1
|
Aswal M, Singhal N, Kumar M. Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly. Sci Data 2023; 10:573. [PMID: 37658065 PMCID: PMC10474267 DOI: 10.1038/s41597-023-02444-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/04/2023] [Indexed: 09/03/2023] Open
Abstract
Escherichia coli are highly diverse bacteria with different pathogenic types, serotypes and phylogenetic types/phylotypes. In recent years, infections with E. coli have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of E. coli. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-β-lactam resistant and the other was multi-drug resistant (resistant to multiple β-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the de-novo approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N50 value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.
Collapse
Affiliation(s)
- Manisha Aswal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
| |
Collapse
|
2
|
NandaKafle G, Blasius LA, Seale T, Brözel VS. Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum. Microorganisms 2023; 11:1457. [PMID: 37374960 DOI: 10.3390/microorganisms11061457] [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: 04/30/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, suggesting that other biological factors play a role in controlling E. coli populations in soil. Free-living protozoa can affect the bacterial population by grazing. We hypothesized that E. coli strains capable of surviving in non-sterile soil possess mechanisms to protect themselves from amoeba predation. We determined the grazing rate of E. coli pasture isolates by using Dictyostelium discoideum. Bacterial suspensions applied to lactose agar as lines were allowed to grow for 24 h, when 4 μL of D. discoideum culture was inoculated in the center of each bacterial line. Grazing distances were measured after 4 days. The genomes of five grazing-susceptible and five grazing-resistant isolates were sequenced and compared. Grazing distance varied among isolates, which indicated that some E. coli are more susceptible to grazing by protozoa than others. When presented with a choice between grazing-susceptible and grazing-resistant isolates, D. discoideum grazed only on the susceptible strain. Grazing susceptibility phenotype did not align with the phylogroup, with both B1 and E strains found in both grazing groups. They also did not align by core genome phylogeny. Whole genome comparisons revealed that the five most highly grazed strains had 389 shared genes not found in the five least grazed strains. Conversely, the five least grazed strains shared 130 unique genes. The results indicate that long-term persistence of E. coli in soil is due at least in part to resistance to grazing by soil amoeba.
Collapse
Affiliation(s)
- Gitanjali NandaKafle
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Lane A Blasius
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Tarren Seale
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
| | - Volker S Brözel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
| |
Collapse
|
3
|
Alegbeleye O, Sant'Ana AS. Survival behavior of six enterotoxigenic Escherichia coli strains in soil and biochar-amended soils. ENVIRONMENTAL RESEARCH 2023; 223:115443. [PMID: 36781014 DOI: 10.1016/j.envres.2023.115443] [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: 12/27/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Some Escherichia coli serotypes are important human pathogens causing diarrhea or in some cases, life threatening diseases. E. coli is also a typical indicator microorganism, routinely used for assessing the microbiological quality of water especially to indicate fecal contamination. The soil is a sink and route of transmission to water and food resources and it is thus important to understand the survival of enterotoxigenic E. coli strains in soil. This study monitored the survival of six E. coli strains in sandy and loam soil. Furthermore, since biochar is a commonly used soil conditioner, the study investigated the impact of biochar amendment (15%) on the survival of the E. coli strains in (biochar-amended) sandy and loam soils. Addition of biochar affected the physicochemical properties of both soils, altering potassium levels, calcium, magnesium, sodium as well as levels of other metal ions. It increased the organic matter of loam soil from 44 g/dm3 to 52 g/dm3, and increased the pH of both sandy and loam soils. Survival and persistence of the E. coli strains generally varied according to soil type, with strains generally surviving better (P ≤ 0.05) in loam soil compared to in sandy soil. In loam soil and biochar amended loam soils, E. coli strains remained culturable until the 150th day with counts ranging between 3.00 and 5.94 ± 0.04 log CFU/g. The effects of biochar on the physicochemical properties of soil and the response of the E. coli strains to biochar amendment was variable depending on soil type.
Collapse
Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
| |
Collapse
|
4
|
Nowicki S, deLaurent ZR, de Villiers EP, Githinji G, Charles KJ. The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing. PLoS One 2021; 16:e0245910. [PMID: 33481909 PMCID: PMC7822521 DOI: 10.1371/journal.pone.0245910] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.
Collapse
Affiliation(s)
- Saskia Nowicki
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Zaydah R. deLaurent
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Etienne P. de Villiers
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katrina J. Charles
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
5
|
Devane ML, Weaver L, Singh SK, Gilpin BJ. Fecal source tracking methods to elucidate critical sources of pathogens and contaminant microbial transport through New Zealand agricultural watersheds - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 222:293-303. [PMID: 29860123 DOI: 10.1016/j.jenvman.2018.05.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/07/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
In New Zealand, there is substantial potential for microbial contaminants from agricultural fecal sources to be transported into waterways. The flow and transport pathways for fecal contaminants vary at a range of scales and is dependent on chemical, physical and biological attributes of pathways, soils, microorganisms and landscape characteristics. Understanding contaminant transport pathways from catchment to stream can aid water management strategies. It is not practical, however to conduct direct field measurement for all catchments on the fate and transport of fecal pathogens due to constraints on time, personnel, and material resources. To overcome this problem, fecal source tracking can be utilised to link catchment characteristics to fecal signatures identifying critical sources. In this article, we have reviewed approaches to identifying critical sources and pathways for fecal microorganisms from agricultural sources, and make recommendations for the appropriate use of these fecal source tracking (FST) tools.
