Empirical assessment of state-and-transition models with a long-term vegetation record from the Sonoran Desert

Resilience-based frameworks, including state-and-transition models (STM), are being increasingly called upon to inform policy and guide ecosystem management, particularly in rangelands. Yet, multiple challenges impede their effective implementation: (1) paucity of empirical tests of resilience concepts, such as alternative states and thresholds, and (2) heavy reliance on expert models, which are seldom tested against empirical data. We developed an analytical protocol to identify unique plant communities and their transitions, and applied it to a long-term vegetation record from the Sonoran Desert (1953-2009). We assessed whether empirical trends were consistent with resilience concepts, and evaluated how they may inform the construction and interpretation of expert STMs. Seven statistically distinct plant communities were identified based on the cover of 22 plant species in 68 permanent transects. We recorded 253 instances of community transitions, associated with changes in species composition between successive samplings. Expectedly, transitions were more frequent among proximate communities with similar species pools than among distant communities. But unexpectedly, communities and transitions were not strongly constrained by soil type and topography. Only 18 transitions featured disproportionately large compositional turnover (species dissimilarity ranged between 0.54 and 0.68), and these were closely associated with communities that were dominated by the common shrub (burroweed, Haplopappus tenuisecta); indicating that only some, and not all, communities may be prone to large compositional change. Temporal dynamics in individual transects illustrated four general trajectories: stability, nondirectional drift, reversibility, and directional shifts that were not reversed even after 2-3 decades. The frequency of transitions and the accompanying species dissimilarity were both positively correlated with fluctuation in precipitation, indicating that climatic drivers require more attention in STMs. Many features of the expert models, including the number of communities and participant species, were consistent with empirical trends, but expert models underrepresented recent increases in cacti while overemphasizing the introduced Lehmann's lovegrass (Eragrostis lehmanniana). Quantification of communities and transitions within long-term vegetation records presents several quantitative metrics such as transition frequency, magnitude of accompanying compositional change, presence of unidirectional trajectories, and lack of reversibility within various timescales, which can clarify resilience concepts and inform the construction and interpretation of STMs.     

Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals (HMs) as well as their genotoxicity in soil after long-term wastewater irrigation

A study was carried out on the residue level of major concern pollutants (PAHs, PCBs and HMs) and the assessment of their genotoxicity in soils obtained from Shenyang, northeast of China which had been subjected to wastewater irrigation for more than 40 years. Topsoils (0-20cm) in paddy fields were sampled along the upper, middle and lower reaches of the wastewater disposal channel. Sixteen USEPA PAHs were determined by High Performance Liquid Chromatography (HPLC) with fluorescence detector, eight PCBs were detected by Gas Chromatography (GC) with electron capture detector, and six heavy metals (Cd, Cu, Pb, Zn, Ni, and Cr) were measured by Atomic Absorption Spectrophotometer (AAS). The genotoxicity effect of soils was examined by Vicia faba micronucleus (MN) test. Archived soils that had undergone a similar history of wastewater irrigation provided by Technical University of Berlin, Germany were subjected to analysis of the above pollutants and Vicia faba/MN test for comparison. Results indicated elevated residues of the studied pollutants (PAHs, especially benzo (a) pyrene, the eight PCB congeners and heavy metals) in both tested and archived soils. The MN frequencies were 2.2-48.4 times higher compared with the control. However, there was no correlation between the MN frequencies and the concentration of pollutants detected. This investigation suggested a potential ecological risk even with a lower level of residual pollutants in soil matrix after long-term wastewater irrigation.     

Travel time and trajectory moments of conservative solutes in two-dimensional convergent flows

We address advective transport of a solute traveling toward a single pumping well in a two-dimensional randomly heterogeneous aquifer. The two random variables of interest are the trajectory followed by an individual particle from the injection point to the well location and the particle travel time under steady-state conditions. Our main objective is to derive the predictors of trajectory and travel time and the associated uncertainty, in terms of their first two statistical moments (mean and variance). We consider a solute that undergoes mass transfer between a mobile and an immobile zone. Based on Lawrence et al. [Lawrence, A.E., Sánchez-Vila, X., Rubin, Y., 2002. Conditional moments of the breakthrough curves of kinetically sorbing solute in heterogeneous porous media using multirate mass transfer models for sorption and desorption. Water Resour. Res. 38 (11), 1248, doi:10.1029/2001WR001006.], travel time moments can be written in terms of those of a conservative solute times a deterministic quantity. Moreover, the moments of solute particles trajectory do not depend on mass transfer processes. The resulting mean and variance of travel time and trajectory for a conservative species can be written as functions of the first, second moments and cross-moments of trajectory and velocity components. The equations are developed from a consistent second order expansion in sigmaY (standard deviation of the natural logarithm of hydraulic conductivity). Our solution can be completely integrated with the moment equations of groundwater flow of Guadagnini and Neuman [Guadagnini, A., Neuman, S.P., 1999a. Nonlocal and localized analyses of conditional mean steady state flow in bounded, randomly non uniform domains 1. Theory and computational approach. Water Resour. Res. 35(10), 2999-3018.,Guadagnini, A., Neuman, S.P., 1999b. Nonlocal and localized analyses of conditional mean steady state flow in bounded, randomly non uniform domains 2. Computational examples. Water Resour. Res. 35(10), 3019-3039.], it is free of distributional assumptions regarding the log conductivity field, and formally includes conditioning. We present analytical expressions for the unconditional case by making use of the results of Riva et al. [Riva, M., Guadagnini, A., Neuman, S.P., Franzetti, S., 2001. Radial flow in a bounded randomly heterogeneous aquifer. Transport in Porous Media 45, 139-193.]. The quality of the solution is supported by numerical Monte Carlo simulations. Potential uses of this work include the determination of aquifer reclamation time by means of a single pumping well, and the demarcation of the region potentially affected by the presence of a contaminant in the proximity of a well, whenever the aquifer is very thin and Dupuit-Forchheimer assumption holds.     

