Microbiology

Event Date: 
Wednesday, May 29, 2013 - 18:00 - 18:15
Institution: 
CSIRO
Title: 

Genotypic associations of Borrelia burgdorferi in mammalian and avian hosts

Abstract: 

Borrelia burgdorferi s. s., the bacterium that causes Lyme disease in North America, occurs as multiple co-circulating genotypes of the ospC gene, an important antigenic outer surface protein C. The diversity of ospC genotypes is thought to arise from fairly specific associations between genotypes and vertebrate hosts, such that different host species act as different “ecological niches” for the pathogen. To evaluate the degree of specificity of B. burgdorferi-host associations, we sampled genotypes of bacteria transmitted to ticks by several mammalian and avian host species. We also examined how the subset of genotypes known to infect humans, considered as human-invasive strains (HIS), is distributed among host species and higher taxonomic levels (birds, shrews, rodents). We adapted a patch occupancy model used for species detection to test for the occurrence probabilities (ψ) and transmission efficiencies (ε) associated with each ospC type. We found that the frequency of specific ospC genotypes varied among host species, demonstrating some support for the niche concept. Indeed, examination of all ospC types concurrently indicated that the ospC frequencies associated with birds and rodents were more similar within the taxonomic group than between groups based on principal components analysis. Conversely, HIS frequencies were more similar across all host species than within a host taxonomic level, implying weaker support for the niche concept. The occupancy model suggests that HIS types occurred more frequently than non-HIS types, but that HIS types generally had lower transmission efficiencies (from hosts to ticks). In several cases, rare genotypes had higher transmission efficiencies, suggesting an evolutionary trade-off between transmission efficiency and maintenance within the host. Our study highlights the importance of American robins (Turdus migratorius) and short-tailed shrews (Blarina brevicauda) in contributing large proportions of HIS types, and offers a novel way of examining occurrence and transmission efficiencies of ospC types within tick vectors, using a likelihood approach.

Event Date: 
Wednesday, May 29, 2013 - 18:15 - 18:30
Institution: 
Macquarie University
Title: 

Dissemination of antibiotic resistance determinants via sewage discharge from Davis Station, Antarctica

Abstract: 

Discharge of untreated or macerated sewage presents a significant risk to Antarctic marine ecosystems by introducing non-native microorganisms that potentially impact microbial communities and threaten health of Antarctic wildlife. Despite these risks, disposal of essentially untreated sewage continues in the Antarctic and sub-Antarctic. As part of an environmental impact assessment of the Davis Station, we investigated carriage of antibiotic resistance determinants in Escherichia coli isolates from marine water and sediments, marine invertebrates (Laturnula and Abatus), birds and mammals within 10 km of the Davis sewage outfall. Class 1 integrons typical of human pathogens and commensals were detected in 12% of E. coli isolates. E. coli carrying these integrons were primarily isolated from the near shore marine water column and the filter feeding mollusc Laturnula. Class 1 integrons were not detected in E. coli isolated from seal (Miroungaleonina, Leptonychotes weddellii) or penguin (Pygoscelis adeliae) feces. However, isolation of E. coli from these vertebrates’ faeces was also low. Consequently, sewage disposal is introducing non-native microorganisms and associated resistance genes into the Antarctic environment. The impact of this “gene pollution” on the diversity and evolution of native Antarctic microbial communities is unknown. 

