1
|
Burg S, Ovaskainen O, Furneaux B, Ivanova N, Abrahamyan A, Niittynen P, Somervuo P, Abrego N. Experimental evidence that root-associated fungi improve plant growth at high altitude. Mol Ecol 2024:e17376. [PMID: 38703052 DOI: 10.1111/mec.17376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high-altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability.
Collapse
Affiliation(s)
- Skylar Burg
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Brendan Furneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Natalia Ivanova
- Canadian Centre for DNA Barcoding, Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Arusyak Abrahamyan
- Canadian Centre for DNA Barcoding, Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- ImmunoCeutica Inc., Guelph, Ontario, Canada
| | - Pekka Niittynen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
2
|
Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
Collapse
Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
| | | |
Collapse
|
3
|
Steach H, Viswanath S, He Y, Zhang X, Ivanova N, Hirn M, Perlmutter M, Krishnaswamy S. Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning. bioRxiv 2023:2023.12.05.570153. [PMID: 38105974 PMCID: PMC10723270 DOI: 10.1101/2023.12.05.570153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The ability to measure gene expression at single-cell resolution has elevated our understanding of how biological features emerge from complex and interdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulation. Biological processes such as transcription, translation, and post-translational or epigenetic modification impose both energetic and specific molecular demands on a cell and are therefore implicitly constrained by the metabolic state of the cell. While metabolomics is crucial for defining a holistic model of any biological process, the chemical heterogeneity of the metabolome makes it particularly difficult to measure, and technologies capable of doing this at single-cell resolution are far behind other multiomics modalities. To address these challenges, we present GEFMAP (Gene Expression-based Flux Mapping and Metabolic Pathway Prediction), a method based on geometric deep learning for predicting flux through reactions in a global metabolic network using transcriptomics data, which we ultimately apply to scRNAseq. GEFMAP leverages the natural graph structure of metabolic networks to learn both a biological objective for each cell and estimate a mass-balanced relative flux rate for each reaction in each cell using novel deep learning models.
Collapse
|
4
|
Apanovich N, Matveev A, Ivanova N, Burdennyy A, Apanovich P, Pronina I, Filippova E, Kazubskaya T, Loginov V, Braga E, Alimov A. Prediction of Distant Metastases in Patients with Kidney Cancer Based on Gene Expression and Methylation Analysis. Diagnostics (Basel) 2023; 13:2289. [PMID: 37443682 DOI: 10.3390/diagnostics13132289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive histological type of cancer in this location. Distant metastases are present in approximately 30% of patients at the time of first examination. Therefore, the ability to predict the occurrence of metastases in patients at early stages of the disease is an urgent task aimed at personalized treatment. Samples of tumor and paired histologically normal kidney tissue from patients with metastatic and non-metastatic ccRCC were studied. Gene expression was analyzed using real-time PCR. The level of gene methylation was evaluated using bisulfite conversion followed by quantitative methylation-specific PCR. Two groups of genes were analyzed in this study. The first group includes genes whose expression is significantly reduced during metastasis: CA9, NDUFA4L2, EGLN3, and BHLHE41 (p < 0.001, ROC analysis). The second group includes microRNA genes: MIR125B-1, MIR137, MIR375, MIR193A, and MIR34B/C, whose increased methylation levels are associated with the development of distant metastases (p = 0.002 to <0.001, ROC analysis). Based on the data obtained, a combined panel of genes was formed to identify patients whose tumors have a high metastatic potential. The panel can estimate the probability of metastasis with an accuracy of up to 92%.
Collapse
Affiliation(s)
- Natalya Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Alexey Matveev
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Natalia Ivanova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Alexey Burdennyy
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Pavel Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Irina Pronina
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Elena Filippova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Tatiana Kazubskaya
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Vitaly Loginov
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Eleonora Braga
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Andrei Alimov
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| |
Collapse
|
5
|
Wu D, Ivanova N. A tale of two codes. Nat Rev Microbiol 2023:10.1038/s41579-023-00921-2. [PMID: 37268864 DOI: 10.1038/s41579-023-00921-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Dongying Wu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
6
|
Nikitin I, Gorbachev V, Velina D, Klokonos M, Mutallibzoda S, Tefikova S, Orlovtseva O, Ivanova N, Posnova G, Bychkova T, Zabalueva Y, Matsikova O. Rosebay willowherb (Chamerion angustifolium) in food products: evaluation of the residual anti-radical activity of polyphenol compounds and N-acetylcystein. CNF 2023. [DOI: 10.2174/1573401319666230330095521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Background:
The composition of polyphenolic compounds in various parts of the
Rosebay willowherb (Chamerion angustifolium) has been studied in detail and published. A
number of these compounds have sufficient antiradical activity (ARA) to create functional foods
based on extracts from this plant that are preventive against free-radical pathologies in humans.
Part of substances with antiradical activity (e.g., vitamins, polyphenol components) are destroyed
during the technological processing of food raw materials, and the values of ARA drop in the finished food product concerning the initial values (before and after technical processing) are not
fully evaluated.
background:
The composition of polyphenolic compounds in various parts of the Rosebay willowherb (Chamerion angustifolium) has been studied in detail and published. A number of these compounds have sufficient antiradical activity (ARA) to create functional foods based on extracts from this plant that are preventive against free-radical pathologies in humans. Part of substances with antiradical activity (e.g., vitamins, polyphenol components) are destroyed during the technological processing of food raw materials, and the values of ARA drop in the finished food product concerning the initial values (before and after technical processing) are not fully evaluated.
Objective:
The object of the study is to study the thermal stability of polyphenol components
possessing ARA (dried at 60°C and 150°C) and evaluate their residual ARA in the finished food
products, N-acetylcysteine (NAC), as one of the known antiradical, was used as a reference substance.
objective:
The object of the study is to study the thermal stability of polyphenol components (Chamerion angustifolium) possessing APA (dried at 60°C and 150°C) and evaluate their residual APA in the finished food products, N-acetylcysteine (NAC), as one of the known antiradical, was used as a reference substance.
Methods:
Spectrophotometric method was used to evaluate the change of ARA in prepared
foods. Gas chromatography-mass spectrometry (GC-MS) was used as an additional method to
evaluate the difference in the chemical composition of polyphenol components.
method:
Spectrophotometric method was used to evaluate the change of APA in prepared foods. Gas chromatography-mass spectrometry (GC-MS) was used as an additional method to evaluate the difference in the chemical composition of polyphenol components (Chamerion angustifolium).