Phenanthrene degradation in Arthrobacter sp. P1-1: initial 1,2-, 3,4- and 9,10-dioxygenation, and meta- and ortho-cleavages of naphthalene-1,2-diol after its formation from naphthalene-1,2-dicarboxylic acid and hydroxyl naphthoic acids

Arthrobacter sp. P1-1, isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Hilo, HI, USA, can decompose phenanthrene (40 mg l⁻¹) completely within 7 days. A detailed phenanthrene metabolism map was constructed based on metabolite analysis and replacement cultures. Initial dioxygenation occurs on 1,2-, 3,4-, and 9,10-C of phenanthrene, dominantly on 3,4-C positions. Rapid accumulation of 5,6- and 7,8-benzocoumarin suggests that phenanthrene-1,2- and -3,4-diols mainly undergo meta-cleavage. However, a trace amount of o-carboxyvinylnaphthoates and diphenic acid indicates a limited extent of ortho-cleavage of the diols. Naphthalene-1,2-diol, as a common and converged metabolite, was formed from 1-[(E)-2-carboxyvinyl]-2-naphthoic acid, naphthalene-1,2-dicarboxylic acid, and 1-hydroxy-2-naphthoic acid in separate culture tests. Naphthalene-1,2-diol is then degraded in a dominant phthalic acid pathway and a minor salicylic acid pathway. Several metabolites of phthalic acid were found, while no salicylic acid metabolites were detected. The strain P1-1 likely has a very diverse set of PAH-degrading enzymes or the enzymes having relaxed substrate-specificity.     

Direct numerical simulations of boundary condition effects on the propagation of density current in wall-bounded and open channels

The propagation of density current under different boundary conditions is investigated using high resolution direct numerical simulations (DNS). A revised Kleiser and Schumann influence-matrix method is used to treat the general Robin type velocity boundary conditions and the related “tau” error corrections in the numerical simulations. Comparison of the simulation results reveals that the boundary conditions change the turbulent flow field and therefore the propagation of the front. This paper mainly focuses on the effects of boundary conditions and initial depth of the dense fluid. The differences in energy dissipation and overall front development in wall-bounded and open channels are examined. Through DNS simulations, it is evident that with the decrease of initial release depth ratio ( $D/H$ ), the effect of the top boundary becomes less important. In wall-bounded channels, there are three distinctive layers in the vertical distribution of energy dissipation corresponding to the contributions from bottom wall, interface, and top wall, respectively. In open channels, there are only two layers with the top one missing due to the shear free nature of the boundary. It is found that the energy dissipation distribution in the bottom layer is similar for cases with the same $D/H$ ratio regardless the top boundary condition. The simulation results also reveal that for low Reynolds number cases, the energy change due to concentration diffusion cannot be neglected in the energy budget. To reflect the real dynamics of density current, the dimensionless Froude number and Reynolds number should be defined using the release depth $D$ as the length scale.     

Molecular characterization of symbiotic algae (Symbiodinium spp.) in soritid foraminifera (Sorites orbiculus) and a scleractinian coral (Orbicella annularis) from St John,US Virgin Islands

