Aaron Maloy - Academia.edu (original) (raw)

Papers by Aaron Maloy

Fundamental to food web analysis is the accurate description of predator prey relationships and c... more Fundamental to food web analysis is the accurate description of predator prey relationships and competitive interactions among organisms. Establishing these connections in marine suspension feeders and small larval forms has proven difficult with conventional methodologies. The following account details the development and initial application of DNA-based methods that allow for the direct dietary analysis and assessment of resource competition in marine organisms and their larvae. An initial approach based on polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was applied to the dietary analysis of several species of adult marine bivalves. In each of two separate studies it was demonstrated that bivalves, typically considered generalist suspension feeders, actively partition food resources thereby reducing direct competition. The sensitivity and accuracy of this approach was further validated by analysing the dietary variation in spatially separated marine m...

Journal of …, 2003

To test the hypothesis that a temporal variation in species-specific spawning times is the mechan... more To test the hypothesis that a temporal variation in species-specific spawning times is the mechanism limiting hybridization and maintaining genetic integrity in a Mytilus edulis (L.) and M. trossulus (Gould) hybrid zone in eastern Maine, mussels from a low intertidal ...

Aquaculture International, 2014

Although biofilms are recognised as important in microbial colonisation, solutions to their inhib... more Although biofilms are recognised as important in microbial colonisation, solutions to their inhibition are predominantly based on planktonic assays. These solutions have limited efficacy against biofilms. Here, a series of biofilm-orientated tests were used to identify anti-biofilm compounds from marine micro-flora. This led to the isolation of a complex of anti-biofilm compounds from an extract of Paenibacillus polymyxa (PPE). A combination of rpHPLC and mass spectrometry identified the principle components of PPE as fusaricidin B (LI-FO4b) and polymyxin D1, with minor contributions from surfactins. This complex (PPE) reduced the biofilm biomass of Bacillus subtilis, Micrococcus luteus, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus bovis. In contrast, ampicillin was only effective against S. aureus. PPE also inhibited a self-assembling marine biofilm (SAMB) in co-incubation assays by 99.3% + 1.9 and disrupted established SAMB by 72.4% + 4.4, while ampicillin showed no significant reduction. The effectiveness of this complex of lipopeptides against single and multispecies biofilms suggests a future role in biofilm prevention strategies.

International Journal of Systematic and Evolutionary Microbiology, 2005

Roseovarius crassostreae sp. nov., a member of the Roseobacter clade and the apparent cause of ju... more Roseovarius crassostreae sp. nov., a member of the Roseobacter clade and the apparent cause of juvenile oyster disease (JOD) in cultured Eastern oysters

Journal of the Marine Biological Association of the United Kingdom, 2011

Improved understanding of the occurrence and spatio-temporal distribution of bivalve larvae holds... more Improved understanding of the occurrence and spatio-temporal distribution of bivalve larvae holds significant benefits for ecological studies, shellfisheries management and aquaculture. Morphological methods for identification have proved difficult to develop because of the small size of these larvae and similarities in their shape and colour. Molecular methods based on DNA extraction can confirm the presence of a species in a plankton sample, but without sample sorting and individual larval analysis, provide no estimate of larval abundance and are incapable of providing an estimate of larval growth rate. Fluorescence in situ hybridization (FISH) using species-specific DNA probes has the potential to resolve these issues. However, utilization of this technique is constrained by the strong autofluorescence, common in marine larvae. Here we evaluate the effect of eight different fixatives on the autofluorescence intensity of bivalve larvae using fluorescein isothiocyanate (FITC) and Cy3 filters. In addition, fifteen autofluorescence reduction treatments were evaluated and their compatibility with FISH assessed. Relative to fresh larvae, chemically fixed larvae had significantly higher autofluorescence in both filter sets. Larvae preserved by freezing at -808C exhibited no significant increase in autofluorescence over a 3-year period. Autofluorescence levels were generally lower with the FITC filter set than the Cy3 filter set. For archived larvae preserved in modified saline ethanol and exhibiting fixative-induced autofluorescence, the autofluorescence intensity could be reduced to 20-30% with saturated Sudan Black B and to 30-40% with Chemicon TM . Both of these autofluorescence reduction treatments were compatible with subsequent FISH protocols using a FITC-labelled probe.

North American Journal of Fisheries Management, 2008

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Marine Ecology Progress Series, 2009

Journal of Plankton Research, 2013

Establishing predatorprey relationships and determining competitive interactions within the plank... more Establishing predatorprey relationships and determining competitive interactions within the plankton community remains a central aim of zooplankton ecology. Using bivalve larvae as a model system, a DNA-based dietary approach using general eukaryotic primers was evaluated. Prey DNA was preferentially amplified using a predator-specific endonuclease restriction enzyme and blocking primer. Application of the blocking primer in isolation resulted in 80% of recombinant clones carrying inserts of non-bivalve origin, increasing to 100% when combined with a restriction enzyme. Further validation was achieved using wild, naturally feeding larvae of Mysella spp. and Ostrea edulis. Of the sequenced clones, 75% originated from centric and pennate diatoms (Bacillariophyta). A further 16% originated from fungi representing the phyla Ascomycota and Basidiomycota. The remaining sequences belonged to flowering plants (Magnoliophyta), single-celled green algae (Prasinophyceae), potential parasites (Ichthyosporea), dinoflagellates (Dinophyceae) and brown algae (Phaeophyceae). No qualitative difference in diet was observed among these two particular species, although the diversity of prey observed suggests that this DNA-based approach is suitable for studying the trophic interactions of marine bivalve larvae. Furthermore, based on sequence alignments, slight modifications to the blocking primer sequence could adapt this basic approach to a wide diversity of consumers within the plankton community.

