Presence-absence Test Research Articles

Comparing maximum entropy modelling methods to inform aquaculture site selection for novel seaweed species

Maximum entropy (maxent) modelling is a widely used method for developing species distribution models (SDMs), but default maxent modelling methods can result in overly complex models with poor transferability. Methods suggested to reduce overfitting include increasing regularisation, using only linear and quadratic features, or applying forward selection of predictors using maximum likelihood (ML) methods. We built models using these options to determine environmental suitability within existing aquaculture zones for eight seaweed species, four red (Rhodophyta: Florideophyceae) and four brown (Ochrophyta: Phaeophyceae), that are being investigated for aquaculture in southern Australia. Forward selection models were the most parsimonious, but we encountered failure of ML methods for Pterocladia lucida (Rhodophyta) due to separation. Separation is a known issue for logistic regression and has recently been recognised in maxent models. Separation occurs where a variable, or combination of variables, is a perfect predictor for a binary response, here, species occurrence, and results in ML parameter estimates tending to infinity. One method for obtaining finite parameter estimates under separation is to apply a Cauchy prior distribution for coefficients. We therefore also built models for each species using a Cauchy-prior version of the forward selection method, and found that these models performed similarly to those built with ML methods. Default models achieved marginally higher predictive performance than other options based on training data metrics, but simpler models performed equivalently to, or better than, default models at predicting independent presence-absence test data. Predictive performance using test data varied considerably between species, but the difference in performance between models within each species was generally small. Our results confirm the concern that default maxent models may suffer from over-fitting and poor transferability. Model transferability and interpretability were important for our purpose, hence, based on the principle of parsimony, forward selection models were preferred. We also found that forward selection models retained similar predictive performance to the best model as assessed by each metric, further supporting use of these models. Where ML methods failed due to separation, the use of the Cauchy-prior method was a viable alternative. Predictions for the region of interest (Spencer Gulf, South Australia) were generated using the most parsimonious models, and Solieria robusta (Rhodophyta) showed the highest predicted suitability of the eight candidate species within existing aquaculture zones, especially in northern Spencer Gulf. Predicted suitability was low for the other Rhodophyta considered, while each of the Phaeophyceae showed moderate to high suitability in at least some southern Spencer Gulf aquaculture zones. These model results help to inform selection of the best candidate species and suitable farming areas for future research.

Microbial counts of mealworm larvae (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from different rearing companies and different production batches

The rising interest in insects for human consumption and the changing regulations in Europe require a profound insight into the food safety of insects reared and sold in Western society. The microbial quality of edible insects has only been studied occasionally. This study aimed at generating an overview of intrinsic parameters (pH, water activity and moisture content) and microbial quality of fresh mealworm larvae and crickets for several rearing companies and for several batches per rearer. In total, 21 batches obtained from 7 rearing companies were subjected to analysis of intrinsic parameters, a range of plate counts and presence-absence tests for Salmonella spp. and Listeria monocytogenes. The microbial counts of the fresh insects were generally high. Different rearing batches from a single rearing company showed differences in microbial counts which could not be explained by variations in intrinsic properties. The largest variations were found in numbers of bacterial endospores, psychrotrophs and fungi. Salmonella spp. and L. monocytogenes were not detected in any of the samples. Altogether, our study shows that large variations were found between batches from individual rearers. As a consequence, no overall differences between rearers could be observed.

Chemical remagnetization and clay diagenesis: testing the hypothesis in the Cretaceous sedimentary rocks of northwestern Montana

Although the migration of fluids is a likely agent of remagnetization for some chemical remanent magnetizations (CRMs), widespread CRMs, which occur in rocks that have not been altered by externally derived fluids, need to explained by another mechanism. We are testing clay diagenesis as a remagnetization mechanism for such CRMs by comparing results from Mesozoic strata in the disturbed belt of Montana where the rocks contain ordered illite/smectite that formed by moderate heating as a result of thrust loading, with equivalent strata on the adjacent Sweetgrass Arch which contain unaltered smectite-rich clay mineral assemblages. The results indicate that the magnetization in the rocks in the Sweetgrass Arch is weak and dominated by a modern viscous component. In contrast, the disturbed belt rocks have higher magnetic intensities and contain a prefolding or early synfolding, reversed tertiary magnetization that is interpreted to be a CRM residing in magnetite and perhaps pyrrhotite. A presence–absence test and the timing of acquisition for the CRM suggest that magnetite authigenesis could be related to the smectite-to-illite conversion.

New methods for the detection of viruses: call for review of drinking water quality guidelines

Drinking water supplies which meet international recommendations for source, treatment and disinfection were analysed. Viruses recovered from 100 L-1,000 L volumes by in-line glass wool filters were inoculated in parallel into four cell culture systems. Cell culture inoculation was used to isolate cytopathogenic viruses, amplify the nucleic acid of non-cytopathogenic viruses and confirm viability of viruses. Over a period of two years, viruses were detected in 23% of 413 drinking water samples and 73% of 224 raw water samples. Cytopathogenic viruses were detected in 6% raw water samples but not in any treated drinking water supplies. Enteroviruses were detected in 17% drinking water samples, adenoviruses in 4% and hepatitis A virus in 3%. In addition to these viruses, astro- and rotaviruses were detected in raw water. All drinking water supplies had heterotrophic plate counts of < 100/mL, total and faecal coliform counts of 0/100 mL and negative results in qualitative presence-absence tests for somatic and F-RNA coliphages (500 mL samples). These results call for a revision of water quality guidelines based on indicator organisms and vague reference to the absence of viruses.