Collapse
Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Ltd. (ESR), P.O. Box 29181, Christchurch, New Zealand.
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd. (ESR), P.O. Box 29181, Christchurch, New Zealand
| | - Shailesh K Singh
- National Institute of Water and Atmospheric Research, 10 Kyle St, Riccarton Christchurch, 8011, New Zealand
| | - Brent J Gilpin
- Institute of Environmental Science and Research Ltd. (ESR), P.O. Box 29181, Christchurch, New Zealand
| |
Collapse
|
6
|
Patterson L, Navarro-Gonzalez N, Jay-Russell MT, Aminabadi P, Antaki-Zukoski E, Pires AFA. Persistence ofEscherichia coliin the soil of an organic mixed crop-livestock farm that integrates sheep grazing within vegetable fields. Zoonoses Public Health 2018; 65:887-896. [DOI: 10.1111/zph.12503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Laura Patterson
- Department Population Health and Reproduction, School of Veterinary Medicine; University of California-Davis; Davis California
| | | | | | - Peiman Aminabadi
- Western Center for Food Safety; University of California-Davis; Davis California
| | | | - Alda F. A. Pires
- Department Population Health and Reproduction, School of Veterinary Medicine; University of California-Davis; Davis California
| |
Collapse
|
7
|
Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH. Appl Environ Microbiol 2018. [PMID: 29523546 DOI: 10.1128/aem.02714-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is deposited into soil with feces and exhibits subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process, and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics, and soil chemistry influence the prevalence of cultivable E. coli in surface soil. Soils from forests and pasture lands had equally high prevalences of E. coli Edge interactions were also observed among land cover types, with proximity to forests and pastures affecting the likelihood of E. coli isolation from surrounding soils. E. coli is thought to be more prevalent in sediments with high moisture, but this was observed only in grass- or crop-dominated lands in this study. Because differing E. coli phylogroups are thought to have differing ecology profiles, isolates were also typed using a novel single-nucleotide polymorphism (SNP) genotyping assay. Phylogroup B1 was the dominant group isolated from soil, as has been reported in all other surveys of environmental E. coli Although differences were small, isolates belonging to phylogroups B2 and D were associated with wooded areas, slightly more acidic soils, and soil sampling after rainfall events. In contrast, isolates from phylogroups B1 and E were associated with pasture lands.IMPORTANCE The consensus is that complex niches or life cycles should select for complex genomes in organisms. There is much unexplained biodiversity in E. coli, and its cycling through complex extrahost environments may be a cause. In order to understand the evolutionary processes that lead to adaptation for survival and growth in soil, an isolate collection that associates soil conditions and isolate genome sequences is required. An equally important question is whether traits selected in soil or other extrahost habitats can be transmitted to E. coli residing in hosts via gene flow. The new findings about the distribution of E. coli in soil at the landscape scale (i) enhance our capability to study how extrahost environments influence the evolution of E. coli and other bacteria, (ii) advance our knowledge of the environmental biology of this microbe, and (iii) further affirm the emerging scientific consensus that E. coli in waterways originates from nonpoint sources not associated with human activity or livestock farming.
Collapse
|
8
|
NandaKafle G, Seale T, Flint T, Nepal M, Venter SN, Brözel VS. Distribution of Diverse Escherichia coli between Cattle and Pasture. Microbes Environ 2017; 32:226-233. [PMID: 28747587 PMCID: PMC5606692 DOI: 10.1264/jsme2.me17030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli is widely considered to not survive for extended periods outside the intestines of warm-blooded animals; however, recent studies demonstrated that E. coli strains maintain populations in soil and water without any known fecal contamination. The objective of this study was to investigate whether the niche partitioning of E. coli occurs between cattle and their pasture. We attempted to clarify whether E. coli from bovine feces differs phenotypically and genotypically from isolates maintaining a population in pasture soil over winter. Soil, bovine fecal, and run-off samples were collected before and after the introduction of cattle to the pasture. Isolates (363) were genotyped by uidA and mutS sequences and phylogrouping, and evaluated for curli formation (Rough, Dry, And Red, or RDAR). Three types of clusters emerged, viz. bovine-associated, clusters devoid of cattle isolates and representing isolates endemic to the pasture environment, and clusters with both. All isolates clustered with strains of E. coli sensu stricto, distinct from the cryptic species Clades I, III, IV, and V. Pasture soil endemic and bovine fecal populations had very different phylogroup distributions, indicating niche partitioning. The soil endemic population was largely comprised of phylogroup B1 and had a higher average RDAR score than other isolates. These results indicate the existence of environmental E. coli strains that are phylogenetically distinct from bovine fecal isolates, and that have the ability to maintain populations in the soil environment.