Journal of Invertebrate Pathology, 2008

The bacterium Roseovarius crassostreae causes seasonal mortalities among commercially produced ea... more The bacterium Roseovarius crassostreae causes seasonal mortalities among commercially produced eastern oysters (Crassostrea virginica) grown in the Northeastern United States. Phylogenetically, the species belongs to a major lineage of marine bacteria (the Roseobacter clade), within which Roseovarius crassostreae is the only known pathogen to be isolated in laboratory culture. The objective of the current study was to determine the location and nature of R. crassostreae interactions with oysters affected by juvenile oyster disease (JOD). Scanning electron microscopy of diseased individuals revealed abundant colonization of the inner shell surfaces by bacteria which were morphologically similar to R. crassostreae. The same types of cells were also observed on and within layers of host-derived conchiolin on the inner valves. Most bacterial cells were alive as determined by the use of a fluorescent viability stain. Further, most were clearly attached at the cell poles, which is consistent with the ability of R. crassostreae to express polar fimbriae. When material from the pallial fluid, soft tissue and inner valve surfaces was cultured, the highest numbers of R. crassostreae were recovered from the inner valves. These samples also contained the greatest abundance of R. crassostreae as a percentage of total colonies. Cloning and sequencing of 16S rRNA genes provided culture-independent evidence of the numerical dominance of R. crassostreae among the bacterial consortia associated with the inner shell surfaces of JOD-affected animals. The ability of R. crassostreae to colonize shell and conchiolin is consistent with the described JOD-pathology and may aid the bacteria in avoiding hemocyte-mediated killing.

Fish & Shellfish Immunology, 2013

This study is to characterize freshwater prawn Macrobrachium rosenbergii GST is belonging to delt... more This study is to characterize freshwater prawn Macrobrachium rosenbergii GST is belonging to delta class using bioinformatics. A full length cDNA of GST-delta was identified from the cDNA library of M. rosenbergii (designated as MrGST) constructed by GS FLX technology. Further, to gain more knowledge on GST-delta, bioinformatics analysis including homology search, domain and motif analysis, multiple sequence alignment carried out. Furthermore, in order to dissect the evolutionary significance, both from origin and structural point of view, phylogenetic tree as well as 3D protein model construction were done. Results of above investigation reveal that cDNA of GST-delta has 879 base pairs (bp) with an ORF holding 648 base pairs which encodes 216 amino acids with a molecular weight of 24.2 kDa. GST has two domains namely, N-terminal glutathione binding site and C-terminal substrate binding site. Structural analysis of MrGST showed that the protein has 35.65% random coils, 44.91% helices, 14.35% extended sheets and 5.09% beta turns. Noteworthy, cysteine in N-terminal and glycine in C-terminal are conserved. It looks like, the amino acids responsible for structural and functions of GST are highly conserved. It is widely reported that GST in mammalian system participates in several diverse functions which are essential for defense of cell from aerophilic free radicals. Probably this unique and important function of GST is contributing to the evolutionary conservation. Nevertheless, further in vitro and in vivo experiments are been carried out to prove the hypothesis "GST is involved in protection against free radicals attack, even in arthropoda phylum".

Diseases of Aquatic Organisms, 2005

We have developed a PCR-assay for the diagnosis of juvenile oyster disease (JOD) based on the det... more We have developed a PCR-assay for the diagnosis of juvenile oyster disease (JOD) based on the detection of Roseovarius crassostreae directly from affected oysters. Species-specific primers are used to amplify the 16S-23S rDNA internal transcribed spacer (ITS) of R. crassostreae, and confirmation of product identity is accomplished by restriction enzyme analysis. No false positives were obtained with either closely related bacterial species or from other DNAs present in oyster samples. The assay has the potential to detect as few as 10 cells of R. crassostreae per oyster when samples are taken from the inner valve surfaces of the animal. Inclusion of material from soft body surfaces is not necessary, and may reduce sensitivity approximately 10-fold. In a JOD-affected population, a positive PCR result was obtained from all oysters from which these bacteria were subsequently cultured. The assay also detected the presence of R. crassostreae in 2 oysters from which no R. crassostreae isolates were recovered. No R. crassostreae was detected by either PCR or bacteriology in oysters from a population that was not exhibiting JOD-signs. This assay is expected to advance regional disease management efforts and provide valuable insights into the disease process and epizootiology of JOD.

