James J. Smith

James J. Smith
Queensland University of Technology | QUT · School of Earth, Environmental and Biological Sciences

29.29
 · 
BSc, PhD, RABSQ (ISO14001)

About

65
Publications
23,525
Reads
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1,084
Citations
Research Experience
January 2012 - present
PGRI University of Adi Buana
Position
January 2004 - December 2012
Queensland University of Technology
Position
January 1994 - December 1996
Montana State University
Position
Education
August 1991 - May 1995
Montana State University
Field of study
  • Microbiology
August 1984 - June 1988
California State University, Long Beach
Field of study
  • Microbiology (minor in Chemistry)

Publications

Publications (65)
Chapter
This chapter describes how microbiology is the science devoted to the study of organisms that are too small to be seen by the naked eye. These micro-organisms are a large and diverse group of free-living forms that exist as single cells or cell clusters. In depth treatment of topics including pathogens in aquatic-related environments, indicators of...
Article
This study examined the potential for Fe mobilization and greenhouse gas (GHG, e.g. CO2, and CH4) evolution in SEQ soils associated with a range of plantation forestry practices and water-logged conditions. Intact, 30-cm-deep soil cores collected from representative sites were saturated and incubated for 35 days in the laboratory, with leachate and...
Article
The study investigates the prevalence of antimicrobial resistance in Campylobacter jejuni and Campylobacter coli in gastroenteritis patients in the eight most populous regions in Australia and compares the prevalence of antimicrobial resistance in Europe and North America. A total of 164 Campylobacter isolates were collected from patients with camp...
Article
Full-text available
Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campy...
Article
Salmonella enterica is a common contaminant of macadamia nut kernels in the subtropical state of Queensland (QLD), Australia. We hypothesized that nonhuman sources in the plantation environment contaminate macadamia nuts. We applied a modified Hald source attribution model to attribute Salmonella serovars and phage types detected on macadamia nuts...
Article
The aim of this study was to investigate the prevalence and distribution of Campylobacter species in a variety of fresh and frozen meat and offal products collected from retail outlets in New South Wales (NSW), Queensland (Qld), and Victoria (Vic). A total of 1,490 chicken, beef, lamb, and pork samples were collected from Australian supermarkets an...
Chapter
A comprehensive review of the discipline of water microbiology with a focus on public health which can be used as a primary Australian legal reference. The chapter covers: indicator and pathogenic microorganisms; test methods, techniques and associated metrology; quality assurance; traditional and emerging technologies and methodologies; sampling;...
Method
Principal associated subcommittee authors (of FT-020 Water Microbiology). General procedures for preparation of homogenates of solid and semi-solid matrices for microbiological analyses. Principally focused on bacteriological analyses, but containing informative reference to virological and protozoan procedures. ISBN 9781760354572 See: https://www....
Chapter
http://www.thomsonreuters.com.au/product/AU/files/91163/3563CHAP115_preview.pdf
Article
Full-text available
Organic compounds in Australian coal seam gas produced water (CSG water) are poorly understood despite their environmental contamination potential. In this study, the presence of some organic substances is identified from government-held CSG water-quality data from the Bowen and Surat Basins, Queensland. These records revealed the presence of polyc...
Article
Wastewater containing human sewage is often discharged with little or no treatment into the Antarctic marine environment. Faecal sterols (primarily coprostanol) in sediments have been used for assessment of human sewage contamination in this environment, but in situ production and indigenous faunal inputs can confound such determinations. Using gas...
Conference Paper
Although Antarctica is considered a pristine wilderness in recent years pathogenic bacteria, potentially of human origin, have been isolated near outfalls where sewage is released directly into the marine environment. Studies monitoring impacts of untreated sewage release into the Antarctic marine environment have isolated enterococci including Ent...
Article
Full-text available
Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica.
Article
