Improving the estimation of rice above-ground biomass based on spatio-temporal UAV imagery and phenological stages.

Introduction: Unmanned aerial vehicles (UAVs) equipped with visible and multispectral cameras provide reliable and efficient methods for remote crop monitoring and above-ground biomass (AGB) estimation in rice fields. However, existing research predominantly focuses on AGB estimation based on canopy spectral features or by incorporating plant height (PH) as a parameter. Insufficient consideration has been given to the spatial structure and the phenological stages of rice in these studies. In this study, a novel method was introduced by fully considering the three-dimensional growth dynamics of rice, integrating both horizontal (canopy cover, CC) and vertical (PH) aspects of canopy development, and accounting for the growing days of rice. Methods: To investigate the synergistic effects of combining spectral, spatial and temporal parameters, both small-scale plot experiments and large-scale field testing were conducted in Jiangsu Province, China from 2021 to 2022. Twenty vegetation indices (VIs) were used as spectral features, PH and CC as spatial parameters, and days after transplanting (DAT) as a temporal parameter. AGB estimation models were built with five regression methods (MSR, ENet, PLSR, RF and SVR), using the derived data from six feature combinations (VIs, PH+CC, PH+CC+DAT, VIs+PH +CC, VIs+DAT, VIs+PH+CC+DAT). Results: The results showed a strong correlation between extracted and ground-measured PH (R2 = 0.89, RMSE=5.08 cm). Furthermore, VIs, PH and CC exhibit strong correlations with AGB during the mid-tillering to flowering stages. The optimal AGB estimation results during the mid-tillering to flowering stages on plot data were from the PLSR model with VIs and DAT as inputs (R 2 = 0.88, RMSE=1111kg/ha, NRMSE=9.76%), and with VIs, PH, CC, and DAT all as inputs (R 2 = 0.88, RMSE=1131 kg/ha, NRMSE=9.94%). For the field sampling data, the ENet model combined with different feature inputs had the best estimation results (%error=0.6%-13.5%), demonstrating excellent practical applicability. Discussion: Model evaluation and feature importance ranking demonstrated that augmenting VIs with temporal and spatial parameters significantly enhanced the AGB estimation accuracy. In summary, the fusion of spectral and spatio-temporal features enhanced the actual physical significance of the AGB estimation models and showed great potential for accurate rice AGB estimation during the main phenological stages.

Effects of Salt Tolerance Training on Multidimensional Root Distribution and Root-Shoot Characteristics of Summer Maize under Brackish Water Irrigation.

To investigate the impact of brackish water irrigation on the multidimensional root distribution and root-shoot characteristics of summer maize under different salt-tolerance-training modes, a micro-plot experiment was conducted from June to October in 2022 at the experimental station in Hohai University, China. Freshwater irrigation was used as the control (CK), and different concentrations of brackish water (S0: 0.08 g·L-1, S1: 2.0 g·L-1, S2: 4.0 g·L-1, S3: 6.0 g·L-1) were irrigated at six-leaf stage, ten-leaf stage, and tasseling stage, constituting different salt tolerance training modes, referred to as S0-2-3, S0-3-3, S1-2-3, S1-3-3, S2-2-3, and S2-3-3. The results showed that although their fine root length density (FRLD) increased, the S0-2-3 and S0-3-3 treatments reduced the limit of root extension in the horizontal direction, causing the roots to be mainly distributed near the plants. This resulted in decreased leaf area and biomass accumulation, ultimately leading to significant yield reduction. Additionally, the S2-2-3 and S2-3-3 treatments stimulated the adaptive mechanism of maize roots, resulting in boosted fine root growth to increase the FRLD and develop into deeper soil layers. However, due to the prolonged exposure to a high level of salinity, their roots below 30 cm depth senesced prematurely, leading to an inhibition in shoot growth and also resulting in yield reduction of 10.99% and 11.75%, compared to CK, respectively. Furthermore, the S1-2-3 and S1-3-3 treatments produced more reasonable distributions of FRLD, which did not boost fine root growth but established fewer weak areas (FLRD < 0.66 cm-3) in their root systems. Moreover, the S1-2-3 treatment contributed to increasing leaf development and biomass accumulation, compared to CK, whereas it allowed for minimizing yield reduction. Therefore, our study proposed the S1-2-3 treatment as the recommended training mode for summer maize while utilizing brackish water resources.