Results:
The residual ARA in the finished products (for caramel and bakery products) was ≈
23.9% for rapidly extractable substances, for polyphenol compounds ≈ 46.1%, and for amino acids and easily hydrolyzable substances ≈ 34.5%.
result:
The residual APA in the finished products (for caramel and bakery products) was ≈ 23.9% for rapidly extractable substances, for polyphenol compounds ≈ 46.1%, and for amino acids and easily hydrolyzable substances ≈ 34.5%.
Conclusion:
Rosebay willowherb extract and N-acetylcysteine are recommended for increasing
the ARA (between 1.6 – 4.9 times) of foods with low ARA (confectionery, bread, or other heavily processed foods) and for diets and diets preventive of free-radical pathologies by adding polyphenolic plant components and cysteine derivatives.
conclusion:
Rosebay willowherb extract (Chamerion angustifolium) and N-acetylcysteine are recommended for increasing the APA (between 1.6 – 4.9 times) of foods with low APA (confectionery, bread, or other heavily processed foods) and for diets and diets preventive of free-radical pathologies by adding polyphenolic plant components and cysteine derivatives.
other:
-
Collapse
|
7
|
Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
Collapse
Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| |
Collapse
|
8
|
Garrett NR, Watkins J, Francis CM, Simmons NB, Ivanova N, Naaum A, Briscoe A, Drinkwater R, Clare EL. Out of thin air: surveying tropical bat roosts through air sampling of eDNA. PeerJ 2023; 11:e14772. [PMID: 37128209 PMCID: PMC10148639 DOI: 10.7717/peerj.14772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 05/03/2023] Open
Abstract
Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.
Collapse
Affiliation(s)
- Nina R. Garrett
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Jonathan Watkins
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Charles M. Francis
- Canadian Wildlife Service, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | | | - Amanda Naaum
- Nature Metrics North America Ltd., Guelph, Ontario, Canada
| | - Andrew Briscoe
- Nature Metrics Ltd., Surrey Research Park, Guildford, United Kingdom
| | - Rosie Drinkwater
- Palaeogenomics group, Department of Veterinary Sciences, Ludwig-Maximillian University Munich, Munich, Germany
| | | |
Collapse
|
9
|
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D, Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 2022; 185:4023-4037.e18. [PMID: 36174579 DOI: 10.1016/j.cell.2022.08.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 01/26/2023]
Abstract
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.
Collapse
Affiliation(s)
- Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania
| | - I Min Chen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA; Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA, USA
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Archaeal Virology Unit, 75015 Paris, France
| | - Valerian V Dolja
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel.
| |
Collapse
|
10
|
Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr 2022; 10:e0234621. [PMID: 35579457 PMCID: PMC9241852 DOI: 10.1128/spectrum.02346-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
Collapse
Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Jacob Ford
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Wing Yin Tam
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Meghan Whalen
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Marcel Huntemann
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alex Spunde
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - I-Min Chen
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T. B. K Reddy
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Ronan O’Malley
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos C. Kyrpides
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
11
|
Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science 2022; 376:1453-1458. [PMID: 35737788 DOI: 10.1126/science.abb3634] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus (Ca.) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
Collapse
Affiliation(s)
- Jean-Marie Volland
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Silvina Gonzalez-Rizzo
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France.,Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Tomáš Tyml
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathalie H Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nandita Nath
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chantal Guidi-Rontani
- Institut de Systématique, Evolution, Biodiversité CNRS UMR 7205, Museum National d'Histoire Naturelle, Paris, France
| | - Susanne Bolte-Kluge
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS FRE3631, Institut de Biologie Paris Seine, Paris, France
| | - Karen M Davies
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Maïtena R Jean
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Jean-Louis Mansot
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Nigel J Mouncey
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Esther R Angert
- Cornell University, College of Agriculture and Life Sciences, Department of Microbiology, Ithaca, NY, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California Merced, School of Natural Sciences, Merced, CA, USA
| | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California San Francisco, San Francisco, CA, USA.,San Francisco State University, San Francisco, CA, USA
| |
Collapse
|
12
|
Eardly B, Meor Osman WA, Ardley J, Zandberg J, Gollagher M, van Berkum P, Elia P, Marinova D, Seshadri R, Reddy TBK, Ivanova N, Pati A, Woyke T, Kyrpides N, Loedolff M, Laird DW, Reeve W. The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host. Front Microbiol 2022; 13:735911. [PMID: 35495676 PMCID: PMC9048898 DOI: 10.3389/fmicb.2022.735911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/10/2022] [Indexed: 11/15/2022] Open
Abstract
Although Medicago sativa forms highly effective symbioses with the comparatively acid-sensitive genus Ensifer, its introduction into acid soils appears to have selected for symbiotic interactions with acid-tolerant R. favelukesii strains. Rhizobium favelukesii has the unusual ability of being able to nodulate and fix nitrogen, albeit sub-optimally, not only with M. sativa but also with the promiscuous host Phaseolus vulgaris. Here we describe the genome of R. favelukesii OR191 and genomic features important for the symbiotic interaction with both of these hosts. The OR191 draft genome contained acid adaptation loci, including the highly acid-inducible lpiA/acvB operon and olsC, required for production of lysine- and ornithine-containing membrane lipids, respectively. The olsC gene was also present in other acid-tolerant Rhizobium strains but absent from the more acid-sensitive Ensifer microsymbionts. The OR191 symbiotic genes were in general more closely related to those found in Medicago microsymbionts. OR191 contained the nodA, nodEF, nodHPQ, and nodL genes for synthesis of polyunsaturated, sulfated and acetylated Nod factors that are important for symbiosis with Medicago, but contained a truncated nodG, which may decrease nodulation efficiency with M. sativa. OR191 contained an E. meliloti type BacA, which has been shown to specifically protect Ensifer microsymbionts from Medicago nodule-specific cysteine-rich peptides. The nitrogen fixation genes nifQWZS were present in OR191 and P. vulgaris microsymbionts but absent from E. meliloti-Medicago microsymbionts. The ability of OR191 to nodulate and fix nitrogen symbiotically with P. vulgaris indicates that this host has less stringent requirements for nodulation than M. sativa but may need rhizobial strains that possess nifQWZS for N2-fixation to occur. OR191 possessed the exo genes required for the biosynthesis of succinoglycan, which is required for the Ensifer-Medicago symbiosis. However, 1H-NMR spectra revealed that, in the conditions tested, OR191 exopolysaccharide did not contain a succinyl substituent but instead contained a 3-hydroxybutyrate moiety, which may affect its symbiotic performance with Medicago hosts. These findings provide a foundation for the genetic basis of nodulation requirements and symbiotic effectiveness with different hosts.
