Cyanobacteria

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, May 27, 2015 - 18:15 - 18:30
Institution: 
University of Western Sydney & Macquarie University
Title: 

Structure, diel functional cycling and viral ecological filtering in the microbiome of a pristine coral atoll in the Indian Ocean

Abstract: 

Given the role of microbes as both indicators and drivers of ecosystem health, establishing baselines in pristine environments is crucial to predicting the response of marine habitats to environmental change.  Here we describe a survey of microbial community composition and metatranscriptomic gene expression across the Indian Ocean, encompassing the first samples from the pristine Salomon Atoll in the Chagos Archipeligo.  We observed strong patterns in beta-diversty  which reflected  Longhurst biogeographical  provinces established  using primary productivity and thermohaline properties of ocean currents.  Samples from within Salomon Atoll showed a highly unique community which was remarkably different even from adjacent samples despite constant water exchange.  This pattern was driven by the dominance of the photosynthetic cyanobacterium Synechococcus within the lagoon, the diel activity of which was responsible for driving shifts in the transcriptional profile of samples.  Inside the lagoon, increases in the expression of genes related to photosynthesis and nutrient cycling associated with the bottom-up control of bacterial populations, however the expression of viral proteins increased five-fold within the lagoon during the day, indicating a concomitant top-down control of bacterial dynamics byphage.  Indeed, genome recruitment against Synechococcus reference genomes suggested  viruses  provide  an  ecological filter for determining the diversity patterns in this system. This study also represented a proof of concept for  using a ‘citizen oceanography’ approach utilzing tools that may easily be adapted to deployment on any ocean going yacht, greatly expanding the scale and outreach of marine microbiology studies. 
 

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, 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, July 30, 2014 - 18:15 - 18:30
Institution: 
Macquarie University
Title: 

Effect of Low Temperature on Tropical and Temperate Isolates of Marine Synechococcus.

Abstract: 

An abundant and globally occurring marine picocyanobacterium, the genus Synechococcus is an important player in oceanic primary production and global carbon cycling. In the complex marine environment, this widespread organism has evolved to successfully colonize and inhabit different environmental niches. Their biogeographic distribution suggests that Synechococcus ecotypes exhibit thermal niche preferences. Temperature is a key environmental variable and the elucidation of the temperature stress acclimation in members of this genus can shed light on the molecular mechanisms involved in their adaptive capability. The growth of four representative Synechococcus isolates of various ecotypes from tropical and temperate regions were monitored under various temperature conditions. This revealed drastic differences in growth rates in correlation with their thermal niche preferences. The temperate strains CC9311 and BL107 displayed higher growth rates at lower temperatures while tropical strains WH8102 and WH8109 grew better at higher temperatures. In order to further elucidate their thermal niche preference, the molecular factors influencing the temperature-related growth patterns were explored through global proteomic analysis of WH8102 and BL107. Whole cell lysates of the strains grown at different temperature conditions were fractionated using 1D SDS-PAGE and analysed using label-free quantitative proteomics. Protein identifications provided 27% and 40% coverage of the whole genome for WH8102 and BL107, respectively. Quantitation of protein expression revealed 22% and 20% of the identified proteins were differentially expressed in WH8102 and BL107, respectively. The results were further investigated using qRT-PCR and PAM fluorometry. Differential expression revealed that low temperature appeared to have a significant effect on the photosynthetic machinery. The light harvesting components, phycobilisomes exhibited a reduced expression which could be the result of protein degradation due to photo-oxidative damage and/or as a mechanism to restore the energy balance disturbed as a consequence of low temperature. The lowered phycobilisome expression is found to be a common low temperature-related response between the tropical and temperate isolates. Within the photosynthetic reaction centres, differences in the expression of some core proteins were observed between the two isolates. The expression of core proteins could correlate with the efficiency of repair mechanisms involved in the replacement of photo-damaged core proteins. This differential expression sheds light on the underlying factors which potentially influence the differences in the thermal ranges of tropical and temperate isolates.

Event Date: 
Wednesday, February 26, 2014 - 18:00 - 18:30
Institution: 
Macquarie University
Title: 

Building Virtual Cyanobacteria: To Metagenomics and Beyond!

Event Date: 
Wednesday, April 24, 2013 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

Comparative Analysis Of Saxitoxin-Producing And Non-Toxic Ecotypes Of Anabaena circinalis

Abstract: 

During bloom events, freshwater cyanobacteria often produce a variety of harmful toxins with devastating health, environmental and economic consequences. The paralytic shellfish toxins are a large group of neurotoxic alkaloids including saxitoxin (STX), which is the most potent identified to date. In Australia, STX production is strain dependent within the cyanobacterium Anabaena circinalis. The following study utilised two strains of cyanobacteria, A. circinalis AWQC131C (131C) and A. circinalis AWQC310F (310F), as model organisms; 131C is a saxitoxin-producer whilst 310F serves as a non-toxic control. We aimed to characterise 131C and 310F at the genomic and proteomic levels using genome sequencing and isobaric tags for relative and absolute quantitation (iTRAQ), respectively, in order to identify key differences in not only their secondary but, primary metabolic pathways.
 
Draft genome sequencing of 131C and 310F revealed a genome length of 4.4 Mbp and a GC content of 37%, and the number of encoded genes was predicted to be 4447 and 4443 for 131C and 310F, respectively. A scan of each genome revealed a total of 740 unique coding regions within 131C, and 651 within 310F. Interestingly, the proteomic profile of 131C was significantly different from 310F. Using iTRAQ, we found that under standard laboratory conditions, 131C was highly abundant in photosynthetic and metabolic proteins compared to the non-toxic control.  This suggests a high C:N ratio and intracellular 2-oxoglutarate concentration and may be a novel site for posttranslational regulation of STX. Overall, 131C is potentially a high energy ecotype likely to inhabit the water surface. Conversely, 310F was more abundant in molecular chaperones and proteins that neutralise reactive oxygen species, indicating activation of cellular stress response. Therefore, 310F seems to be experiencing cellular stress under laboratory conditions and in the environment, may inhabit low-light areas below the water surface.
 
In conclusion, this study has provided an insight into fundamental differences between the toxic 131C and non-toxic 310F strains of A. circinalis. These findings will provide a platform for future experiments and hopefully pave the way to identify the cellular function of STX.

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