Measuring Responses of Dicyandiamide-, 3,4-Dimethylpyrazole Phosphate-, and Allylthiourea-Induced Nitrification Inhibition to Soil Abiotic and Biotic Factors.

Nitrification inhibitors (NIs) such as dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and allylthiourea (AT) are commonly used to suppress ammonia oxidization at different time scales varying from a few hours to several months. Although the responses of NIs to edaphic and temperature conditions have been studied, the influence of the aforementioned factors on their inhibitory effect remains unknown. In this study, laboratory-scale experiments were conducted to assess the short-term (24 h) influence of eight abiotic and biotic factors on the inhibitory effects of DCD, DMPP, and AT across six cropped and non-cropped soils at two temperature conditions with three covariates of soil texture. Simultaneously, the dominant contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to potential ammonia oxidization (PAO) were distinguished using the specific inhibitor 2 phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). Our results revealed that AT demonstrated a considerably greater inhibitory effect (up to 94.9% for an application rate of 75 mg of NI/kg of dry soil) than DCD and DMPP. The inhibitory effect of AT was considerably affected by the relative proportions of silt, sand, and clay in the soil and total PAO. In contrast to previous studies, the inhibitory effects of all three NIs remained largely unaffected by the landcover type and temperature conditions for the incubation period of 24 h. Furthermore, the efficacy of all three tested NIs was not affected by the differential contributions of AOA and AOB to PAO. Collectively, our results suggested a limited influence of temperature on the inhibitory effects of all three NIs but a moderate dependence of AT on the soil texture and PAO. Our findings can enhance the estimation of the inhibitory effect in soil, and pure cultures targeting the AOA and AOB supported ammonia oxidization and, hence, nitrogen dynamics under NI applications.

A spatial prioritization method for identifying potential eco-risk distributions of heavy metals in soil and birds.

Geochemical approaches are popular for evaluations based on heavy metal concentrations in sediments or soils for eco-risk assessment. This study proposes a systematic geochemical approach (SymGeo) to explore six heavy metals in topsoils and bird tissues and organs of the target birds. We assume that the proposed approach based on field-collected heavy metals in topsoils and feathers can predict the areas with the potential risk of the heavy metals in birds. Finite mixture distribution modeling (FMDM) was used to identify background values of the heavy metal concentrations in topsoil. A spatial enrichment factor (EF), potential contamination index (PCI), contamination degree (Cod), and potential ecological risk index (PRI) based on FMDM results for topsoil, and a potential risk index (PRIbird) of heavy metals in the birds, were utilized for systematic prioritization of high eco-risk areas. Using multiple EF, PRI, and Cod results and multiple PRI-based maps of the heavy metals in feathers, we systematically prioritized risk areas where there is a high potential for heavy metal contamination in the birds. Our results indicate that heavy metal concentrations in the feather, liver, and kidney are not spatially cross-autocorrelated but are statistically significantly correlated with some heavy metals in topsoil due to external and internal depositions. Further, multiple EF, Cod, and RI distributions for topsoil, along with the PRI of the feather, showed that adequate coverages for potential risk for birds were greater than 71.05% in the top 30% and 84.69% in the top 20% potential eco-risk priority area of heavy metals in bird liver and kidney. Hence, our proposed approach suggests that assessments of heavy metals in bird feathers and topsoils without bird organs can be utilized to identify spatially high-risk areas. The proposed approach could be improved by incorporating water and sediment samples to enhance the crowdsourcing and the species-specific data.

Topsoil microbial community structure responds to land cover type and environmental zone in the Western Pacific region.