Collapse
Affiliation(s)
| | - Tarren Seale
- Department of Microbiology and Plant Pathology, University of Pretoria
| | - Toby Flint
- Department of Mathematics and Statistics, South Dakota State University
| | - Madhav Nepal
- Department of Biology and Microbiology, South Dakota State University
| | | | - Volker S Brözel
- Department of Biology and Microbiology, South Dakota State University.,Department of Microbiology and Plant Pathology, University of Pretoria
| |
Collapse
|
9
|
Tymensen L, Booker CW, Hannon SJ, Cook SR, Zaheer R, Read R, McAllister TA. Environmental Growth of Enterococci and Escherichia coli in Feedlot Catch Basins and a Constructed Wetland in the Absence of Fecal Input. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5386-5395. [PMID: 28430425 DOI: 10.1021/acs.est.6b06274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population structures of fecal indicator bacteria (FIB) isolated from catch basins, a constructed wetland, and feces from a beef cattle feedlot were compared over a two-year period. Enterococcus hirae accounted for 92% of the fecal isolates, whereas secondary environments were characterized by greater relative abundance of environmentally adapted species including Enterococcus casseliflavus. While enterococci densities in the catch basins and wetland were similar under wet and drought conditions, E. hirae predominated during rainy periods, while E. casseliflavus predominated during drought conditions. Environmentally adapted species accounted for almost half of the erythromycin resistant enterococci isolated from the wetland. Densities of Escherichia coli were also comparable during wet versus drought conditions, and the relative abundance of strains from environmentally adapted clades was greater in secondary environments compared to feces. Unlike enterococci, fewer environmentally adapted E. coli strains were isolated on selective media containing ceftriaxone from the wetland compared to feces, suggesting resistance to this antibiotic may not be well maintained in the absence of selective pressure. Overall, these findings suggest that secondary environments select for environmentally adapted FIB. While these species and clades tend to be of limited clinical relevance, they could potentially serve as reservoirs of antimicrobial resistance.
Collapse
Affiliation(s)
- Lisa Tymensen
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
| | - Calvin W Booker
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Sherry J Hannon
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Shaun R Cook
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Ron Read
- Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary, Alberta, Canada , T1Y 6J4
| | - Tim A McAllister
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| |
Collapse
|
10
|
Weaver L, Karki N, Mackenzie M, Sinton L, Wood D, Flintoft M, Havelaar P, Close M. Microbial transport into groundwater from irrigation: Comparison of two irrigation practices in New Zealand. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 543:83-94. [PMID: 26580730 DOI: 10.1016/j.scitotenv.2015.09.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
UNLABELLED Rising demand on food is leading to an increase in irrigation worldwide to improve productivity. Irrigation, for pastoral agriculture (beef, dairy and sheep), is the largest consumptive use of water in New Zealand. There is a potential risk of leaching of microbial contaminants from faecal matter through the vadose zone into groundwater. Management of irrigation is vital for protection of groundwater from these microbial contaminants and maintain efficient irrigation practices. Our research investigated flood and spray irrigation, two practices common in New Zealand. The aim was to identify the risk of microbial transport and mitigation practices to reduce or eliminate the risk of microbial transport into groundwater. Cowpats were placed on lysimeters over a typical New Zealand soil (Lismore silt loam) and vadose zone and the leachate collected after irrigation events. Samples of both cowpats and leachate were analysed for the microbial indicator Escherichia coli and pathogen Campylobacter species. A key driver to the microbial transport derived from the model applied was the volume of leachate collected: doubling the leachate volume more than doubled the total recovery of E. coli. The persistence of E. coli in the cowpats during the experiment is an important factor as well as the initial environmental conditions, which were more favourable for survival and growth of E. coli during the spray irrigation compared with the flood irrigation. The results also suggest a reservoir of E. coli surviving in the soil. Although the same was potentially true for Campylobacter, little difference in the transport rates between irrigation practices could be seen due to the poor survival of Campylobacter during the experiment. Effective irrigation practices include monitoring the irrigation rates to minimise leachate production, delaying irrigation until 14days post-cowpat deposition and only irrigating when risk of transport to the groundwater is minimal. AIM To compare the risk of microbial contamination of groundwater from cowpats using two irrigation practices onto pasture.