Enterococcus faecalis is one of the leading causes of nosocomial infections and is a common commensal organism in humans and other animals. In this study, we report a draft genome sequence for the E. faecalis strain PF3, isolated from Adélie penguin feces collected from Warriner Island, Antarctica.
Article
Full-text available
Environmental Burkholderia pseudomallei isolated from sandy soil at Castle Hill, Townsville, in the dry tropic region of Queensland, Australia, was inoculated into sterile-soil laboratory microcosms subjected to variable soil moisture. Survival and sublethal injury of the B. pseudomallei strain were monitored by recovery using culture-based methods...
Article
This research sought to determine optimal corn waste stream–based fermentation medium C and N sources and incubation time to maximize pigment production by an indigenous Indonesian Penicillium spp., as well as to assess pigment pH stability. A Penicillium spp. was isolated from Indonesian soil, identified as Penicillium resticulosum, and used to te...
Conference Paper
Full-text available
About 260–270 Mt of suspended sediment are discharged annually from the conterminous USA; approximately 69% derives from Gulf rivers (n = 36), 24% from Pacific rivers (n = 42), and 7% from Atlantic rivers (n = 54). Elevated sediment-associated chemical concentrations relative to baseline levels occur in the reverse order of sediment discharges: Atl...
Article
Bacterially mediated iron redox cycling exerts a strong influence on groundwater geochemistry, but few studies have investigated iron biogeochemical processes in coastal alluvial aquifers from a microbiological viewpoint. The shallow alluvial aquifer located adjacent to Poona estuary on the subtropical Southeast Queensland coast represents a redox-...
Data
Figure 1 Neutrophilic Fe(II)-oxidizing bacterial enrichment culture recovered from Poona estuary-adjacent shallow groundwater (W7) using semi-solid FeS gradient medium (A) Photograph of rust-colored Fe(II) oxidation band due to bacterial growth (arrows); (B) TEM image of unicellular bacterial cells (arrows) associated with Fe oxide precipitates; an...
Article
This study examined the potential for Fe mobilization and greenhouse gas (GHG, e.g. CO2, and CH4) evolution in SEQ soils associated with a range of plantation forestry practices and water-logged conditions. Intact, 30-cm-deep soil cores collected from representative sites were saturated and incubated for 35 days in the laboratory, with leachate and...
Article
Full-text available
We examined the abundance and distribution of neutrophilic, microaerophilic Fe(II)-oxidizing bacteria (FeOB) in aquatic habitats of a highly weathered, subtropical coastal catchment where Fe biogeochemistry is of environmental significance. Laboratory cultivation and microscopy indicated that stalked Gallionella and sheathed Leptothrix-like FeOB we...
Article
Environmental ManagSibelco Australia Limited (SAL), a mineral sand mining operation on North Stradbroke Island, undertakes progressive rehabilitation of mined areas. Initial investigations have found that some areas at SAL's Yarraman Mine have failed to redevelop towards approved criteria. This study, undertaken in 2010, examined ground cover rehab...
Conference Paper
Full-text available
Introduction In addition to causing the general degradation of water quality, nutrients such as N, P and Fe can contribute to toxic blooms of the cyanobacteria, Lyngbya majuscula, which has negative impacts on marine ecology and human health. Lyngbya blooms have been found in close proximity to this study area and in other areas along the coast of...
Conference Paper
Full-text available
During the summer 2009/10, an environmental impact assessment of the sewage outfall was conducted at Davis Station, East Antarctica. An investigation of the nature and extent of impacts to the marine environment associated with current sewage treatment and effluent discharge practices included ecological surveys of macrobiological communities, phys...
Article
Iron (Fe) biogeochemistry is potentially of environmental significance in plantation-forested, subtropical coastal ecosystems where soil disturbance and seasonal water-logging may lead to elevation of Fe mobilization and associated water quality deterioration. Using wet-chemical extraction and laboratory cultivation, we examined the occurrence of F...
Conference Paper
Full-text available
Potential impacts of plantation forestry practices on soil organic carbon and Fe available to microorganisms were investigated in a subtropical coastal catchment. The impacts of harvesting or replanting were largely limited to the soil top layer (0–10 cm depth). The thirty-year-old Pinus plantation showed low soil moisture content (Wc) and relative...
