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Zhang T, Zhang D, Lyu Z, Zhang J, Wu X, Yu Y. Effects of extreme precipitation on bacterial communities and bioaerosol composition: Dispersion in urban outdoor environments and health risks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123406. [PMID: 38244904 DOI: 10.1016/j.envpol.2024.123406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
Concerns about contaminants dispersed by seasonal precipitation have grown due to their potential hazards to outdoor environments and human health. However, studies on the crucial environmental factors influencing dispersion changes in bacterial communities are limited. This research adopted four-season in situ monitoring and sequencing techniques to examine the regional distribution profiles of bioaerosols, bacterial communities, and risks associated with extreme snowfall versus rainfall events in two monsoon cities. In the early-hours of winter snowfall, airborne cultivable bioaerosol concentrations were 4.1 times higher than the reference exposure limit (500 CFU/m3). The concentration of ambient particles (2.5 μm) exceeded 24,910 particles/L (97 μg/m3), positively correlating with the prevalence of cultivable bioaerosols. These bioaerosols contained cultivable bacterial species such as pathogenic Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, and Escherichia coli. Bioaerosol concentrations increased by 53.0% during 50-mm snow extremes. Taxonomic analysis revealed that Pseudomonas, Staphylococcus, and Veillonella were the most abundant bacterial taxa in the initial snowmelt samples during winter precipitation. However, their abundance decreased by 87.6% as snowing continued (24 h). Reduced water base cation concentration also led to a 1.15-fold increase in the Shannon index, indicating a similar yet heightened bacterial diversity. Seasonally, Pedobacter and Massilia showed higher relative abundance (25% and 18%, respectively), presenting increased bacterial transmission to the soil. Furthermore, Pseudomonas was identified in 60% of spring snowstorm samples, suggesting long-distance dispersal of pathogenic bacteria. When these atmospheric aerosol particles carrying biological entities (0.65-1.1 μm) penetrated human alveoli, the calculated hazard ratio was 0.55, which as observed in inhalation exposures. Consequently, this study underscores the risk of seasonal precipitation-enhanced ambient bacterial transmission.
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Affiliation(s)
- Ting Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Dingqiang Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Zhonghang Lyu
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Jitao Zhang
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Xian Wu
- College of Civil Engineering, Liaoning Technical University, Fuxin, 123000, China
| | - Yingxin Yu
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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2
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Power JF, Carere CR, Welford HE, Hudson DT, Lee KC, Moreau JW, Ettema TJG, Reysenbach AL, Lee CK, Colman DR, Boyd ES, Morgan XC, McDonald IR, Craig Cary S, Stott MB. A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nat Commun 2024; 15:179. [PMID: 38167814 PMCID: PMC10762115 DOI: 10.1038/s41467-023-43960-2] [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: 04/18/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
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Affiliation(s)
- Jean F Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Carlo R Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Holly E Welford
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Daniel T Hudson
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
| | - Kevin C Lee
- Te Kura Pūtaiao | School of Science, Te Wānanga Aronui o Tāmaki Makau Rau | Auckland University of Technology, Auckland, 1010, Aotearoa New Zealand
| | - John W Moreau
- School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | | | - Charles K Lee
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Xochitl C Morgan
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian R McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - S Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand.
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3
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Adhikari A, Banerjee P, Thornton T, Jones DH, Adeoye C, Sherpa S. Exposure Levels of Airborne Fungi, Bacteria, and Antibiotic Resistance Genes in Cotton Farms during Cotton Harvesting and Evaluations of N95 Respirators against These Bioaerosols. Microorganisms 2023; 11:1561. [PMID: 37375063 DOI: 10.3390/microorganisms11061561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
The USA is the third-leading cotton-producing country worldwide and cotton farming is common in the state of Georgia. Cotton harvest can be a significant contributor to airborne microbial exposures to farmers and nearby rural communities. The use of respirators or masks is one of the viable options for reducing organic dust and bioaerosol exposures among farmers. Unfortunately, the OSHA Respiratory Protection Standard (29 CFR Part 1910.134) does not apply to agricultural workplaces and the filtration efficiency of N95 respirators was never field-tested against airborne microorganisms and antibiotic resistance genes (ARGs) during cotton harvesting. This study addressed these two information gaps. Airborne culturable microorganisms were sampled using an SAS Super 100 Air Sampler in three cotton farms during cotton harvesting, and colonies were counted and converted to airborne concentrations. Genomic DNA was extracted from air samples using a PowerSoil® DNA Isolation Kit. A series of comparative critical threshold (2-ΔΔCT) real-time PCR was used to quantify targeted bacterial (16S rRNA) genes and major ARGs. Two N95 facepiece respirator models (cup-shaped and pleated) were evaluated for their protection against culturable bacteria and fungi, total microbial load in terms of surface ATP levels, and ARGs using a field experimental setup. Overall, culturable microbial exposure levels ranged between 103 and 104 CFU/m3 during cotton harvesting, which was lower when compared with bioaerosol loads reported earlier during other types of grain harvesting. The findings suggested that cotton harvesting works can release antibiotic resistance genes in farm air and the highest abundance was observed for phenicol. Field experimental data suggested that tested N95 respirators did not provide desirable >95% protections against culturable microorganisms, the total microbial load, and ARGs during cotton harvesting.
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Affiliation(s)
- Atin Adhikari
- Department of Biostatistics, Epidemiology & Environmental Health Sciences, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30460, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taylor Thornton
- Department of Biostatistics, Epidemiology & Environmental Health Sciences, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30460, USA
| | - Daleniece Higgins Jones
- Department of Public Health, College of Education, Health, and Human Sciences, The University of Tennessee, Knoxville, TN 37996, USA
| | - Caleb Adeoye
- Department of Biostatistics, Epidemiology & Environmental Health Sciences, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30460, USA
| | - Sonam Sherpa
- Department of Health Policy and Community Health, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30460, USA
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Budil J, Štenclová P, Kromka A, Lišková P. Development of the Pseudomonas syringae pv. morsprunorum Biofilm Monitored in Real Time Using Attenuated Total Reflection Fourier Transform Infrared Measurements in a Flow Cell Chamber. APPLIED SPECTROSCOPY 2023; 77:500-512. [PMID: 36898963 DOI: 10.1177/00037028231165057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biofilms of sessile Pseudomonas syringae cells formed on top of plant host's leaves or fruits allow surviving harsh environmental conditions (desiccation) and improve their resistance to antibacterial treatments of crops. A better understanding of these biofilms can help minimize their effect on harvests. In the present study, infrared attenuated total reflection spectroscopy coupled with optical and confocal laser scanning microscopy has been applied for the first time to analyze Pseudomonas syringae pathovar morsprunorum biofilm development in real time. The biofilm development was observed within a spectral window 4000-800 cm-1 under constant flow conditions for 72 h. The kinetics of representative integrated band areas (nucleic acids with polysaccharides at 1141-1006 cm-1, amino acid side chains with free fatty acids at 1420-1380 cm-1, proteins at 1580-1490 cm-1, and lipids with proteins at 2935-2915 cm-1) were analyzed with regard to the observed biofilm structure and the following P. syringae biofilm developmental stages were attributed: The inoculation phase, washing of weakly attached bacteria closely followed by recolonization of the vacated surface, the restructuration phase, and finally the maturation phase.