Diseases of Aquatic Organisms, 2007

Biofouling, 2012

Aquaculture Nutrition, 2011

The transition between endogenous and exogenous feeding in hatchery production of fish larvae has... more The transition between endogenous and exogenous feeding in hatchery production of fish larvae has long been a bottleneck to increased production. Identification of alternative prey species with a wider array of nutritional profiles is essential for further expansion and diversification within the aquaculture industry. Traditional morphological methods to identify dietary composition are limited. In this study, we present a novel DNA-based methodology for identifying the gut contents of larval fish that is independent of prey retaining identifiable characteristics. Laser capture microdissection is used to collect ingested material for DNA extraction, thus limiting contaminating DNA originating from the larval fish. PCR is then conducted using universal eukaryotic primers that have the potential to detect a wide diversity of prey items. Using this approach, we identified ingested Artemia salina from hatchery-reared Gadus morhua larvae. Differential length amplification PCR was used to evaluate the effects of DNA degradation on the sensitivity of A. salina detection. Although it was possible to detect A. salina with relatively long (626 bp) fragments, targeting smaller fragments (264 bp) resulted in the highest return of prey sequences. This combined LCM and molecular approach to diet analysis could offer a more complete assessment of the diets of naturally feeding larvae.

Aquaculture, 2007

Juvenile Oyster Disease (JOD) has resulted in mass mortalities of cultured Crassostrea virginica ... more Juvenile Oyster Disease (JOD) has resulted in mass mortalities of cultured Crassostrea virginica in the northeastern United States since the 1980's. Bacteriological analyses of affected oysters have revealed a consistent association of JOD-signs and mortalities with heavy colonization by the novel species Roseovarius crassostreae. Conclusive assignment of etiology has been difficult, however, for two principle reasons. First, JOD-like mortality was reproduced in laboratory-held oysters by challenge with R. crassostreae, but the typical disease signs were not present. Further, because R. crassostreae had only been detected in oyster populations after the onset of JOD, the possibility remained that it was a secondary colonizer. In this study, we document the ability of R. crassostreae to induce JOD-like conchiolin deposition in oysters maintained in laboratory aquaria. Further we report the isolation of R. crassostreae from a first-year crop of C. virginica concurrent with the development of microscopic mantle lesions, which are the first pathological indication of JOD. Consistent with previous studies, these lesions preceded overt JOD-signs and mortalities by less than two weeks. Based on the accumulated evidence, it is now possible to rule out a secondary role for R. crassostreae as a colonizer of already diseased animals, and we conclude that R. crassostreae is the etiological agent of JOD. To avoid potential confusion with other diseases of juvenile oysters, we also propose that JOD be renamed "Roseovarius Oyster Disease" (ROD).

Accurate field data on trophic interactions for suspension feeders are lacking, and new approache... more Accurate field data on trophic interactions for suspension feeders are lacking, and new approaches to dietary analysis are necessary. Polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) was integrated with stable isotope analysis to examine dietary patterns in suspension-feeding Mytilus spp. from seven spatially discrete locations within a semi-enclosed marine bay (Strangford Lough, Northern Ireland) during June 2009. Results of the two methods were highly correlated, reflecting dietary variation in a similar manner. Variation in PCR-DGGE data was more strongly correlated with the principal environmental gradient (distance from the opening to the Irish Sea), while values of d 13 C and d 15 N became progressively enriched, suggesting a greater dependence on animal tissue and benthic microalgae. Diatoms and crustaceans were the most frequently observed phylotypes identified by sequencing, but specific DNA results provided little support for the trophic trends observed in the stable isotope data. This combined approach offers an increased level of trophic insight for suspension feeders and could be applied to other organisms. Communicated by J. P. Grassle.

Current antibiofilm solutions based on planktonic bacterial physiology have limited efficacy in c... more Current antibiofilm solutions based on planktonic bacterial physiology have limited efficacy in clinical and occasionally environmental settings. This has prompted a search for suitable alternatives to conventional therapies. This study compares the inhibitory properties of two biological surfactants (rhamnolipids and a plant-derived surfactant) against a selection of broad-spectrum antibiotics (ampicillin, chloramphenicol and kanamycin). Testing was carried out on a range of bacterial physiologies from planktonic and mixed bacterial biofilms. Rhamnolipids (Rhs) have been extensively characterised for their role in the development of biofilms and inhibition of planktonic bacteria. However, there are limited direct comparisons with antimicrobial substances on established biofilms comprising single or mixed bacterial strains. Baseline measurements of inhibitory activity using planktonic bacterial assays established that broad-spectrum antibiotics were 500 times more effective at inhibiting bacterial growth than either Rhs or plant surfactants. Conversely, Rhs and plant biosurfactants reduced biofilm biomass of established single bacterial biofilms by 74-88 and 74-98 %, respectively. Only kanamycin showed activity against biofilms of Bacillus subtilis and Staphylococcus aureus. Broad-spectrum antibiotics were also ineffective against a complex biofilm of marine bacteria; however, Rhs and plant biosurfactants reduced biofilm biomass by 69 and 42 %, respectively. These data suggest that Rhs and plantderived surfactants may have an important role in the inhibition of complex biofilms.