Nitrification

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, 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, 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.

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