Models for Estimating Abundance from Repeated Counts of an Open Metapopulation

Summary Using only spatially and temporally replicated point counts, Royle (2004b, Biometrics 60, 108–115) developed an N ‐mixture model to estimate the abundance of an animal population when individual animal detection probability is unknown. One assumption inherent in this model is that the animal populations at each sampled location are closed with respect to migration, births, and deaths throughout the study. In the past this has been verified solely by biological arguments related to the study design as no statistical verification was available. In this article, we propose a generalization of the N ‐mixture model that can be used to formally test the closure assumption. Additionally, when applied to an open metapopulation, the generalized model provides estimates of population dynamics parameters and yields abundance estimates that account for imperfect detection probability and do not require the closure assumption. A simulation study shows these abundance estimates are less biased than the abundance estimate obtained from the original N ‐mixture model. The proposed model is then applied to two data sets of avian point counts. The first example demonstrates the closure test on a single‐season study of Mallards (Anas platyrhynchos), and the second uses the proposed model to estimate the population dynamics parameters and yearly abundance of American robins (Turdus migratorius) from a multi‐year study.     

A simple and fast kinetic assay for phytases using phytic acid-protein complex as substrate

Phytase (EC 3.1.3.–) hydrolyzes phytate (IP₆) present in cereals and grains to release inorganic phosphate (P_i), thereby making it bioavailable. The most commonly used method to assay phytase, developed nearly a century ago, measures the P_i liberated from IP₆. This traditional endpoint assay is time-consuming and well known for its cumbersomeness in addition to requiring extra caution for handling the toxic regents used. This article reports a simple, fast, and nontoxic kinetic method adaptable for high throughput for assaying phytase using IP₆–lysozyme as a substrate. The assay is based on the principle that IP₆ forms stable turbid complexes with positively charged lysozyme in a wide pH range, and hydrolysis of the IP₆ in the complex is accompanied by a decrease in turbidity monitored at 600 nm. The turbidity decrease correlates well to the released P_i from IP₆. This kinetic method was found to be useful in assaying histidine acid phytases, including 3- and 6-phytases, a class representing all commercial phytases, and alkaline β-propeller phytase from Bacillus sp. The influences of temperature, pH, phosphate, and other salts on the kinetic assay were examined. All salts, including NaCl, CaCl₂, and phosphate, showed a concentration-dependent interference.     

Shorebird Abundance Estimates in Interior Alaska

Interior Alaska, USA, is the least-studied region in Alaska for breeding shorebirds because of challenging accessibility and expectations of low densities and abundances. We estimated lowland and upland shorebird population sizes on 370,420 ha of military lands in interior Alaska boreal forest from May–July 2016 and 2017. We modified the Program for Regional and International Shorebird Monitoring (PRISM) protocol used elsewhere in Alaska and incorporated a probability-based sampling design and dependent double-observer methods. We pooled all lowland shorebird and all upland shorebird observations and estimated abundance using Huggins closed captures models in Program MARK. Estimated abundances of all lowland and upland shorebirds were 42,239 ± 13,431 (SE) and 3,523 ± 494, respectively. The survey area is important for shorebirds in Alaska. We estimate that military lands in interior Alaska support 45,762 ± 13,925 shorebirds, including 7 species of conservation concern. Higher abundance of lowland shorebirds was best explained by lower elevation, lower percent scrub canopy, and higher percent water on plots. Higher abundance of upland shorebirds was best explained by higher elevation and increased distance to wetland. Our modified Arctic PRISM protocol was effective for surveys in the boreal forest and we recommend continued use of method modifications for future shorebird surveys in boreal forests. Identifying baseline abundances of shorebirds using interior Alaska is an important step in monitoring distributional shifts and potential future population declines. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Microbial community composition and its role in volatile compound formation during the spontaneous fermentation of ice wine made from Vidal grapes

Vidal grape grown in Ili, Xinjiang Autonomous Region, is one of few grapes used to ferment ice wine in China. Microbial community structure and volatile composition during the spontaneous fermentation of ice wine made from Vidal grapes in Ili were investigated using amplicon sequencing technology and headspace solid-phase microextraction/gas chromatography-mass spectrometer technologies. Among bacterial genera, Sphingobium, Pseudomonas and Sphingomonas gradually decreased, while Lactobacillus and Streptococcus increased during the spontaneous fermentation process. As regards fungi, the relative abundance of Vishniacozymaand Cladosporium reduced, but Hanseniaspora sharply raised. Additionally, correlations between microbes and volatile compounds were constructed based on multivariate data analysis. The results revealed that the functional core microbiota (mainly composed of eight bacterial genera and nine fungal genera) during ice wine fermentation showed considerable correlations with the formation of twenty-four volatile compounds in ice wine made from Vidal grapes. For example, Saccharomyces was positively correlated with ethanol, ethyl acetate and isoamylol; Hanseniaspora and Candidawere negatively correlated with hexanol; and Lactobacillus and Streptococcus were positively correlated with 2,3-butanediol, ethanol, ethyl acetate, isoamylol and isoamyl acetate. This studyprovides a reference for understanding the process of ice wine fermentation and improving the quality of ice wine made from Vidal grapes.     

