Kim Handley

Dr Kim Handley is an environmental microbiologist and Senior Research Fellow in the School of Biological Sciences, Faculty of Science, The University of Auckland, and a Royal Society of NZ Rutherford Discovery Fellow. She completed her PhD at the University of Manchester in 2008, where she studied microbial respiratory diversity in hydrothermal marine sediment. This was followed by postdoctoral training at the University of California, Berkeley, where she studied microbial community interactions in the terrestrial subsurface.


Her research focuses on understanding the metabolic capabilities and evolution of natural microbial communities, and the role of these communities in biogeochemical cycling in aquatic and sedimentary environments. She uses environmental genomics and related functional omic techniques to determine the lifestyles of uncultivated microorganisms and community-wide interactions. Dr Handley is currently collaborating with Professor Kathleen Campbell (inaugural Director of Te Ao Mārama – Centre for Fundamental Inquiry) on a project to determine the biological influence on the formation of terrestrial, digitate, silica-rich hot spring deposits morphologically analogous to those discovered by the Spirit rover on Mars. The project aims to identify the microbial associations with these sinters; determine the role these organisms play in structuring the sinters; and understand the functional relationship of microbial communities supported by these systems. Dr Handley’s current research also includes understanding biological processes and genetic novelty in estuaries and aquifers, and she is the environmental metagenomics project lead for Genomics Aotearoa – a collaborative national platform for genomics and bioinformatics research. ​

The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.

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Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.

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