Chapter
Sewage and its microbiology, treatment and disposal are important to the topic of Antarctic wildlife health because disposal of untreated sewage effluent into the Antarctic marine environment is both allowed and commonplace. Human sewage contains enteric bacteria as normal flora, and has the potential to contain parasites, bacteria and viruses whic...
Article
This paper studies the detection limit, selectivity and counting efficiency of an ultraviolet aerodynamic particle sizer spectrometer (UVAPS) with regard to aerosolized fungal spores. The study demonstrated the ability of the instrument for detection and measurement of fungal spores under controlled conditions. A reasonable correlation was found be...
Article
Full-text available
Fluorescent reference strains of bacteria carrying a stable chromosomally integrated single copy of the gfp gene have been developed. A modified version of the gfp gene has been generated by mutagenesis and expressed under the control of the bacteriophage lambda promoter P(L). A cassette comprising bacteriophage Mu transposon arms flanking the modi...
Article
(Translated from German) The requirements for the quality of the measurement results are steadily increasing. In particular, the determination of the uncertainty of microbiological analysis results, which is done by some laboratories, is not mandatory, but is, a great challenge in many microbiology laboratories. The objective is a procedure that is...
Chapter
This chapter describes how microbiology is the science devoted to the study of organisms that are too small to be seen by the naked eye. These micro-organisms are a large and diverse group of free-living forms that exist as single cells or cell clusters. In depth treatment of topics including pathogens in aquatic-related environments, indicators of...
Thesis
Full-text available
Survival, sublethal injury, and recoverability of Escherichia coli, Enterococcus faecalis, SalmoneUla typhi-murium, and Yersinia enterocolitica were investigated by using diffusion chambers over 54 to 56 days of in situ exposure to a polar marine environment (-1.8°C; salinity, 34.5 ppt) at McMurdo Station, Antarctica. Plate counts were used to asse...
Article
Full-text available
McMurdo Station, Antarctica, has discharged untreated sewage into McMurdo Sound for decades. Previous studies delineated the impacted area, which included the drinking water intake, by using total coliform and Clostridium perfringens concentrations. The estimation of risk to humans in contact with the impacted and potable waters may be greater than...
Article
The purpose of the present study was to evaluate techniques for detection of Giardia cysts and Cryptosporidium oocysts in swimming pool filter backwash water. Calcium carbonate flocculation was used for water samples concentration of 1 l filter backwash water samples. Immunomagnetic separation (IMS) was used for separation of cysts and oocysts from...
Article
Fluorescence in situ hybridization (FISH) has been proposed for species-specific detection, and viability determination of Cryptosporidium parvum oocysts. FISH-based viability determination depends on rRNA decay after loss of viability. We examined the effects of RNase(s) and RNase inhibitors on FISH of C. parvum. FISH was performed using a 5'-Texa...
Book
This study focused on ideal methods of detecting C. parvum oocysts which give low detection limits, specific and sensitive detection in concentraded samples, and differentiation of viable from non-viable oocysts; are usable by a water treatment facility and provide quantitative results within a few hours. Potential useful methods are continuous flo...
Article
Land treatment of animal or human waste can result in chemical and microbial contamination of shallow ground water and/or water-ways. We investigated the fate of a host-specific Salmonella bacteriophage and a nonreactive chemical (Br-) tracer when applied to large intact lysimeter soil cores (500 mm diam. by 700 mm high). The soils included a poorl...
Article
During 1998/1999, surface and subsurface sediment samples were collected along the entire length of the Spokane River from its outlet at the northern end of Lake Coeur d'Alene (CDA), Idaho, to Lake Roosevelt on the Columbia River, Washington. The study was conducted to determine if the trace element enrichments observed in Lake CDA and on the flood...
Article
Land application of animal waste can result in bacterial contamination of shallow groundwater and/or waterways. Using 500-mm-diameter barrel lysimeters, we investigated the potential for bacterial indicators to leach through 4 New Zealand soils treated with dairy shed effluent (DSE). DSE was applied to soil lysimeters containing poorly drained Gley...
