Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Waterlogging responses in dune,swale and marsh populations of Spartina patens under field conditions

Summary Soil waterlogging responses were examined in three Spartina patens populations along a steep flooding gradient in coastal Louisiana. Root anatomy and physiological indicators of anaerobic metabolism were examined to identify and compare flooding responses in dune, swale and marsh populations, while soil physicochemical factors were measured to characterize the three habitats. Soil waterlogging increased along the gradient from dune to marsh habitats and was accompanied by increases in root porosity (aerenchyma). Aerenchyma in marsh roots was apparently insufficient to provide enough oxygen for aerobic respiratory demand, as indicated by high root alcohol dehydrogenase activities and low energy charge ratios. Patterns of root metabolic indicators suggest that dune and swale roots generally respired aerobically, while anaerobic metabolism was important in marsh roots. However, in each population, relatively greater soil waterloging was accompanied by differences in enzyme activities leading to malate accumulation. In dune and swale roots under these circumstances, depressed adenylate energy charge ratios may have been the result of an absence of increased ethanol fermentation. These trends suggest that: 1) Aerenchyma formation was an important, albeit incomplete, long-term adaptation to the prevalent degree of soil waterlogging. 2) All populations adjusted root metabolism in response to a relative (short-term) increase in soil waterlogging.     

Distribution,length and weight of roots in young plantations ofEucalyptus grandis W. Hill ex Maiden irrigated with recycled water

Summary The root systems ofEucalyptus grandis W. Hill ex Maiden, irrigated with recycled municipal effluent at two sites in north-western Victoria, Australia, were studied by excavation and coring. Trees at Robinvale were four years-old and were irrigated using micro-sprays that covered only 70% of the ground surface area, whereas at Mildura, effuent was uniformly was uniformly applied to six years-old trees by flood and sprinkler irrigation. At Mildura where roots were excavated from a 2.80×2.80×1.20 m block of soil, a total root length of 1193 m.m⁻² and a total root weight of 3.1 kg m⁻² were estimated in the top metre. For roots >1 mm diameter, 77% of intercepts were at 0–30 cm, whereas only 50% were in the 50–100 cm soil horizon. At both sites where roots in the top 30 cm were studied by coring, the vertical distributions of root intercepts, length and weight were similar. Root length was greatest in the 0–10 cm soil horizon at both sites, and intercepts of roots <1 mm diameter comprised 73% and 81% of all roots at Mildura and Robinvale respectively. Roots <1 mm diameter contributed 85% of total length at both sites, but only 19% and 21% of total weight at Mildura and Robinvale respectively. The horizontal distribution of roots differed at the two sites. With uniform application of effuent at Mildura, root intercepts and length were concentrated in the centre of the irrigation bay, but at Robinvale, the concentration occurred closer to the tree row due mainly to the different method of irrigation. Root weight at both sites was highest within 50 cm of the tree row. Root densities of 0.11 to 0.57 cm cm⁻³ were estimated in the two plantations; these were similar to root densities measured inPinus radiata D. Don plantations up to 46 months old, but were considerably lower than those estimated for pastures. The implications of the results for the management of irrigated plantations of eucalypts are discussed.     

Plant-water relations in wheat as influenced by root pruning

Summary A greenhouse study in which 24, 54 and 71 per cent roots of wheat (Triticum aestivum L.) were pruned on the 73rd day from the date of planting (anthesis stage) showed that during a 7-day period following root pruning, total transpiration and leaf water potential were significantly lower (P=0.05) and the stomatal resistance was significantly higher (P=0.05) where 54 and 71 per cent roots were pruned, as compared to no root pruning or 24 per cent root pruning. The leaf relative water content, however, showed no significant differences. Thus about one-fourth root sytem could be reduced without adversely affecting the plant-water status.     

A model for water transport in the stele of plant roots

Summary The mechanism of water movement across roots is, as yet, not well understood. Some workable black box theories have already been proposed. They, however, assumed unrealistic cell membranes with low values of , or were based on a poor anatomical knowledge of roots. The role of root stele in solute and water transport seems to be especially uncertain. An attempted explanation of the nature of root exudation and root pressure by applying the apoplast canal theory (Katou andFurumoto 1986 a, b) to transport in the root stele is given. The canal equations are solved for boundary conditions based on anatomical and physiological knowledge of the root stele. It is found that the symplast cell membrane, cell wall and net solute transport into the wall apoplast are the essential constituents of the canal system. Numerical analysis shows that the canal system enables the coupled transport of solutes and water into a xylem vessel, and the development of root pressure beyond the level predicted by the osmotic potential difference between the ambient medium and the exudate. Observations on root exudation and root pressure previously reported seem to be explained quite well. It is concluded that the movement of water in the root stele although apparently active is essentially osmotic.Abbreviations J _v ^ex volume exudation per root surface - J₀ non-osmotic exudation - L^r overall radial hydraulic conductivity of an excised root - reflection coefficient - C_s difference in the osmotic concentration between the bathing medium and the exudate - R gas constant - T absolute temperature - C_K molar concentration of K⁺ - C_Cl molar concentration of Cl^– - C_j molar concentration of ion species j - P_j membrane permeability of ion j - z_j valence of ion j - F Faraday constant - V_ix intracellular electric potential with reference to the canal     

