki Emrizal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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Salmaso N. Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes. Front Microbiol 2019; 10:2257. [PMID: 31636614 PMCID: PMC6788347 DOI: 10.3389/fmicb.2019.02257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/17/2019] [Indexed: 12/04/2022] Open
Abstract
In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Harkes P, Suleiman AKA, van den Elsen SJJ, de Haan JJ, Holterman M, Kuramae EE, Helder J. Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents. Sci Rep 2019; 9:13521. [PMID: 31534146 PMCID: PMC6751164 DOI: 10.1038/s41598-019-49854-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.
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Affiliation(s)
- Paula Harkes
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Afnan K A Suleiman
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- KWR Watercycle Research Institute, Groningenhaven 7, 3433, PE, Nieuwegein, The Netherlands
| | - Sven J J van den Elsen
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Johannes J de Haan
- Wageningen University & Research Open Teelten, Edelhertweg 10, Lelystad, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Dept. Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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46
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Speirs LBM, Rice DTF, Petrovski S, Seviour RJ. The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge. Front Microbiol 2019; 10:2015. [PMID: 31572309 PMCID: PMC6753630 DOI: 10.3389/fmicb.2019.02015] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/16/2019] [Indexed: 02/01/2023] Open
Abstract
It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.
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Affiliation(s)
- Lachlan B. M. Speirs
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, VIC, Australia
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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47
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Otto M, Wynands B, Drepper T, Jaeger KE, Thies S, Loeschcke A, Blank LM, Wierckx N. Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas. ACS Synth Biol 2019; 8:1901-1912. [PMID: 31298831 DOI: 10.1021/acssynbio.9b00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribosomal RNA (rRNA) operons have recently been identified as promising sites for chromosomal integration of genetic elements in Pseudomonas putida, a bacterium that has gained considerable popularity as a microbial cell factory. We have developed a tool for targeted integration of recombinant genes into the rRNA operons of various Pseudomonas strains, where the native context of the rRNA clusters enables effective transcription of heterologous genes. However, a sufficient translation of foreign mRNA transcriptionally fused to rRNA required optimization of RNA secondary structures, which was achieved utilizing synthetic ribozymes and a bicistronic design. The generated tool further enabled the characterization of the six rRNA promoter units of P. putida S12 under different growth conditions. The presence of multiple, almost identical rRNA operons in Pseudomonas also allowed the integration of multiple copies of heterologous genetic elements. The integration of two expression cassettes and the resulting disruption of rRNA units only moderately affects growth rates, and the constructs were highly stable over more than 160 generations.
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Affiliation(s)
- Maike Otto
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Benedikt Wynands
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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48
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Díez-Vives C, Nielsen S, Sánchez P, Palenzuela O, Ferrera I, Sebastián M, Pedrós-Alió C, Gasol JM, Acinas SG. Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea. Mol Ecol 2019; 28:2846-2859. [PMID: 30830717 DOI: 10.1111/mec.15068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 01/18/2023]
Abstract
Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Department of Life Sciences (Invertebrate Division), The Natural History Museum of London, London, UK
| | - Shaun Nielsen
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, Australia
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Oswaldo Palenzuela
- Department of Biology, Culture and Pathology of Marine Species, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto Español de Oceanografía, Centro Oceanográfico de Málaga, Fuengirola, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Madrid, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
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