Andrew Mark Osborn

• Ph.D. in Genetics and Microbiology
• Professor (Full) at RMIT University

With the fast-global development of packaging techniques, the potential antimicrobial effect of CO2, as a safe, cheap and readily available gas, makes it the integral component for packaging of meat products. The associated spoilage and/or pathogenic bacteria on raw meat may respond in different ways to elevated CO2 concentrations. The growth of so...

Cheese quality is determined by many dynamic complex interactions that occur between cheese microbiota, metabolites and milk substrates. Here we report that application of multi-omics and data integration (by Data Integration Analysis for Biomarker discovery using Latent components, DIABLO) is able to identify and rank biomarkers (taxa and metaboli...

The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars wa...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Cheese maturation and flavor development results from complex interactions between milk substrates, cheese microbiota and their metabolites. In this study, bacterial 16S rRNA-gene sequencing, untargeted metabolomics (gas chromatography-mass spectrometry) and data integration analyses were used to characterize and differentiate commercial Cheddar ch...

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degrada...

Cheese microbiota and metabolites and their inter-relationships that underpin specific cheese quality attributes remain poorly understood. Here we report that multi-omics and integrative data analysis (multiple co-inertia analysis, MCIA) can be used to gain deeper insights into these relationships and identify microbiota and metabolite fingerprints...

Dumping wastes generated from the oil industry to the local waste disposal facilities remains the most common means of oil waste management. In industrial landfills, the most serious ecological problem is the contamination of soil and local groundwater by landfill leachate. Polycyclic aromatic hydrocarbons (PAHs) represent a hazardous group of harm...

Cheese is a fermented dairy product, harboring diverse microbial communities (microbiota) that change over time and vary depending on the type of cheese and their respective starter and adjunct cultures. These microorganisms play a crucial role in determining the flavor, quality and safety of the final product. Exploring the composition of cheese m...

High-quality drinking water from treatment works is degraded during transport to customer taps through the Drinking Water Distribution System (DWDS). Interactions occurring at the pipe wall-water interface are central to this degradation and are often dominated by complex microbial biofilms that are not well understood. This study uses novel applic...

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which...

Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of...

Genus-level representation of OTUs identified in PET-attached biofilms. Identified bacterial/archaeal genera (16S rRNA gene) comprising PET-attached biofilms across all stations and seasons sampled. OTU counts have been square root transformed. (PDF)

Phylogenetic representation and relative abundances of OTUs comprising PET-and glass-attached communities. Phylogenetic representation (based on 16S rRNA gene-based taxonomy assignment) of abundant OTUs (>0.5% of at least one community) and their relative abundances (pie charts based on log-scaled OTU counts) attached onto PET and glass substrates...

Scanning electron micrograph of marine biofilm members on plastic bottles. Eukaryotic biofilm members living at the surface of a PET plastic bottle after incubation for 5–6 weeks in the coastal North Sea. (a) Diatom members of PET-colonizing community. (b) A mass of interacting eukaryotes (diatoms, algae, possible ciliates) within the PET-colonizin...

Principle Coordinate Ordinations relating variation in plastic (PET) microbiome community composition across season and station variables. PCOs representing similarity of biofilm communities based on counts of OTUs across samples (16S/18S rRNA gene data, see methods for OTU definition). Displayed are comparisons of (a) bacterial/archaeal and (b) eu...

Environmental data (temperature, salinity, chlorophyll fluorescence) and season-sample pairs. Average temperature, salinity, and chlorophyll fluorescence data for each season-station pair used in the dissimilarity matrix for Mantel test. Data were continuously collected by the SmartBuoy system at each station the substrates were deployed and the wa...

Abundance of Fungal OTUs across treatments. Bar graph representing the abundance of reads assigned to fungal OTUs across all treatments (PET-attached, glass-attached, 0.2–3 μm seawater, >3 μm seawater). OTU counts are normalized to the number of samples of each treatment to account for unbalanced representation of each sample type. (PDF)

PERMANOVA/PERMDISP results of pairwise tests comparing bacterial/archaeal (16S rRNA gene) and eukaryotic (18S rRNA gene) community structure across different seasons, stations, and treatments. PERMANOVA was performed on Bray-Curtis dissimilarity matrices based on OTU counts across microbial communities (a: bacterial/archaeal, 16S rRNA gene; b: euka...

