JAMS goes west.
In the best JAMS tradition to foster collaborations and interactions the JAMS community heads to the brand new Hawkesbury Institute for the Environment (HIE) on april 12th. Here researchers from each institute/university will summarize their work and what facilities are available in their organizations. This will be followed by lunch and a round table meeting to discuss the possible collaborations and sharing the facilities. The program for the event is the following:
10:00am Arrivals and introductions
10:15-12:15pm Short research presentations
12:30-1:30pm Lunch sponsored by HIE
1:30-2:30pm Tour of the facilities available at HIE
2:30-4:00pm Roundtable table discussion to explore synergies and collaborations
JAMS goes west.
Retracing the Recent Emergence of Mycobacterium ulcerans.
It is more than 60 years since Mycobacterium ulcerans was shown to be the causative agent of Buruli ulcer yet it is still unclear where the bacterium resides in the environment and how it is transmitted to humans. Limited genome comparisons show that M. ulcerans has the characteristics of a niche-adapted microbe, having evolved recently from the fish-associated, opportunistic human pathogen, Mycobacterium marinum by horizontal gene transfer and reductive evolution. To further understand the relationship between these two species of pathogenic mycobacteria and to gain deeper insights into the evolution of M. ulcerans, we have used high throughput short-read DNA sequencing and compared the genomes of 30 strains of M. ulcerans and 5 strains of M. marinum, a strain collection that spans the known genetic diversity of these two species. We used a nucleotide read-mapping approach and objectively defined a 4,362,138 bp M. ulcerans-M. marinum core genome. Pairwise comparisons of every strain against this core revealed 129,416 variable nucleotide positions (3.0% nucleotide overall variation) across the two species and permitted the construction of a high resolution phylogeny for the complex, confirming that all M. ulcerans strains evolved from a common M. marinum progenitor and have diverged again into two distinct sub- lineages. In conjunction with de novo sequence assembly and gene ortholog clustering techniques, we used this phylogeny as a framework for reconstruction of a putative M. ulcerans most recent common ancestor (MRCA). We show that presence of the pMUM plasmid required for production of the polyketide toxin mycolactone (a potent immunosuppressor), high copy number of the insertion sequence IS2404, and loss/mutation of genes associated with, anaerobic respiration, lipid and cell-wall metabolism were all key attributes of the M. ulcerans MRCA before its global dispersal. Interestingly, intact genes involved with lipid metabolism and the cell wall showed evidence of positive selection with significantly higher dN/dS ratios than M. marinum strains. These data provide clues regarding the characteristics of the niche(s) M. ulcerans occupies and are guiding efforts to control the spread of Buruli ulcer.
Towards a biological Argo float.
Humans have long known about the physical attributes of the ocean – waves, tides, currents and temperatures. Since the 1800’s, deliberate measurements of depth, temperature and velocity have helped to build a low- resolution picture of the dynamic ocean. Argo is an international, collaborative program started in 2000 in which 3000 depth-profiling floats are deployed worldwide. These floats surface routinely and transmit salinity, temperature and depth data via satellite to data handling stations from where it is available to the global research community within 24 hours. Argo data have revolutionised physical oceanography and climate science.
Marine microbial ecology, in particular, how microbial community composition interacts with biogeochemical function in the ocean, is at the low-resolution phase of its history. With deep sequencing, we have the ability to take individual high-resolution samples but we do not yet have the global coverage required to make the connections between the bio and the geochemical.
We have a long-term goal of developing the microbiological equivalent of the Argo float. This requires a lot of hardware and “software” development. Hardware that can automatically sample, filter and process seawater and “software”, the genomic-based assays of microbial community structure that can be automated and miniaturised to work within the hardware. I will describe the development and rationale behind some of our array-based assays that might satisfy these criteria.
Microbial diversity and ecosystem functions, resilience & recovery: Beyond statistical correlation.
