Bacteria

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, September 30, 2015 - 19:00 - 19:45
Institution: 
University of Southern California
Title: 

Microbial evolutionary surprises in the future ocean:  Long-term adaptation of marine nitrogen-fixing cyanobacteria to high CO2

Abstract: 

The globally-distributed marine cyanobacterium Trichodesmium plays a key role in ocean biogeochemical cycles, as it is a major source of newly fixed atmospheric nitrogen to marine food webs.  Trichodesmium N2 fixation rates have been shown to increase under expected future high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity, but its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. My lab has been carrying out a nearly decade-long experimental evolution study with Trichodesmium growing under selection by projected future elevated CO2 levels.  Unexpectedly, selection under high CO2 results in large increases in nitrogen fixation and growth rates that appear to be irreversible, even after adapted cell lines are moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained even after returning to the ancestral environment. These constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, up-regulation of cellular energetic pathways, elevated expression of non-coding intergenic DNA, and increased activity of a potentially regulatory DNA methyltransferase enzyme. Ongoing work in my lab is examining the consequences of multiple nutrient limitation interactions (iron and phosphorus) for the physiology, biochemistry and genetics of Trichodesmium adapted to growing in a more nutrient-limited, acidified future ocean environment.  
 

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, June 24, 2015 - 19:15 - 20:00
Institution: 
University of New South Wales
Title: 

The role of quorum sensing in chitin biodegradation

Abstract: 

The 1011 ton global annual turnover of chitin has generated extensive interest in the regulation of chitin processing enzyme production in bacteria. Some bacteria regulate chitinase production by N-Acyl-L-homoserine lactone (AHL) mediated quorum sensing. In this study, a description of bacterial community succession during chitin particle colonisation and depolymerisation in activated sludge is presented. It was discovered that Betaproteobacteria and Bacteroidetes lineages dominate chitin colonisation in sludge and that AHLs bind to chitin at concentrations that upregulate AHL dependent transcription in bacterial cells associated with the chitin surface. There was no requirement for high cell density (a quorum) at the chitin surface. Further, N-Acetyl glucosamine (GlcNAc), the monomer of the chitin polymer, is shown to inhibit AHL dependent gene transcription representing a previously unrecognised mechanism by which the chitinase reaction product negatively regulates chitinase production. Evidence is presented supporting a role for both competitive inhibition at the AHL binding site of LuxR type transcriptional regulators and catabolite repression. The quorum sensing inhibitor activity of GlcNAc adds to its list of possible therapeutic benefits. 

Event Date: 
Wednesday, April 29, 2015 - 18:15 - 18:30
Institution: 
University of Southern Maine
Title: 

Developing MicroPIE and a Microbial Ontology

Abstract: 

The study of the evolution of microbial traits requires both phylogenetic as well as phenotypic trait information (also called phenomics). Next generation sequencing has enable high throughput (meta)genomic analyses, but collecting phenotypic information, either de novo or from published taxonomic literature, to create character matrices is still tedious and time-consuming. I am part of a team of researchers developing tools to provide faster collection of microbial phenomic information from published literature. We have created a natural language processing tool, Microbial Phenomics Information Extractor, or MicroPIE, that uses existing parsers, machine-learning tools, and a library of microbial-specific terms derived from ~1000 taxonomic descriptions from the Archaea, Bacteroidetes, Cyanobacteria, and Mollicutes. We have also developed an ontology of terms found in prokaryotic taxonomic descriptions, that is organized using a formal logical framework. This ontology will be used to assist MicroPIE in character identification and extraction, facilitate the identification of trait synonyms used in prokaryotic taxonomic descriptions, and to populate character matrices with higher-level character states. The taxon-character matrices extracted using MicroPIE can be combined with phylogenomic trees and analyzed using the Arbor software package, which is a scalable, web-services based platform for conducting phylogenetic comparative analyses to test evolutionary hypotheses. I’ll show some preliminary results from an analysis of trait evolution in cyanobacteria.

