Commonwealth Scientific and Industrial Research Organisation

Event Date: 
Wednesday, August 26, 2015 - 19:00 - 19:45
Institution: 
CSIRO
Title: 

The evolution of mutualistic trait variation in rhizobial symbionts across genetic and geographic scales

Abstract: 

Interactions between plants and nitrogen-fixing rhizobial bacteria are characterized by high genetic diversity for traits important to the outcome of the interaction at the population and species level. However, the selective processes underpinning the generation and maintenance of genetic and phenotypic variation in such interactions are not well understood. I will present an overview of data gathered from a series of experiments using interactions between Acacia spp. and their associated rhizobia, and that address questions regarding the ecological and evolutionary drivers of trait variation across different scales.  Specifically, I will discuss how 1) phylogenetic constraint; 2) within-species local adaptation; 3) nutrient availability; and 4) partner diversity and identity, influence patterns of specialization and community structure in legume-rhizobial mutualistic interactions. Our results suggest that both host-bacterial and bacterial-bacterial interactions are important for understanding evolutionary and ecological dynamics and highlight the importance of designing experiments that span different genetic and geographic scales.

Event Date: 
Wednesday, August 26, 2015 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Effects of temporal pH shifts on ammonia oxidiser community structure and function

Abstract: 

Soil nitrification, the oxidation of ammonia to nitrate, is and driven by bacterial and archaeal autotrophic ammonia oxidisers (AOB and AOA) that carry out the first, rate limiting, step of oxidising ammonia to nitrite.  Previous work has suggested that adaptation and selection in AOA and AOB communities is, to some extent, pH driven.  Acidophilic, acido-neutral, and alkalinophilic groups have been identified by environmental surveys of amoA genes.  These studies of the role of pH in determining ammonia oxidiser community structure and activity have largely relied on spatial pH gradients.  In many managed soil systems (e.g., agricultural systems) edaphic factors (e.g., pH, N concentrations) vary widely temporally and the implications of short term temporal shifts in factors thought to govern oxidiser community structure, and therefore our ability to manipulate edaphic factors to direct community structure, are not well understood.   We investigated the roles of pH in driving nitrifier activity (potential) and community structure over a crop growing season (6 sampling points) in agricultural soils by comparing unamended soils with soils amended with lime to create a temporal pH gradient.  Liming induced a rapid and sustained change in the pH of surface soils (0-10cm), with pH in these soils increasing from 4.8 to 6.5, while in subsurface soils pH increased to a lesser degree after liming (4.3 – 4.5).  After liming, potential nitrification rates increased significantly throughout the production season in both surface and subsurface soils.   TRFLP analysis of total bacterial and archaeal communities showed significant partitioning of the broader communities with soil depth, pH treatment and time, suggesting that microbial communities respond rapidly to changes and that temporal variation in community structure is an important, if often overlooked, factor in assessing microbial diversity patterns. These changes were greater for bacterial, than archaeal, communities. We then utilised amoA gene microarrays to investigate specific AOA and AOB community responses to temporally induced pH changes.  Despite significant changes to ammonia oxidiser function, we saw only very weak changes in community structure of AOA and AOB, suggesting that over shorter temporal periods soil communities are resilient to environmental change and that niche partitioning of ammonia oxidiser communities is likely to be spatially, rather than temporally, governed.

Event Date: 
Wednesday, June 25, 2014 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Biomes of Australian Soil Environments (BASE)

Abstract: 

The Biomes of Australian Soil Environments (BASE) is a soil microbial diversity database faciliatated by Bioplatforms Australia and currently involving 14 Australian agencies. The BASE project is collecting biodiversity data from Australian soils in the form of amplicon sequences and amplication free metagenomic sequences. Sequence data is accompanied by rich contextual data describing soil physical and chemical attributes, land use, overlying vegetation and climate. All information collected is made publicly available via the BASE database. Thus far BASE has collected approximately 900 samples, with data from over 400 of these being currently available. I will briefly introduce the BASE project and its newly deployed database by describing the sampling and sequencing protocols and demonstrating the databases search capabilities.