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Affiliation(s)
- Jakub Budil
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavla Štenclová
- Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alexander Kromka
- Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Lišková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
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5
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Fan C, Xie W, Hu W, Matsusaki H, Kojima T, Zhang D. Number size distribution of bacterial aerosols in terrestrial and marine airflows at a coastal site of Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161238. [PMID: 36586682 DOI: 10.1016/j.scitotenv.2022.161238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Size-differentiated concentration of bacterial aerosols is essential for investigating their dissemination via the atmosphere. In this study, the number size distribution of bacterial aerosols was measured at a coastal site in southwestern Japan (32.324°N, 129.993°E) using a size-segregated eight-stage (>11, 7.0-11, 4.7-7.0, 3.3-4.7, 2.1-3.3, 1.1-2.1, 0.65-1.1, and 0.43-0.65μm) sampler. The results showed that the distribution differed according to the source areas: terrestrial air, oceanic air, or a combination of the two. The distribution in the long-distance transported terrestrial air from the Asian continent was monomodal, with a peak of 3.3-4.7 μm. The distribution in local land breeze air was bimodal, with the peaks at 0.43-1.1 and 3.3-4.7 μm. A similar bimodal distribution was encountered when the local island air and long-distance transported terrestrial air mixed. In contrast, the size distribution did not show clear peaks in the air from either nearby or remote marine areas. According to the air mass backward trajectories, the further the distance the air moved in the 72 h before arriving at the site, the lower the concentration of total bacterial aerosols. The estimation of dry deposition fluxes of bacterial cells showed that the deposition was dominated by cells larger than 1.1 μm with a relative contribution from 70.5 % to 93.7 %, except for the local land breeze cases, where the contributions in the size ranges larger and smaller than 1.1 μm were similar. These results show the distinctive number size distributions and removal processes of bacterial aerosols in different types of air. In addition, they indicate that size-dependent characteristics of airborne bacteria should be considered when studying their activities and roles in the atmospheric environment.
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Affiliation(s)
- Chunlan Fan
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Wenwen Xie
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Hiromi Matsusaki
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Tomoko Kojima
- Department Earth and Environmental Science, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Daizhou Zhang
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan.
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Silva-Sanzana C, Gangas MV, Zavala D, Blanco-Herrera F. A Recipe for Success: Three Key Strategies Used by Aphids and Pseudomonas syringae to Colonize the Phyllosphere. MICROBIAL ECOLOGY 2023; 85:1-8. [PMID: 35039905 PMCID: PMC9849291 DOI: 10.1007/s00248-022-01965-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.
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Affiliation(s)
- Christian Silva-Sanzana
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maria Victoria Gangas
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Diego Zavala
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), ANID, Santiago, Chile
| | - Francisca Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, 8370186, Chile.
- Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), ANID, Santiago, Chile.
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Bhat MA, Eraslan FN, Awad A, Malkoç S, Üzmez ÖÖ, Döğeroğlu T, Gaga EO. Investigation of indoor and outdoor air quality in a university campus during COVID-19 lock down period. BUILDING AND ENVIRONMENT 2022; 219:109176. [PMID: 35599669 PMCID: PMC9116033 DOI: 10.1016/j.buildenv.2022.109176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
The pandemic of COVID-19 currently shadows the world; the whole earth has been on an unprecedented lockdown. Social distancing among people interrupted domestic and international air traffic, suspended industrial productions and economic activities, and had various far-reaching and undetermined implications on air quality. Improvement in air quality has been reported in many cities during the lockdown. On March 22, 2020, the Turkish government enforced strict lockdown measures to reduce coronavirus disease transmission. This lockdown had a significant impact on the movement of people within the country, which resulted in a major drop in worldwide commercial activities. During this period, university campuses were emptied due to the transition to distance education. In this study, various air pollutants sulfur dioxide (SO2), nitrogen dioxide (NO2), ozone (O3), fine particulate matter (PM2.5), total bacteria, and total fungi were measured in different indoor environments at Eskişehir Technical University Campus in Eskişehir, Turkey during COVID-19 lock down period. Also, to calculate the indoor and outdoor ratios (I/O) of the pollutants, simultaneous outdoor measurements were also carried out. The average indoor SO2, NO2, O3, and PM2.5 concentrations in different indoor environments ranged between 2.10 and 54.58, 1.36-30.89, 12.01-39.05, and 21-94 μg/m3, respectively. The total number of bacteria and fungi ranged between 21.83-514.15 and 13.10-83.36 CFU/m3, respectively. Our study intends to give a glimpse to quantify the impact of a pandemic on air quality in different indoor environments in a university campus in Eskişehir, Turkey and calls for follow-up studies. Indoor concentrations were evaluated together with outdoor concentrations. In general, it can be said that the calculated I/O ratios for SO2, NO2, O3, bacteria, and fungi were less than 1 in most indoor environments.
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Affiliation(s)
- Mansoor Ahmad Bhat
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
| | - Fatma Nur Eraslan
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
| | - Alaa Awad
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
| | - Semra Malkoç
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
- Eskişehir Technical University, Environmental Research Center (ÇEVMER), 26555, Eskişehir, Turkey
| | - Özlem Özden Üzmez
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
| | - Tuncay Döğeroğlu
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
| | - Eftade O Gaga
- Eskişehir Technical University, Faculty of Engineering, Department of Environmental Engineering, 26555, Eskişehir, Turkey
- Eskişehir Technical University, Environmental Research Center (ÇEVMER), 26555, Eskişehir, Turkey
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Morris CE, Ramirez N, Berge O, Lacroix C, Monteil C, Chandeysson C, Guilbaud C, Blischke A, Sigurbjörnsdóttir MA, Vilhelmsson OÞ. Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth’s Temperate Zones. Pathogens 2022; 11:pathogens11030357. [PMID: 35335680 PMCID: PMC8951587 DOI: 10.3390/pathogens11030357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 107 cfu g−1 and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.
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Affiliation(s)
- Cindy E. Morris
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
- Correspondence:
| | - Natalia Ramirez
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
| | - Odile Berge
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Christelle Lacroix
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Cécile Monteil
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Charlotte Chandeysson
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Caroline Guilbaud
- INRAE, Pathologie Végétale, F-84140 Montfavet, France; (O.B.); (C.L.); (C.M.); (C.C.); (C.G.)
| | - Anett Blischke
- ÍSOR, Iceland GeoSurvey, Rangárvöllum við Hlíðarfjallsveg, 600 Akureyri, Iceland;
| | | | - Oddur Þ. Vilhelmsson
- Faculty of Natural Resource Sciences, University of Akureyri, 600 Akureyri, Iceland; (N.R.); (M.A.S.); (O.Þ.V.)
