Microbial responses to phenanthrene contamination in soil
The effect of phenanthrene on soil microbial community structure and gene expression was evaluated by 16S rRNA gene microbiome analysis and next generation sequencing of community mRNA. Widespread changes in microbial diversity and functional gene content were revealed. Actinobacteria abundances increased markedly with the addition of phenanthrene, in particular that of Arthrobacter and Mycobacterium, and evidence was also obtained for an increase in the abundance of protozoans. The abundance of transcripts annotated as dioxygenases, heavy metal P-type ATPases, thioredoxins and heat shock proteins increased 1.8-7 fold upon phenanthrene amendment, whereas those of general metabolism were little affected. Custom databases constructed with bacterial or fungal PAH metabolism genes were used to further annotate transcripts, and revealed that increases in PAH-degradatory gene expression occurred for all gene groups investigated. Taxonomic determination of mRNA transcripts showed that the actinobacteria were responsible for most of the de novo expression of transcripts associated with dioxygenases, stress response and detoxification genes. This study is the first combining microbiome and metatranscriptomic approaches to describe microbial community responses to a pollutant in soil, offering information on novel in-situ effects which opens up new directions for research in PAH degradation and bioremediation.
Impact of nutrient addition on microbial community actively decomposing wheat residues and sequestration of carbon in soil
Soils represent a significant terrestrial carbon reservoir and there is considerable interest in increasing or maintaining its size. Recent work has suggested that microbially mediated carbon sequestration into soils may be maximised by ensuring adequate supply of other nutrients (nitrogen, phosphorous, sulphur), thus maintaining high microbial carbon use efficiency. This is particularly important in cropping agriculture systems where appropriate crop-residue management may result in substantial soil carbon and general soil quality improvements.
A soil microcosm experiment was conducted to evaluate the effects of nutrients on the decomposition of wheat residues; specifically the effects on active bacterial community and carbon sequestration. Stable Isotope Probing (SIP) of 16S rDNA using Phylochip microarrays was employed to investigate the bacterial community associated with the decomposition of 13C-labelled wheat straw and incorporation of the carbon into soil humus. Respiration and carbon, nitrogen, phosphorous and sulphur transformations were measured over a 56 day incubation to assess priming effects, both gross and net humification efficiency and carbon sequestration through microbiological action. Soils that received wheat residues only always showed an increase in “new” carbon (13C), although they did not always show an increase in “total” (12C +13C) carbon. Soils receiving nutrients (nitrogen, phosphorous and sulphur) with wheat residues did show an increase in both new and total carbon pools, suggesting availability of nutrients other than carbon influence soil carbon sequestration. Bacterial communities responsible for residue decomposition and carbon sequestration were different for nutrient added and no-nutrient treatments, indicating microbial carbon use efficiency is also influenced by the composition of the active community. Our results suggest that soil carbon:nitrogen:phosphorus:sulphur (C:N:P:S) stoichiometry and bacterial community composition play important roles in determining potential levels of carbon sequestration in agricultural soils.
Sulfur scent for a harmful algae killer
Marine harmful algal blooms (HABs) are dense ephemeral proliferations typically of dinoflagellates, cyanobacteria or diatoms. These HABs can cause illness and death in humans and marine life, or ecosystem alterations affecting food provision and recreational activities. Despite being recognised as a major environmental challenge, little is known about what makes HABs thrive and vanish. For dinoflagellates, which account for 75% of HAB-forming phytoplankton species, bottom-up factors (including: eutrophication, climate change and species dispersal) are common triggers, yet the causes of bloom termination remain obscure.
Parasitoids have been identified as a major cause of termination of coastal harmful algal blooms, but the mechanisms and strategies they have evolved to efficiently infect ephemeral blooms are largely unknown. This study investigated the potential cues for parasite infection by the generalist dinoflagellate parasitoid Parvilucifera sinerae (Perkinsozoa, Alveolata). It showed that P. sinerae was activated from dormancy by Alexandrium minutum cells. Further investigation identified the algal metabolite dimethylsulphide (DMS) as the density-dependent chemical cue for the presence of potential host cells. The presence of DMS allowed the parasitoid to alternate between a sporangium-hosted dormant state and a chemically activated, free-living virulent state. DMS-rich exudates from infection-resistant dinoflagellate species also induced parasitoid activation, which can be interpreted as an example of a co-evolutionary arms race between parasitoid and host. These results further expand the involvement of dimethylated sulphur compounds in marine chemical ecology, where they have been described as foraging cues and chemoattractants for mammals, birds, fish, invertebrates and plankton microbes.
The Summer Course at the Sydney Institute for Marine Science will provide a comprehensive training for students with an interest in marine microbes and ecology. Students with a background in any one of the following areas are encouraged to apply: marine science, ecology, microbiology and biotechnology.
Students will develop an integrative view of the microbes in marine ecosystems in terms of their evolution, diversity, interactions and functional roles.
In September, JAMS was back into top gear, with a bigger audience, and a room with a view. Kent Lim from Macquarie University led off with a talk on his PhD work on the biocontrol agent Pseudomonas strain Pf5. As is often the case in science, things didn’t work out as expected, and Kent found that knocking out suspected pyochelin transporters led to an increase rather than a decrease in efflux of this siderophore and its metabolic precursors. Kent valiantly soldiered on, applying qRT-PCR and Biolog phenotype microarrays to untangle the problem, but unfortunately, this released even more worms from the seemingly-bottomless can provided by strain Pf5. It seems that these transporters may in fact also be regulatory proteins, explaining the unexpected pleiotropic effects of the knockouts.
Marsh Lawson Mushroom Research Unit
Cnr Maze Cr and Blackwattle Creek Rd
University of Sydney Darlington Campus
Chippendale NSW 2008
Prof. Mark Adams to open the new Marsh Lawson Mushroom Research Facility at University of Sydney
It is with great pleasure that I write to invite you to join us for the official launch of the new Marsh Lawson Mushroom Research Unit on Tuesday, 30th October 2012.
This brand new international-class research facility, one of only a handful of such entities in the world, undertakes projects with university academics, pharmaceutical and nutraceutical producers, and conducts independent trials for suppliers to the mushroom industry. It offers a new focus for a broad spectrum of experimental work in the areas of human nutrition, biological science, medicine and agriculture.