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León-Sobrino C, Ramond JB, Coclet C, Kapitango RM, Maggs-Kölling G, Cowan D. Temporal dynamics of microbial transcription in wetted hyperarid desert soils. FEMS Microbiol Ecol 2024; 100:fiae009. [PMID: 38299778 PMCID: PMC10913055 DOI: 10.1093/femsec/fiae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.
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Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- Extreme Ecosystem Microbiomics and Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Clément Coclet
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
| | | | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
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Lee Díaz AS, Minchev Z, Raaijmakers JM, Pozo MJ, Garbeva P. Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress. FEMS Microbiol Ecol 2024; 100:fiad160. [PMID: 38331428 PMCID: PMC10858387 DOI: 10.1093/femsec/fiad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 11/16/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024] Open
Abstract
Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.
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Affiliation(s)
- Ana Shein Lee Díaz
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhivko Minchev
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Jos M Raaijmakers
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - María José Pozo
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Paolina Garbeva
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
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Kammoun I, Hezbri K, Sbissi I, Del Carmen Montero-Calasanz M, Klenk HP, Gtari M, Ghodhbane-Gtari F. Blastococcus carthaginiensis sp. nov., isolated from a monument sampled in Carthage, Tunisia. Int J Syst Evol Microbiol 2023; 73. [PMID: 37994907 DOI: 10.1099/ijsem.0.006178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 °C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1 ω8c and C18 : 1 ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov.
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Affiliation(s)
- Ikram Kammoun
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Karima Hezbri
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Imed Sbissi
- LR Écologie Pastorale, Institut des Régions Arides, Médenine, Tunisia
| | | | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Maher Gtari
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Carthage, Tunisia
- Institut supérieur de Biotechnologie de Sidi Thabet, Université La Manouba, Manouba, Tunisia
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Wang K, Yang S, Yu X, Bai M, Ye H, Xu Y, Zhao L, Wu D, Li X, Weng L, Li Y. Microplastics degradation stimulated by in-situ bioelectric field in agricultural soils. ENVIRONMENT INTERNATIONAL 2023; 177:108035. [PMID: 37329759 DOI: 10.1016/j.envint.2023.108035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 06/09/2023] [Indexed: 06/19/2023]
Abstract
Bioelectric field is a stimulated force to degrade xenobiotic pollutants in soils. However, the effect of bioelectric field on microplastics (MPs) aging is unclear. The degradation behavior of polyvinyl chloride (PVC), polyethylene (PE) and polylactic acid (PLA) was investigated in an agricultural soil microbial electrochemical system in which bioelectric field was generated in-situ by native microbes. Based on the density function theory, the energy gaps between the highest and the lowest occupied molecular orbitals of the three polymers with periodic structure were 4.20, 7.24 and 10.09 eV respectively, and further decreased under the electric field, indicating the higher hydrolysis potential of PLA. Meanwhile, the mass loss of PLA in the closed-circuit group (CC) was the highest on day 120, reaching 8.94%, which was 3.01-3.54 times of that without bioelectric field stimulation. This was mainly due to the enrichment of plastic-degrading bacteria and a robust co-occurrence network as the deterministic assembly process, e.g., the abundance of potential plastic-degrading bacteria on the surface of PLA and PVC in the CC increased by 1.92 and 1.30 times, respectively, compared to the open-circuit group. In terms of functional genes, the xenobiotic biodegradation and metabolism capacity of plasticsphere in the CC were stronger than that in soil, and determined by the bioaccessibility of soil nitrogen and carbon. Overall, this study explored the promoting effect of bioelectric field on the degradation of MPs and reveled the mechanism from quantum chemical calculations and microbial community analysis, which provides a novel perception to the in-situ degradation of MPs.
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Affiliation(s)
- Kai Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Side Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Xin Yu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Mohan Bai
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Huike Ye
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Lixia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Dan Wu
- Tianjin Eco-Environmental Monitoring Center, Tianjin 300191, China.
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China.
| | - Liping Weng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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Rizk SM, Magdy M, De Leo F, Werner O, Rashed MAS, Ros RM, Urzì C. Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt. Front Microbiol 2023; 14:1167083. [PMID: 37275160 PMCID: PMC10232867 DOI: 10.3389/fmicb.2023.1167083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
A large percentage of the world's tangible cultural heritage is made from stone; thus, it deteriorates due to physical, chemical, and/or biological factors. The current study explored the microbial community inhabiting two prehistoric sites with high cultural value in the Memphis necropolis of Egypt (Djoser and Lahun Pyramids) using amplicon-based metabarcoding and culture-dependent isolation methods. Samples were examined by epifluorescent microscopy for biological signs before environmental DNA extraction and in vitro cultivation. The metabarcoding analysis identified 644 bacterial species (452 genera) using the 16S rRNA and 204 fungal species (146 genera) using ITS. In comparison with the isolation approach, an additional 28 bacterial species (13 genera) and 34 fungal species (20 genera) were identified. A total of 19 bacterial and 16 fungal species were exclusively culture-dependent, while 92 bacterial and 122 fungal species were culture-independent. The most abundant stone-inhabiting bacteria in the current study were Blastococcus aggregatus, Blastococcus saxobsidens, and Blastococcus sp., among others. The most abundant rock-inhabiting fungi were Knufia karalitana and Pseudotaeniolina globosa, besides abundant unknown Sporormiaceae species. Based on previous reports, microorganisms associated with biodeterioration were detected on color-altered sites at both pyramids. These microorganisms are potentially dangerous as physical and chemical deterioration factors and require proper conservation plans from a microbiological perspective.
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Affiliation(s)
- Samah Mohamed Rizk
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Filomena De Leo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, Murcia University, Murcia, Spain
| | | | - Rosa M. Ros
- Department of Plant Biology, Faculty of Biology, Murcia University, Murcia, Spain
| | - Clara Urzì
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
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6
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Papatheodorou EM, Papakostas S, Stamou GP. Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns. Microorganisms 2023; 11:microorganisms11030790. [PMID: 36985363 PMCID: PMC10052084 DOI: 10.3390/microorganisms11030790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.
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Affiliation(s)
| | - Spiros Papakostas
- Department of Science and Technology, School of Science and Technology, University Center of International Programmes of Studies, International Hellenic University, 57001 Thessaloniki, Greece
| | - George P Stamou
- Department of Ecology, School of Biology, AUTH, 54124 Thessaloniki, Greece
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Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study. Arch Microbiol 2023; 205:90. [PMID: 36780035 DOI: 10.1007/s00203-023-03432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.