Collapse
Affiliation(s)
- L Weaver
- Institute of Environmental Science and Research Ltd., New Zealand
| | - N Karki
- Institute of Environmental Science and Research Ltd., New Zealand
| | - M Mackenzie
- Institute of Environmental Science and Research Ltd., New Zealand
| | - L Sinton
- Institute of Environmental Science and Research Ltd., New Zealand; Water Micro NZ, Christchurch, New Zealand
| | - D Wood
- Institute of Environmental Science and Research Ltd., New Zealand
| | - M Flintoft
- Institute of Environmental Science and Research Ltd., New Zealand; AquaLinc Research, Christchurch, New Zealand
| | - P Havelaar
- Institute of Environmental Science and Research Ltd., New Zealand; NIWA, Christchurch, New Zealand
| | - M Close
- Institute of Environmental Science and Research Ltd., New Zealand
| |
Collapse
|
11
|
Książczyk M, Kuczkowski M, Dudek B, Korzekwa K, Tobiasz A, Korzeniowska-Kowal A, Paluch E, Wieliczko A, Bugla-Płoskońska G. Application of Routine Diagnostic Procedure, VITEK 2 Compact, MALDI-TOF MS, and PCR Assays in Identification Procedure of Bacterial Strain with Ambiguous Phenotype. Curr Microbiol 2016; 72:570-82. [PMID: 26804795 DOI: 10.1007/s00284-016-0993-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/19/2015] [Indexed: 11/28/2022]
Abstract
In diagnostic microbiology as well as in microbiological research, the identification of a microorganism is a crucial and decisive stage. A broad choice of methods is available, based on both phenotypic and molecular properties of microbes. The aim of this study was to compare the application of phenotypic and molecular tools in bacterial identification on the example of Gram-negative intestine rod with an ambiguous phenotype. Different methods of identification procedure, which based on various properties of bacteria, were applied, e.g., microscopic observation of single-bacterial cells, macroscopic observation of bacterial colonies morphology, the automated system of microorganism identification (biochemical tests), the mass spectrometry method (analysis of bacterial proteome), and genetic analysis with PCR reactions. The obtained results revealed discrepancies in the identification of the tested bacterial strain with an atypical phenotype: mucous morphology of colonies, not characteristic for either E. coli and Citrobacter spp., mass spectrometry analysis of proteome initially assigned the tested strain to Citrobacter genus (C. freundii) and biochemical profiles pointed to Escherichia coli. A decisive method in the current study was genetic analysis with PCR reactions which identified conserved genetic sequences highly specific to E. coli species in the genome of the tested strain.
Collapse
Affiliation(s)
- Marta Książczyk
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.
| | - Maciej Kuczkowski
- Department of Epizootiology and Clinic of Bird and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland
| | - Bartłomiej Dudek
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Anna Tobiasz
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wrocław, Poland
| | - Agnieszka Korzeniowska-Kowal
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wrocław, Poland
| | - Emil Paluch
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.,Department Physicochemistry of Microorganisms, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Alina Wieliczko
- Department of Epizootiology and Clinic of Bird and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland
| | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| |
Collapse
|
12
|
Chamam A, Wisniewski-Dyé F, Comte G, Bertrand C, Prigent-Combaret C. Differential responses of Oryza sativa secondary metabolism to biotic interactions with cooperative, commensal and phytopathogenic bacteria. PLANTA 2015; 242:1439-1452. [PMID: 26303982 DOI: 10.1007/s00425-015-2382-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/28/2015] [Indexed: 06/04/2023]
Abstract
Profiling of plant secondary metabolite allows to differentiate the different types of ecological interactions established between rice and bacteria. Rice responds to ecologically distinct bacteria by altering its content of flavonoids and hydroxycinnamic acid derivatives. Plants' growth and physiology are strongly influenced by the biotic interactions that plants establish with soil bacterial populations. Plants are able to sense and to respond accordingly to ecologically distinct bacteria, by inducing defense pathways against pathogens to prevent parasitic interactions, and by stimulating the growth of root-associated beneficial or commensal bacteria through root exudation. Plant secondary metabolism is expected to play a major role in this control. However, secondary metabolite responses of a same plant to cooperative, commensal and deleterious bacteria have so far never been compared. The impact of the plant growth-promoting rhizobacteria (PGPR) Azospirillum lipoferum 4B on the secondary metabolite profiles of two Oryza sativa L. cultivars (Cigalon and Nipponbare) was compared to that of a rice pathogen Burkholderia glumae AU6208, the causing agent of bacterial panicle blight and of a commensal environmental bacteria Escherichia coli B6. Root and shoot rice extracts were analyzed by reversed-phase high-performance liquid chromatography (RP-HPLC). Principal component analyses (PCAs) pinpointed discriminant secondary metabolites, which were characterized by mass spectrometry. Direct comparison of metabolic profiles evidenced that each bacterial ecological interaction induced distinct qualitative and quantitative modifications of rice secondary metabolism, by altering the content of numerous flavonoid compounds and hydroxycinnamic acid (HCA) derivatives. Secondary metabolism varied according to the cultivars and the interaction types, demonstrating the relevance of secondary metabolic profiling for studying plant-bacteria biotic interactions.
Collapse
Affiliation(s)
- Amel Chamam
- UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
- Université de Lyon, 69622, Lyon, France
- Unité de Recherche Clinique Lariboisière-Saint Louis, 200, rue du Faubourg Saint-Denis, 75010, Paris, France
| | - Florence Wisniewski-Dyé
- UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
- Université de Lyon, 69622, Lyon, France
| | - Gilles Comte
- UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
- Université de Lyon, 69622, Lyon, France
| | - Cédric Bertrand
- Laboratoire de Chimie des Biomolécules et de l'Environnement EA 4215, Université de Perpignan, Via Domitia, 66860, Perpignan, France
| | - Claire Prigent-Combaret
- UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France.
- Université de Lyon, 69622, Lyon, France.
| |
Collapse
|
13
|
Abstract
E. coli's hardiness, versatility, broad palate and ease of handling have made it the most intensively studied and best understood organism on the planet. However, research on E.coli has primarily examined it as a model organism, one that is abstracted from any natural history. But E. coli is far more than just a microbial lab rat. Rather, it is a highly diverse organism with a complex, multi-faceted niche in the wild. Recent studies of 'wild' E. coli have, for example, revealed a great deal about its presence in the environment, its diversity and genomic evolution, as well as its role in the human microbiome and disease. These findings have shed light on aspects of its biology and ecology that pose far-reaching questions and illustrate how an appreciation of E. coli's natural history can expand its value as a model organism.