Event Date: 
Wednesday, May 28, 2014 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Cairneyella

Abstract: 

In September 1999, I collected a small heath plant from a large sandstone outcrop near the Murphy’s Glen campsite in the Blue Mountains west of Sydney. This seedling had been growing in just a few centimetres of sand atop the rock. The shallowness of soil meant its root system was perpendicular to the stem, and spread out like a spider’s web from the base. Heath plants have unusual roots; they’re very fine, being only marginally thicker than a human hair. I took the plant back to the laboratories at University of Western Sydney and carefully cut these hair roots up in small pieces. I surface sterilised the pieces in bleach and placed each piece, numbered and its location in the root system recorded, onto an agar plate. From these tiny root pieces grew a host of very slow growing non-spore producing fungi. Most of these fungi were ericoid mycorrhizal (ERM) fungi – these fungi form a symbiosis with heath plants – facilitating their growth in challenging places such as acid bogs, nutrient poor sands and soils rich in metals such as cadium and zinc. Since 1999, I’ve undertaken quite a bit of work on the most abundant ERM fungus from this one seedling, and with the help of various collaborators we have observed the structures it forms in roots of heath plants, how it enhances the growth of heath seedlings and examined its carbon, nitrogen and phosphorus catabolism. It was, and still is, the most studied Australian ericoid mycorrhizal fungus. 
Upon moving to CSIRO in 2007, I left the last six cultures in the fridge in Dr. Peter McGee’s laboratory and it was here that they remained until 2013 when I retrieved them on Peter’s retirement. Just two of the last six survived the long winter. In late 2013, we had some space on an Illumina run with some other samples – and we sequenced the genome of this fungus. We’ve called it ‘Cairneyella’ after the late Professor John W. G. Cairney. There’s still much to learn about Cairneyella – and I’m seeking collaborators who’d like to share these last cultures and further the body of work on this remarkable fungus.

Event Date: 
Wednesday, April 30, 2014 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

Genetic diversity of Group I Clostridium botulinum and Clostridium sporogenes

Abstract: 

Whilst classified as a single bacterial species, Clostridium botulinum comprises a phylogenetically and physiologically diverse collection of organisms. Members of this species are linked together based solely on the production of botulinum neurotoxin (BoNT); amongst most lethal natural toxin produced. Isolates that do not produce BoNT are taxonomically considered a separate species, such as Clostridium sporogenes. Given the species delineation is based solely on an unstable phenetic trait presents increasing challenges in a post-genomic era, particularly with increasing evidence pointing towards the lateral acquisition of BoNT production in many strains. Here, the pan-genome of Group I C. botulinum and C. sporogenes is presented, describing the genetic diversity of these species, highlighting the incongruent taxonomy of these organisms and presenting insights into the acquisition of BoNT within this group.

Event Date: 
Wednesday, August 28, 2013 - 18:15 - 18:30
Institution: 
CSIRO Canberra
Title: 

Multi-scale spatial patterns of soil microbial communities and biogeochemical processes in three arctic ecosystems

Abstract: 

Microbial communities and their functional role in soil biogeochemical processes vary across spatial scales. Although soil and microbial spatial variability has been studied in various tropical and temperate ecosystems, little information is available from arctic ecosystems. Arctic soils represent a significant proportion of global land mass and contain about one fourth of total soil carbon pool. Soil microbial nitrogen (N) transformations such as nitrification and denitrification have significant implications for N availability and N loss in nutrient-limited arctic ecosystems. This study explored the spatial relationships among microbial communities, functional processes and soil properties in three Canadian arctic ecosystems. Despite adverse climatic conditions and frequent cryopedogenic processes, soil attributes and microbial abundance are highly spatially structured and their spatial autocorrelation is consistent within and between the ecohabitats. However, the zone of spatial autocorrelation is substantially smaller than non-arctic ecosystems. Ammonia-oxidizing and denitrifying communities are spatially structured within 5 m whereas potential nitrification and denitrification are spatially autocorrelated within 40 m in arctic soils. Nitrification activities are driven at small scales (<1 m) by moisture and total organic carbon content whereas gene abundance and other edaphic factors drive at medium (1-10 m) and large (10-100 m) scales. Soil moisture, organic carbon and nitrogen content are the predominant driving factors with nirK abundance also correlated to denitrification across spatial scales. Overall, this study unravels the multi-scale determinants of nitrification and denitrification in Arctic ecosystems.

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 - 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.

Syndicate content