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Microbial generation of methane from organic matter in coal represents an opportunity to improve environmental and economic outcomes of coal seam gas production. This has prompted research interest in microbial communities responsible for its generation. While advances have been made in understanding the overall structure of these communities and in methods to stimulate methane generation through nutrient additions, many questions still remain as to the metabolic roles played by the majority of the taxa in coal seams. One confounding issue faced by the coal seam microbiology community is an inability to compare OTUs (Operational Taxonomic Units) from 16S rDNA community surveys between studies. The aim of this study is to provide a common language for researchers studying coal seam microbes so that any given OTU from a coal seam community can be readily referenced to OTUs from other studies. To meet this aim a new Coal Seam MicroBiome (CSMB) reference set of OTU sequences was constructed from both new data obtained through community surveys of 28 coal seam formation water samples across three eastern Australian coal basins, along with all compatible, publicly available community surveys. To illustrate the power of the CSMB set for enabling comparisons the set was used to compare the co-occurrence of OTUs from publicly available compatible coal seam community surveys. Additionally, 16S rDNA sequence data from all compatible coal seam isolates and/or reconstructed genomes from published studies were mapped to the CSMB set. Resultant analysis revealed that a large number of published surveys have shared CSMB OTUs and a number of isolate and reconstructed genomes matched CSMB OTUs observed in surveys of the coal seam formation waters across the USA, Canada, China, India, Japan and Australia. This report details these observations of co-occurrence, as well as providing information on downloading, mapping and adding new sequences to the CSMB set.

This paper describes a novel species of ericoid mycorrhizal fungus from Australia, Cairneyella variabilis, Midgley and Tran-Dinh, gen. nov. sp. nov. The genome of C. variabilis was sequenced and a draft genome assembled. The draft genome of C. variabilis is 52.4 Mbp in length, and to our knowledge, this is the first study to present a genome of an ericoid mycorrhizal fungus from the southern hemisphere. Using the SignalP and dbCAN bioinformatic pipelines, a study of the catabolic potential of C. variabilis was undertaken and showed genes for an array of degradative enzymes, most of which appear to be secreted from the hyphae, to access a suite of different carbon sources. Isolates of C. variabilis have been previously shown to utilise cellulose, carboxymethyl cellulose (CMC), cellobiose, xylan, pectin, starch and tannic acid for growth, and in the current study, putative enzymes for these processes were revealed. These enzymes likely play key roles in nutrient cycling and other edaphic processes in heathland environments. ITS phylogenetic analyses showed C. variabilis to be distinct from the fungi of the “Hymenoscyphus ericae aggregate”. Refereed/Peer-reviewed

The draft genome sequence of Ruminoclostridium sp. Ne3 was reconstructed from the metagenome of a hydrogenogenic microbial consortium growing on xylan. The organism is likely the primary hemicellulose degrader within the consortium.

Many Bacillus species can produce biosurfactant, although most of the studies on lipopeptide production by this genus have been focused on Bacillus subtilis. Surfactants are broadly used in pharmaceutical, food and petroleum industry, and biological surfactant shows some advantages over the chemical surfactants, such as less toxicity, production from renewable, cheaper feedstocks and development of novel recombinant hyperproducer strains. This study is aimed to unveil the biosurfactant metabolic pathway and chemical composition in Bacillus safensis strain CCMA-560. The whole genome of the CCMA-560 strain was previously sequenced, and with the aid of bioinformatics tools, its biosurfactant metabolic pathway was compared to other pathways of closely related species. Fourier transform infrared (FTIR) and high-resolution TOF mass spectrometry (MS) were used to characterize the biosurfactant molecule. B. safensis CCMA-560 metabolic pathway is similar to other Bacillus species; however, some differences in amino acid incorporation were observed, and chemical analyses corroborated the genetic results. The strain CCMA-560 harbours two genes flanked by srfAC and srfAD not present in other Bacillus spp., which can be involved in the production of the analogue gramicidin. FTIR and MS showed that B. safensis CCMA-560 produces a mixture of at least four lipopeptides with seven amino acids incorporated and a fatty acid chain with 14 carbons, which makes this molecule similar to the biosurfactant of Bacillus pumilus, namely, pumilacidin. This is the first report on the biosurfactant production by B. safensis, encompassing the investigation of the metabolic pathway and chemical characterization of the biosurfactant molecule.

Alternaria alternata is of major significance as a food and feed contaminant and is able to produce a range of mycotoxins that may elicit adverse effects in both animals and humans. We describe the isolation and characterization of five microsatellite markers for studying A. alternata. Marker polymorphism was screened in 64 isolates of A. alternata. The number of alleles per locus ranged from eight to 24, and allelic diversity ranged from 0.425 to 0.882. These markers will be useful in the study of relationships and population genetics amongst isolates of A. alternata.