Collapse
Affiliation(s)
- Bertrand Eardly
- Berks College, Penn State University, Reading, PA, United States
| | - Wan Adnawani Meor Osman
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Julie Ardley
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Margaret Gollagher
- Murdoch University Associate, Murdoch, WA, Australia.,Sustainability and Biosecurity, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Peter van Berkum
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Patrick Elia
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD, United States
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Rekha Seshadri
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - T B K Reddy
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, United States
| | - Matthys Loedolff
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Damian W Laird
- Centre for Water Energy and Waste, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Wayne Reeve
- Centre for Crop and Food Innovation, College of Science, Health, Engineering and Education, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| |
Collapse
|
13
|
Gorbachev V, Klokonos M, Mutallibzoda S, Tefikova S, Orlovtseva O, Ivanova N, Posnova G, Velina D, Zavalishin I, Khayrullin M, Bobkova E, Kuznetsova E, Vorobeva A, Vorobyev D, Nikitin I. Antiradical Potential of Food Products as a Comprehensive Measure of Their Quality. Foods 2022; 11:foods11070927. [PMID: 35407013 PMCID: PMC8997558 DOI: 10.3390/foods11070927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Antiradical potential (ARP) is an important measure of food safety. In addition, it directly or indirectly affects the rate of occurrence of a number of human pathologies. Using a photocolorimetric analysis of DPPH (2,2-diphenyl-1-picrylhydrazyl) solutions, we estimated the antiradical potential of food raw materials, food concentrates, biologically active substances, and wild plants. We conducted approximately 1500 analyses of almost 100 food products selected from 11 food groups: vegetables, milk, meat, fish, cereals and bread, drinks (including tea and coffee), etc. With a confidence interval (CI) of 95%, the average values for animal products range from 15.87 to 18.70 ascorbic acid equivalents per gram of dry matter. For plant materials, the range is 474.54-501.50 equivalents when wild herbs are included and 385.02-408.83 equivalents without taking herbs into account. The antiradical potential of the biologically active substances we studied ranged from 706.84 to 847.77 equivalents per gram of dry matter, which makes it possible to use some of the components to repair products with low ARP values, for example, bread and baked goods, confectionery, milk and dairy products, carbonated drinks, and juice. In this study, a low ARP value is associated with a reduction in the shelf life of products and a deterioration in their organoleptic properties; therefore, we propose using ARP as an important reference for describing the quality of food products and raw food materials.
Collapse
Affiliation(s)
- Victor Gorbachev
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Maria Klokonos
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Sherzodkhon Mutallibzoda
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Svetlana Tefikova
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Olga Orlovtseva
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Natalia Ivanova
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Galina Posnova
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Daria Velina
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
| | - Igor Zavalishin
- Department of Automated Control Systems, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia
- Correspondence: (I.Z.); (I.N.)
| | - Mars Khayrullin
- Research Department, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (M.K.); (E.B.); (E.K.); (A.V.); (D.V.)
| | - Elena Bobkova
- Research Department, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (M.K.); (E.B.); (E.K.); (A.V.); (D.V.)
| | - Elena Kuznetsova
- Research Department, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (M.K.); (E.B.); (E.K.); (A.V.); (D.V.)
| | - Alla Vorobeva
- Research Department, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (M.K.); (E.B.); (E.K.); (A.V.); (D.V.)
| | - Dmitry Vorobyev
- Research Department, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (M.K.); (E.B.); (E.K.); (A.V.); (D.V.)
| | - Igor Nikitin
- Department of Biotechnology of Food Products from Plant and Animal Raw Materials, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), 73 Zemlyanoy Val, 109004 Moscow, Russia; (V.G.); (M.K.); (S.M.); (S.T.); (O.O.); (N.I.); (G.P.); (D.V.)
- Correspondence: (I.Z.); (I.N.)
| |
Collapse
|
14
|
Wu HF, Huang CW, Daga KR, Marklein RA, Ivanova N, Zeltner N. Human pluripotent stem cell-derived functional sympathetic neurons express ACE2 and RAAS components: a framework for studying the effect of COVID-19 on sympathetic responsiveness. Clin Auton Res 2022; 32:59-63. [PMID: 35091835 PMCID: PMC8799422 DOI: 10.1007/s10286-021-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Hsueh-Fu Wu
- Center for Molecular Medicine, University of Georgia, 325 Riverbend Road, Athens, GA, 30602, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Chia-Wei Huang
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kanupriya R Daga
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, Rhodes Center for Animal Dairy Science, University of Georgia, Athens, GA, USA
| | - Ross A Marklein
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, Rhodes Center for Animal Dairy Science, University of Georgia, Athens, GA, USA
| | - Natalia Ivanova
- Center for Molecular Medicine, University of Georgia, 325 Riverbend Road, Athens, GA, 30602, USA
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Nadja Zeltner
- Center for Molecular Medicine, University of Georgia, 325 Riverbend Road, Athens, GA, 30602, USA.
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA.
- Department of Cellular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA.
| |
Collapse
|
15
|
Al-Muzaiqer M, Ivanova N, Klyuev D. Fabrication of Ring-Shaped Deposits of Polystyrene Microparticles Driven by Thermocapillary Mechanism. Materials (Basel) 2021; 14:ma14185267. [PMID: 34576496 PMCID: PMC8464929 DOI: 10.3390/ma14185267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/21/2022]
Abstract
Fabrication of ring-shaped deposits of microparticles on solid surfaces with the desired length scales and morphology of particle arrangements is of great importance when developing modern optical and electronic resonators, chemical sensors, touch screens, field-emission displays, porous materials, and coatings with various functional properties. However, the controlled formation of ring-shaped patterns scaling from a few millimeters up to centimeters with simultaneous control of particle arrangement at the microscale is one of the most challenging problems in advanced materials science and technology. Here, we report a fabrication approach for ring-shaped structures of microparticles on a glass surface that relied on a local thermal impact produced by the subsurface heater and heat sink. Thermocapillary convection in the liquid covering microparticles in combination with evaporative lithography is responsible for the particle transport and the assembling into the ring-shaped patterns. An advantageous feature of this approach is based on the control of thermocapillary flow direction, achieved by changing the sign of the temperature gradient in the liquid, switching between heating and cooling modes. That allows for changing the particle transfer direction to create the ring-shaped deposits and dynamically tune their size and density distribution. We have studied the influence of the power applied to the heat source/sink and the duration of the applied thermal field on the rate of the ring fabrication, the sizes of the ring and the profile of the particle distribution in the ring. The proposed method is flexible to control simultaneously the centimeter scale and microscale processes of transfer and arrangements of particles and can be applied to the fabrication of ring structures of particles of different nature and shape.