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Highlander SK, Wood JM, Gillece JD, Folkerts M, Fofanov V, Furstenau T, Singh NK, Guan L, Seuylemezian A, Benardini JN, Engelthaler DM, Venkateswaran K, Keim PS. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition. PLoS One 2023; 18:e0282428. [PMID: 36947490 PMCID: PMC10032485 DOI: 10.1371/journal.pone.0282428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.
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Affiliation(s)
- Sarah K Highlander
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - John D Gillece
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Megan Folkerts
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Viacheslav Fofanov
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara Furstenau
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Lisa Guan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Arman Seuylemezian
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - James N Benardini
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - David M Engelthaler
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Paul S Keim
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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aroF and cm2: potential molecular markers for the detection of stone-inhabiting Actinobacteria on cultural heritage sites. Arch Microbiol 2023; 205:32. [DOI: 10.1007/s00203-022-03368-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/08/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
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10
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Saadouli I, Marasco R, Mejri L, Hamden H, Guerfali MM, Stathopoulou P, Daffonchio D, Cherif A, Ouzari HI, Tsiamis G, Mosbah A. Diversity and adaptation properties of actinobacteria associated with Tunisian stone ruins. Front Microbiol 2022; 13:997832. [PMID: 36583041 PMCID: PMC9793712 DOI: 10.3389/fmicb.2022.997832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Stone surface is a unique biological niche that may host a rich microbial diversity. The exploration of the biodiversity of the stone microbiome represents a major challenge and an opportunity to characterize new strains equipped with valuable biological activity. Here, we explored the diversity and adaptation strategies of total bacterial communities associated with Roman stone ruins in Tunisia by considering the effects of geo-climatic regions and stone geochemistry. Environmental 16S rRNA gene amplicon was performed on DNA extracted from stones samples collected in three different sampling sites in Tunisia, along an almost 400km aridity transect, encompassing Mediterranean, semiarid and arid climates. The library was sequenced on an Illumina MiSeq sequencing platform. The cultivable Actinobacteria were isolated from stones samples using the dilution plate technique. A total of 71 strains were isolated and identified based on 16S rRNA gene sequences. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. Amplicon sequencing showed that stone ruins bacterial communities were consistently dominated by Cyanobacteria, followed by Proteobacteria and Actinobacteria along the aridity gradient. However, the relative abundance of the bacterial community components changed according to the geo-climatic origin. Stone geochemistry, particularly the availability of magnesium, chromium, and copper, also influenced the bacterial communities' diversity. Cultivable actinobacteria were further investigated to evaluate the adaptative strategies adopted to survive in/on stones. All the cultivated bacteria belonged to the Actinobacteria class, and the most abundant genera were Streptomyces, Kocuria and Arthrobacter. They were able to tolerate high temperatures (up to 45°C) and salt accumulation, and they produced enzymes involved in nutrients' solubilization, such as phosphatase, amylase, protease, chitinase, and cellulase. Actinobacteria members also had an important role in the co-occurrence interactions among bacteria, favoring the community interactome and stabilization. Our findings provide new insights into actinobacteria's diversity, adaptation, and role within the microbiome associated with stone ruins.
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Affiliation(s)
- Ilhem Saadouli
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lassaad Mejri
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Haytham Hamden
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Meriem M’saad Guerfali
- Laboratory of Biotechnology and Nuclear Technologies, LR16CNSTN02, National Centre of Nuclear Sciences and Technologies, Sidi Thabet, Tunisia
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ameur Cherif
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, LMBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia,*Correspondence: Hadda-Imene Ouzari,
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, Agrinio, Greece,George Tsiamis,
| | - Amor Mosbah
- BVBGR-LR11ES31, Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, Ariana, Tunisia,Amor Mosbah,
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11
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Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365. [PMID: 36439792 PMCID: PMC9686282 DOI: 10.3389/fmicb.2022.975365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom,*Correspondence: Maria del Carmen Montero-Calasanz,
| | - Adnan Yaramis
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan P. Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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12
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Jiang X, Wang C, Guo J, Hou J, Guo X, Zhang H, Tan J, Li M, Li X, Zhu H. Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9891-9902. [PMID: 35785964 PMCID: PMC9301914 DOI: 10.1021/acs.est.1c07923] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Airborne microbiome alterations, an emerging global health concern, have been linked to anthropogenic activities in numerous studies. However, these studies have not reached a consensus. To reveal general trends, we conducted a meta-analysis using 3226 air samples from 42 studies, including 29 samples of our own. We found that samples in anthropogenic activity-related categories showed increased microbial diversity, increased relative abundance of pathogens, increased co-occurrence network complexity, and decreased positive edge proportions in the network compared with the natural environment category. Most of the above conclusions were confirmed using the samples we collected in a particular period with restricted anthropogenic activities. Additionally, unlike most previous studies, we used 15 human-production process factors to quantitatively describe anthropogenic activities. We found that microbial richness was positively correlated with fine particulate matter concentration, NH3 emissions, and agricultural land proportion and negatively correlated with the gross domestic product per capita. Airborne pathogens showed preferences for different factors, indicating potential health implications. SourceTracker analysis showed that the human body surface was a more likely source of airborne pathogens than other environments. Our results advance the understanding of relationships between anthropogenic activities and airborne bacteria and highlight the role of airborne pathogens in public health.
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Affiliation(s)
- Xiaoqing Jiang
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Chunhui Wang
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Jinyuan Guo
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Jiaheng Hou
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Xiao Guo
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Haoyu Zhang
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jie Tan
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Mo Li
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Li
- School
of Life Sciences, Peking University, Beijing 100871, China
- Beijing
National Day School, Beijing 100039, China
| | - Huaiqiu Zhu
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30332, United States
- . Phone: 8610-6276-7261
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13
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Bao L, Sun B, Wei Y, Xu N, Zhang S, Gu L, Bai Z. Grape Cultivar Features Differentiate the Grape Rhizosphere Microbiota. PLANTS (BASEL, SWITZERLAND) 2022; 11:1111. [PMID: 35567111 PMCID: PMC9102929 DOI: 10.3390/plants11091111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Rhizosphere microflora are key determinants that contribute to plant growth and productivity, which are involved in improving the uptake of nutrients, regulation of plants' metabolisms and activation of plants' responses against both biotic and abiotic stresses. However, the structure and diversity of the grape rhizosphere microbiota remains poorly described. To gain a detailed understanding of the assembly of rhizosphere microbiota, we investigated the rhizosphere microbiota of nine grape varieties in northern China by high-throughput sequencing. We found that the richness and diversity of bacterial and fungal community networking in the root compartments were significantly influenced by the grape variety. The bacterial linear discriminant analysis showed that Pseudomonas and Rhizobium, which were considered as potential plant-growth-promoting bacteria, were more enriched in Pinot noir, and Nitrosospira was enriched in Gem. The fungal linear discriminant analysis showed that Fusarium was more enriched in Longan, Sporormiella was more enriched in Merlot, Gibberella and Pseudallescheria were more enriched in Gem and Mortierella was more abundant in Cabernet Sauvignon. The 16S rRNA functional prediction indicated that no significance differentiates among the grape varieties. Understanding the rhizosphere soil microbial diversity characteristics of different grape varieties could provide the basis for exploring microbial associations and maintaining the health of grapes.