Soil encompasses diverse microbial communities that are essential for fundamental ecosystem functions such as biogeochemical cycling. To better understand underlying biogeochemical processes, it is necessary to know the structure of soil archaeal and bacterial communities and their responses to edaphic and climate variables within and across various land cover types (LCTs) and environmental zones (ENZs). Here we sampled eighty-nine sites across five ENZs and four LCTs within the Western Pacific region. Through leveraging the second-generation sequencing of topsoil samples, we showed that α-diversity (taxonomic diversity) of archaea strongly varied within LCTs, whereas bacterial α-diversity was significantly controlled by both LCT and ENZ. Soil archaea and bacteria showed global niche differentiation associated with contrasting diversity responses to latitude and differential responses of microbial diversity patterns to edaphic and climate variables within LCTs and ENZs. In contrast to α-diversity, microbial ß-diversity (the compositional dissimilarity between sites) was majorly governed by ENZs, particularly for archaea (P < 0.01). Our results highlight the importance of LCTs and ENZs for understanding soil microbial contributions to nutrient dynamics and ecosystem resilience under land-use intensification and climate change.

Climate and land cover shape the fungal community structure in topsoil.

Globally, soils are subject to radical changes in their biogeochemistry as rampant deforestation and other forms of land use and climate change continue to transform planet Earth. To better understand soil ecosystem functioning, it is necessary to understand the responses of soil microbial diversity and community structure to changing climate, land cover, and associated environmental variables. With next-generation sequencing, we investigated changes in topsoil fungi community structure among different land cover types (from Forest to Cropland) and climate zones (from Hot to Cold zones) in the Western Pacific Region. We demonstrated that climate zones substantially (P = 0.001) altered the soil fungal beta-diversity (change in community composition), but not alpha-diversity (taxonomical diversity). In particular, precipitation, temperature, and also latitude were the best predictors of beta-diversity. Individual fungal classes displayed divergent but strong responses to climate variables and latitude, suggesting niche differentiation at lower taxonomic levels. We also demonstrated that fungal taxonomic diversity differentially responded to latitude across land covers: fungal diversity increased towards lower latitudes in the Forest and Cropland (R2 = 0.19) but increased towards both lower and higher latitudes in Fallow land (R2 = 0.45). Further, alpha-diversity was significantly influenced by soil pH in Forest (P = 0.02), and by diurnal temperature range in Fallow land and mean annual precipitation in Cropland. Collectively, various land cover types had differential influence on the latitude diversity gradient, while climate, and to some extent, edaphic variables, were crucial in shaping soil fungal community structure. Our results can also serve as a baseline for estimating global change impacts on fungal community structure in the Western Pacific Region.

Real-Time Identification of Irrigation Water Pollution Sources and Pathways with a Wireless Sensor Network and Blockchain Framework.

Real-time identification of irrigation water pollution sources and pathways (PSP) is crucial to ensure both environmental and food safety. This study uses an integrated framework based on the Internet of Things (IoT) and the blockchain technology that incorporates a directed acyclic graph (DAG)-configured wireless sensor network (WSN), and GIS tools for real-time water pollution source tracing. Water quality sensors were installed at monitoring stations in irrigation channel systems within the study area. Irrigation water quality data were delivered to databases via the WSN and IoT technologies. Blockchain and GIS tools were used to trace pollution at mapped irrigation units and to spatially identify upstream polluted units at irrigation intakes. A Water Quality Analysis Simulation Program (WASP) model was then used to simulate water quality by using backward propagation and identify potential pollution sources. We applied a "backward pollution source tracing" (BPST) process to successfully and rapidly identify electrical conductivity (EC) and copper (Cu2+) polluted sources and pathways in upstream irrigation water. With the BPST process, the WASP model effectively simulated EC and Cu2+ concentration data to identify likely EC and Cu2+ pollution sources. The study framework is the first application of blockchain technology for effective real-time water quality monitoring and rapid multiple PSPs identification. The pollution event data associated with the PSP are immutable.

Assessing the association and predictability of heavy metals in avian organs, feathers, and bones using crowdsourced samples.

