Why environmental scientists are becoming Bayesians

Advances in computational statistics provide a general framework for the high‐dimensional models typically needed for ecological inference and prediction. Hierarchical Bayes (HB) represents a modelling structure with capacity to exploit diverse sources of information, to accommodate influences that are unknown (or unknowable), and to draw inference on large numbers of latent variables and parameters that describe complex relationships. Here I summarize the structure of HB and provide examples for common spatiotemporal problems. The flexible framework means that parameters, variables and latent variables can represent broader classes of model elements than are treated in traditional models. Inference and prediction depend on two types of stochasticity, including (1) uncertainty, which describes our knowledge of fixed quantities, it applies to all ‘unobservables’ (latent variables and parameters), and it declines asymptotically with sample size, and (2) variability, which applies to fluctuations that are not explained by deterministic processes and does not decline asymptotically with sample size. Examples demonstrate how different sources of stochasticity impact inference and prediction and how allowance for stochastic influences can guide research.     

Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers

Molecular gut content analysis is a popular tool to study food web interactions and has recently been suggested as an alternative source for DNA-based biomonitoring. However, the overabundant consumer's DNA often outcompetes that of its diet during PCR. Lineage-specific primers are an efficient means to reduce consumer amplification while retaining broad specificity for dietary taxa. Here, we designed an amplicon sequencing assay to monitor the eukaryotic diet of mussels and other metazoan filter feeders and explore the utility of mussels as natural eDNA samplers to monitor planktonic communities. We designed several lineage-specific rDNA primers with broad taxonomic suitability for eukaryotes. The primers were tested using DNA extracts of different limnic and marine mussel species and the results compared to eDNA water samples collected next to the mussel colonies. In addition, we analysed several 25-year time series samples of mussels from German rivers. Our primer sets efficiently prevent the amplification of mussels and other metazoans. The recovered DNA reflects a broad dietary preference across the eukaryotic tree of life and considerable taxonomic overlap with filtered water samples. We also show the utility of a reversed version of our primers, which prevents amplification of nonmetazoan taxa from complex eukaryote community samples, by enriching fauna associated with the marine brown algae Fucus vesiculosus. Our protocol will enable large-scale dietary analysis in metazoan filter feeders, facilitate aquatic food web analysis and allow surveying of aquacultures for pathogens. Moreover, we show that mussels and other aquatic filter feeders can serve as complementary DNA source for biomonitoring.     

Detection of aerosolized bacterial spores (Bacillus atrophaeus) using free-flying honey bees (Hymenoptera: Apidae) as collectors

An aerosol cloud of Bacillus atrophaeus (previously B. subtilis variety niger) spores, an anthrax surrogate, was created in a large 0.4 ha (1 ac), bee-containing, open-mesh tent. Bees from a B. atrophaeus uncontaminated hive flying through the cloud adsorbed the spores in statistically significant quantities. After removal of the B. atrophaeus contaminated hive and introduction of another B. atrophaeus uncontaminated hive, the bees again were monitored for the next few days for B. atrophaeus spores. B. atrophaeus spores accumulated on the bees bodies following their exposure to the residual B. atrophaeus contamination in the tent. The spore loads on the bees quickly returned to background levels after the hives were removed from the contaminated tent area. It may therefore be practical to use honey bee colonies to monitor foraging areas for disease-causing spores.     

Detection of aerosolized bacterial spores (<Emphasis Type="Italic">Bacillus atrophaeus</Emphasis>) using free-flying honey bees (Hymenoptera: Apidae) as collectors

An aerosol cloud of Bacillus atrophaeus (previously B. subtilis variety niger) spores, an anthrax surrogate, was created in a large 0.4 ha (1 ac), bee-containing, open-mesh tent. Bees from a B. atrophaeus uncontaminated hive flying through the cloud adsorbed the spores in statistically significant quantities. After removal of the B. atrophaeus contaminated hive and introduction of another B. atrophaeus uncontaminated hive, the bees again were monitored for the next few days for B. atrophaeus spores. B. atrophaeus spores accumulated on the bees bodies following their exposure to the residual B. atrophaeus contamination in the tent. The spore loads on the bees quickly returned to background levels after the hives were removed from the contaminated tent area. It may therefore be practical to use honey bee colonies to monitor foraging areas for disease-causing spores.     

