Characterization and Modeling of Thermostable GH50 Agarases from Microbulbifer elongatus PORT2

Viewing the considerable potential of marine agar as a source for the sustainable production of energy as well as nature-derived pharmaceutics, this work investigated the catalytic activity of three novel GH50 agarases from the mesophilic marine bacterium Microbulbifer elongatus PORT2 isolated from Indonesian coastal seawaters. The GH50 agarases AgaA50, AgaB50, and AgaC50 were identified through genome analysis; the corresponding genes were cloned and expressed in Escherichia coli BL21 (DE3). All recombinant agarases hydrolyzed β-p-nitrophenyl galactopyranoside, indicating β-glycosidase characteristics. AgaA50 and AgaB50 were able to cleave diverse natural agar species derived from Indonesian agarophytes, indicating a promising tolerance of these enzymes for substrate modifications. All three GH50 agarases degraded agarose, albeit with remarkable diversity in their catalytic activity and mode of action. AgaA50 and AgaC50 exerted exolytic activity releasing differently sized neoagarobioses, while AgaB50 showed additional endolytic activity in dependence on the substrate size. Surprisingly, AgaA50 and AgaB50 revealed considerable thermostability, retaining over 75% activity after 1-h incubation at 50 °C. Considering the thermal properties of agar, this makes these enzymes promising candidates for industrial processing.

Occupancy and detection of Wavyrayed Lampmussel Lampsilis fasciola in Ontario, Canada

Freshwater mussels (Bivalvia: Unionidae) are the most imperilled taxon in Canada. To facilitate species recovery efforts, an understanding of species distribution and habitat that supports species persistence is needed. Detecting mussels presents unique challenges, however, requiring considerable effort due to their complex life-histories and widespread declines. Here, observations of the imperilled Wavyrayed Lampmussel (Lampsilis fasciola Rafinesque 1820) from the Grand and Thames rivers, Ontario, Canada were used to quantify species detection and occupancy probabilities, and the relationship between occupancy probability and substrate size. The best model for the data included a river-specific covariate for detection and an intercept model for occupancy. Detection probability of Wavyrayed Lampmussel was higher in the Grand River than the Thames River. Limited variation in substrate size measurements restricted occupancy modeling, but field measurements qualitatively aligned with previous habitat descriptions. Overall, knowledge of species detection and occupancy probabilities for Wavyrayed Lampmussel will not only enhance the understanding of species distribution and habitat associations, but also ensure that the response of the species to threats and recovery actions are captured.

Effect of substrate particle size on burrowing of the juvenile freshwater pearl mussel Margaritifera margaritifera

Juveniles of the endangered freshwater pearl mussel (FPM, Margaritifera margaritifera) live burrowed in stream substrate for the first years of their life. Fine sediments block water exchange within substrate and may cause juvenile mortality and recruitment failure. To better understand the connection between success of juvenile FPM and substrate particle size, it would be important to understand behavioural responses of FPM to varying substrate sizes at this critical life stage. We placed newly detached FPM juveniles in a 7-mm layer of sieved sand sorted into five sizes (< 120, 120–200, 200–250, 250–500 and 500–650 µm) each with 10 replicate dishes, 10 juveniles per dish, with burrowing status monitored for 96 h. Mean dish-specific proportion burrowed (PB) was significantly affected by substrate size, increasing from 52% in the finest sand to 98% in the coarsest sand. Furthermore, the significant substrate × time interaction was observed due to dropped PB (30-34%) in finest sand at 2–4 h time points. Thus, results suggest a clear behavioural response by juvenile FPM to substrate size, with fine sediments triggering surfacing behaviour. Surfacing may indicate stress, can increase predation risk, and expose to drift and/or enable drift of juveniles.

Investigation of Action Pattern of a Novel Chondroitin Sulfate/Dermatan Sulfate 4-O-Endosulfatase

Recently, a novel CS/DS 4-O-endosulfatase was identified from a marine bacterium and its catalytic mechanism was investigated further (Wang, W., et.al (2015) J. Biol. Chem. 290, 7823-7832; Wang, S., et.al (2019) Front. Microbiol. 10:1309). In the study herein, we provide new insight about the structural characteristics of substrate which determine the activity of this enzyme. The substrate specificities of the 4-O-endosulfatase were probed by using libraries of structure-defined CS/DS oligosacccharides issued from synthetic and enzymatic sources. We found that this 4-O-endosulfatase effectively remove the 4-O-sulfate of disaccharide sequences GlcUAβ1-3GalNAc(4S) or GlcUAβ1-3GalNAc(4S,6S) in all tested hexasaccharides. The sulfated GalNac residue is resistant to the enzyme when adjacent uronic residues are sulfated as shown by the lack of enzymatic desulfation of GlcUAβ1-3GalNAc(4S) connected to a disaccharide GlcUA(2S)β1-3GalNAc(6S) in an octasaccharide. The 3-O-sulfation of GlcUA was also shown to hinder the action of this enzyme. The 4-O-endosulfatase exhibited an oriented action from the reducing to the non-reducing whatever the saturation or not of the non-reducing end. Finally, the activity of the 4-O-endosulfatase decreases with the increase of substrate size. With the deeper understanding of this novel 4-O-endosulfatase, such chondroitin sulfate (CS)/dermatan sulfate (DS) sulfatase is a useful tool for exploring the structure-function relationship of CS/DS.

