Altruism investment in the social amoeba

Supervisor(s): Dr Elizabeth Ostrowski and PhD student Ccathleen Broersma

Supervisor’s webpage: Dr Elizabeth Ostrowski – Senior Lecturer in Evolutionary Biology – Massey University

This project will look at variation within and among populations in altruism investment. Briefly, we work on a model organism called Dictyostelium discoideum, a model organism for multicellular development and cooperation. In response to starvation, these single-celled amoebae communicate, aggregate, and differentiate into a multicellular organism. During this process, approximately 20% of cells altruistically give up their lives to form a dead stalk. Their death provides a benefit to the rest, which survive atop the stalk as spores. When multiple strains co-develop to form fruiting bodies, not all strains behave fairly—some contribute fewer cells to the stalk, while gaining all of the advantages of the stalk cells produced by others. This project will contribute to an ongoing project aimed at understanding how often these selfish behaviors arise in natural populations and whether some populations evolve to suppress selfishness and enforce fairness. The student will assist a current PhD student in measuring stalk size and stalk allocation, as a measure of altruism investment, among strains from different populations across the natural range, using a combination of morphological measurements and GFP-reporters that indicate which cells have adopted the spore vs stalk cell fate. See here and here for more about our research, and here for related past research on this topic.

Timeline: 5 weeks (with possibility to extend to 10 weeks)

Testing computational methods for genome sequencing

Supervisor(s): Dr Olin Silander

Supervisor’s webpage: Dr Olin Silander – Senior Lecturer in Genetics – Massey University

Accurate genome sequencing and assembly is a critical technique in computational biology. This is clearly illustrated by the central role genome sequencing has played in controlling the COVID19 outbreak in New Zealand. In this project, the student will apply computational methods similar to those used in sequencing SARS-CoV-2 genomes (the causative agent of COVID19). The aim of this project is to develop improved bioinformatic techniques for genome sequencing of bacteria (also applicable to viruses). The student will learn current bioinformatic/computational methods for genome sequencing and assembly. This work will be done in the same lab that developed the SARS-CoV-2 rapid genome sequencing method used by the NZ government.

New methods for rapid pathogen detection

Supervisor(s): Dr Olin Silander

Supervisor’s webpage: Dr Olin Silander – Senior Lecturer in Genetics – Massey University

There is a pressing need for rapid pathogen detection in clinical and hospital settings. Currently all methods require patient samples to diagnostic labs for testing. In this project, the student will perform pilot tests aimed at developing new sequence-based methods for pathogen detection. The student will learn standard laboratory techniques such as PCR and DNA isolation, as well as more advanced techniques such as multiplex PCR and Nanopore sequencing. It may be possible to extend the period of this scholarship, as additional funds are available to support research on this project.

Can some bacteria provide a refuge for costly antibiotic resistance genes and make resistance harder to eradicate?

Supervisor(s): Professor Tim Cooper

Supervisor’s webpage: Prof Timothy Cooper – Professor of Molecular Biosciences – Massey University

Antibiotic resistance genes confer a benefit to bacteria in environments that contain the relevant antibiotic. When the antibiotic is absent, however, the same genes often confer a small cost, so that they will be selected against and eventually be lost. We have found that these costs differ in different bacterial strain-resistance gene combinations—resistance genes that are costly in some strains have no detectable cost in others. One implication of low costs is that resistance genes might find host strain ‘refuges’ that allow them to persist in a community much longer than would otherwise be expected. We propose to test this hypothesis using by tracking the dynamics of resistance genes in communities consisting of different bacterial strain- resistance gene combinations. This work will involve a range of microbiological and molecular biology skills, including the use of next generation sequencing.

Flexible time over the 2021-2022 summer break

The effects of copper on biofilm formation by Pseudomonas syringae pv. actinidiae, a causal agent of the bacterial canker in kiwifruit

Supervisor(s): Associate Professor Xue-Xian Zhang

Supervisor’s webpage: Associate Professor Xue-Xian Zhang – Associate Professor – Massey University

Copper spraying is among the most effective practices in managing Pseudomonas syringae pv. actinidiae (Psa) infection of kiwifruit orchards in New Zealand, but its effectiveness is threatened by the emergence of copper-resistant (CuR) Psa strains. Much attention has been focused on the detection of CuR strains and underlying resistance genes. There remains a significant gap in our understanding of how the copper-based bactericides work once they are applied to plants. More specifically, the bioavailability of Cu²⁺ and their efficacy in controlling Psa planktonic growth, biofilm formation and lesion development have not been examined in the plant environment.

In this summer project, we aim to determine the precise effects of toxic copper ions on bacterial growth with Psa and other Pseudomonas species. Experiments are designed to test a new hypothesis that copper, when used at low concentrations, can surprisingly enhance biofilm formation. Biofilm is a specific mode of bacterial growth on biotic and abiotic surfaces, showing high levels of antimicrobial resistance. The data will help increase our understanding of copper resistance and contribute to the optimization of copper sprays in order to combat the increase of copper resistance in the Psa pathogen reservoir.