Microorganism

Event Date: 
Wednesday, October 28, 2015 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Key to living in the extreme desert soils of eastern Antarctica: a chemolithotrophic lifestyle

Abstract: 

Mitchell Peninsula is located at the south of the Windmill Islands, Eastern Antarctica. It is described as a nutrient poor, extreme polar desert and limited knowledge on the microbial diversity of  the soils in this area exists. We examined the microbial taxonomic composition and metabolic potential of Mitchell Peninsula soils  using 16S metagenomics and shotgun metagenomics. We found the site to be a potential biodiversity hotspot, containing a high abundance of Candidate Phyla WPS2 and AD3. Subsequently, differential binning was used to recover 23 draft genomes, including 3 genomes from WPS-2 and two from AD3.  Further analysis of the metagenome revealed a novel Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene to be abundant in the bacterial community, despite a lack of evidence for photosynthesis related genes. We believe that unlike many other Antarctic regions, chemolithautrophic carbon fixation via CBB cycle is the dominant carbon fixation pathway, hence this pathway is providing the key to survival is this very dry, hostile environment. 

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, 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, November 26, 2014 - 19:00 - 19:45
Institution: 
UNSW
Title: 

“The microbial friends and foes of seaweeds”

Abstract: 

 

Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in many aquatic ecosystems, yet till recently very little was understood with respect to their associated microbiota. We now know that macroalgae are home to a diverse community of microorganisms, that display both temporal and spatial variation yet remain distinct from the surrounding seawater. Symbiotic interactions between marine microorganisms and macroalgae can have both positive (e.g. providing nutrients and morphogenic cues or protection from biofouling) and negative (e.g. disease) outcomes for the host. This talk will give an overview of the microorganisms typically associated with macroalgae with a focus on the bacterial symbionts. Details of how bacteria successfully colonize macroalgal hosts will be discussed with specific examples of the functional role of microbial epiphytes in macroalgal health (including disease) highlighted from a “holobiont” perspective.

 

Event Date: 
Wednesday, August 27, 2014 - 19:00 - 20:00
Institution: 
Macquarie University
Title: 

"Xenbiotics and Xenogenetics: Human Influence over Microbial Evolution"

Abstract: 

The extent of human effects on planetary and biological processes means that we are now the world’s greatest evolutionary force. Perhaps the best example of human driven selection is the rapid evolution of antibiotic resistance in a wide range of bacterial pathogens. Continued antibiotic use has resulted in the assembly of complex DNA molecules composed of diverse resistance determinants and mobile elements, each with independent phylogenetic origins. These novel plasmids, transposons, integrons and genomic islands are xenogenetic, in that they have arisen in human-dominated ecosystems as a direct result of human activity. Xenogenetic elements are being released via human waste streams along with significant quantities of selective agents and other xenobiotic compounds, creating environmental reactors that foster even more complex interactions between genes, mobile elements and diverse bacterial species. Saturation of the environment with selective agents is also likely to increase the basal rates of mutation, recombination and lateral gene transfer in all bacterial species. Consequently, the antibiotic revolution may now be having unintended, second order consequences that will affect the entire microbial biosphere.

Event Date: 
Wednesday, March 26, 2014 - 19:00 - 20:00
Institution: 
UTS, Australia
Title: 

Feeling Hot Hot Hot: Insights on thermal regulation of microbial carbon fixation and metabolism in a warming ocean

Abstract: 

Ocean warming is expected to affect marine microbial phototrophs directly by influencing their metabolism and capacity for photosynthesis as well as indirectly through altering the supply of resources needed for growth. In turn, changes in phototrophic community composition, biomass and size structure are expected to have cascading impacts on export production, food web dynamics and fisheries yields, as well as the biogeochemical cycling of carbon and other elements. As a result, temperature is a critical parameter in coupled climate-ocean models because it influences not only the magnitude, but also the direction of future ocean productivity.
 
This seminar presents data from several recent oceanographic voyages to suggest that the statistically significant relationships found between temperature and carbon fixation of contemporary ocean microbes is confounded by the availability of co-varying light and nutrient resources, and challenges the notion that satellite-derived sea surface temperature is a suitable proxy for tracking changes in upper ocean biogeochemical function. It will also present laboratory data which demonstrates that thermal selection of photosynthetic microbes (over >100 generations) results in phenotypic trait evolution and shifts in photosynthesis:respiration. Collectively, these data show non-linearity in metabolism of photosynthetic microbes in a warming ocean, pointing to increased variability of responses and potentially less predictability in models.

Event Date: 
Wednesday, January 29, 2014 - 18:00 - 18:15
Institution: 
UC Davis
Title: 

Hi-C Metagenomics: Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Abstract: 

Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of “binning” the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a synthetic metagenome sample to accurately cluster metagenome assembly contigs into a small number of groups that differentiated the genomes of each species. The Hi-C data also associated plasmids with the chromosomes of their host and with each other orders of magnitude more frequently than to other species. We further demonstrated that Hi-C data is highly informative for resolving strain-specific genes and nucleotide substitutions between two closely related E. coli strains, K12 DH10B and BL21 (DE3), indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This application of Hi-C has the potential to provide new perspective in the study of thefine-scale population structure of microbes, how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities, and the genetic architecture ofheterogeneous tumor clone populations.

Event Date: 
Wednesday, November 27, 2013 - 19:00 - 20:00
Institution: 
Deptartment of Civil and Environmental Engineering, MIT
Title: 

The Ocean....from the microscale

Abstract: 

At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment. New technologies, including microfluidics, high-speed video-microscopy and image analysis, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology. I will illustrate this 'natural history approach to microbial ecology' by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) direct evidence for a diverse gallery of microscale microbial hotspots in the ocean; (ii) a new framework for understanding the evolution of microbial diversity in the ocean; and (iii) microfluidic experiments to capture the dramatic chemotactic abilities of bacterial pathogens towards the roiling surface of coral hosts. Through these examples, I hope to show that direct visualization can foster a new layer of understanding in microbial ecology and can help us unlock the ocean's microscale.

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