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Affiliation(s)
- Lijun Bao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (L.B.); (N.X.)
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; (B.S.); (Y.W.); (Z.B.)
| | - Bo Sun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; (B.S.); (Y.W.); (Z.B.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingxue Wei
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; (B.S.); (Y.W.); (Z.B.)
| | - Nan Xu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; (L.B.); (N.X.)
| | - Shiwei Zhang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; (B.S.); (Y.W.); (Z.B.)
| | - Likun Gu
- College of Resources and Environment, Henan University of Engingeering, Zhengzhou 451191, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; (B.S.); (Y.W.); (Z.B.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Institute of Innovation, Xiongan New Area Baoding 071000, China
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14
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Schiro G, Chen Y, Blankinship JC, Barberán A. Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape. Environ Microbiol 2022; 24:4094-4107. [PMID: 35384241 DOI: 10.1111/1462-2920.15998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joseph C Blankinship
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
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15
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Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano. DIVERSITY 2021. [DOI: 10.3390/d14010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth.
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16
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Jiang ZM, Zhang BH, Sun HM, Zhang T, Yu LY, Zhang YQ. Properties of Modestobacter deserti sp. nov., a Kind of Novel Phosphate-Solubilizing Actinobacteria Inhabited in the Desert Biological Soil Crusts. Front Microbiol 2021; 12:742798. [PMID: 34803963 PMCID: PMC8602919 DOI: 10.3389/fmicb.2021.742798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Three Gram-stain-positive, aerobic, motile actinobacterial strains designated as CPCC 205119T, CPCC 205215, and CPCC 205251 were isolated from different biological soil crust samples collected from Tengger Desert, China. The 16S rRNA gene sequence comparison of these three strains showed they had almost identical 16S rRNA genes, which were closely related to members of the family Geodermatophilaceae, with the highest similarities of 96.3–97.3% to the species of Modestobacter. In the phylogenetic tree based on 16S rRNA gene sequences, these isolates clustered into a subclade next to the branch containing the species of Modestobacter lapidis and Modestobacter multiseptatus, within the lineage of the genus Modestobacter. The comparative genomic characteristics (values of ANI, dDDH, AAI, and POCP) and the phenotypic properties (morphological, physiological, and chemotaxonomic characteristics) of these isolates readily supported to affiliate them to the genus Modestobacter as a single separate species. For which, we proposed that the isolates CPCC 205119T, CPCC 205215, and CPCC 205251 represent a novel species of the genus Modestobacter as Modestobacter deserti sp. nov. CPCC 205119T (=I12A-02624=NBRC 113528T=KCTC 49201T) is the type strain. The genome of strain CPCC 205119T consisted of one chromosome (4,843,235bp) containing 4,424 coding genes, 48 tRNA genes, five rRNA genes, three other ncRNA genes, and 101 pseudogenes, with G+C content of 74.7%. The whole-genome sequences analysis indicated that this species contained alkaline phosphatase genes (phoA/phoD), phosphate transport-related genes (phoU, phnC, phnD, phnE, phoB, phoH, phoP, phoR, pitH, ppk, pstA, pstB, pstC, and pstS), trehalose-phosphate synthase gene (otsA), trehalose 6-phosphate phosphatase gene (otsB) and other encoding genes for the properties that help the microorganisms to adapt to harsh environmental conditions prevalent in deserts. Strains of this species could solubilize tricalcium phosphate [Ca3(PO4)2] and phytin, assimilate pyrophosphate, thiophosphate, dithiophosphate, phosphoenol pyruvate, 2-deoxy-d-glucose-6-phosphate, and cysteamine-S-phosphate.
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Affiliation(s)
- Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bing-Huo Zhang
- College of Life Science, Jiujiang University, Jiujiang, China
| | - Hong-Min Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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17
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Gat D, Reicher N, Schechter S, Alayof M, Tarn MD, Wyld BV, Zimmermann R, Rudich Y. Size-Resolved Community Structure of Bacteria and Fungi Transported by Dust in the Middle East. Front Microbiol 2021; 12:744117. [PMID: 34858365 PMCID: PMC8631519 DOI: 10.3389/fmicb.2021.744117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
The atmosphere plays an important role in transporting microorganisms on a global scale, yet the processes affecting the composition of the airborne microbiome, the aerobiome, are not fully outlined. Here we present the community compositions of bacteria and fungi obtained by DNA amplicon-sequencing of aerosol samples collected in a size-resolved manner during nine consecutive days in central Israel. The campaign captured dust events originating from the Sahara and the Arabian deserts, as well as days without dust ("clear days"). We found that the source of the aerosol was the main variable contributing to the composition of both fungal and bacterial communities. Significant differences were also observed between communities representing particles of different sizes. We show evidence for the significant transport of bacteria as cell-aggregates and/or via bacterial attachment to particles during dust events. Our findings further point to the mixing of local and transported bacterial communities, observed mostly in particles smaller than 0.6 μm in diameter, representing bacterial single cells. Fungal communities showed the highest dependence on the source of the aerosols, along with significant daily variability, and without significant mixing between sources, possibly due to their larger aerodynamic size and shorter atmospheric residence times. These results, obtained under highly varied atmospheric conditions, provide significant assurances to previously raised hypotheses and could set the course for future studies on aerobiome composition.
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Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
- Joint Mass Spectrometry Centre (JMSC), Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shai Schechter
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Alayof
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D. Tarn
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Bethany V. Wyld
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre (JMSC), Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Munich, Germany
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
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18
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Tong X, Leung MHY, Shen Z, Lee JYY, Mason CE, Lee PKH. Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. MICROBIOME 2021; 9:213. [PMID: 34724986 PMCID: PMC8562002 DOI: 10.1186/s40168-021-01166-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail. RESULTS Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography. CONCLUSIONS Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.