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9
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Galbán S, Justel A, González S, Quesada A. Local meteorological conditions, shape and desiccation influence dispersal capabilities for airborne microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146653. [PMID: 34030336 DOI: 10.1016/j.scitotenv.2021.146653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
The atmosphere plays an important role in the dispersal of microorganisms, as well as in the connectivity of most of the planet's ecosystems. In recent decades, interest in microbial diversity and dispersion in the atmosphere has increased due to its importance in various fields. However, there are few studies on the abundance of airborne microorganisms and the factors, such as meteorology, that affect their distribution. Likewise, the physical-mathematical models attempting to reproduce their possible origins also require integrating some biological features. We collected airborne microorganisms under different meteorological conditions at a sampling station over a 12-day period to expand the knowledge about abundance of airborne microorganisms, their relationship with atmospheric conditions and their possible origins with a biological perspective. Total abundance and size distribution of microorganisms were measured in all samples using epifluorescence techniques. Their possible origins were estimated using refined mathematical simulation models of the air masses back-trajectories considering dry deposition. Our results showed microbial abundance values similar to those found in temperate regions over land surface. In our contribution we report a clear relationship between the abundance and, considered as a whole, local meteorological conditions. Despite most of the captured particles were small spherical microorganisms (diameter < 20 μm), large filamentous microorganisms, surprisingly up to 400 μm, were also found. We demonstrate the possibility that these large microorganisms can have their origin at long distances, showing thus probability of remarkable long dispersal, without ruling out a nearby origin, when their equivalent spherical diameter (ESD) and drying capacity are considered.
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Affiliation(s)
- Sofía Galbán
- Department of Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana Justel
- Department of Mathematics, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergi González
- Antarctic Group, Meteorology State Agency (AEMET), 08005 Barcelona, Spain
| | - Antonio Quesada
- Department of Biology, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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10
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Fragola M, Perrone MR, Alifano P, Talà A, Romano S. Seasonal Variability of the Airborne Eukaryotic Community Structure at a Coastal Site of the Central Mediterranean. Toxins (Basel) 2021; 13:518. [PMID: 34437389 PMCID: PMC8402549 DOI: 10.3390/toxins13080518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
The atmosphere represents an underexplored temporary habitat for airborne microbial communities such as eukaryotes, whose taxonomic structure changes across different locations and/or regions as a function of both survival conditions and sources. A preliminary dataset on the seasonal dependence of the airborne eukaryotic community biodiversity, detected in PM10 samples collected from July 2018 to June 2019 at a coastal site representative of the Central Mediterranean, is provided in this study. Viridiplantae and Fungi were the most abundant eukaryotic kingdoms. Streptophyta was the prevailing Viridiplantae phylum, whilst Ascomycota and Basidiomycota were the prevailing Fungi phyla. Brassica and Panicum were the most abundant Streptophyta genera in winter and summer, respectively, whereas Olea was the most abundant genus in spring and autumn. With regards to Fungi, Botrytis and Colletotrichum were the most abundant Ascomycota genera, reaching the highest abundance in spring and summer, respectively, while Cryptococcus and Ustilago were the most abundant Basidiomycota genera, and reached the highest abundance in winter and spring, respectively. The genus community structure in the PM10 samples varied day-by-day, and mainly along with the seasons. The impact of long-range transported air masses on the same structure was also proven. Nevertheless, rather few genera were significantly correlated with meteorological parameters and PM10 mass concentrations. The PCoA plots and non-parametric Spearman's rank-order correlation coefficients showed that the strongest correlations generally occurred between parameters reaching high abundances/values in the same season or PM10 sample. Moreover, the screening of potential pathogenic fungi allowed us to detect seven potential pathogenic genera in our PM10 samples. We also found that, with the exception of Panicum and Physcomitrella, all of the most abundant and pervasive identified Streptophyta genera could serve as potential sources of aeroallergens in the studied area.
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Affiliation(s)
- Mattia Fragola
- Department of Mathematics and Physics, University of Salento, Via per Arnesano, 73100 Lecce, Italy; (M.F.); (M.R.P.)
| | - Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, Via per Arnesano, 73100 Lecce, Italy; (M.F.); (M.R.P.)
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy; (P.A.); (A.T.)
| | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Monteroni, 73100 Lecce, Italy; (P.A.); (A.T.)
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, Via per Arnesano, 73100 Lecce, Italy; (M.F.); (M.R.P.)
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11
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Draft Genome Sequences of Pseudomonas spp. Isolated from Berry Surfaces in Commercial Cranberry Bogs in Massachusetts, USA. Microbiol Resour Announc 2021; 10:e0020421. [PMID: 34236228 PMCID: PMC8265235 DOI: 10.1128/mra.00204-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The surfaces of plants are colonized by a rich diversity of microbes but are largely unexplored. Here, we present the draft genome sequences of five Pseudomonas spp. isolated from cultivated cranberry fruit surfaces. Although the isolates represent four different species, their genomes all contain conserved iron sequestration and uptake genes.
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12
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Huang S, Hu W, Chen J, Wu Z, Zhang D, Fu P. Overview of biological ice nucleating particles in the atmosphere. ENVIRONMENT INTERNATIONAL 2021; 146:106197. [PMID: 33271442 DOI: 10.1016/j.envint.2020.106197] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 05/14/2023]
Abstract
Biological particles in the Earth's atmosphere are a distinctive category of ice nucleating particles (INPs) due to their capability of facilitating ice crystal formation in clouds at relatively warm temperatures. Field observations and model simulations have shown that biological INPs affect cloud and precipitation formation and regulate regional or even global climate, although there are considerable uncertainties in modeling and large gaps between observed and model simulated contribution of biological particles to atmospheric INPs. This paper overviews the latest researches about biological INPs in the atmosphere. Firstly, we describe the primary ice nucleation mechanisms, and measurements and model simulations of atmospheric biological INPs. Secondly, we summarize the ice nucleating properties of biological INPs from diverse sources such as soils or dust, vegetation (e.g., leaves and pollen grains), sea spray, and fresh waters, and controlling factors of biological INPs in the atmosphere. Then we review the abundance and distribution of atmospheric biological INPs in diverse ecosystems. Finally, we discuss the open questions in further studies on atmospheric biological INPs, including the requirements for developing novel detection techniques and simulation models, as well as the comprehensive investigation of characteristics and influencing factors of atmospheric biological INPs.
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Affiliation(s)
- Shu Huang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China.
| | - Jie Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhijun Wu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Daizhou Zhang
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Pingqing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China.