Microbes are the most dominant and diverse group of organisms on planet Earth. They are pivotal to global ecosystem function, carrying out all critical biogeochemical cycling and directly or indirect shape the Earth’s climate. Despite this, their role is not explicitly considered in climate or ecosystem models. This is largely because of their enormous diversity and the lack of theoretical and experimental approaches to illustrate and quantify the magnitude of microbial regulation of ecosystem functions. There are a growing number of studies that provide evidence of the statistical relationship between microbial community and ecosystem function, but such approaches are unable to differentiate between the correlative and casual effects. In this presentation, using a novel diversity dilution approach, I will illustrate the direct role of microbial diversity and community composition in ecosystem function and sustainability, and argue for their explicit inclusion in predictive models.
Differences downunder: macropodids, methane and metagenomics.
The agricultural sector accounts for a large amount of Australia’s greenhouse gas emissions, and strategies that reduce the production and (or) release of methane from ruminant livestock has resurfaced as a viable research topic. While there has been a relatively intense focus on better understanding how rumen microbiology, nutrition and (or) animal genetics might be targeted and productively altered to reduce these emissions; less attention has been directed towards the comparative study of those native Australian herbivores thought to produce small amounts of methane during feed digestion. These animals include the Australian macropodids (kangaroos and wallabies), which have evolved to retain a foregut microbiota that effectively converts plant biomass into nutrients for the host animal; and appears to do so with much less methane emitted. Our research group in Brisbane has used metagenomics approaches with a view to characterize the foregut microbiota of the Tammar wallaby (Macropus eugenii). There is a reduced number of methanogenic archaea resident in the macropodid foregut compared to ruminants, but the species present appear to have some unique attributes relative to their counterparts from other environments. We have also used a combination of metagenomic data and cultivation-based methods to identify and isolate several “new” bacteria that support feed digestion and fermentation schemes consistent with a low methane emitting phenotype. The structure-function relationships inherent to these interesting gut microbiomes warrant further investigation.
The World’s Tipping Point: How genes, enzymes, microbes and plants regulate greenhouse gas release from Arctic Soils.
Arctic soils contain as much carbon as the tropical rainforest. This carbon sequestered in permafrost is in danger of being released to the atmosphere. In this talk, I will discuss what regulates greenhouse gas release from Arctic soils and how, surprisingly, carbon containing greenhouse gases are not the key greenhouse gasses determining how warming Arctic soils influence our global climate. Drawing on the longest running climate change experiment in the Arctic, I will discuss how genes, enzymes, and microbial communities interact with one-another and with soil/plant properties to regulate greenhouse gas release at the field and continental scale. The role and importance of scale in determining biological interactions will be examined and what the implications of such scales are on our climate’s future.
Making and breaking dimethylsulfide in salt marsh sediments
DMSP (dimethylsulfoniopropionate) is a key organic compound in the sulfur cycle with ~10^9 tons of this anti-stress compatible solute being made each year by marine phytoplankton, macro-algae and some salt marsh plants. The DMSP that is liberated is catabolised in a series of different microbial reactions that comprise a massive set of biotransformations in the global sulfur cycle. Some of the reaction products, such as DMS (dimethylsulfide), have major environmental consequences in their own right, from climate regulation to animal behaviour. Our work investigates microbial populations that cycle DMSP and DMS in coastal intertidal sediments. Combining geochemical and molecular biological approaches, such as stable isotope probing (SIP) and targeted high throughput sequencing, we are identifying the main microbial players that catabolise DMSP and DMS in oxic and anoxic parts of intertidal sediments alongside the key genes and cognate biochemical pathways that contribute to the turnover of these influential molecules. Early work led to the observation of a vertical microbial population structure within the salt marsh sediment, partially linked to the sulfur cycle biochemistry of this ecosystem. SIP experiments are allowing the characterisation of active microbial processing of DMSP and DMS compounds by separate new bacterial groups, closely associated to salt marsh plants and within the oxic sediment layer. This work is filling in major gaps in our knowledge of the global organic S cycle and the role of microbial populations in major environmental biochemical processes.
Genetically controlled network architecture in the filamentous fungus Neurospora crassa constrains amino acid translocation
Effective nutrient translocation in fungi is essential for nutrient cycling, mycorrhizal symbioses, virulence and substrate utilization. An interconnected mycelial network is proposed to influence resource translocation, but has not been empirically tested. By comparing amino acid translocation in Neurospora crassa colonies defective in network formation and translocation between wild type colonies of different developmental ages, we can gain insight into the influence of network formation on nutrient translocation.