Rochelle M Soo

Rochelle M Soo
The University of Queensland | UQ · School of Chemistry and Molecular Biosciences

BCA, BBMedSc, MSc, PhD

About

36
Publications
7,191
Reads
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1,572
Citations
Citations since 2016
18 Research Items
1234 Citations
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Introduction
I'm a Postdoctoral Research Fellow at the Australian Centre for Ecogenomics under the supervision of Prof. Hugenholtz. My focus is on basal non-photosynthetic Cyanobacteria, looking at both evolution and metabolism. Previously I worked as a lab technician for 4 years at the Australian Institute of Marine Science with Dr. Webster and Dr. Hoj after studying as an MSc student at TRU at the University of Waikato focusing on bacterial communities on Mt Erebus, Antarctica with Prof. Cary.
Additional affiliations
July 2019 - present
The University of Queensland
Position
  • Fellow
August 2015 - present
The University of Queensland
Position
  • PostDoc Position
May 2015 - August 2015
The University of Queensland
Position
  • Research Assistant
Education
October 2011 - May 2015
The University of Queensland
Field of study
  • Microbial Genomics
February 2005 - August 2007
The University of Waikato
Field of study
  • Molecular Biology
February 2000 - November 2004
Victoria University of Wellington
Field of study
  • Human Genetics, E-commerce and Marketing