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13
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Ruiz-Gil T, Acuña JJ, Fujiyoshi S, Tanaka D, Noda J, Maruyama F, Jorquera MA. Airborne bacterial communities of outdoor environments and their associated influencing factors. ENVIRONMENT INTERNATIONAL 2020; 145:106156. [PMID: 33039877 DOI: 10.1016/j.envint.2020.106156] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 05/16/2023]
Abstract
Microbial entities (such bacteria, fungi, archaea and viruses) within outdoor aerosols have been scarcely studied compared with indoor aerosols and nonbiological components, and only during the last few decades have their studies increased. Bacteria represent an important part of the microbial abundance and diversity in a wide variety of rural and urban outdoor bioaerosols. Currently, airborne bacterial communities are mainly sampled in two aerosol size fractions (2.5 and 10 µm) and characterized by culture-dependent (plate-counting) and culture-independent (DNA sequencing) approaches. Studies have revealed a large diversity of bacteria in bioaerosols, highlighting Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as ubiquitous phyla. Seasonal variations in and dispersion of bacterial communities have also been observed between geographical locations as has their correlation with specific atmospheric factors. Several investigations have also suggested the relevance of airborne bacteria in the public health and agriculture sectors as well as remediation and atmospheric processes. However, although factors influencing airborne bacterial communities and standardized procedures for their assessment have recently been proposed, the use of bacterial taxa as microbial indicators of specific bioaerosol sources and seasonality have not been broadly explored. Thus, in this review, we summarize and discuss recent advances in the study of airborne bacterial communities in outdoor environments and the possible factors influencing their abundance, diversity, and seasonal variation. Furthermore, airborne bacterial activity and bioprospecting in different fields (e.g., the textile industry, the food industry, medicine, and bioremediation) are discussed. We expect that this review will reveal the relevance and influencing factors of airborne bacteria in outdoor environments as well as stimulate new investigations on the atmospheric microbiome, particularly in areas where air quality is a public concern.
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Affiliation(s)
- Tay Ruiz-Gil
- Doctorado en Ciencias de Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - So Fujiyoshi
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Microbial Genomics and Ecology, Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - Daisuke Tanaka
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Jun Noda
- Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan; Graduate School of Veterinary Science, Rakuno Gakuen University, Hokkaido, Japan
| | - Fumito Maruyama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Microbial Genomics and Ecology, Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile; Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Japan.
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14
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Els N, Greilinger M, Reisecker M, Tignat-Perrier R, Baumann-Stanzer K, Kasper-Giebl A, Sattler B, Larose C. Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria. Front Microbiol 2020; 11:980. [PMID: 32508790 PMCID: PMC7251065 DOI: 10.3389/fmicb.2020.00980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022] Open
Abstract
We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphere continuously onto quartzfiber air filters using a DIGITEL high volume PM10 sampler. The bacterial and fungal communities, sequenced using Illumina MiSeq, as well as the chemical components of the atmosphere were compared to those of a late season snow profile. Results reveal strong dynamics in the composition of bacterial and fungal communities in air and snow. In fall the two compartments were similar, suggesting a strong interaction between them. The overlap diminished as the season progressed due to an evolution within the snowpack throughout winter and spring. Certain bacterial and fungal genera were only detected in air samples, which implies that a distinct air microbiome might exist. These organisms are likely not incorporated in clouds and thus not precipitated or scavenged in snow. Although snow appears to be seeded by the atmosphere, both air and snow showed differing bacterial and fungal communities and chemical composition. Season and alpha diversity were major drivers for microbial variability in snow and air, and only a few chemical markers were identified as important in explaining microbial diversity. Air microbial community variation was more related to chemical markers than snow microbial composition. For air microbial communities Cl–, TC/OC, SO42–, Mg2+, and Fe/Al, all compounds related to dust or anthropogenic activities, were identified as related to bacterial variability while dust related Ca2+ was significant in snow. The only common driver for snow and air was SO42–, a tracer for anthropogenic sources. The occurrence of chemical compounds was coupled with boundary layer injections in the free troposphere (FT). Boundary layer injections also caused the observed variations in community composition and chemistry between the two compartments. Long-term monitoring is required for a more valid insight in post-depositional selection in snow.
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Affiliation(s)
- Nora Els
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Marion Greilinger
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria.,Zentralanstalt für Meteorologie und Geodynamik (ZAMG), Vienna, Austria
| | - Michael Reisecker
- Avalanche Warning Service Tyrol, Department of Civil Protection, Federal State Government of Tyrol, Innsbruck, Austria
| | - Romie Tignat-Perrier
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
| | | | - Anne Kasper-Giebl
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Catherine Larose
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
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15
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Community Structure and Influencing Factors of Airborne Microbial Aerosols over Three Chinese Cities with Contrasting Social-Economic Levels. ATMOSPHERE 2020. [DOI: 10.3390/atmos11040317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As an important part of atmospheric aerosol, airborne bacteria have major impacts on human health. However, variations of airborne community structure due to human-induced activities and their possible impact on human health have not been well understood. In this study, we sampled atmospheric microbial aerosols in three Chinese cities (Shanghai, Xiamen, and Zhangzhou) with contrasting social-economic levels and analyzed the bacterial composition using high-throughput sequencing methods. A high similarity of the predominant phyla was observed in three cities but the relative abundances were quite different. At the genus level, the most dominant genus in Shanghai and Xiamen was Deinococcus while the most dominant genus in Zhangzhou was Clostridium. The different characteristics of airborne bacterial in the three cities above may be ascribed to the environmental variables affected by human over-activities such as the vehicle exhausts and coal-burning emissions in Shanghai, the tourist aggregation and construction works in Xiamen, the extensive uses of chemical fertilizers, and agricultural activities in Zhangzhou. The variation of the bacterial community and the pathogenic bacteria detected in three cities would have a potential threat to human health.
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16
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Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation. Appl Environ Microbiol 2019; 85:AEM.01567-19. [PMID: 31562166 DOI: 10.1128/aem.01567-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
Airborne bacteria that nucleate ice at relatively warm temperatures (>-10°C) can interact with cloud water droplets, affecting the formation of ice in clouds and the residency time of the cells in the atmosphere. We sampled 65 precipitation events in southeastern Louisiana over 2 years to examine the effect of season, meteorological conditions, storm type, and ecoregion source on the concentration and type of ice-nucleating particles (INPs) deposited. INPs sensitive to heat treatment were inferred to be biological in origin, and the highest concentrations of biological INPs (∼16,000 INPs liter-1 active at ≥-10°C) were observed in snow and sleet samples from wintertime nimbostratus clouds with cloud top temperatures as warm as -7°C. Statistical analysis revealed three temperature classes of biological INPs (INPs active from -5 to -10°C, -11 to -12°C, and -13 to -14°C) and one temperature class of INPs that were sensitive to lysozyme (i.e., bacterial INPs, active from -5 to -10°C). Significant correlations between the INP data and abundances of taxa in the Bacteroidetes, Firmicutes, and unclassified bacterial divisions implied that certain members of these phyla may possess the ice nucleation phenotype. The interrelation between the INP classes and fluorescent dissolved organic matter, major ion concentrations (Na+, Cl-, SO4 2-, and NO3 -), and backward air mass trajectories indicated that the highest concentrations of INPs were sourced from high-latitude North American and Asian continental environments, whereas the lowest values were observed when air was sourced from marine ecoregions. The intra- and extracontinental regions identified as sources of biological INPs in precipitation deposited in the southeastern United States suggests that these bioaerosols can disperse and affect meteorological conditions thousands of kilometers from their terrestrial points of origin.IMPORTANCE The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that implicated specific bacterial taxa as the source of the ice nucleation activity. The abundance of biological INPs was highest in precipitation from winter storms and implied that their in-cloud concentrations were sufficient to affect the formation of ice and precipitation in nimbostratus clouds.