Collapse
Affiliation(s)
- Mohammed Al-Muzaiqer
- Photonics and Microfluidics Laboratory, X-BIO Institute, University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia; (M.A.-M.); (D.K.)
- Microfiltration Processes Laboratory, WCRC “Advanced Digital Technologies” University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia
| | - Natalia Ivanova
- Photonics and Microfluidics Laboratory, X-BIO Institute, University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia; (M.A.-M.); (D.K.)
- Microfiltration Processes Laboratory, WCRC “Advanced Digital Technologies” University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia
- Correspondence:
| | - Denis Klyuev
- Photonics and Microfluidics Laboratory, X-BIO Institute, University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia; (M.A.-M.); (D.K.)
- Microfiltration Processes Laboratory, WCRC “Advanced Digital Technologies” University of Tyumen, 6 Volodarskogo, 625003 Tyumen, Russia
| |
Collapse
|
16
|
Williams TJ, Allen MA, Ivanova N, Huntemann M, Haque S, Hancock AM, Brazendale S, Cavicchioli R. Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake. Front Microbiol 2021; 12:674758. [PMID: 34140946 PMCID: PMC8204192 DOI: 10.3389/fmicb.2021.674758] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/23/2021] [Indexed: 01/25/2023] Open
Abstract
Organic Lake in Antarctica is a marine-derived, cold (−13∘C), stratified (oxic-anoxic), hypersaline (>200 gl–1) system with unusual chemistry (very high levels of dimethylsulfide) that supports the growth of phylogenetically and metabolically diverse microorganisms. Symbionts are not well characterized in Antarctica. However, unicellular eukaryotes are often present in Antarctic lakes and theoretically could harbor endosymbionts. Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenome-assembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al., 2020). At 158,228 bp (encoding 194 genes), the genome of Ca. Organicella extenuata is among the smallest known bacterial genomes and similar to the genome of Ca. Pinguicoccus supinus (163,218 bp, 205 genes). Ca. Organicella extenuata retains a capacity for replication, transcription, translation, and protein-folding while lacking any capacity for the biosynthesis of amino acids or vitamins. Notably, the endosymbiont retains a capacity for fatty acid synthesis (type II) and iron–sulfur (Fe-S) cluster assembly. Metagenomic analysis of 150 new metagenomes from Organic Lake and more than 70 other Antarctic aquatic locations revealed a strong correlation in abundance between Ca. Organicella extenuata and a novel ciliate of the genus Euplotes. Like Ca. Pinguicoccus supinus, we infer that Ca. Organicella extenuata is an endosymbiont of Euplotes and hypothesize that both Ca. Organicella extenuata and Ca. Pinguicocccus supinus provide fatty acids and Fe-S clusters to their Euplotes host as the foundation of a mutualistic symbiosis. The discovery of Ca. Organicella extenuata as possessing genetic code 4 illustrates that in addition to identifying endosymbionts by sequencing known symbiotic communities and searching metagenome data using reference endosymbiont genomes, the potential exists to identify novel endosymbionts by searching for unusual coding parameters.
Collapse
Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Natalia Ivanova
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| |
Collapse
|
17
|
Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol 2021; 12:632731. [PMID: 34017316 PMCID: PMC8129789 DOI: 10.3389/fmicb.2021.632731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/02/2021] [Indexed: 01/21/2023] Open
Abstract
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
Collapse
Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Devon Payne
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jian-Yu Jiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Rebecca Lau
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katherine B Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alicia Clum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alex Spunde
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Manoj Pillay
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Krishnaveni Palaniappan
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Mikhailova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - I-Min Chen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Dimitrios Stamatis
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - T B K Reddy
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronan O'Malley
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris Daum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicole Shapiro
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos C Kyrpides
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Emiley Eloe-Fadrosh
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| |
Collapse
|
18
|
Mitrofanova I, Ivanova N, Kuzmina T, Mitrofanova O, Zubkova N. In vitro Regeneration of Clematis Plants in the Nikita Botanical Garden via Somatic Embryogenesis and Organogenesis. Front Plant Sci 2021; 12:541171. [PMID: 33777060 PMCID: PMC7994861 DOI: 10.3389/fpls.2021.541171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 02/09/2021] [Indexed: 05/27/2023]
Abstract
The effects of growth regulators, namely, 6-benzylaminopurine (BAP) and thidiazuron (TDZ), on the morphogenic capacity of 13 cultivars of clematis plants, in terms of their morphological structure formation, shoot regeneration, and somatic embryo development, are presented. The clematis cultivars 'Alpinist,' 'Ay-Nor,' 'Bal Tsvetov,' 'Crimson Star,' 'Crystal Fountain,' 'Kosmicheskaya Melodiya,' 'Lesnaya Opera,' 'Madame Julia Correvon,' 'Nevesta,' 'Nikitsky Rosovyi,' 'Nikolay Rubtsov,' 'Serenada Kryma,' and 'Vechniy Zov' were taken in collection plots of the Nikita Botanical Gardens for use in study. After explant sterilization with 70% ethanol (1 min), 0.3-0.4% Cl2 (15 min), and 1% thimerosal (10 min), 1-cm long segments with a single node were introduced to an in vitro culture. The explants were established on the basal MS medium supplemented with BAP (2.20-8.90 μM) and 0.049 μM NAA, or TDZ (3.0; 6.0, and 9.0 μM) with 30 g/L sucrose and 9 g/L agar. The medium with 0.89 μM BAP served as the control. Culture vessels and test tubes with the explants were maintained in plant growth chamber-controlled conditions: with a 16-h photoperiod, under cool-white light fluorescent lamps with a light intensity of 37.5 μmol m-2 s-1, at a temperature of 24 ± 1°C. Histological analysis demonstrated that adventitious bud and somatic embryo formation in studied clematis cultivars occurred at numerous areas of active meristematic cell zones. The main role of plant growth regulators and its concentrations were demonstrated. It was determined that maximum adventitious microshoot regeneration without any morphological abnormalities formed on the media supplemented with BAP or TDZ. 4.40 μM BAP, or 6.0 μM TDZ were optimal cytokinin concentrations for micropropagation. The explants of 'Alpinist,' 'Ay-Nor,' 'Crimson Star,' 'Crystal Fountain,' 'Nevesta,' and 'Serenada Kryma' cultivars displayed high morphogenetic capacity under in vitro culturing. During indirect somatic embryogenesis, light intensity 37.5 μmol m-2 s-1 stimulated a higher-number somatic embryo formation and a temperature of 26°C affected somatic embryo development. Active formation of primary and secondary somatic embryos was also demonstrated. 2.20 μM BAP with 0.09 μM IBA affected the high-number somatic embryo formation for eight cultivars. Secondary somatic embryogenesis by the same concentration of BAP was induced. The frequency of secondary somatic embryogenesis was higher in 'Crystal Fountain' (100%), 'Crimson Star' (100%), 'Nevesta' (97%), and 'Ay-Nor' (92%) cultivars. Based on these results, the methodology for direct somatic embryogenesis and organogenesis of studied clematis cultivars has been developed.