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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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19
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Draft Genome Sequences of Blastococcus sp. Clones TML/M2B and TML/C7B, with Different Motilities, Isolated in a Laboratory. Microbiol Resour Announc 2021; 10:10/12/e00121-21. [PMID: 33766900 PMCID: PMC7996459 DOI: 10.1128/mra.00121-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Two novel Blastococcus sp. clones, TML/M2B and TML/C7B, with 2 stable different growth phenotypes, were isolated from a laboratory tissue culture. The draft genome sequences generated through genomic sequencing of clones TML/M2B and TML/C7B contain 4 and 2 contigs, respectively. The respective genome sizes are 4.10 Mb and 4.11 Mb, with GC contents of 74.17% and 74.14%. Two novel Blastococcus sp. clones, TML/M2B and TML/C7B, with 2 different stable growth phenotypes, were isolated from a laboratory tissue culture. The draft genome sequences generated through genomic sequencing of clones TML/M2B and TML/C7B contain 4 and 2 contigs, respectively. The respective genome sizes are 4.10 Mb and 4.11 Mb, with G+C contents of 74.17% and 74.14%, respectively.
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20
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Liu S, Wang T, Lu Q, Li F, Wu G, Jiang Z, Habden X, Liu L, Zhang X, Lukianov DA, Osterman IA, Sergiev PV, Dontsova OA, Sun C. Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert. Front Microbiol 2021; 12:604999. [PMID: 33790875 PMCID: PMC8005632 DOI: 10.3389/fmicb.2021.604999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/22/2021] [Indexed: 02/04/2023] Open
Abstract
Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter "pDualrep2" system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested "ESKAPE" pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1-16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8-11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.
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Affiliation(s)
- Shaowei Liu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Wang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qinpei Lu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feina Li
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Gang Wu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhongke Jiang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xugela Habden
- College of Life Science, Xinjiang Normal University, Urumchi, China
| | - Lin Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaolin Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Dmitry A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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21
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Salam LB, Obayori OS, Ilori MO, Amund OO. Acenaphthene biodegradation and structural and functional metagenomics of the microbial community of an acenaphthene-enriched animal charcoal polluted soil. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jiang H, Chen Y, Hu Y, Wang Z, Lu X. Soil Bacterial Communities and Diversity in Alpine Grasslands on the Tibetan Plateau Based on 16S rRNA Gene Sequencing. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Tibetan Plateau, widely known as the world’s “Third Pole,” has gained extensive attention due to its susceptibility to climate change. Alpine grasslands are the dominant ecosystem on the Tibetan Plateau, albeit little is known about the microbial community and diversity among different alpine grassland types. Here, soil bacterial composition and diversity in the upper soils of five alpine grassland ecosystems, alpine meadow (AM), alpine steppe (AS), alpine meadow steppe (AMS), alpine desert (AD), and alpine desert steppe (ADS), were investigated based on the 16S rRNA gene sequencing technology. Actinobacteria (46.12%) and Proteobacteria (29.67%) were the two dominant soil bacteria at the phylum level in alpine grasslands. There were significant differences in the relative abundance at the genus level among the five different grassland types, especially for the Rubrobacter, Solirubrobacter, Pseudonocardia, Gaiella, Haliangium, and Geodermatophilus. Six alpha diversity indices were calculated based on the operational taxonomic units (OTUs), including Good’s coverage index, phylogenetic diversity (PD) whole tree index, Chao1 index, observed species index, Shannon index, and Simpson index. The Good’s coverage index value was around 0.97 for all the grassland types in the study area, meaning the soil bacteria samplings sequenced sufficiently. No statistically significant difference was shown in other diversity indices’ value, indicating the similar richness and evenness of soil bacteria in these alpine grasslands. The beta diversity, represented by Bray–Curtis dissimilarity and the non-metric multidimensional scaling (NMDS), showed that OTUs were clustered within alpine grasslands, indicating a clear separation of soil bacterial communities. In addition, soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), pH, and soil water content (SWC) were closely related to the variations in soil bacterial compositions. These results indicated that soil bacterial taxonomic compositions were similar, while soil bacterial community structures were different among the five alpine grassland types. The environmental conditions, including SOM, TN, TP, pH, and SWC, might influence the soil bacterial communities on the Tibetan Plateau.
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Wang Q, Li Z, Li X, Ping Q, Yuan X, Agathokleous E, Feng Z. Interactive effects of ozone exposure and nitrogen addition on the rhizosphere bacterial community of poplar saplings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142134. [PMID: 33254895 DOI: 10.1016/j.scitotenv.2020.142134] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 06/12/2023]
Abstract
It is widely documented that elevated ground-level ozone (O3) has negative effects on tree physiological characteristics, and in return, affects forest ecosystem function. However, the effect may be modified by soil nitrogen (N) availability. Numerous studies have focused on the aboveground part of trees under elevated O3 alone or in combination with soil N; however, little is known about the response of soil bacterial communities. Here, we investigated the effects of O3 (charcoal-filtered air, CF, versus ambient air +40 ppb of O3, E-O3), N addition (0 kg ha-1 yr-1, N0, versus 200 kg ha-1 yr-1, N200), and their combination on rhizosphere soil bacterial communities of hybrid poplar, using an MiSeq targeted amplicon sequencing of the bacterial 16S rRNA gene. E-O3 significantly decreased bacterial abundance, and N200 significantly decreased the α-diversity. The negative impacts of N200 on α-diversity were alleviated by E-O3. Nitrogen and E-O3-N200 combination altered bacterial community composition, with a significant increase in the relative abundance of Proteobacteria and Bacteroidetes and a decrease in the abundance of Firmicutes. From an ecological network analysis, E-O3, alone and in combination with N200, complicated the co-occurrence network of bacterial communities by inducing a microbial survival strategy, shifting the hub species from RB41 to Bacillus and Blastococcus. Conversely, N200 led to simplification and decentralization of the co-occurrence network. These findings demonstrate that the rhizosphere bacterial communities exhibit divergent responses to E-O3 and N200, suggesting the need to consider the stability of the belowground ecosystem to optimize plantation management in response to environmental changes.
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Affiliation(s)
- Qi Wang
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhengzhen Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing 100085, China
| | - Xuewei Li
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Qin Ping
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing 100085, China
| | - Xiangyang Yuan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Haidian District, Beijing 100085, China
| | - Evgenios Agathokleous
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- Key Laboratory of Agrometeorology of Jiangsu Province, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China.
