Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.     

Colour discrimination and associative learning in hatchling lizards incubated at ‘hot’ and ‘cold’ temperatures

The ability of an animal to acquire, process and learn from information in their environment is thought to be fundamental to fitness. We currently have a poor understanding of the learning ability of young animals within the first few months of their life, the types of learning they use and the extent of their learning ability. Furthermore, an animal’s developmental environment, such as nest incubation temperature, may profoundly influence motor and cognitive skills. We first tested the ability of hatchling three-lined skinks (Bassiana duperreyi) incubated at ‘hot’ and ‘cold’ temperatures to solve an instrumental (motor) task before assessing their ability to learn colour associations in a multi-stage instrumental task, with a choice reversal. While 53 (88.3 %) lizards successfully completed the training phase, 14 (46.7 %) of the ‘hot’ incubated and none of the ‘cold’ incubated lizards successfully completed the instrumental task. Thirteen of these lizards rapidly learnt to discriminate colours, and this culminated in eight individuals successfully completing a choice reversal. Hatchling B. duperreyi demonstrated surprisingly rapid learning, and these results highlight the potentially important role of cognition during development and ultimately, in fitness.     

Predicting the multiple pathways of plant succession

Classical concepts view succession as a deterministic, mechanistic regeneration of the disturbed community, and thus have limited applicability to fire-prone ecosystems, A recently developed multiple pathway succession model appears to have more realism and applicability in frequently disturbed ecosystems. It includes a set of species-specific attributes that are vital to reproduction and survival, and permits variable succession pathways depending on the stand's age (and thus species composition) when disturbed. Examples from Australia and the northern Rocky Mountains (USA) are presented, as are approaches to refining and improving the model.     

Bioaccumulation of polychlorinated biphenyls in ranid frogs and northern water snakes from a hazardous waste site and a contaminated watershed

Livers of bullfrogs (Rana catesbeiana) from a polychlorinated biphenyl (PCB) contaminated watershed and hazardous waste site located in Pickens County, South Carolina, contained significantly higher concentrations of PCBs (2.33 and 2.26 ppm, respectively) than those from a reference site (0.05 ppm). Green frogs (R. clamitans) from the two contaminated sites also accumulated higher levels of PCBs (2.37 and 3.88 ppm, respectively) than those from the reference site (0.02 ppm). No temporal variation was observed in PCB concentrations of bullfrogs or green frogs from the contaminated sites between 1992 and 1993. Levels of PCBs in the livers of northern water snakes (Nerodia sipedon) were significantly higher in snakes from the contaminated watershed (13.70 ppm) than in those from the waste site (2.29 ppm) and two reference sites (2.50 and 1.23 ppm). When compared to frogs, significantly higher bioaccumulation occurred in water snakes from the contaminated watershed. No significant differences in PCB levels were found with respect to sex or body size (snout-vent length (SVL) or body mass) for frogs or snakes. PCBs were detected also in eggs of both frogs and snakes. Results of this study provide baseline data and document the bioaccumulation of PCB residues in frog and snake tissues; however, the significance of these tissue residues to reproduction, survival, growth/development, and population dynamics in contaminated habitats is unknown.     

Comparison of beach bacterial water quality indicator measurement methods

Three methods (membrane filtration, multiple tube fermentation, and chromogenic substrate technology kits manufactured by IDEXX Laboratories, Inc.) are routinely used to measure indicator bacteria for beach water quality. To assess comparability of these methods, quantify within-laboratory variability for each method, and place that variability into context of variability among laboratories using the same method, 22 southern California laboratories participated in a series of intercalibration exercises. Each laboratory processed three to five replicates from thirteen samples, with total coliforms, fecal coliforms or enterococci measured depending on the sample. Results were generally comparable among methods, though membrane filtration appeared to underestimate the other two methods for fecal coliforms, possibly due to clumping. Variability was greatest for the multiple tube fermentation method. For all three methods, within laboratory variability was greater than among laboratories variability.     

Co-composting of acid waste bentonites and their effects on soil properties and crop biomass

Acid waste bentonite is a byproduct from vegetable oil bleaching that is acidic (pH < 3.0) and hydrophobic. These materials are currently disposed of in landfills and could potentially have a negative impact on the effective function of microbes that are intolerant of acidic conditions. A study was undertaken using three different sources of acid waste bentonites, namely soybean oil bentonite (SB), palm oil bentonite (PB), and rice bran oil bentonite (RB). These materials were co-composted with rice husk, rice husk ash, and chicken litter to eliminate their acid reactivity and hydrophobic nature. The organic carbon (OC) content, pH, exchangeable cations, and cation exchange capacity (CEC) of the acid-activated bentonites increased significantly after the co-composting phase. In addition, the hydrophobic nature of these materials as measured using the water drop penetration time (WDPT) decreased from >10 800 s to 16 to 80 s after composting. Furthermore, these composted materials showed positive impacts on soil physical attributes including specific surface area, bulk density, and available water content for crop growth. Highly significant increases in maize biomass (Zea mays L.) production over two consecutive cropping cycles was observed in treatments receiving co-composted bentonite. The study clearly demonstrates the potential for converting an environmentally hazardous material into a high-quality soil conditioner using readily available agricultural byproducts. It is envisaged that the application of these composted acid waste bentonites to degraded soils will increase productivity and on-farm income, thus contributing toward food security and poverty alleviation.     