Primer constructs used for amplicon sequencing, including indices (i5/i7) used. See Kozich et al, 2013 for dual indexing strategy. (XLSX)

Results of linear discriminant analysis test to identify differentially abundant bacterial/archaeal OTUs for treatment, station, and season comparisons using LEfSe. Discriminant OTUs (based on16S rRNA gene analysis) identified, using class and subclass distinctions, in comparisons of: (a) PET-associated, particle-attached (>3 μm) and free-living (0...

Results of linear discriminant analysis test to identify differentially abundant eukaryotic OTUs for treatment, station, and season comparisons using LEfSe. Discriminant OTUs (based on18S rRNA gene analysis) identified, using class and subclass distinctions, in comparisons of: (a) PET-associated, particle-attached (>3 μm) and free-living (0.2 μm-3...

Arctic ecosystems are threatened by pollution from recently detected extreme atmospheric nitrogen (N) deposition events in which up to 90% of the annual N deposition can occur in just a few days. We undertook the first assessment of the fate of N from extreme deposition in High Arctic tundra and are presenting the results from the whole ecosystem 1...

This study describes the temporal and spatial variability of bacterial communities within a combined sewer system in England. Sampling was conducted over 9 months in a sewer system with intensive monitoring of hydraulic conditions. The bacterial communities were characterized by 16S rRNA gene-targeted terminal restriction fragment length polymorphi...

Drinking water quality deteriorates during transportation through Drinking Water Distribution Systems (DWDS), microbial activity and ecology, particularly within biofilms that occur on the inner-pipe surface of DWDS, are emerging as important drivers in the degradation process. Yet, we have little real-world applicable understanding of the DWDS bio...

Polycyclic aromatic hydrocarbons (PAHs) are a major class of organic hydrocarbons with high molecular weight that originate from both natural and anthropogenic sources. Sixteen PAHs are included in the U.S Environmental Protection agency list of priority pollutants due to their mutagenic, carcinogenic, toxic and teratogenic properties. In this stud...

The Arctic region is a unique environment, subject to extreme environmental conditions, shaping life therein and contributing to its sensitivity to environmental change. The Arctic is under increasing environmental pressure from anthropogenic activity and global warming. The unique microbial diversity of Arctic regions, that has a critical role in...

Arctic ecosystems are under pressure from climate change and atmospheric nitrogen (N) deposition. However knowledge of the ecology of microbial communities and their responses to such challenges in Arctic tundra soil remain limited, despite the central role these organisms play for ecosystem functioning. We utilised a plot-scale experiment in High...

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Coln...

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, b...

We are living in the ‘Plastic Age’, but unfortunately our non-human relatives with whom we share our planet are not adapted to cope with the thousands of tons of plastic waste entering rivers, seas and oceans each year. Plastic poses both physical and chemical threats to aquatic life. It leads to damage or death of animals following plastic entangl...

Background: Synthetic microplastics (≤5-mm fragments) are emerging environmental contaminants that have been found to accumulate within coastal marine sediments worldwide. The ecological impacts and fate of microplastic debris are only beginning to be revealed, with previous research into these topics having primarily focused on higher organisms a...

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to...

In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upo...

Fig. S1. Variation in monthly pelagic nutrient concentrations in Jennycliff Bay (5.3497 N, 04.1331 W) in the Western English Channel. (A) nitrite, (B) nitrate, (C) ammonium, (D) silicate, (E) phosphate. Inset legends show water depth in metres. Data are from the PML Benthic Survey Data Inventory (Woodward et al., 2013). (F) Variation in monthly tem...

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in sea water, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially-driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approxim...

Bacterial communities in samples of wastewater and biofilms were analysed using terminal-restriction fragment length polymorphism in order to assess the level of variation found in bacterial communities in combined sewers. Samples were collected between November and July at two sites in the sewer system in Nantes, France. Biofilms were collected bo...

Arctic ecosystems are threatened by pollution from extreme atmospheric nitrogen (N) deposition events in which up to 80% of the total annual N deposition can occur in just a few days. These events are now occurring due to an increase in the long-range transport of reactive N species from pollution sources at lower latitudes, and exacerbated by incr...