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Genderjahn S, Lewin S, Horn F, Schleicher AM, Mangelsdorf K, Wagner D. Living Lithic and Sublithic Bacterial Communities in Namibian Drylands. Microorganisms 2021; 9:235. [PMID: 33498742 PMCID: PMC7911874 DOI: 10.3390/microorganisms9020235] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/26/2022] Open
Abstract
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.
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Affiliation(s)
- Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Simon Lewin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Anja M. Schleicher
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Anorganic Chemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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25
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Andreani J, Million M, Baudoin JP, Ominami Y, Khalil JYB, Frémond C, Khelaifia S, Levasseur A, Raoult D, La Scola B. Klenkia terrae resistant to DNA extraction in germ-free mice stools illustrates the extraction pitfall faced by metagenomics. Sci Rep 2020; 10:10228. [PMID: 32576848 PMCID: PMC7311423 DOI: 10.1038/s41598-020-66627-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 05/14/2020] [Indexed: 11/09/2022] Open
Abstract
Over the past decade, metagenomics has become the preferred method for exploring complex microbiota such as human gut microbiota. However, several bias affecting the results of microbiota composition, such as those due to DNA extraction, have been reported. These bias have been confirmed with the development of culturomics technique. In the present study, we report the contamination of a gnotobiotic mice unit with a bacterium first detected by gram staining. Scanning electron microscopy and transmission electron microscopy permitted to detect a bacterium with a thick cell wall. However, in parallel, the first attempt to identify and culture this bacterium by gene amplification and metagenomics of universal 16S rRNA failed. Finally, the isolation in culture of a fastidious bacterium not detected by using universal PCR was successfully achieved by using a BCYE agar plate with CO2 atmosphere at 30 °C. We performed genome sequencing of this bacterium using a strong extraction procedure. The genomic comparison allowed us to classify this bacterium as Klenkia terrae. And finally, it was also detected in the stool and kibble that caused the contamination by using specific qPCR against this bacterium. The elucidation of this contamination provides additional evidence that DNA extraction could be a bias for the study of the microbiota. Currently, most studies that strive to analyze and compare the gut microbiota are based on metagenomics. In a gnotobiotic mice unit contaminated with the fastidious Actinobacteria Klenkia terrae, standard culture, 16S rRNA gene amplification and metagenomics failed to identify the micro-organism observed in stools by gram-staining. Only a procedure based on culturomics allowed us to identify this bacterium and to elucidate the mode of contamination of the gnotobiotic mice unit through diet.
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Affiliation(s)
- Julien Andreani
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France
| | | | - Yusuke Ominami
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, 24-14, Nishi-shimbashi 1-chome, Minato-ku, Tokyo, 105-8717, Japan
| | | | - Cécile Frémond
- Phenomin-TAAM, UPS44, Centre National de la Recherche Scientifique, Orléans, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France.,Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France, Marseille, France. .,Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.
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26
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Tarlachkov SV, Shevchuk TV, Montero-Calasanz MDC, Starodumova IP. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. Bioinformatics 2020; 36:1668-1672. [PMID: 31711117 DOI: 10.1093/bioinformatics/btz840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/30/2019] [Accepted: 11/10/2019] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION A small amount of research is focused on investigation of rhodopsins in cultivated bacteria isolated from non-aquatic environments. Furthermore, the abundance of these proteins in strains from hot and arid habitats was not reported previously. Since there is an insignificant amount of such isolates, the enigmatic role of the rhodopsins in dry ecological niches is still poorly understood. The members of the family Geodermatophilaceae could be used as interesting objects to search for new rhodopsin genes that will provide novel insights into versatility and importance of these proteins in non-aquatic conditions. RESULTS This is the first report of the abundance of different rhodopsins in cultivated bacteria isolated from hot and arid ecological niches. A total of 31 rhodopsin genes were identified in 51 analyzed genomes of strains belonging to the family Geodermatophilaceae. Overall, 88% of the strains harbouring rhodopsins are isolated from non-aquatic environments. It was found that 82% of strains belonging to the genus Geodermatophilus have at least one gene as compared to 38% of strains of other genera which contain rhodopsins. Analysis of key amino acids revealed two types of the studied proteins: DTE type (putative proton pump) and NDQ type (putative sodium pump). Proton pumps were divided into two subtypes (DTEW and DTEF) according to phylogenetic analysis and the presence of highly conserved tryptophan or phenylalanine at position 182. Among all studied rhodopsins DTEF subtype is the most unique one, identified only in this family. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sergey V Tarlachkov
- All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research.,Department of Plant Molecular Biology and Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Taras V Shevchuk
- Department of Plant Molecular Biology and Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Maria Del Carmen Montero-Calasanz
- Plant and Microbial Biology Research Group, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Irina P Starodumova
- All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC Pushchino Scientific Center for Biological Research
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27
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Antonelli F, Esposito A, Calvo L, Licursi V, Tisseyre P, Ricci S, Romagnoli M, Piazza S, Guerrieri F. Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing. PLoS One 2020; 15:e0227639. [PMID: 31917800 PMCID: PMC6952188 DOI: 10.1371/journal.pone.0227639] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022] Open
Abstract
Black patinas are very common biological deterioration phenomena on lapideous artworks in outdoor environments. These substrates, exposed to sunlight, and atmospheric and environmental agents (i.e. wind and temperature changes), represent extreme environments that can only be colonized by highly versatile and adaptable microorganisms. Black patinas comprise a wide variety of microorganisms, but the morphological plasticity of most of these microorganisms hinders their identification by optical microscopy. This study used Next-Generation Sequencing (NGS) (including shotgun and amplicon sequencing) to characterize the black patina of the travertine embankments (muraglioni) of the Tiber River in Rome (Italy). Overall, the sequencing highlighted the rich diversity of bacterial and fungal communities and allowed the identification of more than one hundred taxa. NGS confirmed the relevance of coccoid and filamentous cyanobacteria observed by optical microscopy and revealed an informative landscape of the fungal community underlining the presence of microcolonial fungi and phylloplane yeasts. For the first time high-throughput sequencing allowed the exploration of the expansive diversity of bacteria in black patina, which has so far been overlooked in routine analyses. Furthermore, the identification of euendolithic microorganisms and weathering agents underlines the biodegradative role of black patina, which has often been underestimated. Therefore, the use of NGS to characterize black patinas could be useful in choosing appropriate conservation treatments and in the monitoring of stone colonization after the restoration interventions.