Collapse
Affiliation(s)
- Zachary D Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States; BEACON Center for the Study of Evolution in Action, East Lansing, United States
| |
Collapse
|
14
|
Walker V, Bruto M, Bellvert F, Bally R, Muller D, Prigent-Combaret C, Moënne-Loccoz Y, Comte G. Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:495-502. [PMID: 23360460 DOI: 10.1094/mpmi-12-12-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for 'PR37Y15' but not 'DK315', as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.
Collapse
|
15
|
Amin MGM, Forslund A, Bui XT, Juhler RK, Petersen SO, Lægdsmand M. Persistence and leaching potential of microorganisms and mineral N in animal manure applied to intact soil columns. Appl Environ Microbiol 2013; 79:535-42. [PMID: 23124240 PMCID: PMC3553777 DOI: 10.1128/aem.02506-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/30/2012] [Indexed: 11/20/2022] Open
Abstract
Pathogens may reach agricultural soils through application of animal manure and thereby pose a risk of contaminating crops as well as surface and groundwater. Treatment and handling of manure for improved nutrient and odor management may also influence the amount and fate of manure-borne pathogens in the soil. A study was conducted to investigate the leaching potentials of a phage (Salmonella enterica serovar Typhimurium bacteriophage 28B) and two bacteria, Escherichia coli and Enterococcus species, in a liquid fraction of raw pig slurry obtained by solid-liquid separation of this slurry and in this liquid fraction after ozonation, when applied to intact soil columns by subsurface injection. We also compared leaching potentials of surface-applied and subsurface-injected raw slurry. The columns were exposed to irrigation events (3.5-h period at 10 mm h(-1)) after 1, 2, 3, and 4 weeks of incubation with collection of leachate. By the end of incubation, the distribution and survival of microorganisms in the soil of each treatment and in nonirrigated columns with injected raw slurry or liquid fraction were determined. E. coli in the leachates was quantified by both plate counts and quantitative PCR (qPCR) to assess the proportions of culturable and nonculturable (viable and nonviable) cells. Solid-liquid separation of slurry increased the redistribution in soil of contaminants in the liquid fraction compared to raw slurry, and the percent recovery of E. coli and Enterococcus species was higher for the liquid fraction than for raw slurry after the four leaching events. The liquid fraction also resulted in more leaching of all contaminants except Enterococcus species than did raw slurry. Ozonation reduced E. coli leaching only. Injection enhanced the leaching potential of the microorganisms investigated compared to surface application, probably because of a better survival with subsurface injection and a shorter leaching path.
Collapse
|
16
|
Brennan FP, Grant J, Botting CH, O'Flaherty V, Richards KG, Abram F. Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistentEscherichia coli. FEMS Microbiol Ecol 2012; 84:75-85. [DOI: 10.1111/1574-6941.12038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/14/2023] Open
Affiliation(s)
- Fiona P. Brennan
- Ecological Sciences Group; The James Hutton Institute; Craigiebucker, Aberdeen; Scotland
| | - Jim Grant
- Ashtown Research Centre; Teagasc; Dublin; Ireland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex; University of St. Andrews; St. Andrews; Fife; UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory; Department of Microbiology; School of Natural Sciences and Ryan Institute; National University of Ireland, Galway; Galway; Ireland
| | | | - Florence Abram
- Functional Environmental Microbiology; Department of Microbiology; School of Natural Sciences; National University of Ireland, Galway; Galway; Ireland
| |
Collapse
|
17
|
Didelot X, Méric G, Falush D, Darling AE. Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics 2012; 13:256. [PMID: 22712577 PMCID: PMC3505186 DOI: 10.1186/1471-2164-13-256] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/30/2012] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. This diversity of lifestyles has made it a particular focus of interest for studies of genetic variation, mainly with the aim to understand how a commensal can become a deadly pathogen. Many whole genomes of E. coli have been fully sequenced in the past few years, which offer helpful data to help understand how this important species evolved. Results We compared 27 whole genomes encompassing four phylogroups of Escherichia coli (A, B1, B2 and E). From the core-genome we established the clonal relationships between the isolates as well as the role played by homologous recombination during their evolution from a common ancestor. We found strong evidence for sexual isolation between three lineages (A+B1, B2, E), which could be explained by the ecological structuring of E. coli and may represent on-going speciation. We identified three hotspots of homologous recombination, one of which had not been previously described and contains the aroC gene, involved in the essential shikimate metabolic pathway. We also described the role played by non-homologous recombination in the pan-genome, and showed that this process was highly heterogeneous. Our analyses revealed in particular that the genomes of three enterohaemorrhagic (EHEC) strains within phylogroup B1 have converged from originally separate backgrounds as a result of both homologous and non-homologous recombination. Conclusions Recombination is an important force shaping the genomic evolution and diversification of E. coli, both by replacing fragments of genes with an homologous sequence and also by introducing new genes. In this study, several non-random patterns of these events were identified which correlated with important changes in the lifestyle of the bacteria, and therefore provide additional evidence to explain the relationship between genomic variation and ecological adaptation.