Collapse
Affiliation(s)
- Irina Mitrofanova
- Plant Biotechnology and Virology Laboratory, Plant Developmental Biology, Biotechnology and Biosafety Department, FSFIS “The Nikita Botanical Gardens – National Scientific Center of the RAS,”Yalta, Russia
| | - Natalia Ivanova
- Plant Biotechnology and Virology Laboratory, Plant Developmental Biology, Biotechnology and Biosafety Department, FSFIS “The Nikita Botanical Gardens – National Scientific Center of the RAS,”Yalta, Russia
| | - Tatyana Kuzmina
- Structural Botany and Plant Reproductive Biology Section, FSFIS “The Nikita Botanical Gardens – National Scientific Center of the RAS,”Yalta, Russia
| | - Olga Mitrofanova
- Plant Biotechnology and Virology Laboratory, Plant Developmental Biology, Biotechnology and Biosafety Department, FSFIS “The Nikita Botanical Gardens – National Scientific Center of the RAS,”Yalta, Russia
| | - Natalya Zubkova
- Floriculture Laboratory, FSFIS “The Nikita Botanical Gardens – National Scientific Center of the RAS,”Yalta, Russia
| |
Collapse
|
19
|
|
20
|
Pons JC, Paez-Espino D, Riera G, Ivanova N, Kyrpides NC, Llabrés M. VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics 2021; 37:1805-1813. [PMID: 33471063 PMCID: PMC8830756 DOI: 10.1093/bioinformatics/btab026] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/11/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022] Open
Abstract
Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Joan Carles Pons
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | | | - Gabriel Riera
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Berkeley, 94720, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Berkeley, 94720, USA
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| |
Collapse
|
21
|
Hristova M, Bozhilov S, Hristov N, Tancheva Y, Ivanova N, Penkova-Radicheva M. Invasive Molar Pregnancy in a Woman Aged 55 Years: A Case Report. Open Access Maced J Med Sci 2020. [DOI: 10.3889/oamjms.2020.5536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Gestational trophoblastic diseases (GTDs) are a group of rare human tumors by abnormal trophoblastic proliferation. GTD is neoplasia that develops from the trophoblastic element of blastocyst. In this case, some specific features of the trophoblast are retained, while the hCG (Human Chorionic Gonadotropin) synthesis and invasion potential of the underlying tissues are preserved.
CASE REPORT: We reported a 55-year-old patient with invasive (destructive) mole hydatidiform “FIGO I” with invasion in myometrium wall. This diagnostic was suggested by abnormal (dysfunctional) vaginal bleeding, amenorrhea period, and low abdominal pain. Our paraclinical investigation was physical examination, transabdominal, and transvaginal ultrasound and complete blood count. Transabdominal and transvaginal ultrasound reveal enlarged uterus volume, with dimensions 18/12/5 cm and with Doppler rich blood supply through myometrium and endometrium. Therapeutic method applied was abdominal hysterectomy and bilateral salpingo-oophorectomy. Anatomopathological report revealed a complete invasive mole. After the surgical intervention, the patient was no treated with methotrexate as prophylactic chemotherapy (recommended by oncologists) because the level of β-hCG was very low.
CONCLUSION: Examining the tissue after a miscarriage in women at extreme ages should raise a suspicion of mole. Molar pregnancy should be excluded in these cases.
Collapse
|
22
|
Peña A, Busquets A, Gomila M, Mulet M, Gomila RM, Garcia-Valdes E, Reddy TBK, Huntemann M, Varghese N, Ivanova N, Chen IM, Göker M, Woyke T, Klenk HP, Kyrpides N, Lalucat J. High-quality draft genome sequences of Pseudomonas monteilii DSM 14164 T, Pseudomonas mosselii DSM 17497 T, Pseudomonas plecoglossicida DSM 15088 T, Pseudomonas taiwanensis DSM 21245 T and Pseudomonas vranovensis DSM 16006 T: taxonomic considerations. Access Microbiol 2020; 1:e000067. [PMID: 32974501 PMCID: PMC7491935 DOI: 10.1099/acmi.0.000067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164T), Pseudomonas mosselii (DSM 17497T), Pseudomonas plecoglossicida (DSM 15088T), Pseudomonas taiwanensis (DSM 21245T) and Pseudomonas vranovensis (DSM 16006T). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species.
Collapse
Affiliation(s)
- Arantxa Peña
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Antonio Busquets
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Margarita Gomila
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Magdalena Mulet
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain
| | - Rosa M Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
| | - T B K Reddy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Neha Varghese
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - I-Min Chen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Jorge Lalucat
- Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain
| |
Collapse
|
23
|
Abrego N, Crosier B, Somervuo P, Ivanova N, Abrahamyan A, Abdi A, Hämäläinen K, Junninen K, Maunula M, Purhonen J, Ovaskainen O. Fungal communities decline with urbanization-more in air than in soil. ISME J 2020; 14:2806-2815. [PMID: 32759974 PMCID: PMC7784924 DOI: 10.1038/s41396-020-0732-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 11/09/2022]
Abstract
Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially due to the methodological difficulties in comprehensively surveying fungi. Here we show that both aerial and soil fungal communities are greatly poorer in urban than in natural areas. Strikingly, a fivefold reduction in fungal DNA abundance took place in both air and soil samples already at 1 km scale when crossing the edge from natural to urban habitats. Furthermore, in the air, fungal diversity decreased with urbanization even more than in the soil. This result is counterintuitive as fungal spores are known to disperse over large distances. A large proportion of the fungi detectable in the air are specialized to natural habitats, whereas soil fungal communities comprise a large proportion of habitat generalists. The sensitivity of the aerial fungal community to anthropogenic disturbance makes this method a reliable and efficient bioindicator of ecosystem health in urban areas.