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Affiliation(s)
- Federica Antonelli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Ludovica Calvo
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | | | - Sandra Ricci
- Biology Laboratory, Istituto Superiore per la Conservazione e per il Restauro (ISCR), Rome, Italy
| | - Manuela Romagnoli
- Department of Innovation of Biological Systems, Food and Forestry (DIBAF), Tuscia University, Viterbo, Italy
| | - Silvano Piazza
- Department of Cellular, Computational and Integrative Biology–CIBIO, University of Trento, Trento, Italy
| | - Francesca Guerrieri
- Center for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Epigenetics and epigenomic of hepatocellular carcinoma, U1052, Cancer Research Center of Lyon (CRCL), Lyon, France
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28
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Modestobacter excelsi sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil. Syst Appl Microbiol 2019; 43:126051. [PMID: 31892483 DOI: 10.1016/j.syapm.2019.126051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three Modestobacter strains isolated from a high altitude Atacama Desert soil. The isolates, strains 1G6T, 1G14 and 1G50, showed chemotaxonomic and morphological properties characteristic of members of the genus Modestobacter. The peptidoglycan contained meso-diaminopimelic acid, the whole cell sugars were glucose and ribose (diagnostic sugars) and arabinose, the predominant menaquinone was MK-9(H4), polar lipid patterns contained diphosphatidylglycerol, glycophosphatidylinositol, phosphatidylethanolamine (diagnostic component), phosphatidylglycerol and phosphatidylinositol while whole cellular fatty acid profiles consisted of complex mixtures of saturated, unsaturated iso- and anteiso-components. The isolates were shown to have different BOX-PCR fingerprint and physiological profiles. They formed a distinct phyletic line in Modestobacter 16S rRNA gene trees, were most closely related to the type strain of Modestobacter italicus (99.9 % similarity) but were distinguished from this and other closely related Modestobacter type strains using a combination of phenotypic properties. Average nucleotide identity and digital DNA:DNA hybridization similarities between the draft genome sequences of isolate 1G6T and M. italicus BC 501T were 90.9 % and 42.3 %, respectively, indicating that they belong to different species. Based on these phenotypic and genotypic data it is proposed that the isolates be assigned to a novel species in the genus Modestobacter, namely as Modestobacter excelsi with isolate 1G6T (=DSM 107535T =PCM 3004T) as the type strain. Analysis of the whole genome sequence of M. excelsi 1G6T (genome size of 5.26 Mb) showed the presence of genes and gene clusters that encode for properties that are in tune with its adaptation to extreme environmental conditions that prevail in the Atacama Desert biome.
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29
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Guesmi S, Chouchane H, Neifar M, Hosni F, Cherif A, Sghaier H. Radiation-inducible radioprotective exopolysaccharides of Bacillus siamensis CV5 from irradiated roots of Cistanche violacea to decrease free radical damage produced by ionizing radiation. Int J Radiat Biol 2019; 95:1552-1563. [DOI: 10.1080/09553002.2019.1649501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sihem Guesmi
- National Agronomy Institute (INAT), Avenue Charles Nicolle, Mahrajène, Tunisia
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Habib Chouchane
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Mohamed Neifar
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Faouzi Hosni
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
| | - Haïtham Sghaier
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, Tunisia
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30
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Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
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Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
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31
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Montero-Calasanz MDC, Yaramis A, Nouioui I, Igual JM, Spröer C, Castro JF, Schumann P, Klenk HP, Urzì C. Modestobacter italicus sp. nov., isolated from Carrara marble quarry and emended descriptions of the genus Modestobacter and the species Modestobacter marinus, Modestobacter multiseptatus, Modestobacter roseus and Modestobacter versicolor. Int J Syst Evol Microbiol 2019; 69:1537-1545. [DOI: 10.1099/ijsem.0.003282] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Adnan Yaramis
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - José Mariano Igual
- 2Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Cathrin Spröer
- 3Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jean Franco Castro
- 4Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beauchef 851, Santiago, Chile
| | - Peter Schumann
- 3Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- 1School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Clara Urzì
- 5Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
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León-Sobrino C, Ramond JB, Maggs-Kölling G, Cowan DA. Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil. Front Microbiol 2019; 10:1054. [PMID: 31139170 PMCID: PMC6527771 DOI: 10.3389/fmicb.2019.01054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/26/2019] [Indexed: 11/13/2022] Open
Abstract
Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.
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Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow M. Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol 2018; 41:427-436. [PMID: 29789182 DOI: 10.1016/j.syapm.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 01/20/2023]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12T and G. obscurus DSM 43160T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12T (CECT 9483T=NCIMB 15089T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.
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Affiliation(s)
- Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | | | - Tara Rahmani
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, United Kingdom
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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Hezbri K, Nouioui I, Rohde M, Spröer C, Schumann P, Gtari M, Klenk HP, Montero-Calasanz MDC, Ghodhbane-Gtari F. Blastococcus xanthinilyticus sp. nov., isolated from monument. Int J Syst Evol Microbiol 2018; 68:1177-1183. [PMID: 29458502 DOI: 10.1099/ijsem.0.002646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, non-motile, coccoid, Gram-stain-positive actinobacterium, designated BMG 862T, was isolated from a marble sample collected from the Bulla Regia monument, Northern Tunisia. Its taxonomic position was determined using a polyphasic approach. Results from chemotaxonomic analyses showed MK-9(H4), MK-8(H4) and MK-9(H2) as the predominant menaquinones. The major polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, hydroxy-phosphatidylethanolamine and three unidentified phospholipids. The fatty acids consisted of significant amounts (≥10 %) of iso-C16 : 0, C17 : 1ω8c, iso-C15 : 0 and C16 : 1ω7c. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons showed that strain BMG 862T belongs to the genus Blastococcus, being most closely related to Blastococcus saxobsidens (=DSM 44509T) (99.5 %) and Blastococcus capsensis (=DSM 46835T=CECT 8876T) (99.3 %). The genomic DNA G+C content of the organism was 74.7 mol%. Results of DNA-DNA hybridization and physiological tests allowed differentiation of strain BMG 862T from related species. The strain was also characterized by its ability to hydrolyse xanthine. On the basis of phenotypic and molecular characteristics, strain BMG 862T (=DSM 46842T=CECT 8884T) represents the type strain of a novel species of the genus Blastococcus, for which the name Blastococcus xanthinilyticus sp. nov. is proposed.