Birds are bioindicators for research on the relationship between environmental heavy metal concentration levels and accumulation levels in bird tissues. We use roadkill samples, collected by citizen science participants, to investigate the accumulation levels and associations of seven heavy metals in internal organs (heart, liver, and kidney), feathers (primary and breast), and bones (sternum and femur) of two focal species, Amaurornis phoenicurus and Gallinula chloropus. We found that heavy metal accumulation varied by target tissue, and that variables are associated with bird species and heavy metal type. Although Zn and Cu were highest by concentration among both species, Cu was mostly accumulated in internal organs, As in feathers, and Pb in bones. Concentrations of As, Ni, and Pb in feathers of both focal species were lower than those reported in literature, whereas Cd and Cr were above toxic levels. The results also showed that spatial correlation for heavy metal concentration among bird tissues were weaker than non-spatial correlation, suggesting low spatial autocorrelations and variability. In addition, multiple regression analysis revealed significant correlation for Cr, As, and Pb estimations in A. phoenicurus heart, sternum, and kidney, respectively; and potentially Cr in G. chloropus femur by using feathers. These results support the feasibility of using feathers as indicators of As, Cr, and Pb heavy metal contamination to enhance our understanding of heavy metal accumulation in birds, although caution is required for feather-based estimations of Cd, Cu, and Ni concentration.

Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature.

Ammonia oxidizing archaea (AOA) and bacteria (AOB) are thought to contribute differently to soil nitrification, yet the extent to which their relative abundances influence the temperature response of nitrification is poorly understood. Here, we investigated the impact of different AOA to AOB ratios on soil nitrification potential (NP) across a temperature gradient from 4 °C to 40 °C in twenty different organic and inorganic fertilized soils. The temperature responses of different relative abundance of ammonia oxidizers for nitrification were modeled using square rate theory (SQRT) and macromolecular rate theory (MMRT) models. We found that the proportional nitrification rates at different temperatures varied among AOA to AOB ratios. Predicted by both models, an optimum temperature (Topt) for nitrification in AOA dominated soils was significantly higher than for soils where AOA and AOB abundances are within the same order of magnitude. Moreover, the change in heat capacity ( Δ C P ‡ ) associated with the temperature dependence of nitrification was positively correlated with Topt and significantly varied among the AOA to AOB ratios. The temperature ranges for NP decreased with increasing AOA abundance for both organic and inorganic fertilized soils. These results challenge the widely accepted approach of comparing NP rates in different soils at a fixed temperature. We conclude that a shift in AOA to AOB ratio in soils exhibits distinguished temperature-dependent characteristics that have an important impact on nitrification responses across the temperature gradient. The proposed approach benefits the accurate discernment of the true contribution of fertilized soils to nitrification for improvement of nitrogen management.

Assessing thermodynamic parameter sensitivity for simulating temperature responses of soil nitrification.

Soil nitrification responses to temperature have major implications for the global nitrogen cycle. Temperature sensitivity of soil nitrification has been modeled using several mathematical models, yet the extent to which model-generated thermodynamic parameters are accurate and sensitive in describing temperature sensitivity is unclear. In this study, we performed global sensitivity analysis to identify the key thermodynamic parameters that are most influential when simulating the temperature response of the soil nitrification potential (NP) across two different temperature gradients (4-40 °C and 20-45 °C) which are imposed upon sixteen different soils with square root growth (SQRT) and macromolecular rate theory (MMRT) models. We found that two thermodynamic parameters stand out as moderately to highly sensitive, and are uniquely identifiable in each model, regardless of the temperature range. The minimum and maximum measured temperatures seem to have no impact on the list of sensitive parameters but do influence the parameter ranges, especially for the SQRT model. However, parameters that control the minimum temperature and curvature of the NP response curve (Tmin and ΔC‡P) were found to have little to no sensitivity to SQRT and MMRT model outputs, respectively. We show that the parameter sensitivity and range of measured temperatures influence the complementary model's ability to describe the temperature sensitivity of soil nitrification. Our proposed framework enhances the accurate interpretation of existing thermodynamic parameters that explain the temperature sensitivity of soil biochemical processes, and provides methodological recommendations for future temperature sensitivity studies.

Adherens junction-associated pores mediate the intercellular transport of endosomes and cytoplasmic proteins.