Endophyte differentiation inCasuarina actinorhizae

Summary This is an ultrastructural study of development of infected cells in nitrogen fixing root nodules ofCasuarina spp. While several aspects of development are similar to those found in many other actinorhizae, unusual aspects of development of the host cell and differentiation of the endophyte inCasuarina are correlated with unusual changes in the wall of the infected cell. Instead of vesicles the endophyte forms atypical hyphae in mature infected cells. These unusual hyphal forms are termed intracellular hyphae. Intracellular hyphae are nonseptate hyphae which originate and terminate within the same host cell, and have a varying diameter and a multidirectional growth and branching pattern. A laminate surface layer previously undescribed on hyphae ofFrankia is a feature common to mostCasuarina endophytic hyphae and is probably similar chemically to the laminae comprising the multilamellate envelope of endophytic vesicles in other actinorhizae.This paper is Florida Agricultural Experiment Station Journal Series No. 7350.     

A new mutant class of soybean lacks urease in leaves but not in leaf-derived callus or in roots

Summary We reported earlier the recovery of two classes of soybean urease mutants in soybean (Glycine max L. Merr. cv. Williams). Class I mutants lack the embryo-specific urease while class II mutants lack the activities of both urease isozymes, the embryo-specific and the ubiquitous urease, the latter found in all tissues examined. We report here the recovery of a true-breeding mutant, aj3, which represents the third phenotypic class: normal levels of embryo-specific urease and little or no ubiquitous urease. Unlike class II mutant plants which lack urease in all tissue, aj3 lacks urease activity only in leaves (ca. 2% normal activity); its roots have near normal urease activity. Callus derived from leaves of aj3 has 14% to 40% the urease activity of Williams 82 callus. This partial reduction in urease activity in aj3 callus is sufficient to reduce growth with urea as sole nitrogen source and to confer resistance to 50 mM urea added to callus maintenance medium. Leaves of aj3 produce more than 40 times the urease antigen expected from their urease activity. The aj3 trait is due to a single recessive lesion which is not allelic with lesions at theEu2, Eu3 (class II) orEu1 (class I) loci. We designate the aj3 genotype aseu4/eu4.     

Structural analysis of the phytophagous insect guilds associated with the roots of Centaurea maculosa Lam. C. diffusa Lam., and C. vallesiaca Jordan in Europe:

Summary During extensive field surveys in central and eastern Europe, 21 herbivorous root insect species were found on Centaurea maculosa ssp. rhenana Boreau, 12 species on C. diffusa Lam. and 11 species on C. vallesiaca Jordan, representing 12 families in 4 orders. The large geographic distribution (species-area function), the high number of Centaurea spp. present (host speciation rate), and the high apparency of the rosettes and the rich food resources offered by the roots during winter, together with their poor accessibility, correlate with the high number of specialist feeders associated with the roots of C. maculosa and C. diffusa. The members of the taxonomically diverse root entomofauna exploit specific structures of the tap root (food niches). Interspecific competition among members of food niches, as well as species-specific responses to different phenological stages (for oviposition) and tissues (for larval development) are thought to be responsible for the high predictability in guild structure. The relatively low levels of host plant attack (two thirds of the roots were unattacked) and the fact that food niches remained unoccupied in most of the regions suggest, however, that the majority of the studied guilds do not represent equilibrium assemblages. Ecological (different habitats), climatic (transitional zone) and historical (ancient pre-Pleistocene communities) factors could account for the highest values of species diversity, infestation levels, species packing and food niche utilization, which are found on C. maculosa in E. Austria/NW. Hungary, compared to other regions. A positive correlation between species packing (number of root-feeding species per population) and infestation rates (percent of roots attacked) was only found for the more stable, semi-natural habitats. A comparative analysis of the regional root insect guilds of C. maculosa with corresponding data for the phytophagous insects associated with the flower heads revealed distinct taxonomical differences, but a high degree of numerical and structural similarity. The different geographical regions are similarly ranked for host plant attack, herbivore pressure, average species packing and level of food niche utilization.     

Root and microbial biomass dynamics under the canopy of the desert shrub Zygophyllum dumosum

Summary A study was done to evaluate the influence of soil moisture and rainfall on root and microbial biomass production under the canopy of the desert shrub Zygophyllum dumosum. During the study period the root biomass production increased following the early rains but subsequently declined, remaining fairly constant thoroughout the season. In contrast microbial biomass and soil organic matter increased during the rainy season and declined with the onset of the dry summer period. Based on our results we suggest that the moisture event and not the amount and the organic matter content regulate root and microbial biomass production at the 0 to 10 cm soil layer.Contribution of the Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel. paper no. 2617-E, 1989 series