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17
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Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast. Proc Natl Acad Sci U S A 2019; 116:18900-18910. [PMID: 31484768 DOI: 10.1073/pnas.1908858116] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The foliar plant pathogen Pseudomonas syringae can establish large epiphytic populations on leaf surfaces before apoplastic colonization. However, the bacterial genes that contribute to these lifestyles have not been completely defined. The fitness contributions of 4,296 genes in P. syringae pv. syringae B728a were determined by genome-wide fitness profiling with a randomly barcoded transposon mutant library that was grown on the leaf surface and in the apoplast of the susceptible plant Phaseolus vulgaris Genes within the functional categories of amino acid and polysaccharide (including alginate) biosynthesis contributed most to fitness both on the leaf surface (epiphytic) and in the leaf interior (apoplast), while genes involved in type III secretion system and syringomycin synthesis were primarily important in the apoplast. Numerous other genes that had not been previously associated with in planta growth were also required for maximum epiphytic or apoplastic fitness. Fourteen hypothetical proteins and uncategorized glycosyltransferases were also required for maximum competitive fitness in and on leaves. For most genes, no relationship was seen between fitness in planta and either the magnitude of their expression in planta or degree of induction in planta compared to in vitro conditions measured in other studies. A lack of association of gene expression and fitness has important implications for the interpretation of transcriptional information and our broad understanding of plant-microbe interactions.
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18
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Liu H, Hu Z, Zhou M, Hu J, Yao X, Zhang H, Li Z, Lou L, Xi C, Qian H, Li C, Xu X, Zheng P, Hu B. The distribution variance of airborne microorganisms in urban and rural environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:898-906. [PMID: 30823344 DOI: 10.1016/j.envpol.2019.01.090] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/26/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Microorganisms are ubiquitous in the atmosphere, where they can disperse for a long distance. However, it remains poorly understood how these airborne microorganisms vary and which factors influence the microbial distribution in different anthropogenic activity regions. To explore the regional differences of bacteria and fungi in airborne particles, PM2.5 and PM10 samples were collected in the urban and rural areas of Hangzhou. The bacterial and fungal communities in the urban atmosphere was more similar to each other than those in the rural atmosphere. Analyses conducted by the concentration weighted trajectory model demonstrated that the local environment contributed more to the similarity of airborne bacteria and fungi compared with the atmospheric transport. The concentrations of local air pollutants (PM2.5, PM10, NO2, SO2 and CO) were positively correlated with the similarity of the bacterial and fungal communities. Additionally, the concentrations of these air pollutants in the urban site were about 1.5 times than those in the rural site. This implicated that anthropogenic activity, which is the essential cause of air pollutants, influenced the similarity of airborne bacteria and fungi in the urban area. This work ascertains the outdoor bacterial and fungal distribution in the urban and the rural atmosphere and provides a prospective model for studying the contributing factors of airborne bacteria and fungi.
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Affiliation(s)
- Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zhichao Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zheng Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiangyang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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19
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Dommergue A, Amato P, Tignat-Perrier R, Magand O, Thollot A, Joly M, Bouvier L, Sellegri K, Vogel T, Sonke JE, Jaffrezo JL, Andrade M, Moreno I, Labuschagne C, Martin L, Zhang Q, Larose C. Methods to Investigate the Global Atmospheric Microbiome. Front Microbiol 2019; 10:243. [PMID: 30967843 PMCID: PMC6394204 DOI: 10.3389/fmicb.2019.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
The interplay between microbes and atmospheric physical and chemical conditions is an open field of research that can only be fully addressed using multidisciplinary approaches. The lack of coordinated efforts to gather data at representative temporal and spatial scales limits aerobiology to help understand large scale patterns of global microbial biodiversity and its causal relationships with the environmental context. This paper presents the sampling strategy and analytical protocols developed in order to integrate different fields of research such as microbiology, -omics biology, atmospheric chemistry, physics and meteorology to characterize atmospheric microbial life. These include control of chemical and microbial contaminations from sampling to analysis and identification of experimental procedures for characterizing airborne microbial biodiversity and its functioning from the atmospheric samples collected at remote sites from low cell density environments. We used high-volume sampling strategy to address both chemical and microbial composition of the atmosphere, because it can help overcome low aerosol and microbial cell concentrations. To account for contaminations, exposed and unexposed control filters were processed along with the samples. We present a method that allows for the extraction of chemical and biological data from the same quartz filters. We tested different sampling times, extraction kits and methods to optimize DNA yield from filters. Based on our results, we recommend supplementary sterilization steps to reduce filter contamination induced by handling and transport. These include manipulation under laminar flow hoods and UV sterilization. In terms of DNA extraction, we recommend a vortex step and a heating step to reduce binding to the quartz fibers of the filters. These steps have led to a 10-fold increase in DNA yield, allowing for downstream omics analysis of air samples. Based on our results, our method can be integrated into pre-existing long-term monitoring field protocols for the atmosphere both in terms of atmospheric chemistry and biology. We recommend using standardized air volumes and to develop standard operating protocols for field users to better control the operational quality.
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Affiliation(s)
- Aurelien Dommergue
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, UMR6096 CNRS–Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Romie Tignat-Perrier
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Olivier Magand
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Alban Thollot
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Muriel Joly
- Institut de Chimie de Clermont-Ferrand, UMR6096 CNRS–Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Laetitia Bouvier
- Laboratory for Meteorological Physics (LaMP), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Karine Sellegri
- Laboratory for Meteorological Physics (LaMP), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Timothy Vogel
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Jeroen E. Sonke
- Géosciences Environnement Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université de Toulouse, Toulouse, France
| | - Jean-Luc Jaffrezo
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Marcos Andrade
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andrés, La Paz, Bolivia
- Department of Atmospheric and Oceanic Sciences, University of Maryland, College Park, MD, United States
| | - Isabel Moreno
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | - Lynwill Martin
- South African Weather Service, Stellenbosch, South Africa
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Catherine Larose
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
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Bardin M, Leyronas C, Troulet C, Morris CE. Striking Similarities Between Botrytis cinerea From Non-agricultural and From Agricultural Habitats. FRONTIERS IN PLANT SCIENCE 2018; 9:1820. [PMID: 30568671 PMCID: PMC6290265 DOI: 10.3389/fpls.2018.01820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.