 

Event Date: 
Wednesday, May 29, 2013 - 19:00 - 19:45
Institution: 
CSIRO
Title: 

Sediment Biobarriers for Chlorinated Aliphatic Hydrocarbons in Groundwater Reaching Surface Water

Abstract: 

 
This study explored the potential of eutrophic river sediments to attenuate the infiltration of chlorinated aliphatic hydrocarbon (CAH)-polluted groundwater discharging into the Zenne River near Brussels, Belgium. Active biotic reductive dechlorination of CAHs in the riverbed was suggested by a high dechlorination activity in batch- and column biodegradation tests performed with sediment samples, and by the detection of dechlorination products in sediment pore water. Halorespiring Dehalococcoides spp. were present in large numbers in the riverbed as shown by quantification of their 16S rRNA and reductive dehalogenase genes. By using DGGE-fingerprint analysis of relevant nucleic acid markers, it was shown that the Zenne River sediments were inhabited by a metabolically diverse bacterial community. A large diversity of sulfate-reducing bacteria, Geobacteraceae and methanogens, which potentially compete with halorespiring bacteria for electron resources, was identified. The high organic carbon level in the top of the riverbed, originating from organic matter deposition from the eutrophic surface water, resulted in a homogeneous microbial community structure that differed from the microbial community structure of the sediment underneath this layer. Monitoring of CAH concentrations and stable isotope ratios of the CAHs (δ13C) and the water (δ2H and δ18O), allowed to identify different biotic and abiotic CAH attenuation processes and to delineate their spatial distribution in the riverbed. Reductive dechlorination of the CAHs was the most widespread attenuation process, followed by dilution by unpolluted groundwater discharge and by surface water-mixing. During a 21-month period, the extent of reductive dechlorination ranged from 27 to 89% and differed spatially but was remarkably stable over time, whereas the extent of abiotic CAH attenuation ranged from 6 to 94%, showed large temporal variations, and was often the main process contributing to the reduction of CAH discharge into the river. Although CAHs were never detected in the surface water, CAHs were not completely removed from the discharging groundwater at specific locations in the riverbed with high groundwater influx rates. Therefore, it was concluded that an increase in the extent of biotransformation in the riverbed is needed for acceptance of the Zenne biobarrier as a viable remedial option for attenuation of discharging CAH-polluted groundwater.

Event Date: 
Wednesday, April 24, 2013 - 19:15 - 20:00
Institution: 
University of Technology Sydney
Title: 

Observing the developing infant gut microbiome with time-series metagenomics.

Abstract: 

The human body plays host to a complex microbial ecosystem, the
development of which begins around the time of birth. Routine monitoring
of the development of microbial ecosystems in newborns (or other
environments) using metagenomic methods is currently extremely
challenging and expensive. I will describe some recent technological
advances that could enable routine sequencing and computational analysis
of hundreds of metagenomes, and demonstrate their application on samples
taken from a developing infant gut microbiome. In this study forty-five
samples were subjected to transposon-catalyzed Illumina library prep and
metagenomic sequencing on a HiSeq 2000 instrument. The resulting data
was subjected to analysis of microbial community structure using a new
approach called phylogenetic Edge Principal Component Analysis (Edge
PCA) that can identify which lineages in a phylogeny explain the
greatest degree of variation among the samples. We also investigate the
population genomics of Bacteroides thetaiotaomicron, one of the dominant
members of the gut microbial community.

Event Date: 
Wednesday, April 24, 2013 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

Comparative Analysis Of Saxitoxin-Producing And Non-Toxic Ecotypes Of Anabaena circinalis

Abstract: 

During bloom events, freshwater cyanobacteria often produce a variety of harmful toxins with devastating health, environmental and economic consequences. The paralytic shellfish toxins are a large group of neurotoxic alkaloids including saxitoxin (STX), which is the most potent identified to date. In Australia, STX production is strain dependent within the cyanobacterium Anabaena circinalis. The following study utilised two strains of cyanobacteria, A. circinalis AWQC131C (131C) and A. circinalis AWQC310F (310F), as model organisms; 131C is a saxitoxin-producer whilst 310F serves as a non-toxic control. We aimed to characterise 131C and 310F at the genomic and proteomic levels using genome sequencing and isobaric tags for relative and absolute quantitation (iTRAQ), respectively, in order to identify key differences in not only their secondary but, primary metabolic pathways.
 