Article
Survival, recoverability and sublethal injury of two strains of Listeria monocytogenes, Scott A and an environmental strain KM, on exposure to sea water at 12.8 or 20.8 degrees C was determined using in situ diffusion chambers. Plate counts were used to assess recoverability and injury while 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) reduction...
Article
The tetrazolium salts INT and CTC are frequently used as indicators of bacterial respiration. Mechanisms of tetrazolium reduction to formazan in eukaryotic cells have been proposed, however those in prokaryotes remain largely unresolved. We undertook studies to determine the sites, and degree of coupling for INT and CTC reduction in the aerobic Esc...
Article
The effects of substrates of primary aerobic dehydrogenases, and inorganic phosphate on aerobic INT and CTC reduction in Escherichia coli were examined. In general, INT produced less formazan than CTC, but INT (+) cell counts remained near values of CTC (+) cells. INT and CTC (+) cell numbers were higher than plate counts on R2A medium using succin...
Article
Untreated sewage has been released from McMurdo Station, Antarctica, into McMurdo Sound for several years. In this study organic carbon degradation was compared in seawater from McMurdo Sound at −1.8°C and 20°C using the BOD test. The ultimate BOD was 3 times larger at 20°C than at −1.8°C following 25 days of incubation. On the basis of on these fi...
Article
Full-text available
Survival, sublethal injury, and recoverability of Escherichia coli, Enterococcus faecalis, Salmonella typhimurium, and Yersinia enterocolitica were investigated by using diffusion chambers over 54 to 56 days of in situ exposure to a polar marine environment (-1.8 degrees C; salinity, 34.5 ppt) at McMurdo Station, Antarctica. Plate counts were used...
Article
Full-text available
Examines the survival and recoverability of enteric bacteria exposed to the antarctic marine environment in McMurdo Sound, Antarctica. Correlation between cold temperatures and the survival of enteric bacteria; Physiological responses and recoverability an enteric bacterial indicator; Exposure of the bacteria to in situ marine conditions.
Article
Interactions between copper ions and exopolymer from the marine film-forming bacterium Alteromonas atlantica were evaluated by a two-phase model that treats the polymer as if it exists in a phase separate from the bulk solution. The model takes into account electrostatic interactions and molecular volume changes within the polymer phase to determin...
Article
The spatial distribution and movement of the sewage plume from McMurdo Station, Antarctica, was investigated in the ocean under the early summer ice. Samples of seawater were obtained via holes drilled through the ice and analysed for coliform bacteria. Ocean currents were also examined to determine their effect on the movement of the plume. High d...
Article
Full-text available
EPThis communication reports the presence of polysaccharides in biofilms formed by pure and mixed cultures of Desulfovibrio desulfuricans and Pseudomonas fluorescens on mild and stainless steel surfaces. The results of colorimetric assays, indicating significant differences between the amounts of neutral sugars present in these biofilms, were suppo...
Article
A method was developed for the quantitation of pyruvyl groups in microbial polymers using mild acid hydrolysis, o-phenylenediamine labeling, reversed-phase high-performance liquid chromatography (RP-HPLC), and fluorescence detection. The method was used to determine the pyruvate content of various microbial exopolysaccharides and to estimate the ab...
Article
Full-text available
In 1996 the U.S. Geological Survey (USGS) converted its National Stream Quality Accounting Network Program (NASQAN) into a national flux-based water quality monitoring program in the Mississippi, Columbia, Colorado, and Rio Grande Basins. Suspended sediment flux estimates for temporal spans • year generally are accurate to within ±15% or better. Di...

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Projects

Projects (9)
Project
Ice free coast and associated habitats (terrestrial and nearshore marine) are extremely rare in Antarctica, comprising less than 0.05% of the continent. Yet this is where human activity is concentrated in Antarctica and is where Antarctic Stations are generally built. This project is examining human impacts in marine ecosystems at Australia's Antarctic Stations, ranging from the effects of sewage and hydrocarbons in the marine environment to the impacts of abandoned waste disposal sites.