Collapse
Affiliation(s)
- Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK.
| | | | | | | |
Collapse
|
18
|
Byappanahalli MN, Yan T, Hamilton MJ, Ishii S, Fujioka RS, Whitman RL, Sadowsky MJ. The population structure of Escherichia coli isolated from subtropical and temperate soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 417-418:273-9. [PMID: 22264918 DOI: 10.1016/j.scitotenv.2011.12.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 12/06/2011] [Accepted: 12/20/2011] [Indexed: 05/19/2023]
Abstract
While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous microflora.
Collapse
|
19
|
Edge TA, El-Shaarawi A, Gannon V, Jokinen C, Kent R, Khan IUH, Koning W, Lapen D, Miller J, Neumann N, Phillips R, Robertson W, Schreier H, Scott A, Shtepani I, Topp E, Wilkes G, van Bochove E. Investigation of an Escherichia coli environmental benchmark for waterborne pathogens in agricultural watersheds in Canada. JOURNAL OF ENVIRONMENTAL QUALITY 2012; 41:21-30. [PMID: 22218170 DOI: 10.2134/jeq2010.0253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Canada's National Agri-Environmental Standards Initiative sought to develop an environmental benchmark for low-level waterborne pathogen occurrence in agricultural watersheds. A field study collected 902 water samples from 27 sites in four intensive agricultural watersheds across Canada from 2005 to 2007. Four of the sites were selected as reference sites away from livestock and human fecal pollution sources in each watershed. Water samples were analyzed for Campylobacter spp., Salmonella spp., Escherichia coli O157:H7, Cryptosporidium spp., Giardia spp., and the water quality indicator E. coli. The annual mean number of pathogen species was higher at agricultural sites (1.54 ± 0.07 species per water sample) than at reference sites (0.75 ± 0.14 species per water sample). The annual mean concentration of E. coli was also higher at agricultural sites (491 ± 96 colony-forming units [cfu] 100 mL(-1)) than at reference sites (53 ± 18 cfu 100 mL(-1)). The feasibility of adopting existing E. coli water quality guideline values as an environmental benchmark was assessed, but waterborne pathogens were detected at agricultural sites in 80% of water samples with low E. coli concentrations (<100 cfu 100 mL(-1)). Instead, an approach was developed based on using the natural background occurrence of pathogens at reference sites in agricultural watersheds to derive provisional environmental benchmarks for pathogens at agricultural sites. The environmental benchmarks that were derived were found to represent E. coli values lower than geometric mean values typically found in recreational water quality guidelines. Additional research is needed to investigate environmental benchmarks for waterborne pathogens within the context of the "One World, One Health" perspective for protecting human, domestic animal, and wildlife health.
Collapse
Affiliation(s)
- T A Edge
- Water Science & Technology, National Water Research Institute, Environment Canada, Burlington, ON L7R 4A6, Canada.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Environmental patterns are imposed on the population structure of Escherichia coli after fecal deposition. Appl Environ Microbiol 2010; 77:211-9. [PMID: 21075897 DOI: 10.1128/aem.01880-10] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intestinal microbe Escherichia coli is subject to fecal deposition in secondary habitats, where it persists transiently, allowing for the opportunity to colonize new hosts. Selection in the secondary habitat can be postulated, but its impact on the genomic diversity of E. coli is unknown. Environmental selective pressure on extrahost E. coli can be revealed by landscape genetic analysis, which examines the influences of dispersal processes, landscape features, and the environment on the spatiotemporal distribution of genes in natural populations. We conducted multilocus sequence analysis of 353 E. coli isolates from soil and fecal samples obtained in a recreational meadow to examine the ecological processes controlling their distributions. Soil isolates, as a group, were not genetically distinct from fecal isolates, with only 0.8% of genetic variation and no fixed mutations attributed to the isolate source. Analysis of the landscape genetic structure of E. coli populations showed a patchy spatial structure consistent with patterns of fecal deposition. Controlling for the spatial pattern made it possible to detect environmental gradients of pH, moisture, and organic matter corresponding to the genetic structure of E. coli in soil. Ecological distinctions among E. coli subpopulations (i.e., E. coli reference collection [ECOR] groups) contributed to variation in subpopulation distributions. Therefore, while fecal deposition is the major predictor of E. coli distributions on the field scale, selection imposed by the soil environment has a significant impact on E. coli population structure and potentially amplifies the occasional introduction of stress-tolerant strains to new host individuals by transmission through water or food.