Collapse
Affiliation(s)
- Nerea Abrego
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland.
| | - Brittni Crosier
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Natalia Ivanova
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada.,Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Arusyak Abrahamyan
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Amir Abdi
- Trycksbackantie 20, 10360, Mustio, Finland
| | - Karoliina Hämäläinen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Kaisa Junninen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI-80101, Joensuu, Finland
| | - Minna Maunula
- Department of Microbiology, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jenna Purhonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.,School of Resource Wisdom, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.,Department of Music, Art and Culture Studies, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| |
Collapse
|
24
|
Jarett JK, Džunková M, Schulz F, Roux S, Paez-Espino D, Eloe-Fadrosh E, Jungbluth SP, Ivanova N, Spear JR, Carr SA, Trivedi CB, Corsetti FA, Johnson HA, Becraft E, Kyrpides N, Stepanauskas R, Woyke T. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME J 2020; 14:2527-2541. [PMID: 32661357 PMCID: PMC7490370 DOI: 10.1038/s41396-020-0705-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Our current knowledge of host-virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host-virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus-host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host-virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed "Piggyback-the-Winner" theory.
Collapse
Affiliation(s)
- Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,AnimalBiome, Oakland, CA, USA
| | - Mária Džunková
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | | | | | | | - Hope A Johnson
- California State University Fullerton, Fullerton, CA, USA
| | - Eric Becraft
- University of North Alabama, Florence, AL, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California, Merced, CA, USA.
| |
Collapse
|
25
|
Sheremet A, Jones GM, Jarett J, Bowers RM, Bedard I, Culham C, Eloe-Fadrosh EA, Ivanova N, Malmstrom RR, Grasby SE, Woyke T, Dunfield PF. Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil. Environ Microbiol 2020; 22:3143-3157. [PMID: 32372527 DOI: 10.1111/1462-2920.15054] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/01/2022]
Abstract
Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.
Collapse
Affiliation(s)
- Andriy Sheremet
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada
| | - Gareth M Jones
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada
| | - Jessica Jarett
- Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA
| | - Robert M Bowers
- Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA
| | - Isaac Bedard
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada
| | - Cassandra Culham
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada
| | | | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
26
|
Ivanova N. Biomimetic optics: liquid-based optical elements imitating the eye functionality. Philos Trans A Math Phys Eng Sci 2020; 378:20190442. [PMID: 32008449 PMCID: PMC7015283 DOI: 10.1098/rsta.2019.0442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
The optical systems mimicking the eye functions are of great importance in various applications including consumer electronics, medical equipment, machine vision systems and robotics. This optics offers advantages over traditional optical technologies such as the superior adaptation to changing conditions and the comprehensive range of functional characteristics at miniature sizes. This paper presents a review on the recent progress in the development of human eye-inspired optical systems. Liquid-based and elastomer-based tunable optical elements are discussed with the focus on the actuation mechanism, optical performance and the possibility of integration into artificial eye systems. This article is part of the theme issue 'Bioinspired materials and surfaces for green science and technology (part 3)'.
Collapse
|
27
|
Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
Background Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
Collapse
Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia.
| |
Collapse
|
28
|
Zhu X, Campanaro S, Treu L, Seshadri R, Ivanova N, Kougias PG, Kyrpides N, Angelidaki I. Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem. Microbiome 2020; 8:22. [PMID: 32061251 PMCID: PMC7024554 DOI: 10.1186/s40168-019-0780-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/27/2019] [Indexed: 05/03/2023]
Abstract
Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.
Collapse
Affiliation(s)
- Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121, Padua, Italy
- CRIBI Biotechnology Center, University of Padua, 35131, Padua, Italy
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark.
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121, Padua, Italy.
| | - Rekha Seshadri
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark.
- Soil and Water Resources Institute, Hellenic Organisation-DEMETER, 57001, Thermi-, Thessaloniki, Greece.
| | - Nikos Kyrpides
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Building 115, DK-2800, Kgs. Lyngby, Denmark
| |
Collapse
|
29
|
Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J 2019; 14:659-675. [PMID: 31754206 PMCID: PMC7031533 DOI: 10.1038/s41396-019-0557-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 11/09/2022]
Abstract
Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus ‘Cellulosimonas argentiregionis’. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.
Collapse
Affiliation(s)
- Devin F R Doud
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Robert M Bowers
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Frederik Schulz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Markus De Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Angela Tarver
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Evan Glasgow
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kirk Vander Meulen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sam Deutsch
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Yasuo Yoshikuni
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent Northen
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia Ivanova
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA.
| |
Collapse
|
30
|
Akhaladze D, Grachev N, Kachanov D, Talypov S, Merkulov N, Uskova N, Andreev E, Rabaev G, Ivanova N, Varfolomeeva S. Liver resection for atypical giant focal nodular hyperplasia. Journal of Pediatric Surgery Case Reports 2019. [DOI: 10.1016/j.epsc.2019.101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
31
|
Auezova R, Ivanova N, Akshulakov S, Zhetpisbaev B, Kozhakhmetova A, Ryskeldiyev N, Mustafin K, Teltayev D, Auezova L. Isocitrate dehydrogenase 1 mutation is associated with reduced levels of inflammation in glioma patients. Cancer Manag Res 2019; 11:3227-3236. [PMID: 31114362 PMCID: PMC6489560 DOI: 10.2147/cmar.s195754] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/05/2019] [Indexed: 12/25/2022] Open
Abstract
Background: Glioma patients with mutant isocitrate dehydrogenase have improved survival; this could be in part due to the suppressive effect of mutant IDH on the level of chronic inflammation. This study aimed to prospectively analyze the association of IDH1 mutation status with preoperative levels of blood inflammatory markers: neutrophil–lymphocyte ratio (NLR), platelet–lymphocyte ratio (PLR), C-reactive protein (CRP), and red cell distribution width (RDW) in gliomas. Patients and methods: Receiver operating characteristic curves for cutoff value determination, various bivariate tests, and survival analyses (Kaplan–Meier curves and Cox regression) were performed. Results: Patients with mutant IDH1 had reduced levels of NLR (P<0.032) and CRP (P<0.008). Moreover, these patients showed better median overall survival compared to those without IDH1 mutation (P<0.000). In univariate analysis, IDH1 mutation status (P<0.000), NLR (P<0.000), PLR (P<0.008), and CRP (P<0.001) were among the factors associated with survival. By multivariate analysis, IDH1 mutation (P<0.044) and NLR<2.65 (P<0.022) remained independent factors associated with better survival; other independent variables were tumor grade (P<0.000) and location in noneloquent area (P<0.015). Conclusion: The obtained results show that IDH1 mutation is associated with lower levels of chronic inflammation that could account for an improved prognosis in this group of patients.