Comparative study of 222Rn/220Rn progeny concentration and estimation of age-dependent dose due to inhalation of radon progeny for different body organs

In the present study, the age-dependent doses due to inhalation of short lived decay progeny of radon, i.e., ²¹⁴Po to different body organs have been calculated for the inhabitants of the Jammu district, Jammu &; Kashmir, India. The estimated age-dependent doses for different body organs due to inhalation of radon progeny through air for all age groups varied between 0.002E-06 and 0.10 n Svy^?1 which were found to be well within the recommended limit of 1000 µ Svy^?1 (ICRP). The progeny concentration of radon and thoron was calculated and compared by two different techniques. The attached and un-attached progeny concentration of radon and thoron was calculated by using a passive time integrating, deposition-based technique. The measured attached and un-attached radon and thoron progeny concentrations have been cross-checked by on-line active technique, i.e., Flow-mode Integrated Sampler. A weak positive correlation has been observed between the two devices. The median value of un-attached fraction was found to be 0.15 and 0.12 for thoron and radon progeny, respectively and found to have a log-normal distribution. A good positive correlation has been observed between radon and thoron progeny concentrations.     

Measurements of total and culturable bacteria in the alfresco atmosphere using a wet-cyclone sampler

Alfresco (def. clean, outdoor) airborne bacteria were collected with a commercially available wet-cyclone bioaerosol sampler to demonstrate its use, sample processing and resultant observations of total and culturable bacteria in mid-summer in the mid-Willamette River Valley, OR. Some critiques of the system are given. The maximum and minimum total and culturable airborne bacterial concentrations in the samples were 5.9 × 10⁵ and 8.8 × 10² cells m⁻³, and 1.3 × 10⁴ and 3.1 CFU m⁻³, respectively. What is thought to be a diurnal cycle was also observed for both fractions with highest concentrations during the day and lowest at dawn and dusk. The culturable bacteria as a percentage of the total, was maximal at mid-day (≈ 3%) and minimal at early morning and late evening (≈ 0.5–2%). Contrarily, the total bacteria in the downwind dust plume of a grass seed combine was 2.9 × 10⁶ cells m⁻³ and of these approximately 73% were culturable, a much greater culturable percentage than found in the alfresco outdoor atmosphere.     

A new sampler for collection of interstitial water from sandy sediments

An inexpensive, easily constructed apparatus for collecting interstitial water from sandy substrates is described and evaluated against two other devices. Results indicate that these samplers yield comparable dissolved oxygen determinations, but vary in terms of repeatability, efficiency, construction complexity and sturdiness.     

The tom-tom corer: a new design of the Kajak corer for use in meiofauna sampling

A new corer, the tom-tom, is a modification of the basic Kajak design. New modifications increase the efficiency of the corer in soft muds and increase the stability of the corer during ascent and descent. A stepped release trigger mechanism allows the corer to trip easily in even the softest muds, and a Phleger “bomb’ weight adds stability to the device. The corer can be deployed in a slow, controlled descent from small as well as large boats to reduce bow-wave. Four cores (4.50 cm inner diameter) are taken simultaneously in a fixed spatial pattern. Limited comparative sampling revealed that the tom-tom collected more meiofauna than a Van Veen grab and attained numbers statistically indistinguishable from diver-collected cores (only small sample sizes were available however). The corer will be most efficient in sediments without an extremely well-developed, suspendable layer, and most practical for smaller vessels in environments where diver collected cores are precluded by depth, strong currents or poor visibility. Although used in meiofauna collection, the corer should be appropriate for any sampling needs requiring a relatively undisturbed core.