Collapse
|
21
|
Farnleitner AH, Ryzinska-Paier G, Reischer GH, Burtscher MM, Knetsch S, Kirschner AKT, Dirnböck T, Kuschnig G, Mach RL, Sommer R. Escherichia coli and enterococci are sensitive and reliable indicators for human, livestock and wildlife faecal pollution in alpine mountainous water resources. J Appl Microbiol 2010; 109:1599-608. [PMID: 20629798 PMCID: PMC3154642 DOI: 10.1111/j.1365-2672.2010.04788.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS This study evaluated the applicability of standard faecal indicator bacteria (SFIB) for alpine mountainous water resources monitoring. METHODS AND RESULTS Escherichia coli, enterococci (ENTC) and Clostridium perfringens were investigated by standard or frequently applied phenotypic and genotypic methods in a broad range of animal and human faecal sources in a large alpine mountainous area. Clostridium perfringens occurred only in human, livestock and carnivorous source groups in relevant average concentrations (log 4·7-7·0CFU g(-1) ) but not in herbivorous wildlife sources. Escherichia coli proved to be distributed in all faecal source groups with remarkably balanced average concentrations (log 7·0-8·4CFU g(-1) ). Except for single faecal samples from the cattle source group, prevalence rates for ENTC source groups were generally >87% with average concentrations of log 5·3-7·7 CFUg(-1) . To test the faecal indication capacity in the environment, faecal prevalence data were comparatively analysed with results from the concurrently performed multi-parametric microbial source tracking effort on karst spring water quality from the investigated alpine mountainous catchment (Reischer et al. 2008; Environ Microbiol 10:2598-2608). CONCLUSION Escherichia coli and enterococci are reliable faecal indicators for alpine mountainous water resources monitoring, although E. coli is the more sensitive one. Clostridium perfringens did not prove to be an indicator of general faecal pollution but is suggested a conservative microbial source tracking marker for anthropogenic faecal influence. SIGNIFICANCE AND IMPACT OF THE STUDY Applicability of SFIB is currently hotly debated. This is the first study providing comprehensive information on the applicability of SFIB at alpine mountainous habitats.
Collapse
Affiliation(s)
- A H Farnleitner
- Institute for Chemical Engineering, Research Area Applied Biochemistry and Gene Technology, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Vienna, Austria.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Trevisan D, Dorioz JM, Poulenard J, Quetin P, Prigent Combaret C, Merot P. Mapping of critical source areas for diffuse fecal bacterial pollution in extensively grazed watersheds. WATER RESEARCH 2010; 44:3847-3860. [PMID: 20569961 DOI: 10.1016/j.watres.2010.04.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 04/06/2010] [Accepted: 04/28/2010] [Indexed: 05/29/2023]
Abstract
Microbial contamination of surface waters frequently occurs on permanent natural grasslands subject to extensive grazing. Management of these problems requires developing methods to identify critical source areas that are responsible of significant losses of fecal microorganisms. In this study, GIS analysis of watersheds was used to calculate the flow of fecal bacteria (Escherichia coli) to the outflow of a watershed by summing bacterial flows in runoff from pixels containing cowpats. Calculations were performed in two steps: (i) identification of pixels with bacteria and runoff by modeling the distribution of cowpats and variable sources of surface runoff, and (ii) parameterization by inverse analysis of deterministic and stochastic functions for bacterial emission from cowpats and for retention during their transmission to the watershed outflow. During bacterial transport in water flow, bacterial retention on the soil surface has a large influence. Despite this effect, bacterial concentration in runoff remains high. In general, cowpat age, runoff volumes and the location and proportions of bacteria-emitting and non-emitting surfaces determine critical source areas and bacterial flows at the watershed outflow. These data are discussed in terms of feasibility of solutions for management of watercourses and grazing practices.
Collapse
Affiliation(s)
- Dominique Trevisan
- INRA, UMR 42 CARRTEL, 75 avenue de Corzent, F74203 Thonon les bains, France.
| | | | | | | | | | | |
Collapse
|
23
|
Lejzerowicz F, Pawlowski J, Fraissinet-Tachet L, Marmeisse R. Molecular evidence for widespread occurrence of Foraminifera in soils. Environ Microbiol 2010; 12:2518-26. [PMID: 20406290 DOI: 10.1111/j.1462-2920.2010.02225.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Environmental SSU rDNA-based surveys are contributing to the dramatic revision of eukaryotic high-level diversity and phylogeny as the number of sequence data increases. This ongoing revolution gives the opportunity to test for the presence of some eukaryotic taxa in environments where they have not been found using classical microscopic observations. Here, we test whether the foraminifera, a group of single-celled eukaryotes, considered generally as typical for the marine ecosystems are present in soil. We performed foraminiferal-specific nested PCR on 20 soil DNA samples collected in contrasted environments. Unexpectedly, we found that the majority of the samples contain foraminiferal SSU rDNA sequences. In total, we obtained 49 sequences from 17 localities. Phylogenetic analysis clusters them in four groups branching among the radiation of early foraminiferal lineages. Three of these groups also include sequences originated from previous freshwater surveys, suggesting that there were up to four independent colonization events of terrestrial and/or freshwater ecosystems by ancestral foraminifera. As shown by our data, foraminifera are a widespread and diverse component of soil microbial communities. Yet, identification of terrestrial foraminiferal species and understanding of their ecological role represent an exciting challenge for future research.