Intercellular endosomes (IEs) are endocytosed vesicles shuttled through the adherens junctions (AJs) between two neighboring epidermal cells during Drosophila dorsal closure. The cell-to-cell transport of IEs requires DE-cadherin (DE-cad), microtubules (MTs) and kinesin. However, the mechanisms by which IEs can be transported through the AJs are unknown. Here, we demonstrate the presence of AJ-associated pores with MTs traversing through the pores. Live imaging allows direct visualization of IEs being transported through the AJ-associated pores. By using an optogenetic dimerization system, we observe that the dimerized IE-kinesin complexes move across AJs into the neighboring cell. The AJ-associated pores also allow intercellular movement of soluble proteins. Importantly, most epidermal cells form dorsoventral-oriented two-cell syncytia. Together, we present a model in which an AJ-associated pore mediates the intercellular transport of IEs and proteins between two cells in direct contact.

Smurf Downregulates Echinoid in the Amnioserosa To Regulate Drosophila Dorsal Closure.

Drosophila dorsal closure is a morphogenetic movement that involves flanking epidermal cells, assembling actomyosin cables, and migrating dorsally over the underlying amnioserosa to seal at the dorsal midline. Echinoid (Ed)-a cell adhesion molecule of adherens junctions (AJs)-participates in several developmental processes. The disappearance of Ed from the amnioserosa is required to define the epidermal leading edge for actomyosin cable assembly and coordinated cell migration. However, the mechanism by which Ed is cleared from amnioserosa is unknown. Here, we show that Ed is cleared in amnioserosa by both transcriptional and post-translational mechanisms. First, Ed mRNA transcription was repressed in amnioserosa prior to the onset of dorsal closure. Second, the ubiquitin ligase Smurf downregulated pretranslated Ed by binding to the PPXY motif of Ed. During dorsal closure, Smurf colocalized with Ed at AJs, and Smurf overexpression prematurely degraded Ed in the amnioserosa. Conversely, Ed persisted in the amnioserosa of Smurf mutant embryos, which, in turn, affected actomyosin cable formation. Together, our results demonstrate that transcriptional repression of Ed followed by Smurf-mediated downregulation of pretranslated Ed in amnioserosa regulates the establishment of a taut leading edge during dorsal closure.

Novel transport function of adherens junction revealed by live imaging in Drosophila.

Adherens junctions are known for their role in mediating cell-cell adhesion. DE-cadherin and Echinoid are the principle adhesion molecules of adherens junctions in Drosophila epithelia. Here, using live imaging to trace the movement of endocytosed Echinoid vesicles in the epithelial cells of Drosophila embryos, we demonstrate that Echinoid vesicles co-localize and move with Rab5-or Rab11-positive endosomes. Surprisingly, these Echinoid-containing endosomes undergo directional cell-to-cell movement, through adherens junctions. Consistent with this, cell-to-cell movement of Echinoid vesicles requires the presence of DE-cadherin at adherens junctions. Live imaging further revealed that Echinoid vesicles move along adherens junction-associated microtubules into adjacent cells, a process requiring a kinesin motor. Importantly, DE-cadherin- and EGFR-containing vesicles also exhibit intercellular movement. Together, our results unveil a transport function of adherens junctions. Furthermore, this adherens junctions-based intercellular transport provides a platform for the exchange of junctional proteins and signaling receptors between neighboring cells.

Capulet and Slingshot share overlapping functions during Drosophila eye morphogenesis.

BACKGROUND: CAP/Capulet (Capt), Slingshot (Ssh) and Cofilin/Twinstar (Tsr) are actin-binding proteins that restrict actin polymerization. Previously, it was shown that low resolution analyses of loss-of-function mutations in capt, ssh and tsr all show ectopic F-actin accumulation in various Drosophila tissues. In contrast, RNAi depletion of capt, tsr and ssh in Drosophila S2 cells all affect actin-based lamella formation differently. Whether loss of these three related genes might cause the same effect in the same tissue remains unclear. METHODS: Loss-of-function mutant clones were generated using the MARCM or EGUF system whereas overexpression clones were generated using the Flip-out system. Immunostaining were then performed in eye imaginal discs with clones. FRAP was performed in cultured eye discs. RESULTS: Here, we compared their loss-of-function phenotype at single-cell resolution, using a sheet of epithelial cells in the Drosophila eye imaginal disc as a model system. Surprisingly, we found that capt and ssh, but not tsr, mutant cells within and posterior to the morphogenetic furrow (MF) shared similar phenotypes. The capt/ssh mutant cells possessed: (1) hexagonal cell packing with discontinuous adherens junctions; and (2) largely complementary accumulation of excessive phosphorylated myosin light chain (p-MLC) and F-actin rings at the apical cortex. We further showed that the capt/ssh mutant phenotypes depended on the inactivation of protein kinase A (PKA) and activation of Rho. CONCLUSIONS: Although Capt, Ssh and Tsr were reported to negatively regulate actin polymerization, we found that Capt and Ssh, but not Tsr, share overlapping functions during eye morphogenesis.