Certain strains of Aspergillus niger produce ochratoxin A in food and in animal feeds. Six polymorphic microsatellite markers suitable for population analysis were developed for A. niger through screening published sequences for microsatellite repeats. Polymorphism was evaluated for 28 isolates of A. niger, including toxigenic strains. Loci displayed six to 13 alleles. Investigation of cross-species amplifications with Aspergillus carbonarius and Aspergillus japonicus showed limited success.

Aspergillus flavus and Aspergillus parasiticus cause perennial infection of agriculturally important crops in tropical and subtropical areas. Invasion of crops by these fungi may result in contamination of food and feed by potent carcinogenic aflatoxins. Consumption of aflatoxin contaminated foods is a recognised risk factor for human hepatocellular carcinoma (HCC) and may contribute to the high incidence of HCC in Southeast Asia. This study conducted a survey of Vietnamese crops (peanuts and corn) and soil for the presence of aflatoxigenic fungi and used microsatellite markers to investigate the genetic diversity of Vietnamese Aspergillus strains. From a total of 85 samples comprising peanut (25), corn (45) and soil (15), 106 strains were isolated. Identification of strains by colony morphology and aflatoxin production found all Vietnamese strains to be A. flavus with no A. parasiticus isolated. A. flavus was present in 36.0% of peanut samples, 31.1% of corn samples, 27.3% of farmed soil samples and was not found in virgin soil samples. Twenty-five per cent of the strains produced aflatoxins. Microsatellite analysis revealed a high level of genetic diversity in the Vietnamese A. flavus population. Clustering, based on microsatellite genotype, was unrelated to aflatoxin production, geographic origin or substrate origin.

Vietnamese coffee beans were investigated for the presence of ochratoxigenic Aspergilli. Ninety-three percent of the coffee samples studied were positive for A. niger. No other ochratoxigenic species were present. HPLC analysis determined that 8.7% of the A. niger strains were positive for ochratoxin A (OA) production. There was no significant difference in the level of contamination or incidence of toxigenic strains in samples that had been rejected by manual sorting and those that were destined for human consumption. No OA-producing fungi were uncovered in a fresh coffee bean sample analysed, suggesting that the OA problem most likely occurs post-harvest.

Chemical investigations of a microfungus Xylaria sp. isolated from the Australian rainforest tree Glochidion ferdinandi have afforded two new natural products, 2-hydroxy-6-methyl-8-methoxy-9-oxo-9H-xanthene-1-carboxylic acid (1) and 2-hydroxy-6-hydroxymethyl-8-methoxy-9-oxo-9H-xanthene-1-carboxylic acid (2). Compound 1 has previously been synthesised but only partially characterised. Methylation of 1 using diazomethane afforded the crystalline compound 2,8-dimethoxy-6-methyl-9-oxo-9H-xanthene-1-carboxylic acid methyl ester (3), whose structure was determined by single crystal X-ray analysis. This paper reports the full spectroscopic characterisation of compounds 1–3 by NMR, UV, IR and MS data. All compounds were inactive in a brine shrimp lethality assay and several antimicrobial screens.

Methane generation by microbial activity or biogenesis is a significant source of coal bed methane (Faiz and Hendry, 2006; Strapoć et al, 2011). Being able to stimulate microbial methane generation in a coal seam reservoir has the potential to add significant value to depleted or undersaturated fields. Several laboratory studies have demonstrated that this process can be stimulated through the addition of inorganic nutrients (Jones et al, 2010; Orem et al, 2010). These studies, performed at atmospheric pressure on crushed coal, provide encouraging support for the concept of inducing in-situ biogenic methanogenesis and increasing gas-in-place in coal bed methane reservoirs. Important questions, however, remain about how laboratory results relate to what occurs in the reservoir. This extended abstract presents the results from a series of core flooding experiments conducted at reservoir pressure and temperature on intact coal core samples. Nutrient consumption is characterised by measuring the nutrient balance between the inflow and outflow waters. Gas content is measured through a helium flood at the end of the experiment, during which the pore pressure is dropped to atmospheric pressure to drive off any adsorbed gas. These experiments confirm that microbial gas generation does occur at reservoir pressure and temperature, and at high enough rates to rapidly increase gas content.

Mycotoxins are toxic secondary metabolites produced by filamentous fungi that may occur in almost all food commodities but particularly in cereals, oilseeds and nuts. They are recognised as an unavoidable risk and are found in the world’s most important food and feed crops, including maize, wheat, and barley. When present in foods in sufficiently high levels,mycotoxins pose a significant food safety risk and health hazard. Besides negative health impacts, mycotoxin contamination of food and feeds has a major worldwide economic impact. Mycotoxin contamination of foods is the subject of increasing international importance due toanumberofworldwide issues, includingglobalisation of food trade, global food security and climate change. Innovative strategies to meet the menace of mycotoxin contamination are required, and a greater understanding of the ecology of mycotoxigenic fungi and the molecular regulation of mycotoxin production may aide in the development of such strategies.