Monitoring of Horizontal Gene Transfer from Agricultural Microorganisms to Soil Bacteria and Analysis of Microbial Community in Soils

2012 ◽  
Vol 22 (4) ◽  
pp. 563-566 ◽  
Author(s):  
Sung Eun Kim
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Soil Bacteria

scholarly journals Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA

2007 ◽  
Vol 74 (2) ◽  
pp. 495-502 ◽  
Author(s):  
Dhritiman Ghosh ◽  
Krishnakali Roy ◽  
Kurt E. Williamson ◽  
David C. White ◽  
K. Eric Wommack ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Bacteria ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Viral Dna

ABSTRACT Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment. In this study we employed atrazine-impregnated Bio-Sep beads (a cell immobilization matrix) to sample active microbiota from soils with prior pesticide exposure history. Once recovered from soil, the bead communities were induced with mitomycin C (MC), and viral and bacterial abundances were determined to evaluate the incidence of inducible prophage in soil bacteria. The inducible fraction calculated within bead communities was high (ca. 85%) relative to other studies in aquatic and sedimentary environments. Moreover, the bacterial genes encoding 16S rRNA and trzN, a chlorohydrolase gene responsible for dehalogenation of atrazine, were detected by PCR in the viral DNA fraction purified from MC-induced bead communities. A diverse collection of actinobacterial 16S rRNA gene sequences occurred within the viral DNA fraction of induced, water-equilibrated beads. Similar results were observed in induced atrazine-equilibrated beads, where 77% of the cloned sequences were derived from actinobacterial lineages. Heterogeneous 16S rRNA gene sequences consisting of fragments from two different taxa were detected in the clone libraries. The results suggest that lysogeny is a prevalent reproductive strategy among soil bacteriophages and that the potential for horizontal gene transfer via transduction is significant in soil microbial communities.

scholarly journals Impacts of transgenic plants and microorganisms on soil biota

2001 ◽  
Vol 54 ◽  
pp. 105-110 ◽  
Author(s):  
M. O'Callaghan ◽  
T.R. Glare
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Transgenic Plants ◽  
Recent Work ◽  
Soil Bacteria ◽  
Genetically Modified ◽  
Soil Invertebrates ◽  
Soil Biota ◽  
Soil Ecosystem ◽  
Natural Systems

Little is known about the impacts of transgenic plants and microorganisms on soil biota and processes despite the large number of field releases of transgenic crops Recent work has shown that transgenic plants can cause changes in the soil biota (both invertebrates and microorganisms) associated with these plants Often the changes are transient but their impact on the soil ecosystem remains unknown Horizontal gene transfer from genetically modified (GM) bacteria to indigenous soil bacteria has been demonstrated but movement of genes from transgenic plants if it occurs at all has not yet been detected in natural systems Soil invertebrates appear to play an important role in horizontal gene transfer between bacteria in soil

scholarly journals Mycelia as a focal point for horizontal gene transfer among soil bacteria

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tom Berthold ◽  
Florian Centler ◽  
Thomas Hübschmann ◽  
Rita Remer ◽  
Martin Thullner ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Soil Bacteria ◽  
Focal Point

scholarly journals Horizontal gene transfer in an acid mine drainage microbial community

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Jiangtao Guo ◽  
Qi Wang ◽  
Xiaoqi Wang ◽  
Fumeng Wang ◽  
Jinxian Yao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Acid Mine

scholarly journals Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer

2021 ◽  
Vol 12 ◽  
Author(s):  
Abdullah Ibn Mafiz ◽  
Yingshu He ◽  
Wei Zhang ◽  
Yifan Zhang
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Soil Bacteria ◽  
Community Gardens ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Urban Community Gardens

Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.

Microbial communities and their interactions in biofilm systems: an overview

2004 ◽  
Vol 49 (11-12) ◽  
pp. 327-336 ◽  
Author(s):  
S. Wuertz ◽  
S. Okabe ◽  
M. Hausner
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Enrichment Culture ◽  
Community Analysis ◽  
Microbial Populations ◽  
Community Members ◽  
Biofilm Architecture

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

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