Soil

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, November 27, 2013 - 18:15 - 18:30
Institution: 
School of Civil and Environmental Engineering, UNSW
Title: 

Metal(loid) bioaccessibility dictates microbial community composition in acid sulfate soil horizons and sulfidic drain sediments

Abstract: 

 
Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically-disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing.  Diversity analyses were problematic due to the high microbiological heterogeneity between each geochemical replicate.  Taxonomic analyses combined with measurements of metal(loid) bioaccessibility identified significant correlations to genera (5 % phylogenetic distance) abundances. A number of correlations between genera abundance and bioaccessible Al, Cr, Co, Cu, Mn, Ni, Zn, and As concentrations were observed, indicating that metal(loid) tolerance influences microbial community compositions in these types of landscapes.  Of note, Mn was highly bioaccessible (≤ 24 % total soil Mn); and Mn bioaccessibility positively correlated to Acidobacterium abundance, but negatively correlated to Holophaga abundance and two unidentified archaeal genera belonging to Crenarchaeota were also correlated to bioaccessible Mn concentrations, suggesting these genera can exploit Mn redox chemistry. 

Event Date: 
Wednesday, February 27, 2013 - 15:15 - 15:45
Institution: 
University of Western Sydney
Title: 

Responses of soil fungi to global change: effects of elevated atmospheric CO2, temperature and drought

Abstract: 

Fungi are central to forest carbon and nutrient cycles in Australian sclerophyll forest soils, but little is known about how they will respond to future global change. Our recent research has used a combination of controlled environment glasshouse and field experimentation to investigate the interactive effects of elevated atmospheric CO2 concentration [CO2], increased temperature and drought on Australian eucalypt soil fungal biodiversity.
 
In a glasshouse experiment, seedlings of two eucalypt species (Eucalyptus saligna and E. sideroxylon) were grown in field soil for 5 months under sub-ambient (290 µl l-1), ambient (400 µl l-1) and elevated (650 µl l-1) atmospheric CO2 conditions at both ambient (26°C) and elevated temperature (30°C). Multivariate analyses conducted on molecular data generated from soil and hyphal ingrowth bags (which select for mycorrhizal fungal mycelia) showed a significant (P < 0.035) separation between fungal communities associated with the two different tree species. While there was an effect of [CO2] and temperature, the response was plant species dependent with the exception of the combined elevated [CO2] and elevated temperature treatment (650 µl l-1 CO2 and 30oC) which clustered together regardless of tree species.
 
In the field experiment, E. saligna trees were grown in 12 whole tree chambers for three years under controlled temperature conditions and exposed to either ambient (ca. 380 µl l-1) or elevated (ca. 640 µl l-1) atmospheric [CO2] and different watering regimes to simulate drought. Multivariate analyses of molecular data showed that elevated [CO2] intensified the effect of drought stress by significantly altering fungal community composition.
 
Collectively, our data demonstrate that alterations to atmospheric [CO2], temperature and drought conditions modify soil fungal communities associated with Australian eucalypts. We are currently investigating the knock-on effects of these changes for fungal driven soil processes given the potential for soil microorganisms to significantly influence the direction and magnitude of terrestrial ecosystem/atmosphere feedbacks that regulate global change.

JAMS REPORT
Maria-Luisa Gutierrez-Zamora

The JAMS rendezvous this October 31st took place in the fourth floor of the Museum with a magnificent view of Sydney, and began with an ad hoc presentation featuring sulphurous scents and sexy fangs. Katherina Petrou (UTS) initiated us in the science of the sulphur cycle in the oceans and how this process is dominated by the production of dimethylsulfoniopropionate (DMSP) by microalgae and its decomposition into dimethylsulphide (DMS), a strong odorous chemoattractant for a range of marine organisms. In tackling the mystery of how harmful algal blooms disappear, Katherina discovered that DMS produced by the dinoflagellate Alexandrium minutum (causative agent of toxic algal blooms) was the chemical cue for the infection of its parasitoid Parvilucifera sinerae.  An elegant video illustrated how DMS at 300 nM was able to activate the parasitoid spores from a dormant state to leave the sporangium (an infected A. minutum cell) in transit to infect other cells and propagate. Activation only occurred in the range of 30 to 300 nM indicating that the effect was dependent on cell density. Thus, Katherina’s work showed that DMS plays an important role in the biological control of toxic algal blooms in the oceans. Her results contribute to the better understanding of marine chemical ecology.

