Nitrogen metabolism

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, 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, 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: 
Tuesday, July 24, 2012 - 19:00 - 20:00
Institution: 
MIT
Title: 

Relating the biogeography of nitrogen fixing phytoplankton and the nutrient environment in the ocean

Abstract: 

 

Nitrogen fixation may support as much as half of local productivity in some subtropical regions and is the major source of fixed nitrogen to the ocean, maintaining global productivity on long timescales. We use a combination of numerical models and ecological theory to interpret the relationship of nitrogen fixation and nutrient resources (fixed nitrogen, phosphorus and iron) in the global open ocean. We find that the ratio of the supply rates of iron and fixed nitrogen can accurately predict the biogeography of nitrogen fixers to the extent that it can be constrained by current observations.

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