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Affiliation(s)
- Karima Hezbri
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar, Faculté des Sciences de Tunis, 2092 Tunis, Tunisia
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Manfred Rohde
- Central Facility for Microscopy, HZI - Helmholtz Centre for Infection Research Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Maher Gtari
- Institut National des Sciences Appliquées et de Technologie, Université Carthage, Centre Urbain Nord BP 676-1080 Tunis Cedex, Tunisia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Maria Del Carmen Montero-Calasanz
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar, Faculté des Sciences de Tunis, 2092 Tunis, Tunisia
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Ghedira K, Harigua-Souiai E, Ben Hamda C, Fournier P, Pujic P, Guesmi S, Guizani I, Miotello G, Armengaud J, Normand P, Sghaier H. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Sci Rep 2018; 8:759. [PMID: 29335550 PMCID: PMC5768760 DOI: 10.1038/s41598-017-18839-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
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Affiliation(s)
- Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
- Université de Carthage, Faculté des Sciences de Bizerte, Tunis, 7021, Tunisia
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Sihem Guesmi
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- National Agronomy Institute (INAT), Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- Associated with Laboratory "Biotechnology and Nuclear Technology" (LR16CNSTN01) & Laboratory "Biotechnology and Bio-Geo Resources Valorization" (LR11ES31), Sidi Thabet Technopark, 2020, Tunisia
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Montero-Calasanz MDC, Meier-Kolthoff JP, Zhang DF, Yaramis A, Rohde M, Woyke T, Kyrpides NC, Schumann P, Li WJ, Göker M. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae. Front Microbiol 2017; 8:2501. [PMID: 29312207 PMCID: PMC5742155 DOI: 10.3389/fmicb.2017.02501] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/01/2017] [Indexed: 11/13/2022] Open
Abstract
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dao-Feng Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Adnan Yaramis
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
- Department of Biotechnology, Middle East Technical University, Ankara, Turkey
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Peter Schumann
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Markus Göker
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Miotello G, Ktari A, Gueddou A, Nouioui I, Ghodhbane-Gtari F, Armengaud J, Gtari M. Proteogenomics data for deciphering Frankia coriariae interactions with root exudates from three host plants. Data Brief 2017; 14:73-76. [PMID: 28765834 PMCID: PMC5526514 DOI: 10.1016/j.dib.2017.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/22/2017] [Accepted: 07/05/2017] [Indexed: 10/28/2022] Open
Abstract
Frankia coriariae BMG5.1 cells were incubated with root exudates derived from compatible (Coriaria myrtifolia), incompatible (Alnus glutinosa) and non-actinorhizal (Cucumis melo) host plants. Bacteria cells and their exoproteomes were analyzed by high-throughput proteomics using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with two protein sequence databases derived from the closely-related genomes from strains BMG5.1 andDg1, the Frankia symbiont of Datisca glomerata. The tandem mass spectrometry data accompanying the manuscript describing the database searches and comparative analysis (Ktari et al., 2017, doi.org/10.3389/fmicb.2017.00720) [1] have been deposited to the ProteomeXchange with identifiers PXD005979 (whole cell proteomes) and PXD005980 (exoproteome data).
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Affiliation(s)
- Guylaine Miotello
- CEA, DRF/JOLIOT/DMTS/SPI/Li2D, Lab Innovative Technologies for Detection and Diagnostic, Bagnols-sur-Cèze, France
| | - Amir Ktari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Abdellatif Gueddou
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Imen Nouioui
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Jean Armengaud
- CEA, DRF/JOLIOT/DMTS/SPI/Li2D, Lab Innovative Technologies for Detection and Diagnostic, Bagnols-sur-Cèze, France
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
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Gat D, Mazar Y, Cytryn E, Rudich Y. Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6709-6718. [PMID: 28422476 DOI: 10.1021/acs.est.7b00362] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.
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Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization , Rishon Lezion 7528809, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
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40
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Rasuk MC, Ferrer GM, Kurth D, Portero LR, Farías ME, Albarracín VH. UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities. Photochem Photobiol 2017; 93:865-880. [DOI: 10.1111/php.12759] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/03/2017] [Indexed: 11/27/2022]
Affiliation(s)
- María Cecilia Rasuk
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Gabriela Mónica Ferrer
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Daniel Kurth
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Luciano Raúl Portero
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - María Eugenia Farías
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
| | - Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; S. M. de Tucumán Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
- Centro Integral de Microscopía Electrónica; CCT-Tucumán; CONICET; Universidad Nacional de Tucumán; Tucumán Argentina
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41
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Wilhelm RC, Cardenas E, Leung H, Szeitz A, Jensen LD, Mohn WW. Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing. Front Microbiol 2017; 8:537. [PMID: 28443069 PMCID: PMC5386986 DOI: 10.3389/fmicb.2017.00537] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/14/2017] [Indexed: 12/23/2022] Open
Abstract
Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting. Using a variety of experimental approaches, including stable isotope probing with 13C-labeled cellulose in soil microcosms, we demonstrated that harvesting led to a decrease in net respiration and cellulolytic activity. The decrease in cellulolytic activity was associated with an increased relative abundance of thermophilic, cellulolytic fungi (Chaetomiaceae), coupled with a decreased relative abundance of cellulolytic bacteria, particularly members of Opitutaceae, Caulobacter, and Streptomycetaceae. In general, harvesting led to an increase in stress-tolerant taxa (i.e., also non-cellulolytic taxa), though our results indicated that OM retention mitigated population shifts via buffering against abiotic changes. Stable-isotope probing improved shotgun metagenome assembly by 20-fold and enabled the recovery of 10 metagenome-assembled genomes of cellulolytic bacteria and fungi. Our study demonstrates the putative cellulolytic activity of a number of uncultured taxa and highlights the mineral soil layer as a reservoir of uncharacterized diversity of cellulose-degraders. It also and contributes to a growing body of research showing persistent changes in microbial community structure in the decades following forest harvesting.
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Affiliation(s)
- Roland C. Wilhelm
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - Hilary Leung
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - András Szeitz
- Pharmaceutical Analytical Suite, Faculty of Pharmaceutical Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Lionel D. Jensen
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British ColumbiaVancouver, BC, Canada
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Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau. Appl Environ Microbiol 2017; 83:AEM.03020-16. [PMID: 28087533 DOI: 10.1128/aem.03020-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023] Open
Abstract
Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.