Spatial Mapping of Riverbed Grain-Size Distribution Using Machine Learning

Recent alluvial sediments in riverbeds play a significant role in controlling hydrologic exchange flows (HEFs) in river systems. The alluvial layer is usually associated with strong heterogeneity in physical properties (e.g., permeability and hydraulic conductivity), which affects local HEFs and therefore biogeochemical processes. The spatial distribution of these physical properties needs to be determined to inform the numerical models used to reveal the realistic hydro-biogeochemical behaviors. Such information can be obtained based on the intrinsic link between sediment grain-size distribution and hydraulic properties where sediment texture information is available. However, grain-size measurements are usually spatially sparse and do not have adequate coverage and resolution, particularly for a relatively large domain such as the Hanford Reach of the Columbia River. In this paper, we adopted machine learning (ML) approaches for categorizing and mapping the spatial distributions of riverbed substrate grain size and filling in missing areas of substrate data using the ML models along the reach. Such ML models for substrate size mapping were trained at 13,372 locations using measured substrate sizes along with observed and simulated attributes, including bathymetric attributes (e.g., elevation, slope, and aspect ratio) from LIDAR and bathymetric surveys, and hydrodynamic properties (e.g., water depth, velocity, shear stress, and their statistical moments). An ensemble bagging-based ML technique, Random Forest, was adopted to identify the most influential factors as predictors to develop the predictive models with over-fitting issues addressed. The models were evaluated with respect to each individual substrate size class and the lumped group, and then used to generate the final substrate size maps covering all the grid cells in the numerical modeling domain.

Citizen science via social media revealed conditions of symbiosis between a marine gastropod and an epibiotic alga

Environmental factors promote symbiosis, but its mechanism is not yet well understood. The alga Pseudocladophora conchopheria grows only on the shell of an intertidal gastropod Lunella correensis, and these species have a close symbiotic relationship which the alga reduces heat stress of the gastropod. In collaboration with general public, we investigated how environmental conditions alter the symbiotic interaction between the alga and the gastropod. Information about the habitats of each gastropod and images of shells was obtained from the Japanese and Korean coasts via social media. We constructed the hierarchical Bayesian model using the data. The results indicated that the proportion of shell area covered by P. conchopheria increased as the substrate size utilized by the gastropod increased. Meanwhile, temperature did not affect the proportion of P. conchopheria on the shell. These suggested that the alga provides no benefits for the gastropod on small substrates because gastropod can reduce the heat stress by diving into the small sediment. Further, the gastropod’s cost incurred by growing the alga on the shell seems to be low as the algae can grow even in cooler places where no benefits of heat resistance for gastropods. Different environments can yield variable conditions in symbiosis.

Effects of tributary size on the resource supply and physical habitat at tributary junctions along two mainstem rivers

Tributary junctions are regarded as ecologically important due to unique habitat present; however, there is limited understanding of the drivers of habitat attributes at these locations. Using six sites across two mainstem rivers, we tested whether tributary size relative to main stem governs the strength and direction of response of substrate size, stream temperature, and nutrient and coarse particulate organic matter (CPOM) concentration. We found that only phosphorus and CPOM concentration showed a significant relationship with relative tributary size. Small tributaries contributed high concentrations, whereas concentrations in larger tributaries resembled the main stem. Often, tributary exports were enough to increase the resource concentration in the main stem by 40%. Substrate coarsened by ∼60% downstream of tributaries. Temperature asynchrony was observed, where tributaries contributed water between 2.8 °C cooler to 1.9 °C warmer than the main stem within one diel period. Our results highlight the importance of small tributaries for whole network functioning. However, large spatiotemporal variability revealed how habitat attributes are highly context-dependent in these locations and may be difficult to predict in both scientific and management settings.

The Influence of Substrate Size Changes on the Coil Resistance of the Wireless Power Transfer System

Wireless power transfer (WPT) technology has been widely used in many fields. Nevertheless, in the field of high power transmission, such as the WPT system of electric vehicles, the power transmission efficiency of WPT system lags behind that of wired charging due to losses brought by substrate shielding materials. In this regard, the conduction resistance of Litz-wire coils without substrate is analyzed first in this paper. Secondly, the induction resistance of the coil with single-layer and double-layer substrate materials is modeled. Then, through the establishment of a coil simulation and experimental platform with a single-layer substrate, a contrastive analysis of the variation trend of coil equivalent series resistance (coil ESR) at changing thickness and area and constant volume of the substrate is carried out in combination with the theory. The variation law of coil ESR at changing thickness and area and constant volume of double-layer substrate is also explored at the end of this paper. This is expected to contribute to the reduction of coil losses in the WPT system through a systematic study of the influence of substrate size changes on the coil resistance of the WPT system.