Indicator organisms for assessing sanitization during composting of plant wastes

The potential for using plant pathogens and seeds as indicator organisms for assessing sanitization of plant wastes during composting was tested in bench-scale flask and large-scale systems. Plasmodiophora brassicae was unsuitable due to high temperature tolerance in dry to moist composts, and detection of viable inoculum post-composting using bioassay plants not corresponding with that using TaqMan® PCR, possibly due to preservation of nucleic acids at elevated temperatures. Several other plant pathogens (Sclerotinia sclerotiorum, Microdochium nivale, Phytophthora cinnamomi and Phytophthora nicotianae) were unsuitable due their low temperature tolerance. Fusarium oxysporum f.sp. cepae and f.sp. radicis-lycopersici chlamydospores and tomato seeds were suitable indicators due to their moderate temperature tolerance and ease of viability testing post-composting. Abutilon seeds were more tolerant than tomato seeds of compost temperatures ?52 °C but more prone to degradation at lower temperatures and therefore less suitable as indicators. Relationships between compost temperature during exposures of 2-10 days and subsequent viability of the above chlamydospores or seeds enabled the sanitizing effect of composting processes to be predicted within 2-6 days. Plant waste type (woody or vegetable) had a small but significant effect on the relationship for tomato seeds but not for F. oxysporum chlamydospores.     

Salt-induced land and water degradation in the Aral Sea basin: A challenge to sustainable agriculture in Central Asia

Expansion of irrigated agriculture in the Aral Sea Basin in the second half of the twentieth century led to the conversion of vast tracks of virgin land into productive agricultural systems resulting in significant increases in employment opportunities and income generation. The positive effects of the development of irrigated agriculture were replete with serious environmental implications. Excessive use of irrigation water coupled with inadequate drainage systems has caused large‐scale land degradation and water quality deterioration in downstream parts of the basin, which is fed by two main rivers, the Amu‐Darya and Syr‐Darya. Recent estimates suggest that more than 50% of irrigated soils are salt‐affected and/or waterlogged in Central Asia. Considering the availability of natural and human resources in the Aral Sea Basin as well as the recent research addressing soil and water management, there is cause for cautious optimism. Research‐based interventions that have shown significant promise in addressing this impasse include: (1) rehabilitation of abandoned salt‐affected lands through halophytic plant species; (2) introduction of 35‐day‐old early maturing rice varieties to withstand ambient soil and irrigation water salinity; (3) productivity enhancement of high‐magnesium soils and water resources through calcium‐based soil amendments; (4) use of certain tree species as biological pumps to lower elevated groundwater levels in waterlogged areas; (5) optimal use of fertilizers, particularly those supplying nitrogen, to mitigate the adverse effects of soil and irrigation water salinity; (6) mulching of furrows under saline conditions to reduce evaporation and salinity buildup in the root zone; and (7) establishment of multipurpose tree and shrub species for biomass and renewable energy production. Because of water withdrawals for agriculture from two main transboundary rivers in the Aral Sea Basin, there would be a need for policy level interventions conducive for enhancing interstate cooperation to transform salt‐affected soil and saline water resources from an environmental and productivity constraint into an economic asset.     

Taxonomy of groundwater quality using multivariate and spatial analyses in the Tuticorin District,Tamil Nadu,India

A holistic appraisal of the quality of groundwater from the Tuticorin District has been conducted using multivariate statistical and spatial analyses. The objectives of the study were to delineate the spatial and temporal variabilities in groundwater quality and to understand its suitability for human uses. A total of 100 groundwater samples were collected and analyzed for major cations and anions during pre-monsoon and post-monsoon. Water quality index rating was calculated to quantify overall water quality for human consumption. The PRM samples exhibit poor quality in greater percentage when compared with POM due to the dilution after rainfall. Correlation, factor analysis, and plot of the factor scores reflect the seawater intrusion and weathering process. The mineral stability diagrams indicated that the groundwater is in equilibrium with kaolinite and Ca-montmorillonite, whereas Gibbs plot showed that the chemical composition of groundwater in both districts is controlled by the natural weathering processes irrespective of seasons. The major water type identified in this study is the Ca²⁺–Mg²⁺–HCO₃ ^? type, which degrades into predominantly Na⁺–Cl^?–SO₄ ^2? more saline groundwater toward the coast.