Collapse
Affiliation(s)
- Raushan Auezova
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Natalia Ivanova
- Scientific Department, Polenov Russian Scientific Research Institute of Neurosurgery (a branch of Federal Almazov North-West Medical Research Center), Ministry of Health of the Russian Federation, Saint-Petersburg, Russia
| | - Serik Akshulakov
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Berik Zhetpisbaev
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Aizhan Kozhakhmetova
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Nurzhan Ryskeldiyev
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Khalit Mustafin
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Daniyar Teltayev
- Department of Pathology of the Central Nervous System, National Center for Neurosurgery, Astana, Kazakhstan
| | - Lizette Auezova
- Bioactive Molecules Research Group, Department of Chemistry and Biochemistry, Faculty of Sciences-II, Lebanese University, Beirut, Lebanon
| |
Collapse
|
32
|
Rojas-Rojas FU, Sánchez-López D, Tapia-García EY, Arroyo-Herrera I, Maymon M, Humm E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Hirsch AM, Ibarra JA, Estrada-de Los Santos P. Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources. Curr Microbiol 2019; 76:566-574. [PMID: 30820638 DOI: 10.1007/s00284-019-01657-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/20/2019] [Indexed: 02/06/2023]
Abstract
Burkholderia cenocepacia TAtl-371 was isolated from the rhizosphere of a tomato plant growing in Atlatlahucan, Morelos, Mexico. This strain exhibited a broad antimicrobial spectrum against bacteria, yeast, and fungi. Here, we report and describe the improved, high-quality permanent draft genome of B. cenocepacia TAtl-371, which was sequenced using a combination of PacBio RS and PacBio RS II sequencing methods. The 7,496,106 bp genome of the TAtl-371 strain is arranged in three scaffolds, contains 6722 protein-coding genes, and 99 RNA only-encoding genes. Genome analysis revealed genes related to biosynthesis of antimicrobials such as non-ribosomal peptides, siderophores, chitinases, and bacteriocins. Moreover, analysis of bacterial growth on different carbon and nitrogen sources shows that the strain retains its antimicrobial ability.
Collapse
Affiliation(s)
- Fernando Uriel Rojas-Rojas
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - David Sánchez-López
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Erika Yanet Tapia-García
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Ivan Arroyo-Herrera
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Maskit Maymon
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Ethan Humm
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Manoj Pillay
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | | | - Neha Varghese
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Natalia Mikhailova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Dimitrios Stamatis
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - T B K Reddy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - J Antonio Ibarra
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Paulina Estrada-de Los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico.
| |
Collapse
|
33
|
Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R. A Comparison of Microbial Genome Web Portals. Front Microbiol 2019; 10:208. [PMID: 30853946 PMCID: PMC6395428 DOI: 10.3389/fmicb.2019.00208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs. We assessed both the bioinformatics tools and the data content of BioCyc, KEGG, Ensembl Bacteria, KBase, IMG, and PATRIC. For each portal, our assessment compared and tallied the available capabilities. The strengths of BioCyc include its genomic and metabolic tools, multi-search capabilities, table-based analysis tools, regulatory network tools and data, omics data analysis tools, breadth of data content, and large amount of curated data. The strengths of KEGG include its genomic and metabolic tools. The strengths of Ensembl Bacteria include its genomic tools and large number of genomes. The strengths of KBase include its genomic tools and metabolic models. The strengths of IMG include its genomic tools, multi-search capabilities, large number of genomes, table-based analysis tools, and breadth of data content. The strengths of PATRIC include its large number of genomes, table-based analysis tools, metabolic models, and breadth of data content.
Collapse
Affiliation(s)
- Peter D. Karp
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | | | - Markus Krummenacker
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Mario Latendresse
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Peter Midford
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Wai Kit Ong
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Suzanne Paley
- Bioinformatics Research Group, SRI International, Menlo Park, CA, United States
| | - Rekha Seshadri
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| |
Collapse
|
34
|
Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018. [PMID: 29521452 DOI: 10.1111/1462-2920.14090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
Collapse
Affiliation(s)
- Kathleen M Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Cody M B Porter
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Tara L Harmer
- Biology Program, Stockton University, Galloway, NJ, USA
| | - John H Paul
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kirsten M Antonen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Megan K Bridges
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Gary J Camper
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christie K Campla
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Leila G Casella
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Eva Chase
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - James W Conrad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Mercedez C Cruz
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Darren S Dunlap
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Laura Duran
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth M Fahsbender
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Dawn B Goldsmith
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ryan F Keeley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Matthew R Kondoff
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Breanna I Kussy
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Marannda K Lane
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Stephanie Lawler
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittany A Leigh
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Courtney Lewis
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Lygia M Lostal
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Devon Marking
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Evan C McClenthan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Emily A McIntyre
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jessica A Mine
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Swapnil Modi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittney D Moore
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - William A Morgan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kaleigh M Nelson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kimmy N Nguyen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nicholas Ogburn
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - David G Parrino
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Anangamanjari D Pedapudi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Rebecca P Pelham
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Amanda M Preece
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth A Rampersad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jason C Richardson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christina M Rodgers
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brent L Schaffer
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nancy E Sheridan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Michael R Solone
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Zachery R Staley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Maki Tabuchi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ramond J Waide
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Pauline W Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Suzanne Young
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rich Boden
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | | | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
35
|
Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. Corrigendum: Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 2018; 9:373. [PMID: 29576763 DOI: 10.3389/fmicb.2018.00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/19/2018] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article on p. 1154 in vol. 8, PMID: 28694797.].
Collapse
Affiliation(s)
- Chrizelle W Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Puseletso Manyaka
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Wai Y Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Juanita R Avontuur
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | | | - Neha Varghese
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
36
|
Ivanova N, Pereira CF, Lee DF. Ihor R. Lemischka (1953–2017). Dev Cell 2018. [DOI: 10.1016/j.devcel.2017.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
37
|
Yassin AF, Langenberg S, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Ivanova N, Woyke T, Kyrpides NC. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. PLoS One 2017; 12:e0188914. [PMID: 29216246 PMCID: PMC5720513 DOI: 10.1371/journal.pone.0188914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
Collapse
Affiliation(s)
- Atteyet F. Yassin
- Institut für medizinische Mikrobiologie und Immunologie der Universität Bonn, Bonn, Germany
- * E-mail:
| | - Stefan Langenberg
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Manoj Pillay
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Krishnaveni Palaniappan
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Neha Varghese
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Natalia Mikhailova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - T. B. K. Reddy
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Chris Daum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| |
Collapse
|
38
|
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 2017; 8:2264. [PMID: 29234309 PMCID: PMC5712423 DOI: 10.3389/fmicb.2017.02264] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
Collapse
Affiliation(s)
- Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto Rico
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tullis Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jonathan A Eisen
- College of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane Moser
- Desert Research Institute, Las Vegas, NV, United States
| | | |
Collapse
|
39
|
Odintsova G, Chugunova A, Ivanova N. Reproductive behaviour in women with epilepsy. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.3777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
40
|
Osman WAM, van Berkum P, León-Barrios M, Velázquez E, Elia P, Tian R, Ardley J, Gollagher M, Seshadri R, Reddy TBK, Ivanova N, Woyke T, Pati A, Markowitz V, Baeshen MN, Baeshen NN, Kyrpides N, Reeve W. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 2017; 12:58. [PMID: 28975015 PMCID: PMC5613336 DOI: 10.1186/s40793-017-0270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022] Open
Abstract
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
Collapse
Affiliation(s)
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genetica and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| |
Collapse
|
41
|
Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G. Draft genome sequence of Dethiobacter alkaliphilus strain AHT1 T, a gram-positive sulfidogenic polyextremophile. Stand Genomic Sci 2017; 12:57. [PMID: 28943998 PMCID: PMC5609068 DOI: 10.1186/s40793-017-0268-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/08/2017] [Indexed: 12/01/2022] Open
Abstract
Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.