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Gaylarde C, Baptista-Neto JA, Ogawa A, Kowalski M, Celikkol-Aydin S, Beech I. Epilithic and endolithic microorganisms and deterioration on stone church facades subject to urban pollution in a sub-tropical climate. BIOFOULING 2017; 33:113-127. [PMID: 28054493 DOI: 10.1080/08927014.2016.1269893] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
Weathering of two church facades in Rio de Janeiro was caused substantially by salts, mainly halite and gypsum, detected by SEM and chemical analyses, which cause physical stresses by deposition within the rock. Biofilm populations, determined by SEM and as operational taxonomic units (OTUs), degraded stone by penetration, solubilization and redeposition of minerals on their surfaces. Endolithic cyanobacteria were associated with gypsum deposits. Microbiomes were typical for high-stress environments, high salt, intense insolation, low water and low nutrients (eg halophilic Rubrobacter, Salinicola, Sterigmatomyces). The main colonizers on the church most affected by traffic (Nossa Senhora da Candelária - CA) were Actinobacteria; Gammaproteobacteria (chiefly Pseudomonas) were predominant on the site situated in a leafy square (São Francisco de Paula - SF). Major Gammaproteobacteria on CA were halophilic Halomonas and Rhodobacteriaceae. Fungal OTUs on both churches were principally dimorphic, yeast-like basidiomycetes. Many OTUs of thermophilic microorganisms (eg the Thermomicrobia class, Chloroflexi) were present. This is the first use of next generation sequencing (NGS) to study microbial biofilm interactions with metamorphic and granite buildings in an intensely urban, sub-tropical climate.
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Affiliation(s)
- Christine Gaylarde
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | | | - Akiko Ogawa
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Matthew Kowalski
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Sukriye Celikkol-Aydin
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Iwona Beech
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
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Hezbri K, Louati M, Nouioui I, Gtari M, Rohde M, Spröer C, Schumann P, Klenk HP, Ghodhbane-Gtari F, Montero-Calasanz MDC. Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus. Int J Syst Evol Microbiol 2016; 66:4864-4872. [PMID: 27553620 DOI: 10.1099/ijsem.0.001443] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-reaction-positive actinobacterium, designated BMG 804T, was isolated from an archaeological Roman pool located in Gafsa, Tunisia. The strain grew as dry bright orange colonies at 30 °C and pH 6.0-8.0. It contained meso-diaminopimelic acid in the cell wall. The whole-cell sugars consisted of glucose, rhamnose and ribose. Polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, an unidentified glycolipid and two unidentified phospholipids. MK-9(H4) was the predominant menaquinone. The fatty acid profile contained major amounts (>5 %) of C17 : 1ω8c, C16 : 1ω7c, iso-C15 : 0, iso-C16 : 0 and iso-C16 : 1H. The 16S rRNA gene sequence of BMG 804T showed 99.4 % as highest sequence similarity with Blastococcussaxobsidens. DNA-DNA hybridization between strain BMG 804T and B.saxobsidens DSM 44509T was 48.6±6.6 %. The G+C content of the DNA was 73.7 mol%. On the basis of the phenotypic and genotypic characteristics, including DNA-DNA hybridization results, BMG 804T (=DSM 46835T=CECT 8876T) is proposed as the type strain of a novel species Blastococcuscapsensis sp. nov. Emended descriptions of the genus Blastococcus and the species Blastococcus aggregatus, B. saxobsidens, Blastococcus jejuensis and Blastococcus endophyticus are also proposed.
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Affiliation(s)
- Karima Hezbri
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Moussa Louati
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Imen Nouioui
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Manfred Rohde
- Central Facility for Microscopy, HZI - Helmholtz Centre for Infection Research Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Maria Del Carmen Montero-Calasanz
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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King P, Pham LK, Waltz S, Sphar D, Yamamoto RT, Conrad D, Taplitz R, Torriani F, Forsyth RA. Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes. PLoS One 2016; 11:e0160124. [PMID: 27482891 PMCID: PMC4970769 DOI: 10.1371/journal.pone.0160124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/05/2016] [Indexed: 12/15/2022] Open
Abstract
We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.
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Affiliation(s)
- Paula King
- FLIR Systems, Inc., La Jolla, California, United States of America
- Singlera Genomics, Inc., La Jolla, California, United States of America
| | - Long K. Pham
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Shannon Waltz
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Dan Sphar
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Douglas Conrad
- Department of Medicine, Division of Pulmonary Medicine, UC San Diego Health System, San Diego, California, United States of America
| | - Randy Taplitz
- Department of Medicine, Division of Infectious Diseases and Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health System, San Diego, California, United States of America
| | - Francesca Torriani
- Department of Medicine, Division of Infectious Diseases and Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health System, San Diego, California, United States of America
| | - R. Allyn Forsyth
- FLIR Systems, Inc., La Jolla, California, United States of America
- Singlera Genomics, Inc., La Jolla, California, United States of America
- Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
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Hezbri K, Ghodhbane-Gtari F, Montero-Calasanz MDC, Nouioui I, Rohde M, Spröer C, Schumann P, Klenk HP, Gtari M. Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert. Int J Syst Evol Microbiol 2016; 66:3828-3834. [PMID: 27381197 DOI: 10.1099/ijsem.0.001272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A black-pigmented, aerobic actinobacterium, tolerant to ionizing radiation, designated BMG 825T, was isolated from desert limestone dust in Tunisia. The strain grew within the temperature range 10-40 °C, at pH 5.5-11.0 and in the presence of 2 % NaCl. The DNA G+C content was 75.7 mol%, and its cell-wall peptidoglycan contained meso-diaminopimelic acid. Sugars of whole-cell hydrolysates were galactose, glucose, and trace amounts of ribose and mannose. The predominant menaquinone was MK-9(H4), and the major fatty acids were iso-C16 : 0 and C16 : 1ω7c. The polar lipid profile comprised phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and an unspecified glycolipid. 16S rRNA gene sequence analysis revealed that the strain fell into the genus Geodermatophilus, showing the highest similarity with Geodermatophilus poikilotrophus DSM 44209T (99.1 %). DNA-DNA hybridization results, phylogenetic distinctiveness and phenotypic properties supported the classification of this strain as a representative of a novel species of the genus Geodermatophilus, for which the name Geodermatophilus pulveris sp. nov. is proposed. The type strain is BMG 825T (=CECT 9003T=DSM 46839T).
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Affiliation(s)
- Karima Hezbri
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Faten Ghodhbane-Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
| | - Maria Del Carmen Montero-Calasanz
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.,School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Manfred Rohde
- Central Facility for Microscopy HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne NE1 7RU, UK
| | - Maher Gtari
- Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis El Manar (FST) & Université de Carthage (INSAT), 2092 Tunis, Tunisia
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Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing. Appl Microbiol Biotechnol 2016; 100:8537-48. [DOI: 10.1007/s00253-016-7656-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
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