Publications

Publications (36)
Article
Full-text available
An uncultured non-photosynthetic basal lineage of the Cyanobacteria, the Melainabacteria, was recently characterised by metagenomic analyses of aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorella-vorus, originally described in 1972 appears to be the first cultured representative of the Melainabacteria based on a 1...
Article
Full-text available
Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groun...
Article
Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem r...
Article
Full-text available
Coral reefs provide habitat for an array of marine invertebrates that host symbiotic microbiomes. Photosynthetic symbionts including Symbiodinium dinoflagellates and diatoms potentially influence the diversity of their host-associated microbiomes by releasing carbon-containing photosynthates and other organic compounds that fuel microbial metabolis...
Article
Tramway Ridge, located near the summit of Mount Erebus in Antarctica, is probably the most remote geothermal soil habitat on Earth. Steam fumaroles maintain moist, hot soil environments creating extreme local physicochemical differentials. In this study a culture-independent approach combining automated rRNA intergenic spacer analysis (ARISA) and a...
Article
Rhodococcus globerulus (R. globerulus) isolated from soil beneath Eucalyptus sp. was found to live on the monoterpenes 1,8-cineole, p-cymene and (R)- and (S)-limonene as sole sources of carbon and energy. Previous metabolic studies revealed that R. globerulus is capable of living on 1,8-cineole, the main monoterpene component of eucalyptus essentia...
Article
Full-text available
Intensification of production across agriculture, horticulture, forestry, biodiversity restoration and other plant-related industries is urgently needed to meet expanding demand for food and materials, sustainability and climate change targets and to remain profitable under harsh post-pandemic conditions. This review appraises biochar, a charcoal-l...
Article
In this study we compared the faecal microbiomes of wild joey koalas (Phascolarctos cinereus) to those of adults, including their mothers, to establish whether gut microbiome maturation and inheritance in the wild is comparable to that seen in captivity. Our findings suggest that joey koala microbiomes slowly shift towards an adult assemblage betwe...
Article
The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala (Phascolarctos cinereus). Joey koalas are thought to be inoculated with microorganisms by feeding on specialised maternal faeces (pap). We found that compared to faeces, pap has hig...
Article
Full-text available
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, th...
Article
Full-text available
Background Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptus foliage but many individuals will not feed on particular Eucalyptus species that are adequate food for other individuals, eve...
Article
For well over a hundred years, members of the bacterial phylum Cyanobacteria have been considered strictly photosynthetic microorganisms, reflected in their classification as “blue-green algae” in the botanical code. Recently, genomes recovered from environmental sequencing surveys representing two major uncultured basal lineages (classes) of Cyano...
Article
Full-text available
The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attribu...
Data
Metabolic pathways enriched in the koala metagenomic dataset, compared to that of the wombat Predicted CDSs from each marsupial co-assembly were annotated based on KEGG Orthology (KO) using the KEGG Automatic Annotation Server (Moriya et al., 2007). KO annotations were weighted by average coverage of associated contigs per sample time-point and nor...
Data
Co-assembly statistics of Vombatiformes fecal communities All time-points from each host dataset were co-assembled de novo (CLC) following stringent quality control of raw reads (adaptor trimming with SeqPrep and quality trimming with Nesoni). Co-assemblies were then validated by mapping high-quality paired reads from each time-point back to the co...
Data
Bin statistics of quality population genomes extracted from koala and wombat metagenomes, ranked by median abundance
Data
Metabolic pathways enriched in the wombat metagenomic dataset, compared to that of the koala Predicted CDSs from each marsupial co-assembly were annotated based on KEGG Orthology (KO) using the KEGG Automatic Annotation Server. KO annotations were weighted by average coverage of associated contigs per sample time-point and normalized to overall cov...
Data
Shotgun sequencing statistics of Vombatiformes fecal communities Fecal samples representing multiple time-points from a captive koala and captive wombat were sequenced, generating a total of 90.7 Gb and 22.0 Gb of raw data, respectively.
Data
Intra-community diversity in metabolic potential among top population genomes within each community, colored by phylum The 15 most abundant quality population genomes from the (A) koala and (B) wombat communities were annotated based on KEGG Orthology (KO) (Moriya et al., 2007). Annotations were assigned to all corresponding KEGG pathways according...
Data
Taxonomic makeup (%) of Zagget the koala fecal microbiomes across sample time-points Shotgun reads corresponding to 16S rRNA sequences were identified with HMMs and mapped to the Greengenes 97% database (McDonald et al., 2012), and the resulting community makeup was assessed at each taxonomic level (including unmapped reads). Lineages with less tha...
Data
Taxonomic makeup (%) of Phil the wombat fecal microbiomes across sample time-points Shotgun reads corresponding to 16S rRNA sequences were identified with HMMs and mapped to the Greengenes 97% database (McDonald et al., 2012), and the resulting community makeup was assessed at each taxonomic level (including unmapped reads). Lineages with less than...
Data
The majority of 16S and 18S rRNA reads extracted from koala and wombat metagenomic samples are bacterial Reads mapping to 16S and 18S rRNA genes were extracted from quality-filtered shotgun sequencing samples using hidden Markov models and mapped to the SILVA 98% database (Quast et al., 2013). Table values are kingdom-level percentages of all extra...
Article
The origin of oxygenic photosynthesis in Cyanobacteria led to the rise of oxygen on Earth ~2.3 billion years ago, profoundly altering the course of evolution by facilitating the development of aerobic respiration and complex multicellular life. Here we report the genomes of 41 uncultured organisms related to the photosynthetic Cyanobacteria (class...
Preprint
Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from huma...
Preprint
Full-text available
Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from huma...
Preprint
Full-text available
Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a non-photosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of standard draft population genomes from huma...
Article
Full-text available
Bacteria associated with three coral species, Acropora tenuis, Pocillopora damicornis and Tubastrea faulkneri, were assessed before and after coral mass spawning on Ningaloo Reef in Western Australia. Two colonies of each species were sampled before and after the mass spawning event and two additional samples were collected for P. damicornis after...
Article
Full-text available
Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR) sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont compos...
Article
Marine sponges are critical components of benthic environments; however, their sessile habit, requirement to filter large volumes of water and complex symbiotic partnerships make them particularly vulnerable to the effects of global climate change. We assessed the effect of elevated seawater temperature on bacterial communities in larvae of the Gre...
Article
Full-text available
Cultivation of sponges is being explored to supply biomaterial for the pharmaceutical and cosmetics industries. This study assesses the impact of various cultivation methods on the microbial community within the sponge Rhopaloeides odorabile during: (1) in situ cultivation under natural environmental conditions, (2) ex situ cultivation in small flo...
Article
Full-text available
Crustose coralline algae (CCA) are key reef-building primary producers that are known to induce the metamorphosis and recruitment of many species of coral larvae. Reef biofilms (particularly microorganisms associated with CCA) are also important as settlement cues for a variety of marine invertebrates, including corals. If rising sea surface temper...
Article
Full-text available
Bacillus thuringiensis is a Gram-positive bacterium that produces crystalline endotoxins and is widely considered an environmentally safe insecticide to control mosquitoes and a number of agriculture pests. Bacteria closely related to B. thuringiensis have recently been discovered in association with diseased sponges, which has raised concerns that...
Article
Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme...
Article
Only a few studies have looked at microbial biogeography in soils and whether microorganisms are endemic to an area is still debatable. Tramway Ridge, a geothermal area on Mount Erebus, Antarctica, provides a unique opportunity due to its isolation and extreme conditions to explore the possibilities of microbial endemism and to identify novel Bacte...

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