 

Event Date: 
Wednesday, April 29, 2015 - 18:00 - 18:15
Institution: 
University of New South Wales (UNSW)
Title: 

Bacterial secondary metabolite prodigiosin inhibit biofilm development by cleaving extracellular DNA

Abstract: 

Prodigiosin a bacterial secondary metabolite is a heterocyclic compound belongs to the class of tripyrrole, synthesized by various strains of bacteria includes Serratia species. Research on prodigiosin is under limelight for past 10 years from clinical and pharmacological aspects in relevance to its potential to be drug for cancer therapy by inducing apoptosis in several cancer cell lines. Reports suggest that prodigiosin promotes oxidative damage to DNA in presence of copper ion and consequently lead to inhibition of cell-cycle progression and inducing cell death. However, prodigiosin has not been previously implicated in biofilm inhibition. We performed experiments to reveal any link between prodigiosin and biofilm inhibition through degradation of extracellular DNA which plays a major role in biofilm establishment. Our study showed that prodigiosin (extracted from Serratia culture) has strong DNA cleaving property but does not intercalate with nitrogenous bases of DNA. Using P. aeruginosa PA14 wild-type strain as a model organism we showed that bacterial cells treated with prodigiosin showed significant reduction in its cells surface hydrophobicity and consequently affecting surface energies and physico-chemical property essential for bacterial adhesion and aggregation. We also found that prodigiosin did not influence planktonic growth of P. aeruginosa however, was successful in inhibiting the establishment of biofilms includes decrease in biofilm thickness, adhesion to substratum, decrease in biovolume, microcolony formation and also significantly dispersed pre-established biofilm of P. aeruginosa. This novel function on the biofilm inhibition of prodigiosin could be used to interfere with risks associated with bacterial biofilms. 

Event Date: 
Wednesday, February 25, 2015 - 17:00 - 17:30
Institution: 
University of Southern Maine
Title: 

Prochlorococcus: the “invisible forest” in the ocean’s Outback.

Abstract: 

The smallest, most abundant phototroph in the world, Prochlorococcus, dominates the base of the food web in the “Outback” of the world’s oceans, the nutrient-depleted ocean gyres. This unicellular, marine cyanobacterium, unknown only 30 years ago, is an oligotrophic specialist with a streamlined genome and reduced cellular requirement for the limited resources available in this environment. Based on physiological and molecular analyses of isolated strains from different oceans and depths, two broad groupings of Prochlorococcus were characterized: high- and low-light adapted “ecotypes”. Within these broad groupings are many subclades, some of which have been shown to dominate under certain temperature and light conditions. Through additional culture-based studies, my lab has been exploring nutrient physiology and other physiological characteristics that may contribute to the ecology and evolution of other Prochlorococcus subgroups. Some subgroups have the capacity to utilize nitrate, which was not the case for the initial isolates of Prochlorococcus, and others differ in their pigmentation. We have also found that Prochlorococcus regulates its uptake velocity and specific affinity for inorganic and organic phosphorus under P stress conditions. Examining the physiology, ecology and genomics of Prochlorococcus isolates and natural populations is providing insights into how these tiny photosynthesizing cells create a stable, yet invisible forest in the deserts of the world’s oceans.

Event Date: 
Wednesday, January 28, 2015 - 18:00 - 18:15
Institution: 
University of New South Wales
Title: 

Biomining and methanogenesis for resource extraction from asteroids

Abstract: 

As spacecraft fuel is a limited resource, creating a readily available source for hydrocarbon-based fuels in space will reduce launch cost and increase operating time of spacecraft. Biomethanation is viable for Earth-based operations, thus applications in space under controlled conditions have potential. This study proposes a sustainable environment for methanogens on Near-Earth Objects. Vacuum and desiccation effects, at 0.025% Earth atmospheric pressure, are conducted on three bacterial and three Archaea strains to test post-exposure viability. Cell degradation and colony size reduction was quantified for aerobic strains. Adverse effects were exhibited more so in gram-negative than gram-positive strains. Archaea showed limited to no cell degradation, providing evidence that vacuum effects, at these pressures, will have minor effects on in-situ biofuel operations. If successful, a sustainable and cost-effective method of metal extraction and producing methane based fuel reservoirs could revolutionise in-situ resource and fuel resupply of spacecraft, thus enhancing spacefaring capabilities.

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