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approxima...

Arctic ecosystems are threatened by pollution from both chronic and acute, extreme atmospheric N depositions. Here we report the difference in N (15 N) recovery from the first-ever field simulation of extreme N deposition events (short-term) and snowpack chronic N deposition after 10-years (long-term), within the plant-soil system in the high arcti...

Microorganisms have a crucial role to play in the cycling of nutrients within glacial environments. These systems are often nutrient-limited, and so biogeochemical reactions, which ensure the availability of nutrients for microbial communities, are critical for the maintenance of these systems. This study uses molecular biology to characterise the...

Biofilms are ubiquitous within drinking water distribution systems (DWDS), attached to the inner pipe surface via a matrix of extracellular polymeric substances (EPS). If the external shear forces exceed the internal EPS strength, biofilm will be mobilised into the bulk water with potential aesthetic, chemical and biological implications. However,...

Poster presents methods and initial results regarding the characterisation of the physical (cells and EPS) and community structure of biofilms developed within a full-scale drinking water distribution system test facility. For more information please see Fish et al. (2015), PLoS ONE: http://journals.plos.org/plosone/article?id=10.1371/journal.pone....

The quality of a soil is often viewed in relation to its ability to suppress plant disease and enhance agricultural productivity. A soil is considered suppressive when, in spite of favourable conditions for disease incidence and development, a pathogen cannot become established, or establishes but produces no disease, or establishes and produces di...

Arctic ecosystems are threatened by pollution from acute, extreme atmospheric N deposition events. Such events can deposit ~40% (perhaps reaching 80%) of annual atmospheric N input as acidic rainfall (pH 4) in less than a week. These events are a result of polluted air masses from the mid-latitude travelling to the high-latitude with minimal disper...

Introduction Biofilms develop on the inner surface of drinking water distribution pipelines (Figure 1). A microbially produced matrix of extracellular polymeric substances (EPS) provides adhesion and physical stability to the biofilm. If the adhesive forces of the EPS (primarily considered as proteins and carbohydrates) are overcome the biofilm wi...

To determine the spatial and temporal variability in the abundance, structure and composition of planktonic bacterial assemblages sampled from a small, looped water distribution system and to interpret results with respect to hydraulic conditions. Water samples were collected from five sampling points, twice a day at 06:00 h and 09:00 h on a Monday...

The cryosphere presents some of the most challenging conditions for life on earth. Nevertheless, (micro)biota survive in a range of niches in glacial systems, including water-filled depressions on glacial surfaces termed cryoconite holes (centimetre to metre in diameter and up to 0.5 m deep) that contain dark granular material (cryoconite). In this...

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Sequences were screened for chimeras by the submitter using Bellerophon NA. ##Assembly-Data-START## Assembly Method :: Bioedit v. Version 7.0 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

PCR based assays were developed in this study to quantitatively predict pea footrot infections in agricultural soils prior to cultivation. Pea footrot disease due to Nectria haematococca (anamorph Fusarium solani f.sp. pisi) is linked to the presence of six pea pathogenicity (PEP) genes (PDA1, PEP1, PEP2, PEP3, PEP4 and PEP5). Whilst molecular assa...

Ammonia oxidation is a key microbial process within the marine N-cycle. Sediment and water column samples from two contrasting sites in the English Channel (mud and sand) were incubated (up to 14 weeks) in CO2-acidified seawater ranging from pH 8.0 to pH 6.1. Additional observations were made off the island of Ischia (Mediterranean Sea), a natural...

Footrot disease due to Nectria haematococca is an economically important disease of peas all over the world where peas are grown. The combined effect of pathogenicity genes on disease severity has not been adequately addressed. Hence in this research, molecular PCR-based assays have been developed and/or used to detect all six (PDA, PEP1, PEP2, PEP...

Poster presentation on bacterial colonization of LDPE fragments in coastal sediment microcosms (SETAC Europe 21st Annual Meeting, 2011).