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Affiliation(s)
- Marc Bardin
- Pathologie Végétale, INRA, Montfavet, France
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Honeyman AS, Day ML, Spear JR. Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA. PeerJ 2018; 6:e5961. [PMID: 30498637 PMCID: PMC6252068 DOI: 10.7717/peerj.5961] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/16/2018] [Indexed: 01/15/2023] Open
Abstract
Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.
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Affiliation(s)
| | - Maria L Day
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
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Jimenez-Sanchez C, Hanlon R, Aho KA, Powers C, Morris CE, Schmale DG. Diversity and Ice Nucleation Activity of Microorganisms Collected With a Small Unmanned Aircraft System (sUAS) in France and the United States. Front Microbiol 2018; 9:1667. [PMID: 30158903 PMCID: PMC6104180 DOI: 10.3389/fmicb.2018.01667] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
Many microbes relevant to crops, domestic animals, and humans are transported over long distances through the atmosphere. Some of these atmospheric microbes catalyze the freezing of water at higher temperatures and facilitate the onset of precipitation. We collected microbes from the lower atmosphere in France and the United States with a small unmanned aircraft system (sUAS). 55 sampling missions were conducted at two locations in France in 2014 (an airfield in Pujaut, and the top of Puy de Dôme), and three locations in the U.S. in 2015 (a farm in Blacksburg, Virginia, and a farm and a lake in Baton Rouge, Louisiana). The sUAS was a fixed-wing electric drone equipped with a remote-operated sampling device that was opened once the aircraft reached the desired sampling altitude (40-50 meters above ground level). Samples were collected on agar media (TSA, R4A, R2A, and CA) with and without the fungicide cycloheximide. Over 4,000 bacterial-like colonies were recovered across the 55 sUAS sampling missions. A positive relationship between sampling time and temperature and concentrations of culturable bacteria was observed for sUAS flights conducted in France, but not for sUAS flights conducted in Louisiana. A droplet freezing assay was used to screen nearly 2,000 colonies for ice nucleation activity, and 15 colonies were ice nucleation active at temperatures warmer than -8°C. Sequences from portions of 16S rDNA were used to identify 503 colonies from 54 flights to the level of genus. Assemblages of bacteria from sUAS flights in France (TSA) and sUAS flights in Louisiana (R4A) showed more similarity within locations than between locations. Bacteria collected with sUAS on TSA in France and Virginia were significantly different across all levels of classification tested (P < 0.001 for class, order, family, and genus). Principal Coordinates Analysis showed a strong association between the genera Curtobacterium, Pantoea, and Pseudomonas from sUAS flights in Virginia, and Agrococcus, Lysinibacillus, and Paenibacillus from sUAS flights in France. Future work aims to understand the potential origin of the atmospheric microbial assemblages collected with sUAS, and their association with mesoscale atmospheric processes.
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Affiliation(s)
- Celia Jimenez-Sanchez
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Regina Hanlon
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Ken A. Aho
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
| | - Craig Powers
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Cindy E. Morris
- INRA, Plant Pathology Research Unit, Provence Alpes Côtes d'Azur Research Center, Montfavet, France
| | - David G. Schmale
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Dorati F, Barrett GA, Sanchez-Contreras M, Arseneault T, José MS, Studholme DJ, Murillo J, Caballero P, Waterfield NR, Arnold DL, Shaw LJ, Jackson RW. Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators. Microorganisms 2018; 6:microorganisms6020032. [PMID: 29690522 PMCID: PMC6027264 DOI: 10.3390/microorganisms6020032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/09/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their natural plant host e.g., water courses, soil, non-host plants. This exposes them to a variety of eukaryotic predators such as nematodes, insects and amoebae present in the environment. Nematodes and amoeba in particular are bacterial predators while insect herbivores may act as indirect predators, ingesting bacteria on plant tissue. We therefore postulated that bacteria are probably under selective pressure to avoid or survive predation and have therefore developed appropriate coping mechanisms. We tested the hypothesis that plant pathogenic Pseudomonas syringae are able to cope with predation pressure and found that three pathovars show weak, but significant resistance or toxicity. To identify the gene systems that contribute to resistance or toxicity we applied a heterologous screening technique, called Rapid Virulence Annotation (RVA), for anti-predation and toxicity mechanisms. Three cosmid libraries for P. syringae pv. aesculi, pv. tomato and pv. phaseolicola, of approximately 2000 cosmids each, were screened in the susceptible/non-toxic bacterium Escherichia coli against nematode, amoebae and an insect. A number of potential conserved and unique genes were identified which included genes encoding haemolysins, biofilm formation, motility and adhesion. These data provide the first multi-pathovar comparative insight to how plant pathogens cope with different predation pressures and infection of an insect gut and provide a foundation for further study into the function of selected genes and their role in ecological success.
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Affiliation(s)
- Federico Dorati
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | - Glyn A Barrett
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | | | - Tanya Arseneault
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Research and Development Centre, Quebec, J3B 3E6, Canada.
| | - Mateo San José
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | | | - Jesús Murillo
- Instituto de Agrobiotecnología, Universidad Pública de Navarra, 31192 Mutilva, Spain.
| | - Primitivo Caballero
- Instituto de Agrobiotecnología, Universidad Pública de Navarra, 31192 Mutilva, Spain.
| | - Nicholas R Waterfield
- Department of Biology and Biochemistry, University of Bath, Bath, BA1 9BJ, UK.
- Warwick Medical School, University of Warwick, Warwick, CV4 7AL, UK.
| | - Dawn L Arnold
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, BS16 1QY, UK.
| | - Liz J Shaw
- School of Archaeology, Geography and Environmental Science, University of Reading, Reading, RG6 6AX, UK.
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
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24
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Soubeyrand S, Garreta V, Monteil C, Suffert F, Goyeau H, Berder J, Moinard J, Fournier E, Tharreau D, Morris CE, Sache I. Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data. PHYTOPATHOLOGY 2017; 107:1199-1208. [PMID: 28677479 DOI: 10.1094/phyto-02-17-0070-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791 . A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.
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Affiliation(s)
- Samuel Soubeyrand
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Vincent Garreta
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Caroline Monteil
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Frédéric Suffert
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Henriette Goyeau
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Julie Berder
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Jacques Moinard
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Elisabeth Fournier
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Didier Tharreau
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Cindy E Morris
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Ivan Sache
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
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Active microorganisms thrive among extremely diverse communities in cloud water. PLoS One 2017; 12:e0182869. [PMID: 28792539 PMCID: PMC5549752 DOI: 10.1371/journal.pone.0182869] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 07/25/2017] [Indexed: 12/27/2022] Open
Abstract
Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104 bacteria and archaea mL-1 and ~102−103 eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.