Collapse
Affiliation(s)
- Franck Lejzerowicz
- Ecologie Microbienne, UMR CNRS, USC INRA, Université de Lyon, Université Lyon 1, 43, Boulevard du 11 Novembre 1918, F 69622 Villeurbanne, France
| | | | | | | |
Collapse
|
24
|
Characterization of environmentally persistent Escherichia coli isolates leached from an Irish soil. Appl Environ Microbiol 2010; 76:2175-80. [PMID: 20154122 DOI: 10.1128/aem.01944-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soils are typically considered to be suboptimal environments for enteric organisms, but there is increasing evidence that Escherichia coli populations can become resident in soil under favorable conditions. Previous work reported the growth of autochthonous E. coli in a maritime temperate Luvic Stagnosol soil, and this study aimed to characterize, by molecular and physiological means, the genetic diversity and physiology of environmentally persistent E. coli isolates leached from the soil. Molecular analysis (16S rRNA sequencing, enterobacterial repetitive intergenic consensus PCR, pulsed-field gel electrophoresis, and a multiplex PCR method) established the genetic diversity of the isolates (n = 7), while physiological methods determined the metabolic capability and environmental fitness of the isolates, relative to those of laboratory strains, under the conditions tested. Genotypic analysis indicated that the leached isolates do not form a single genetic grouping but that multiple genotypic groups are capable of surviving and proliferating in this environment. In physiological studies, environmental isolates grew well across a broad range of temperatures and media, in comparison with the growth of laboratory strains. These findings suggest that certain E. coli strains may have the ability to colonize and adapt to soil conditions. The resulting lack of fecal specificity has implications for the use of E. coli as an indicator of fecal pollution in the environment.
Collapse
|
25
|
Fremaux B, Prigent-Combaret C, Beutin L, Gleizal A, Trevisan D, Quetin P, Jocteur-Monrozier L, Rozand C. Survival and spread of Shiga toxin-producing Escherichia coli in alpine pasture grasslands. J Appl Microbiol 2009; 108:1332-43. [PMID: 19778349 DOI: 10.1111/j.1365-2672.2009.04527.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To determine the fate of Shiga toxin-producing Escherichia coli (STEC) strains defecated onto alpine grassland soils. METHODS AND RESULTS During the summers of 2005 and 2006, the field survival of STEC was monitored in cowpats and underlying soils in four different alpine pasture units. A most probable number (MPN)-PCR stx assay was used to enumerate STEC populations. STEC levels ranged between 3.9 and 5.4 log(10) CFU g(-1) in fresh cowpats and slowly decreased until their complete decay (inactivation rates k < 0.04 day(-1)). PFGE typing of STEC strains isolated from faecal and soil samples assessed the persistence of various clonal types for at least 2 months in cowpats and their vertical dispersal down through the soil at a depth up to at least 20 cm. STEC cells counts in soil were always below 2 log(10) CFU g(-1), regardless of the pasture unit investigated. The soil became rapidly free of detectable STEC once the cowpat had decomposed. The eight STEC strains isolated during this study belonged to six distinct serotypes and tested positive for the gene(s) stx2, including the stx2g and stx2 NV206 variants. CONCLUSIONS STEC were able to persist in cowpats and disseminate down through the soil but were unable to establish. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides useful information concerning the ecology of STEC in alpine pasture grasslands and may have implications for land and cattle management.
Collapse
Affiliation(s)
- B Fremaux
- Unité de Microbiologie Alimentaire et Prévisionnelle-Ecole Nationale Vétérinaire de Lyon, Marcy l'Etoile, France.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Hodgson CJ, Bulmer N, Chadwick DR, Oliver DM, Heathwaite AL, Fish RD, Winter M. Establishing relative release kinetics of faecal indicator organisms from different faecal matrices. Lett Appl Microbiol 2009; 49:124-30. [PMID: 19422475 DOI: 10.1111/j.1472-765x.2009.02630.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS A laboratory assay for comparative characterization of various faecal matrices with respect to faecal indicator organism (FIO) release using, artificial rain water. METHODS AND RESULTS Fresh sheep and beef-cattle faeces, dairy cattle slurry and beef cattle farm yard manure (FYM) were collected from commercial units in south-west England and applied to 20 randomized 1 m(2) plots established on permanent grassland. Representative samples from each faecal matrix (n = 5) were collected on four occasions over 16 days. One gram of each sample was transferred to a sterile vial to which 9 ml of standard local rain was carefully pipetted. The vial was then rotated through 360 degrees, 20 times in 60 s to 'simulate' a standardized interaction of the faecal material with rainfall, providing an assay of comparative release potential. Appropriate decimal dilutions were prepared from the eluent. Following agitation, with a sterile spatula, the remaining faecal material and eluent in the vials were vortex mixed for 60 s before decimal dilutions were prepared from the resulting mixture, providing a quantitative assessment of the total FIO in the sample from which percentage release could be determined. Bacterial concentrations were enumerated in duplicate by membrane filtration following standard methods for FIO. Significant differences in release kinetics of Escherichia coli and enterococci from each of the faecal matrices were determined. CONCLUSIONS Differences in release from each faecal substrate and between FIO type (E. coli and intestinal enterococci) were observed in this laboratory study. The order of release of E. coli from the faecal matrices (greatest to least, expressed as a percentage of the total present) was dairy cattle slurry > beef cattle FYM > beef-cattle faeces > sheep faeces. For intestinal enterococci the order of percentage release was dairy cattle slurry > beef-cattle faeces > beef cattle FYM > sheep faeces. SIGNIFICANCE AND IMPACT OF THE STUDY This laboratory-based method provides the first data on the relative release kinetics of FIO from different faecal matrices in rain water. This is fundamental information needed to parameterize laboratory-based microbial models and inform approaches to field and catchment risk assessment.
Collapse
|