The exchange of Symbiodinium symbionts among scleractinian and soritid hosts could facilitate acclimatization to changing conditions by establishing novel symbiotic unions better tuned to prevailing conditions. In this study, we compare the communities of Symbiodinium spp. in neighboring populations of Orbicella annularis and Sorites orbiculus from St. John, US Virgin Islands, using operational taxonomic unit (OTU) clustering of cloned internal transcribed spacer 2 (ITS-2) rDNA sequences. We tested for partitioning of Symbiodinium OTUs by host and depth within and between two sites to explore the potential for symbiont exchange between hosts and light-dependent microhabitat specialization. An apparent lack of overlap in Symbiodinium communities (13 OTUs representing 7 clades) hosted by O. annularis and S. orbiculus suggests that exchange among these hosts does not occur. A low number of novel clade G ITS-2 sequences were found in one O. annularis and one S. orbiculus. A phylogenetic analysis of these sequences revealed them to be sub-clade G2 Symbiodinium, which are most commonly hosted by excavating clionid sponges. A permutational MANOVA revealed within host differences in the partitioning of Symbiodinium OTUs by site but not depth. This finding highlights the potential roles of either dissimilar environmental conditions between sites, or at least partial separation between populations, in determining the types of Symbiodinium contained in different hosts on a spatial scale of a few kilometers.     

Effects of Arbuscular mycorrhizal fungi isolated from white clovers (Trifolium repens L) on soil bacteria and fungi

White clover potted experiments were performed to investigate the effects of seven indigenous arbuscular mycorrhizal fungi (AMF) communities isolated from different test plots subjected to long-term fertilisation on soil enzyme activities, number of soil bacteria and fungi. The results showed that the inoculation of arbuscular mycorrhizal fungi communities increased the mycorrhizal infection rate of the plants and promoted the growth of plants. The Mnp treatment was most effective. The shoot biomass, root biomass, potassium and nitrogen uptake of the white clover in Mnp treatment group were increased by 61.54%, 84.00%, 62.50% and 46.71% respectively, compared with those in non-inoculation treatment. The inoculation of AMF communities had little effect on the number of bacteria in the soil, but significantly increased the number of soil fungi. Mnk treatment group had the highest number of fungi in the soil, which was 9.91 times that of the non-inoculation treatment group. The catalase and dehydrogenase activities were both significantly improved in Mnp treatment by 28.12% and 205.38% respectively, compared with those of the control treatment (-M). The urease, invertase and cellulase activities reached the highest levels in the Mck treatment; they were increased by 142.79%, 41.17% and 77.62% respectively, compared with those of the control treatment. Pearson correlation analysis showed that the soil enzyme activity was not correlated with the mycorrhizal infection rate, but correlated with the spore number of the AMF community. The impact of AMF community on soil quality is important for us to understand the function of the ecosystems. Relevant study provides important guidance for maintaining the balance of the soil-plant system and the development of sustainable agriculture.     

Effect of red mud addition on the fractionation and bio-accessibility of Pb,Zn and As in combined contaminated soil

Using soil incubation experiments, the effect of red mud addition on the fractionation and bioaccessibility of Pb, Zn and As in combined contaminated soil was studied. The results showed that red mud addition could significantly decrease the concentration of HOAc-extractable Pb and Zn in soil. Compared with the control, 5% red mud addition could significantly reduce the concentrations of HOAc-extractable Pb and Zn in soil after 1, 2 and 3 months of incubation [62.5, 65.3 and 73.5% decrease (Pb), 56.7, 65.8 and 67.4% decrease (Zn)]. Whereas adding red mud could remarkably increase the concentrations of specific absorbed As and residual As in soil. The result of a simple bioavailability extraction test (SBET) indicated that all treatments with red mud addition markedly reduced the concentration of bioaccessible Zn but increased the concentration of bioaccessible As in soil, while having little effect on the concentration of bioaccessible Pb in soil. After 3 months incubation, all treatments including 1, 2 and 5% red mud addition reduced the concentration of bioaccessible Zn by 53.1–56.7% compared with the control, but increased the concentration of bioaccessible As by 1.81–6.25 times. The results suggested that red mud is an additive with potential for the remediation soil contaminated soil by combinations of heavy metals, although it should be added based on the different heavy metals in the soil. Combined use of red mud and hyperaccumulators to remediate heavy metal contaminated soil needs further study.     

A dynamic study of the sorption and the transport processes of cadmium in calcareous sandy soils

The interactions of Cd2+ with silica and calcite were observed through laboratory dynamic experiments. Cd2+ sorption processes were characterised as a function of reaction kinetics in aqueous solutions saturated or not with respect to calcite. Chromatographic column experiments show that Cd2+ sorption on silica can be considered as a reversible equilibrate reaction which depends on water composition and pH. For a porous medium composed by a mixture of silica and calcite, the Cd2+ migration behaviours are predominantly controlled by calcite. The amount and the reversibility of sorbed Cd on calcite are strongly affected by kinetic limitations. Stirred flow through reactor experiments provide an original method to separate and characterise the 'fast' and 'slow' Cd sorption on calcite processes. The 'fast' Cd reversible adsorption isotherms and the rate of Cd subsequent uptake by 'slow' reactions are determined. In addition, the inhibition of calcite dissolution is observed as a function of sorbed Cd in order to provide a complete mechanistic database for coupled transport-geochemistry models.