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Perspectives on the Future of Ice Nucleation Research: Research Needs and Unanswered Questions Identified from Two International Workshops. ATMOSPHERE 2017. [DOI: 10.3390/atmos8080138] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Failor KC, Schmale DG, Vinatzer BA, Monteil CL. Ice nucleation active bacteria in precipitation are genetically diverse and nucleate ice by employing different mechanisms. ISME JOURNAL 2017; 11:2740-2753. [PMID: 28753208 DOI: 10.1038/ismej.2017.124] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 06/02/2017] [Accepted: 06/15/2017] [Indexed: 11/09/2022]
Abstract
A growing body of circumstantial evidence suggests that ice nucleation active (Ice+) bacteria contribute to the initiation of precipitation by heterologous freezing of super-cooled water in clouds. However, little is known about the concentration of Ice+ bacteria in precipitation, their genetic and phenotypic diversity, and their relationship to air mass trajectories and precipitation chemistry. In this study, 23 precipitation events were collected over 15 months in Virginia, USA. Air mass trajectories and water chemistry were determined and 33 134 isolates were screened for ice nucleation activity (INA) at -8 °C. Of 1144 isolates that tested positive during initial screening, 593 had confirmed INA at -8 °C in repeated tests. Concentrations of Ice+ strains in precipitation were found to range from 0 to 13 219 colony forming units per liter, with a mean of 384±147. Most Ice+ bacteria were identified as members of known and unknown Ice+ species in the Pseudomonadaceae, Enterobacteriaceae and Xanthomonadaceae families, which nucleate ice employing the well-characterized membrane-bound INA protein. Two Ice+ strains, however, were identified as Lysinibacillus, a Gram-positive genus not previously known to include Ice+ bacteria. INA of the Lysinibacillus strains is due to a nanometer-sized molecule that is heat resistant, lysozyme and proteinase resistant, and secreted. Ice+ bacteria and the INA mechanisms they employ are thus more diverse than expected. We discuss to what extent the concentration of culturable Ice+ bacteria in precipitation and the identification of a new heat-resistant biological INA mechanism support a role for Ice+ bacteria in the initiation of precipitation.
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Affiliation(s)
- K C Failor
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - D G Schmale
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - B A Vinatzer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - C L Monteil
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA.,CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, Saint-Paul-lès-Durance, France.,INRA, UR0407 Pathologie Végétale, Montfavet cedex, France
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28
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Weil T, De Filippo C, Albanese D, Donati C, Pindo M, Pavarini L, Carotenuto F, Pasqui M, Poto L, Gabrieli J, Barbante C, Sattler B, Cavalieri D, Miglietta F. Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms. MICROBIOME 2017; 5:32. [PMID: 28283029 PMCID: PMC5345179 DOI: 10.1186/s40168-017-0249-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/27/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust. RESULTS Our metagenomic analysis revealed that sandstorms can move not only fractions but rather large parts of entire microbial communities far away from their area of origin and that this microbiota contains several of the most stress-resistant organisms on Earth, including highly destructive fungal and bacterial pathogens. In particular, we provide first evidence that winter-occurring dust depositions can favor a rapid microbial contamination of sensitive sink habitats after snowmelt. CONCLUSIONS Airborne microbial depositions accompanying extreme meteorological events represent a realistic threat for ecosystem and public health. Therefore, monitoring the spread and persistence of storm-travelling alien microbes is a priority while considering future trajectories of climatic anomalies as well as anthropogenically driven changes in land use in the source regions.
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Affiliation(s)
- Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Carlotta De Filippo
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Florence, Italy
- Institute of Agricultural Biology and Biotechnology, National Research Council (IBBA-CNR), Via Moruzzi 1, 56124 Pisa, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Lorenzo Pavarini
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Federico Carotenuto
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Florence, Italy
| | - Massimiliano Pasqui
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Florence, Italy
| | - Luisa Poto
- Institute for the Dynamics of Environmental Processes, National Research Council (IDPA-CNR), Via Torino 155, 30172 Mestre, Venice Italy
| | - Jacopo Gabrieli
- Institute for the Dynamics of Environmental Processes, National Research Council (IDPA-CNR), Via Torino 155, 30172 Mestre, Venice Italy
| | - Carlo Barbante
- Institute for the Dynamics of Environmental Processes, National Research Council (IDPA-CNR), Via Torino 155, 30172 Mestre, Venice Italy
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino 155, 30172 Mestre, Venice Italy
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Duccio Cavalieri
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Florence, Italy
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence Italy
| | - Franco Miglietta
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Florence, Italy
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29
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Pietsch RB, Vinatzer BA, Schmale DG. Diversity and Abundance of Ice Nucleating Strains of Pseudomonas syringae in a Freshwater Lake in Virginia, USA. Front Microbiol 2017; 8:318. [PMID: 28337177 PMCID: PMC5343033 DOI: 10.3389/fmicb.2017.00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/15/2017] [Indexed: 12/03/2022] Open
Abstract
The bacterium Pseudomonas syringae is found in a variety of terrestrial and aquatic environments. Some strains of P. syringae express an ice nucleation protein (hereafter referred to as Ice+) allowing them to catalyze the heterogeneous freezing of water. Though P. syringae has been sampled intensively from freshwater sources in France, little is known about the genetic diversity of P. syringae in natural aquatic habitats in North America. We collected samples of freshwater from three different depths in Claytor Lake, Virginia, USA between November 2015 and June 2016. Samples were plated on non-selective medium (TSA) and on medium selective for Pseudomonas (KBC) and closely related species to estimate the total number of culturable bacteria and of Pseudomonas, respectively. A droplet freezing assay was used to screen colonies for the Ice+ phenotype. Ice+ colonies were then molecularly identified based on the cts (citrate synthase) gene and the 16S rDNA gene. Phylogenetic analysis of cts sequences showed a surprising diversity of phylogenetic subgroups of P. syringae. Frequencies of Ice+ isolates on P. syringae selective medium ranged from 0 to 15% per sample with the highest frequency being found in spring. Our work shows that freshwater lakes can be a significant reservoir of Ice+ P. syringae. Future work is needed to determine the contribution of P. syringae from freshwater lakes to the P. syringae populations present in the atmosphere and on plants and, in particular, if freshwater lakes could be an inoculum source of P. syringae-caused plant disease outbreaks.