Event Date: 
Wednesday, October 31, 2012 - 06:15 - 06:30
Institution: 
CSIRO
Title: 

Impact of nutrient addition on microbial community actively decomposing wheat residues and sequestration of carbon in soil

Abstract: 

 
Soils represent a significant terrestrial carbon reservoir and there is considerable interest in increasing or maintaining its size.   Recent work has suggested that microbially mediated carbon sequestration into soils may be maximised by ensuring adequate supply of other nutrients (nitrogen, phosphorous, sulphur), thus maintaining high microbial carbon use efficiency.  This is particularly important in cropping agriculture systems where appropriate crop-residue management may result in substantial soil carbon and general soil quality improvements.
A soil microcosm experiment was conducted to evaluate the effects of nutrients on the decomposition of wheat residues; specifically the effects on active bacterial community and carbon sequestration.  Stable Isotope Probing (SIP) of 16S rDNA using Phylochip microarrays was employed to investigate the bacterial community associated with the decomposition of 13C-labelled wheat straw and incorporation of the carbon into soil humus.  Respiration and carbon, nitrogen, phosphorous and sulphur transformations were measured over a 56 day incubation to assess priming effects, both gross and net humification efficiency and carbon sequestration through microbiological action.  Soils that received wheat residues only always showed an increase in “new” carbon (13C), although they did not always show an increase in “total” (12C +13C) carbon.  Soils receiving nutrients (nitrogen, phosphorous and sulphur) with wheat residues did show an increase in both new and total carbon pools, suggesting availability of nutrients other than carbon influence soil carbon sequestration.  Bacterial communities responsible for residue decomposition and carbon sequestration were different for nutrient added and no-nutrient treatments, indicating microbial carbon use efficiency is also influenced by the composition of the active community.  Our results suggest that soil carbon:nitrogen:phosphorus:sulphur (C:N:P:S) stoichiometry and bacterial community composition play important roles in determining potential levels of carbon sequestration in agricultural soils.

Event Date: 
Wednesday, June 27, 2012 - 19:15 - 20:00
Institution: 
Faculty of Agriculture & Environment, University of Sydney, Sydney, NSW.
Title: 

Sulfur cycling in the rhizosphere: the role of sulfatase and sulfonatase diversity.

Abstract: 

Growth of healthy, high-yielding crop plants requires a stable input not only of nitrogen and phosphorus, but also of sulfur (S). Although S is naturally present in soils, it is usually bound in organic form as sulfate esters or sulfonates, which are not directly bioavailable to plants. Sulfur can be supplemented by addition of inorganic fertilizer, but most sulfate for plant nutrition is provided by microbial turnover of organically-bound sulfur. To identify the rhizosphere organisms responsible for this turnover, we focused on the key genes atsA, which encodes arylsulfatase, and asfA, which is required for aryldesulfonation. Functional T-RFLP analysis was used to analyse atsA diversity in a range of agricultural and natural soils, and clear atsA community differences associated with land use and soil/bedrock types were observed, which were mirrored in the arylsulfatase activity of the cultivable fraction of the population. Soil arylsulfatase activity is routinely assayed as a measure of soil health, but these data highlight the need for detailed studies on arylsulfatase gene diversity in the soil. Sulfonatase diversity was measured in rhizospheres of field-grown wheat plants and in a sulfate-limited Agrostis-dominated grassland, and the effect of adding sulfate in long-term or short-term treatments was tested. Functional asfA community analysis showed that desulfonation genes from both wheat and Agrostis rhizospheres were dominated by Variovorax and Polaromonas species. This distribution of taxa was also found in a cultivation-dependent analysis, and these genera appear to be key players in rhizosphere sulfonate transformations in several environments. Increasing our understanding of the rhizosphere microbes that catalyse soil organosulfur turnover will allow us to develop management practices to maximize soil sulfur availability, and minimize the costs associated with fertilization.

Event Date: 
Wednesday, August 31, 2011 - 18:15 - 18:30
Institution: 
CSIRO
Title: 

High Alpine Bacteria Display Strong Landscape Scale Distributions

Abstract: 

Soil microorganisms dominate terrestrial biogeochemical cycles; however, we know very little about their spatial distribution and how changes in the distributions of specific groups of microbes translate into landscape and global patterns of biogeochemical processes. I use a nested sampling scheme at scales ranging from 2 to 2,000 m to show that bacteria from a high-alpine landscape have significant spatial autocorrelation in community composition up to a distance of 240 m. While this pattern is strongly predictable, the average diversity only increases by 5% across the entire landscape. This pattern is best explained changes in the relative abundance of specific bacterial clades in response to the soil environment across the landscape.

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