Limitations of highly sensitive enzymatic presence-absence tests for detection of waterborne coliforms and Escherichia coli.

This study presents evidence for the unfeasibility of enzymatic presence-absence tests to detect one total coliform or one Escherichia coli organism in 100 ml of drinking water within a working day. The results of field trials with prototype chemiluminometric procedures indicated that the sensitivity-boosting measures that are essential to achieve the required speed compromise the specificity of the tests.

Detection and occurrence of waterborne bacterial and viral pathogens

Detection and occurrence of waterborne bacterial and viral pathogens

Evaluation of the Autoanalysis Colilert test for detection and enumeration of total coliforms

The Autoanalysis Colilert (AC) test was compared with the membrane filter (MF), 10-tube multiple-tube fermentation (MTF) technique, and the presence-absence test as described in Standard Methods for the Examination of Water and Wastewater for the detection and enumeration of total coliforms in water. The methods were evaluated with 31 samples from seven different sources. Each sample was analyzed by each of the techniques, using replicate 100-ml sample volumes. A total of 582 confirmed tubes were positive by the MTF test, and 533 tubes were positive by the AC test. Statistical analysis of the most-probable-number comparability data showed a statistically significant difference in the number of positive tubes, with the MTF test resulting in more positive tubes. There were no statistically significant differences in precision between the two methods. All the methods were comparable in detection of total coliforms. Levels of heterotrophic bacteria generally encountered in drinking water did not interfere with detection or enumeration of coliforms by the AC test.

Inexpensive, Disposable Presence-Absence Test for Coliforms and Escherichia coli in Water

Six-ounce (151-g) Whirl-Pak® bags containing 3.05g of dehydrated Presence-Absence (P-A) Broth and 5 mg of 4-methylumbelliferyl-β-D-glucuronide (MUG) were pasteurized with 10 kGy of gamma irradiation. To conduct a “bag” P-A test, 100 ml of water sample were added to a bag. The bag was closed, the medium was dissolved by massaging the bag for about 15 sec, and the bag was then placed in a rack for incubation. The bag method was compared with P-A tests conducted in 160-ml glass bottles and 200-ml polysulfone bottles, as well as with a 5-tube Laury] Tryptose Broth (LTB) most-probable-number (MPN) method. Twenty-nine surface-water samples (11 streams, 7 rivers, and 11 lakes), 9 well-water samples, and 2 sewage effluents were examined. Chi-square analyses of the results revealed that no significant difference (P≤0.1) existed among the different P-A tests. The hydrolysis of MUG provided excellent Escherichia coli detection and was easiest to determine in the bags.

Detection, Isolation and Identification of Osmotolerant Yeasts from High-Sugar Products

A simple presence-absence test for detection of small numbers of osmotolerant yeasts in foods was developed. Yeast extract glucose 50 broth [consisting of 0.5% (w/w) yeast extract and 50% (w/w) glucose] was used as enrichment medium and was incubated with agitation at 30°C. The detection was done by (a) microscope and (b) streaking 0.03 ml of enrichment culture on selective yeast extract glucose 50 agar and incubation at 30°C for 5–7 d. If no yeast cells were observed under the microscope within 10 d of incubation, the product sample was judged as “free from osmotolerant yeasts.” In accordance with this method 28 strains of osmotolerant yeasts were isolated from 27 spoiled high-sugar products. Twenty-four strains were identified as Zygosaccharomyces rouxii, 2 Zygosaccharomyces bailii and 1 each as Torulaspora delbrueckii and Debaryomyces hansenii.

The influence of increasing numbers of nonindicator organisms upon the detection of indicator organisms by the membrane filter and presence–absence tests

Municipal water samples were analyzed by membrane filter (MF) procedures for total coliforms, "background" counts, and 24-and 48-h, 35 °C plate counts. Presence–absence (P–A) tests were done on the samples for total coliforms and other indicator bacteria. The frequency of detection of indicator organisms by P–A tests was better than twice that recovered by MF analyses. When the 24-h plate count data were grouped into counting ranges of 0, 1–100, 101–1000, and &gt; 1000, a marked inhibition effect was observed with total coliform MF recoveries on samples producing plate counts &gt; 1000/mL. When the "background" and 48-h plate count results were placed in the corresponding counting ranges, inhibition of indicator organisms in the total coliform MF analyses was not observed. No inhibition effect was observed in the recovery of indicator organisms by P–A tests at any of the counting range levels. The presence of an apparent inhibition effect by high numbers of bacteria in a sample was shown to be influenced by the incubation period and type of count parameter, as well as the isolation technique for detection of indicator organisms.