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Affiliation(s)
- Renée B Pietsch
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Boris A Vinatzer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech Blacksburg, VA, USA
| | - David G Schmale
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech Blacksburg, VA, USA
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Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK. Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens. Microb Genom 2016; 2:e000089. [PMID: 28348830 PMCID: PMC5359406 DOI: 10.1099/mgen.0.000089] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/13/2016] [Indexed: 12/24/2022] Open
Abstract
Many bacterial pathogens are well characterized but, in some cases, little is known about the populations from which they emerged. This limits understanding of the molecular mechanisms underlying disease. The crop pathogen Pseudomonas syringae sensu lato has been widely isolated from the environment, including wild plants and components of the water cycle, and causes disease in several economically important crops. Here, we compared genome sequences of 45 P. syringae crop pathogen outbreak strains with 69 closely related environmental isolates. Phylogenetic reconstruction revealed that crop pathogens emerged many times independently from environmental populations. Unexpectedly, differences in gene content between environmental populations and outbreak strains were minimal with most virulence genes present in both. However, a genome-wide association study identified a small number of genes, including the type III effector genes hopQ1 and hopD1, to be associated with crop pathogens, but not with environmental populations, suggesting that this small group of genes may play an important role in crop disease emergence. Intriguingly, genome-wide analysis of homologous recombination revealed that the locus Psyr 0346, predicted to encode a protein that confers antibiotic resistance, has been frequently exchanged among lineages and thus may contribute to pathogen fitness. Finally, we found that isolates from diseased crops and from components of the water cycle, collected during the same crop disease epidemic, form a single population. This provides the strongest evidence yet that precipitation and irrigation water are an overlooked inoculum source for disease epidemics caused by P. syringae.
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Affiliation(s)
- Caroline L Monteil
- 4Laboratoire de Bioénergétique Cellulaire, Institut de Biosciences et Biotechnologies d'Aix-Marseille, CEA, 13108, Saint-Paul-lès-Durance, France.,3INRA, UR0407 Pathologie Végétale, Montfavet cedex, France.,1Institute of Life Science, College of Medicine, Swansea University, Swansea, UK.,2Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - Koji Yahara
- 1Institute of Life Science, College of Medicine, Swansea University, Swansea, UK.,5National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Leonardos Mageiros
- 1Institute of Life Science, College of Medicine, Swansea University, Swansea, UK
| | - Guillaume Méric
- 7The Milner Centre for Evolution, Department of Biology and Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - Bryan Swingle
- 8School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Cindy E Morris
- 3INRA, UR0407 Pathologie Végétale, Montfavet cedex, France
| | - Boris A Vinatzer
- 2Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - Samuel K Sheppard
- 7The Milner Centre for Evolution, Department of Biology and Biotechnology, University of Bath, Claverton Down, Bath, UK.,9Department of Zoology, University of Oxford, Oxford, UK
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31
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Karise R, Dreyersdorff G, Jahani M, Veromann E, Runno-Paurson E, Kaart T, Smagghe G, Mänd M. Reliability of the entomovector technology using Prestop-Mix and Bombus terrestris L. as a fungal disease biocontrol method in open field. Sci Rep 2016; 6:31650. [PMID: 27530075 PMCID: PMC4987692 DOI: 10.1038/srep31650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/21/2016] [Indexed: 11/09/2022] Open
Abstract
Botrytis cinerea Pers.:Fr. is a major plant pathogen, and a new approach is needed for its control in strawberry to minimise the increasing use of synthetic fungicides. The biofungicide Prestop-Mix, which contains Gliocladium catenulatum, is effective against Botrytis infections; however, the need for frequent applications increases the costs for farmers. Here, we demonstrate that bumble bees, Bombus terrestris L., effectively disseminate the preparation onto flowers in open field conditions. Over the course of three years, we found a highly significant decrease in the rate of Botrytis infection. Pathogen control was achieved with relatively low numbers of G. catenulatum spores per flower, even using flowers that are not highly attractive to bumble bees. An even distribution of spores was detected up to 100 m from the hives, either due to primary inoculation by bumble bees or secondary distribution by other flower visitors such as honey bees and solitary bees. We showed that the application of a biocontrol agent by bumble bees is reliable for the use of environmentally friendly pest control strategies in northern climatic conditions. This low cost technology is especially relevant for organic farming. This study provides valuable information for introducing this method into practice in open strawberry fields.
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Affiliation(s)
- Reet Karise
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
| | - Gerit Dreyersdorff
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
| | - Mona Jahani
- Department of Crop Protection, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Eve Veromann
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
| | - Eve Runno-Paurson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
| | - Tanel Kaart
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51014 Tartu, Estonia
| | - Guy Smagghe
- Department of Crop Protection, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Marika Mänd
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51014 Tartu, Estonia
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32
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Hall SJ, Dry IB, Blanchard CL, Whitelaw-Weckert MA. Phylogenetic Relationships of Pseudomonas syringae pv. syringae Isolates Associated with Bacterial Inflorescence Rot in Grapevine. PLANT DISEASE 2016; 100:607-616. [PMID: 30688599 DOI: 10.1094/pdis-07-15-0806-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudomonas syringae pv. syringae causes extensive yield losses in wine-grape production in some Australian cool-climate vineyards. Putative P. syringae pv. syringae isolates from infected grapevines within a range of vineyards were genotyped using RNA polymerase β-subunit (rpoB) and multilocus sequence typing (MLST) using primers for glyceraldehyde-3-phosphate dehydrogenase (gapA), citrate synthase (gltA), DNA gyrase B (gyrB), and σ factor 70 (rpoD). The isolates were also evaluated for pathogenicity by inoculation of detached grapevine leaves. The isolates were grouped by MLST data into two well-supported clades, each containing a mixture of pathogenic and nonpathogenic grapevine isolates, indicating that P. syringae pv. syringae in Australian vineyards is genetically diverse. Each clade also contained P. syringae pv. syringae from nongrape hosts pathogenic to grapevine, demonstrating a lack of host specificity and possible potential for cross-infection of grape and other horticultural crops. Furthermore, the isolation of pathogenic P. syringae pv. syringae isolates from grapevine sucker shoots suggests that sucker shoots may allow overwintering of the pathogen. The vineyard quarantine status of P. syringae pv. syringae may need to be reconsidered, due to its easy dispersal through pruning equipment.
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Affiliation(s)
- Stewart J Hall
- National Wine and Grape Industry Centre, Charles Sturt University, New South Wales Department of Primary Industries, Wagga Wagga, NSW, Australia 2650
| | - Ian B Dry
- CSIRO Agriculture, Hartley Grove, Urrbrae, SA, Australia 5064
| | - Christopher L Blanchard
- ARC Industrial Transformation Training Centre for Functional Grains, Charles Sturt University
| | - Melanie A Whitelaw-Weckert
- National Wine and Grape Industry Centre, Charles Sturt University, New South Wales Department of Primary Industries
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A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLoS One 2014; 9:e105547. [PMID: 25184292 PMCID: PMC4153583 DOI: 10.1371/journal.pone.0105547] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/22/2014] [Indexed: 11/19/2022] Open
Abstract
The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated.
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