Collapse
Affiliation(s)
- Emily Denise Melton
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, RAS, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lex Overmars
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Alla L Lapidus
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State, University, St. Petersburg, Russia
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Nikos C Kyrpides
- Joint Genome Institute, Walnut Creek, CA USA.,Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA USA
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Microbial Systems Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
42
|
Kirov L, Mushanov E, Dimitrov H, Ivanova N, Georgiev B. [PP.28.06] ISK PROFILE OF PATIENTS WITH TYPE 2 DIABETES AND ARTERIAL HYPERTENSION IN BULGARIAN GENERAL POPULATION. J Hypertens 2017. [DOI: 10.1097/01.hjh.0000523942.04740.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
43
|
Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci 2017; 12:46. [PMID: 28775794 PMCID: PMC5534035 DOI: 10.1186/s40793-017-0258-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage.
Collapse
Affiliation(s)
- Vera Y. Matrosova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Elena K. Gaidamakova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Olga Grichenko
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Polina Klimenkova
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Robert P. Volpe
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Rok Tkavc
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Gözen Ertem
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
| | - Isabel H. Conze
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- University of Bielefeld, Bielefeld, Germany
| | - Evelyne Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - Wei Gu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | | | - Yan Xu
- Los Alamos National Laboratory, Los Alamos, NM USA
| | | | - Michael Woolbert
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD USA
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michael J. Daly
- Uniformed Services University of the Health Sciences, School of Medicine, Bethesda, MD USA
| |
Collapse
|
44
|
Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 2017; 8:1154. [PMID: 28694797 PMCID: PMC5483467 DOI: 10.3389/fmicb.2017.01154] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022] Open
Abstract
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
Collapse
Affiliation(s)
- Chrizelle W Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Puseletso Manyaka
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Wai Y Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Juanita R Avontuur
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | - Neha Varghese
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Chris Daum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, AthensGA, United States
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| |
Collapse
|
45
|
Laviad-Shitrit S, Göker M, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Woyke T, Klenk HP, Kyrpides NC, Halpern M. High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482 T, isolated from raw cow milk. Stand Genomic Sci 2017; 12:31. [PMID: 28491240 PMCID: PMC5422911 DOI: 10.1186/s40793-017-0242-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 04/07/2017] [Indexed: 01/29/2023] Open
Abstract
Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.
Collapse
Affiliation(s)
- Sivan Laviad-Shitrit
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.,Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, Israel
| |
Collapse
|
46
|
Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76 T, isolated from Glycine max (L.) Merr. Stand Genomic Sci 2017; 12:26. [PMID: 28270909 PMCID: PMC5336687 DOI: 10.1186/s40793-017-0238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76T are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76T genome contains a low GC content region with symbiotic nod and fix genes, indicating the presence of a symbiotic island integration. A comparison of five B. elkanii genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76T were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules on Clark (rj1), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76T to introduce various effector molecules into this host to enable nodulation.
Collapse
Affiliation(s)
- Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
47
|
Patil Y, Müller N, Schink B, Whitman WB, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Junghare M. High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11 T (DSM 29698). Stand Genomic Sci 2017; 12:24. [PMID: 28250895 PMCID: PMC5322786 DOI: 10.1186/s40793-017-0236-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/26/2017] [Indexed: 11/10/2022] Open
Abstract
Anaerobium acetethylicum strain GluBS11T belongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11T and provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method. It comprises in total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124 RNA genes and 867 pseudogenes. The G + C content was 43.51 mol %. The annotated genome of strain GluBS11T contains putative genes coding for the pentose phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff pathway and the tricarboxylic acid cycle. The genome revealed the presence of most of the necessary genes required for the fermentation of glucose and gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for production of formate was not identified.
Collapse
Affiliation(s)
- Yogita Patil
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany
| | | | | | - Alicia Clum
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | | | - T B K Reddy
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | - Chris Daum
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE-Joint Genome Institute, Walnut Creek, CA USA
| | - Madan Junghare
- Department of Biology, Microbial Ecology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School of Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| |
Collapse
|
48
|
Baltrus DA, Dougherty K, Arendt KR, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Arnold AE. Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genom 2017; 3:e000101. [PMID: 28348879 PMCID: PMC5361626 DOI: 10.1099/mgen.0.000101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 12/04/2016] [Indexed: 01/03/2023] Open
Abstract
Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.
Collapse
Affiliation(s)
- David A Baltrus
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kevin Dougherty
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kayla R Arendt
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | - Alicia Clum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | | | - T B K Reddy
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Chris Daum
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Tanja Woyke
- 2Joint Genome Institute, Walnut Creek, CA, USA
| | - A Elizabeth Arnold
- 1School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.,3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
49
|
Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 2017; 8:195. [PMID: 28265262 PMCID: PMC5317091 DOI: 10.3389/fmicb.2017.00195] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
Collapse
Affiliation(s)
- Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Olga M Sigalova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia
| | - Olga Kovaleva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Nikolai A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | | | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Oleg N Reva
- Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa
| | - Margarita L Miroshnichenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia
| | | |
Collapse
|
50
|
Klonowska A, López-López A, Moulin L, Ardley J, Gollagher M, Marinova D, Tian R, Huntemann M, Reddy TBK, Varghese N, Woyke T, Markowitz V, Ivanova N, Seshadri R, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W. High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. Stand Genomic Sci 2017; 12:7. [PMID: 28116041 PMCID: PMC5240323 DOI: 10.1186/s40793-016-0212-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/26/2016] [Indexed: 11/12/2022] Open
Abstract
Rhizobium mesoamericanum STM6155 (INSCD = ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. The 6,927,906 bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501T. Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.
Collapse
Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France ; IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Aline López-López
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France ; IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| |
Collapse
|