Activated sludge under free ammonia treatment using gel immobilization technology for long-term partial nitrification with different initial biomass

To achieve stable partial nitrification, activated sludge from a wastewater treatment plant using free ammonia (FA) inhibition was immobilized in a polyvinyl alcohol carrier. After FA treatment at 16.44 mg L⁻¹ for 1 day, due to the increased growth rate gap between ammonium-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), AOB enrichment and NOB inhibition were achieved within 12 days, with AOB and NOB accounting for 65.61 and 0.05%, respectively. Subsequently, with dissolved oxygen concentrations of 4−5 mg L⁻¹, pH of 7.6–7.8 and temperature of 25 ± 1 °C, the immobilized carrier made of activated sludge achieved more than 90% and more than 86% of nitrite accumulation rate at the influent ammonia concentration of 90−110 mg L⁻¹ and 35−50 mg L⁻¹, respectively. After 50 days operation, the NOB content was 0.10%, indicating the immobilized carrier provided favorable conditions for maintaining the low NOB content. Furthermore, due to the low NOB content in the inoculum and the oxygen-limited environment formed by the increase in the AOB numbers in the carrier, immobilized carrier with different initial biomass (1, 2.5 and 5%) can achieve stable partial nitrification.     

Responses of pea and wheat to textile wastewater reclaimed by suspended sequencing batch bioreactors

Availability of good quality water for crop irrigation is a big challenge in developing countries due to limited resources of clean water. Textile industry consumes a huge amount of water during dyeing process and consequently it releases high strength wastewater into wastewater streams. The present study was designed with the objective to use textile wastewater treated in sequencing batch bioreactor for irrigation purpose. Wastewater containing 100 mg/L reactive black-5 azo dye amended with different co-substrates was treated using mixed liquor suspended solids (MLSS) and two previously isolated dye-degrading bacterial strains (Psychrobacter alimentarius KS23 and Staphylococcus equorum KS26). About 90% color and COD removal in case of dye-containing wastewater amended either with mineral salts + yeast extract or only yeast extract was achieved in 24 h after treatment with mixed culture (MLSS + KS23 + KS26). The treated wastewater was applied for irrigation of pea and wheat plants under controlled conditions. Untreated dye-contaminated wastewater was used as a control for comparison. A significant positive effect of treated dye wastewater amended with different co-substrates on the seed germination index, root and shoot length and biomass was observed in response to application of dye-containing wastewater treated with MLSS and dye-degrading bacterial strains compared to untreated control. Results of this study reveal that the dye-degrading microbial cultures could be used to enhance the treatment efficiency of dye-contaminated wastewater that can be utilized for irrigation of crops and biomass production.     

Rhizomicrobiomics of Caesalpinia bonducella,a wonder plant for PCOS treatment

Plant and rhizobacterial interactions contribute partly to a plant’s medicinal properties and are well studied through metagenomics. In this study, 16S rDNA, 18S rDNA, and ITS meta-sequencing were performed using the genomic DNA obtained from the rhizosphere of Caesalpinia bonducella—a medicinal shrub widely used to treat polycystic ovary syndrome (PCOS). Of the 665 Operational Taxonomic Units (OTUs) obtained from 16S rDNA sequencing, 23.9% comprised of microbes that increase the therapeutic value of plants (Bacillus, Paenibacillus), 6.4% belonged to stress and drought tolerant microbes (Pseudomonas, Rhizobium, Serratia), 8% belonged to plant-growth promoting rhizobacteria—predominantly Proteobacteria, and Firmicutes and the remaining were the microbes performing various other functions. Alpha diversity indexing by GAIA-metagenomics tool revealed the presence of a highly diverse group of microbes in the rhizosphere of C. bonducella; Chao.1 index (665), Shannon Weiner index (3.53), Simpson index (0.83) and Fisher index (106.13). The highly diverse microbes lingering around the roots of C. bonducella could possibly be due to a strong symbiotic association with the plant; root exudates nourish the microbes and the microbes in turn enrich the medicinal value of the plant.     

On the merits and feasibility of wildlife monitoring for conservation: a case study from Katavi National Park,Tanzania

Although long‐term monitoring is viewed as an essential part of conserving wildlife populations, it is currently carried out in surprisingly few protected areas in Africa. Here, data from a 16‐year vehicle transect monitoring programme in Katavi National Park, western Tanzania, are presented. These data provide information on large mammal densities, identify declines in populations of several large mammal species as based on encounter rates, support worrying trends observed in aerial census data and shed light on the effectiveness of recent changes in legal protection. Ground and aerial surveys confirmed that waterbuck, topi, warthog, lion and spotted hyaena populations are all in decline and that this should be a cause for concern. Counting animals by driving vehicle transects is relatively easy and inexpensive to carry out, and data here show that such counts have several pay‐offs for conservation managers especially in identifying population declines; counts should be employed more often in East Africa and elsewhere.