Differential adhesion and actomyosin cable collaborate to drive Echinoid-mediated cell sorting.

Cell sorting involves the segregation of two cell populations into `immiscible' adjacent tissues with smooth borders. Echinoid (Ed), a nectin ortholog, is an adherens junction protein in Drosophila, and cells mutant for ed sort out from the surrounding wild-type cells. However, it remains unknown which factors trigger cell sorting. Here, we dissect the sequence of this process and find that cell sorting occurs when differential expression of Ed triggers the assembly of actomyosin cable. Conversely, Ed-mediated cell sorting can be rescued by recruitment of Ed, via homophilic or heterophilic interactions, to the wild-type cell side of the clonal interface, even when differential Ed expression persists. We found, unexpectedly, that when actomyosin cable was largely absent, differential adhesion was sufficient to cause limited cell segregation but with a jagged tissue border (imperfect sorting). We propose that Ed-mediated cell sorting is driven both by differential Ed adhesion that induces cell segregation with a jagged border and by actomyosin cable assembly at the interface that smoothens this border.

Echinoid regulates Flamingo endocytosis to control ommatidial rotation in the Drosophila eye.

Planar cell polarity (PCP) refers to a second polarity axis orthogonal to the apicobasal axis in the plane of the epithelium. The molecular link between apicobasal polarity and PCP is largely unknown. During Drosophila eye development, differentiated photoreceptors form clusters that rotate independently of the surrounding interommatidial cells (ICs). Here, we demonstrate that both Echinoid (Ed), an adherens junction-associated cell adhesion molecule, and Flamingo (Fmi), a PCP determinant, are endocytosed via a clathrin-mediated pathway in ICs. Interestingly, we found that Ed binds the AP-2 adaptor and is required for the internalization of Fmi into ICs. Loss of ed led to increased amounts of Fmi on the cell membrane of non-rotating ICs and also to the misrotation of photoreceptor clusters. Importantly, overexpression of fmi in ICs alone was sufficient to cause misrotation of the adjacent photoreceptor clusters. Together, we propose that Ed, when internalized by AP-2, undergoes co-endocytosis with, and thereby decreases, Fmi levels on non-rotating ICs to permit correct rotation of ommatidial clusters. Thus, co-endocytosis of Ed and Fmi provides a link between apicobasal polarity and PCP.

Echinoid is a component of adherens junctions that cooperates with DE-Cadherin to mediate cell adhesion.

Echinoid is an immunoglobulin domain-containing transmembrane protein that modulates cell-cell signaling by Notch and the EGF receptors. We show that, in the Drosophila wing disc epithelium, Echinoid is a component of adherens junctions that cooperates with DE-Cadherin in cell adhesion. Echinoid and beta-catenin (a DE-Cadherin interacting protein) each possess a C-terminal PDZ domain binding motif that binds to Bazooka/PAR-3; these motifs redundantly position Bazooka to adherens junctions. Echinoid also links to actin filaments by binding to Canoe/AF-6/afadin. Moreover, interfaces between Echinoid- and Echinoid+ cells, like those between DE-Cadherin- and DE-Cadherin+ cells, are deficient in adherens junctions and form actin cables. These characteristics probably facilitate the strong sorting behavior of cells that lack either of these cell-adhesion molecules. Finally, cells lacking either Echinoid or DE-Cadherin accumulate a high density of the reciprocal protein, further suggesting that Echinoid and DE-Cadherin play similar and complementary roles in cell adhesion.