Soil biology

Event Date: 
Wednesday, October 28, 2015 - 18:15 - 18:30
Institution: 
UTS
Title: 

Heterogeneity in diazotroph diversity and activity within a putative hotspot for marine nitrogen fixation

Abstract: 

Australia’s tropical waters represent predicted “hotspots” for nitrogen (N2) fixation based on empirical and modelled data. However, the identity, activity and ecology of N2 fixing bacteria (diazotrophs) within this region are virtually unknown. By coupling DNA and cDNA sequencing of nitrogenase genes (nifH) with size fractionated N2 fixation rate measurements, we elucidated diazotroph dynamics across the shelf region of the Arafura and Timor Seas (ATS) and oceanic Coral Sea during Austral spring and winter. During spring, Trichodesmium dominated ATS assemblages, comprising 60% of nifH DNA sequences, while Candidatus Atelocyanobacterium thalassa (UCYN-A) comprised 42% in the Coral Sea. In contrast, during winter the relative abundance of heterotrophic unicellular diazotrophs (∂-proteobacteria and gamma-24774A11) increased in both regions, concomitant with a marked decline in UCYN-A sequences, whereby this clade effectively disappeared in the Coral Sea. Conservative estimates of N2 fixation rates ranged from < 1 to 91 nmol L-1 d-1, and size fractionation indicated that unicellular organisms dominated N2 fixation during both spring and winter, but average unicellular rates were up to 10-fold higher in winter than spring. Relative abundances of UCYN-A1 and gamma-24774A11 nifH transcripts negatively correlated to silicate and phosphate, suggesting an affinity for oligotrophy. Our results indicate that Australia’s tropical waters are indeed hotspots for N2 fixation, and that regional physicochemical characteristics drive differential contributions of cyanobacterial and heterotrophic phylotypes to N2 fixation.

Event Date: 
Wednesday, November 26, 2014 - 18:00 - 18:15
Institution: 
UWS
Title: 

Clues of sexual reproduction in the Arbuscular Mycorrhizal Fungi: a putatively ancient asexual land-plant symbiont

Abstract: 

Arbuscular Mycorrhizal Fungi (AMF) are an ancient group of obligate land-plant symbionts which form a mutualistic symbiosis with the roots of over 80% of land plants  and are found in the majority of terrestrial ecosystems. The filamentous hyphae of these fungi grow throughout the soil, scavanging for water and nutrients and transfer these to the plant in exchange for plant produced sugars.  As a result, extensive underground networks can form where multiple fungal individuals can be connected to a single plant and a single fungus can be connected to multiple plants simultaneously.  AMF do not have cells, rather nuclei flow freely through a common cytoplasm and genetically distinct individuals of a species are capable of anastomosis – or hyphal fusion – where cytoplasmic and nuclear exchange may occur. Curiously, these fungi have been once classified as ‘ancient asexuals’ due the lack of any observable sexual structures and an assumed purely clonal life-style. I present recent insights from the genome of the model AMFRhizophagus irregularis which contains evidence of a genetic tool kit which looks more like that of a sexually reproducing organism. I highlight the extreme expansion of a group of MATA-HMG genes which normally act as master- regulators of sex in fungi and present insights into the structure and function of these genes from a survey of local and global populations of R. irregularis individuals along with transcriptional evidence via QRT-PCR that a subset of these genes have a functional involvement in AMF partner recognition and possibly sexual reproduction.

Event Date: 
Wednesday, October 29, 2014 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Ammonia-oxidizing bacteria play redundant roles with ammonia-oxidizing archeae in acidic soil

Abstract: 