Footrot disease due to N. haematococca (anamorph Fusarium solani f. sp. pisi) is a globally, economically important disease of peas. The disease has been linked to the presence of six pea pathogenicity (PEP) genes (PDA1, PEP1, PEP2, PEP3, PEP4 and PEP5) inherent in pathogenic forms of the causal fungus N. haematococca MPIV. The disease is prevented...

Synthetic thermoplastics constitute the majority by percentage of anthropogenic debris entering the Earth's oceans. Microplastics (≤5-mm fragments) are rapidly emerging pollutants in marine ecosystems that may transport potentially toxic chemicals into macrobial food webs. This commentary evaluates our knowledge concerning the interactions between...

Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofaun...

We measured benthic denitrification (DN) and dissimilatory reduction of nitrate to ammonium (DNRA) using the isotope-pairing technique in three tropical estuaries in Thailand (Mae Klong), Indonesia (Cisadane), and Fiji (Vunidawa-Rewa) during rainy, dry, and intermediate seasons along the salinity gradient of each estuary. DNRA dominated. Anammox (A...

Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction...

Footrot disease due to Nectria haematococca (anamorph Fusarium solani f.sp. pisi) is an economically important disease of peas globally. However, our ability to predict accurately the likelihood of footrot infections is limited because there is no method to determine inoculum density prior to planting. In this research, a PCR-based assay was develo...

Bacillus species suppress phytopathogens by producing lipopeptide antibiotics, hydrolytic enzymes, siderophores and other secondary metabolites. Three bacterial strains Bacillus subtilis NH-100 (EU627167), B. subtilis NH-160 (EU627169) and Bacillus sp. NH-217 (EU627170) with proven ability to suppress red rot disease on sugarcane plants were furthe...

Microbiology in Urban Water Systems (MUWS) is an integrated project, which aims to characterize the microorganisms found in both potable water distribution systems and sewer networks. These large infrastructure systems have a major impact on our quality of life, and despite the importance of these systems as major components of the water cycle, lit...

This study presents a new coupon sampling device that can be inserted directly into the pipes within water distribution systems (WDS), maintaining representative near wall pipe flow conditions and enabling simultaneous microscopy and DNA-based analysis of biofilms formed in situ. To evaluate this sampling device, fluorescent in situ hybridization (...

b>M icrobiology in U rban W ater S ystems (MUWS) is an integrated project, which aims to characterize the microorganisms found in both potable water distribution systems and sewer networks. These large infrastructure systems have a major impact on our quality of life, and despite the importance of these systems as major components of the water cycl...

Despite the fact that microorganisms are important for both the function of sewers and potential ecological or public health risk due to sewer failures, little is currently known about the diversity of microbial communities present within the sewers. Sewer biofilms are in this context of particular interest as the microbial load in biofilms is sign...

Estuarine sediments are the location for significant bacterial removal of anthropogenically derived inorganic nitrogen, in particular nitrate, from the aquatic environment. In this study, rates of benthic denitrification (DN), dissimilatory nitrate reduction to ammonium (DNRA), and anammox (AN) at three sites along a nitrate concentration gradient...

Microphytobenthic biofilms in estuarine sediments, consisting of photosynthetic microalgae, heterotrophic bacteria and their associated exopolymers, contain high concentrations of water-soluble colloidal carbohydrates that can be separated using ethanol precipitation into low molecular weight. (LMW) carbohydrate and colloidal extracellular polymeri...

The aim of this study was to develop molecular assays for investigating the presence and diversity of pathogenicity genes from the pea footrot pathogen Nectria haematococca (anamorph Fusarium solani f.sp. pisi) in soils. Polymerase chain reaction (PCR) assays were developed to amplify four N. haematococca pathogenicity genes (PDA, PEP1, PEP3 and PE...

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons...

Aims: To provide an independent assessment of azoxystrobin effects on nontarget soil bacteria and fungi and generate some baseline information on azoxystrobin's persistence in soil. Methods and results: Plate based assay showed that azoxystrobin exhibited differential toxicity upon cultured fungi at different application rates. While (14)C label...

There is now compelling evidence that microbially mediated reactions impart a significant effect upon the dynamics, composition, and abundance of nutrients in glacial melt water. Consequently, we must now consider ice masses as ecosystem habitats in their own right and address their diversity, functional potential, and activity as part of alpine an...