Draft genome sequencing of 131C and 310F revealed a genome length of 4.4 Mbp and a GC content of 37%, and the number of encoded genes was predicted to be 4447 and 4443 for 131C and 310F, respectively. A scan of each genome revealed a total of 740 unique coding regions within 131C, and 651 within 310F. Interestingly, the proteomic profile of 131C was significantly different from 310F. Using iTRAQ, we found that under standard laboratory conditions, 131C was highly abundant in photosynthetic and metabolic proteins compared to the non-toxic control.  This suggests a high C:N ratio and intracellular 2-oxoglutarate concentration and may be a novel site for posttranslational regulation of STX. Overall, 131C is potentially a high energy ecotype likely to inhabit the water surface. Conversely, 310F was more abundant in molecular chaperones and proteins that neutralise reactive oxygen species, indicating activation of cellular stress response. Therefore, 310F seems to be experiencing cellular stress under laboratory conditions and in the environment, may inhabit low-light areas below the water surface.
 
In conclusion, this study has provided an insight into fundamental differences between the toxic 131C and non-toxic 310F strains of A. circinalis. These findings will provide a platform for future experiments and hopefully pave the way to identify the cellular function of STX.

Event Date: 
Wednesday, March 27, 2013 - 18:15 - 18:30
Institution: 
Hawkesbury Institute for the Environment, University of Western Sydney
Title: 

Effect of Huanglongbing on the structure and functional diversity of microbial communities associated with citrus.

Abstract: 

Plant-microbe interactions lie at the heart of plant performance and ecology. It has been postulated that disruption of multi-trophic interactions in a stable ecosystem under the influence of invading phytopathogens will cause community reorganization and changes in the local feedback interactions. However, there is a paucity of knowledge on the extent to which such community shifts may occur, on the dynamics of changes and on the putative effects regarding the functioning of ecosystems. We have used Citrus-‘Candidatus Liberibacter asiaticus’ [Las, causal agent of devastating Huanglongbing (HLB) disease] as a host pathogen model to characterize the structure, function and interactions of plant-associated microbial communities. We applied a suit of metagenomic techniques to provide detailed census of citrus associated microbiomes. Our results confirmed that Las is the sole causal agent of HLB in Florida and revealed that HLB significantly re-structures the composition of native microbial community present either in leaf, roots and rhizosphere of citrus. Functional microarray (Geochip) and shotgun metagenomic sequencing showed that HLB has severe effects on various functional guilds of bacteria involved in key ecological processes including nitrogen cycling and carbon fixation. Overall, the metagenomic studies provided evidence that change in plant physiology mediated by Las infection could elicit shifts in the composition and functional potential of plant associated microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus producing agro-ecosystems.

Event Date: 
Wednesday, February 27, 2013 - 16:15 - 16:45
Institution: 
California Institute of Technology
Title: 

Bridging the gap between ‘omics generated hypotheses and metabolic function of microorganisms in the environment.

Abstract: 

Rapid advancements in environmental ‘omics approaches (e.g. metagenomics, transcriptomics, proteomics) have provided a fresh perspective on the metabolic potential of uncultured microorganisms in nature.  However, our ability to directly test hypotheses regarding the ecophysiology of microorganisms in their natural environment remains a challenge.  New applications of whole cell fluorescence microscopy, stable isotope tracers and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS), provide direct cell-specific isotopic, elemental and phylogenetic information on the metabolic roles of environmental microorganisms and microbial associations.   This presentation will introduce the FISH-nanoSIMS method and highlight its utility for the field of microbial ecology through a case study of uncultured methane-consuming archaeal-bacterial symbioses in deep-sea sediments.

JAMS REPORT
Tom Jeffries
 
January JAMS got the new year off to a good start with a solid turnout and some stimulating talks. First up was Olivier Laczka who took us in to the technical realm of biosensors. Olivier’s work has focused on developing cost-effective tools for the rapid identification of micro-organisms relevant to industry and has led to several Patents.

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