 
It is widely accepted that ammonia-oxidizing achaea (AOA) dominates ammonia oxidization, the rate-limiting step in the nitrification process, in acidic soils, but their counterpart ammonia-oxidizing bacteria (AOB) which are ubiquitous in acidic soils should not be neglected. Researches about the functions of AOB in acidic soils are very few. Here, we investigated the abundance and community of AOA and AOB in acidic soils (pH 3.35 ~ 4.46) with nine different treatments (Ctrol, N, NK, NP, NPK, N+CaO, NK+CaO, NP+CaO, NPK+CaO) and found that significant positive correlations between potential nitrification rate (PNR) with the total amoA gene copy numbers of AOA and AOB. The community of AOB but not of AOA responded to CaO significantly. Moreover, microcosms incubation with different concentration CaO (N+0, 500, 1000, 2000 ppm CaO, pH 3.42 ~ 4.37) showed that the abundance of AOB amoA gene significantly increased in N+1000 and N+2000 treatments at day 7 while the abundance of AOA amoA gene significantly increased in N and N+500 treatments at day 60. The community of AOA and AOB changed significantly during the incubation. Phylogenetic analysis of bacterial and archaeal amoA gene in treatment N+1000 revealed that AOA belonged to group 1.1a-associated increased whereas that belonged to group 1.1b decreased significantly during the incubation.  AOB belonged to Cluster 10 increased significantly at day 7 but decreased during the last incubation while AOB belonged to Cluster 3a.1 and 3a.2 showed reverse trends during the incubation. Additionally, AOB belonged to Cluster 7 were obligately observed at day 7. Moreover, we studied the activity of ammonia oxidizers in treatments N, N+1000 and N+CaO with 13CO2-DNA-stable isotope probing incubation for 30 days. Interestingly, 13C-labeled carbon source was significantly assimilated into the amoA gene of AOB but not AOA at day 7 and the reverse result was observed at day 30 in treatment N+1000 though it was acidic soil. Significant assimilation of 13C-labeled carbon source was detected in AOA amoA gene in treatments N and N+CaO during the incubation. Taken together, these results suggested that AOB responded to the disturbance significantly then drove the ammonia oxidization in acidic soils, meaning that AOB played redundant roles with AOA in acidic soils though the two groups of ammonia oxidizers had special niches.

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, February 26, 2014 - 15:15 - 15:45
Institution: 
Singapore Centre on Environmental Life Sciences Engineering
Title: 

Dissecting Structure-Function Relationships In Complex Microbial Communities Using Perturbation Transcriptomics

Abstract: 

Application of ‘omics technologies, including high-throughput nucleic acid sequencing and advanced mass spectrometry, show huge potential to increase our understanding of bioprocesses occurring in both natural and engineering microbial ecosystems. Field studies of such systems are inherently complicated, while laboratory reactor models involve extensive community modifications following inoculation and may not accurately reflect the biology of the source community. Here we develop a complementary approach to dissecting structure-function relationships of complex microbial communities, by applying experimental perturbations to freshly sourced, intact communities in a controlled fashion. In an investigation examining nitrogen transformation in wastewater treatment, we use metatranscriptomics in a time series design (n=20 samples) to study changes associated with onset of oxygenation. This stimulus switches the community between de-nitrification and nitrification phases of the nitrogen cycle, thus modeling a key aspect of wastewater process control. This model permits identification of functional genes, in both known and previously unknown taxa, and represents a readily adaptable model studying structure-function relationships in microbial communities. If time permits, I will discuss how this perturbation metatranscriptomics approach has implications for improving our ability to perform metagenome assembly.

Event Date: 
Wednesday, November 27, 2013 - 18:00 - 18:15
Institution: 
Hawkesbury Institute for the Environment, UWS
Title: 

Organic phosphorus acquisition may be a functional driver of community structure for ectomycorrhizal fungi in a tri-partite symbiosis

Abstract: 

 
Alnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria, and while their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts. We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus and nitrogen as compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii. At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than those from P. menziesii, while potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites.  At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host. Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic phosphorus acquisition abilities relative to non-Frankia ECM hosts.  This shift, in combination with chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities. 

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, January 30, 2013 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

Changes in soil microbial community precede changes in plant community along a chronosequence

Abstract: 

Shrubs in semiarid ecosystems facilitate the establishment of other plant species under their canopies and promote changes in these understory plant communities as they grow. To better understand whether plant community dynamics are linked to changes in soil microbes, we characterized soil microbial communities in gaps (interspaces) and under Retama sphaerocarpa shrubs of three different size/age classes. Different methodological approaches including pyrosequencing of 16S rDNA, phospholipid-fatty acid (PLFA) analysis and microbial activity indicators were combined to characterize both the structure and function of microbial communities along the chronosequence. Small shrubs induced an increase in soil bacterial and fungal biomass, a stimulation of microbial activity and changes in the relative abundance of several bacterial groups, preceding aboveground increase in plant richness and biomass. Shrubs promoted a significant increase of Bacteroidetes, Betaproteobacteria and Gammaproteobacteria abundance in detriment of Actinobacteria and Firmicutes without changes in overall bacterial diversity. Some changes in the microbial community increased with shrub age while other did not, being microbial communities in gaps and under the canopy of large shrubs the most differentiated. We argue that the observed changes in composition and function of soil microbial communities may promote the increase in plant growth and understory species richness along the chronosequence. This emphasizes the importance of plant-soil interactions on defining the structure and composition of both plant and soil microbial communities and their impact on ecosystem functioning.

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