Soil Moisture Regulation under Mulched Drip Irrigation Influences the Soil Salt Distribution and Growth of Cotton in Southern Xinjiang, China.

Water deficiency, together with soil salinization, has been seriously restricting sustainable agriculture around the globe for a long time. Optimal soil moisture regulation contributes to the amelioration of soil water and salinity for crops, which is favorable for plant production. A field experiment with five soil water lower limit levels (T1: 85% FC, T2: 75% FC, T3: 65% FC, T4: 55% FC, and T5: 45% FC, where FC is the field capacity) was conducted in southern Xinjiang in 2018 to investigate the responses of soil water-salt dynamics and cotton performance to soil moisture regulation strategies. The results indicated that in the horizontal direction, the farther away the drip irrigation belt, the lower the soil moisture content and the greater the soil salinity. In the vertical direction, the soil moisture and soil salinity increased first and then decreased with an increase in soil depth after irrigation, and the distribution was similar to an ellipse. Moreover, the humid perimeter of soil water and the leaching range of soil salt increased with a decrease in the soil moisture lower limit. Though more soil salt was leached out for the T5 treatment at the flowering stage due to the higher single irrigation amount, soil salinity increased again at the boll setting stage owing to the long irrigation interval. After the cotton was harvested, soil salt accumulated in the 0-100 cm layer and the accumulation amount followed T3 > T5 > T1 > T2 > T4. Moreover, with a decline of soil moisture lower limit, both plant height and nitrogen uptake decreased significantly while the shoot-root ratio increased. Compared with the yield (7233.2 kg·hm-2) and water use efficiency (WUE, 1.27 kg·m-3) of the T1 treatment, the yield for the T2 treatment only decreased by 1.21%, while the WUE increased by 10.24%. Synthetically, considering the cotton yield, water-nitrogen use efficiency, and soil salt accumulation, the soil moisture lower limit of 75% FC is recommended for cotton cultivation in southern Xinjiang, China.

Mapping the potential for offshore aquaculture of salmonids in the Yellow Sea.

Mariculture has been one of the fastest-growing global food production sectors over the past three decades. With the congestion of space and deterioration of the environment in coastal regions, offshore aquaculture has gained increasing attention. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two important aquaculture species and contribute to 6.1% of world aquaculture production of finfish. In the present study, we established species distribution models (SDMs) to identify the potential areas for offshore aquaculture of these two cold-water fish species considering the mesoscale spatio-temporal thermal heterogeneity of the Yellow Sea. The values of the area under the curve (AUC) and the true skill statistic (TSS) showed good model performance. The suitability index (SI), which was used in this study to quantitatively assess potential offshore aquaculture sites, was highly dynamic at the surface water layer. However, high SI values occurred throughout the year at deeper water layers. The potential aquaculture areas for S. salar and O. mykiss in the Yellow Sea were estimated as 52,270 ± 3275 (95% confidence interval, CI) and 146,831 ± 15,023 km2, respectively. Our results highlighted the use of SDMs in identifying potential aquaculture areas based on environmental variables. Considering the thermal heterogeneity of the environment, this study suggested that offshore aquaculture for Atlantic salmon and rainbow trout was feasible in the Yellow Sea by adopting new technologies (e.g., sinking cages into deep water) to avoid damage from high temperatures in summer. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-022-00141-2.

The complete mitochondrial genome of Montiporavietnamensis (Scleractinia, Acroporidae).

Montiporavietnamensis Veron, 2000 (Cnidaria, Anthozoa, Scleractinia, Acroporidae) is an uncommon, but distinctive species of stony coral. The complete mitochondrial genome of M.vietnamensis was sequenced in this study for the first time, based on 32 pairs of primers newly designed according to seven species in the family Acroporidae. The mitogenome of M.vietnamensis has a circular form and is 17,885 bp long, including 13 protein-coding genes (PCGs), 2 tRNA (tRNAMet, tRNATrp), 2 rRNA genes and a putative control-region. The base composition of the complete mitogenome was 24.8% A, 14.2% C, 24.2% G and 36.8% T, with a higher AT content (61.6%) than GC content (38.4%). Based on 13 protein-coding genes, a Maximum Likelihood phylogenetic analysis showed that M.vietnamensis is clustered in the genus Montipora which belongs to the family Acroporidae. More stony coral species should be sequenced for basic molecular information and to help confirm the taxonomic status and evolutionary relationships of Scleractinia in the future.

Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes.

Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.

Insights on the mechanism of Fe doped ZnO for tightly-bound extracellular polymeric substances tribo-catalytic degradation: The role of hydration layers at the interface.

The control of interfacial microbial pollution is of great significance for water safety. Herein, the tribo-catalysis ability of zinc oxide (ZnO) has been investigated, which can realize the control of tightly-bound extracellular polymeric substances (T-EPS) in water under dark environment. The DFT calculation proves the Fe doping introduces the impurity level and decreases the work function from 5.071 eV to 5.045 eV, improves the charge separation of ZnO, and eventually enhances the catalytic reaction efficiency. Characterizing the catalytic reaction process by three-dimensional fluorescence (3D EEM) and fluorescence regional integration (FRI) method, it is found that the T-EPS solution can be degraded 75.8% by Fe-ZnO in 12 min, while ZnO can only degrade 32.2%. Combining with high-resolution scanning probe microscope (HR-SPM) and attenuated total reflection method (ATR-FTIR), hydration layers consist with hydroxyl layer (∼0.23 nm) and water molecular layer (∼0.27 nm) are observed at the interface between Fe-ZnO and T-EPS solution, and terminal hydroxyl group (OHt) is considered to be the active site for the generation of radicals. This study provides an idea for exploring the mechanism of tribo-catalytic reaction and shows its application prospect in the field of microbial inhibition in water.

Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China).

A Gram-strain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacterium, designated SM6T, was isolated from surface seawater collected in Daya Bay (Guangdong, China). Phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis, phylogenomic analysis of single-copy gene families and whole genome data showed that strain SM6T belonged to the genus Vibrio. The closest phylogenetic relatives of SM6T were Vibrio plantisponsor MSSRF60T (97.38 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis R-40492T (97.27 %), Vibrio aestuarianus ATCC 35048T (97.21 %) and Vibrio sagamiensis LC2-047T (97.3 %). Growth of strain SM6T occurred at 10-45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum 6.0) and in the presence of 0-10 % (w/v) NaCl (optimum 3-8 %). The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1 ω7c or/and C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c). The DNA G+C content of the assembled genomic sequences was 47.37 % for strain SM6T. Average nucleotide identity values between SM6T and its reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further showed that the strains shared less than 70 % similarity. On the basis of evidence from the present polyphasic study, strain SM6T is considered to represent a novel species of the genus Vibrio, for which the name Vibrio agarilyticus sp. nov. is proposed. The type strain is SM6T (=KCTC 82076T=MCCC 1K04327 T).

Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater.

A Gram-stain-negative, aerobic, gliding, reddish-orange-coloured, rod-shaped strain, designated SR4T, was isolated from surface seawater sampled at Luhuitou fringing reef (South China Sea). Phylogenetic analyses based on the 16S rRNA gene, phylogenomic analysis of single-copy gene families and whole genome data affiliated it to the genus Flammeovirga. It was most closely related to Flammeovirga yaeyamensis NBRC 100898T (97.99 % 16S rRNA gene similarity). The genome average nucleotide identity and DNA-DNA relatedness values between strain SR4T and its reference strains were less than 74.2 and 16.3 %, respectively. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 1-6 % (w/v) NaCl (optimum, 2-4 %). The dominant fatty acids were C16 : 0, iso-C15 : 0 and C20 : 4 ω6,9,12,15c. The polar lipid profile of strain SR4T comprised phosphatidylethanolamine, two glycolipids, two aminophospholipids and three unidentified lipids. The major respiratory quinone was MK-7. The DNA G+C content of strain SR4T was 34.20 mol%. On the basis of the polyphasic evidence, strain SR4T is proposed as representing a novel species of the genus Flammeovirga, for which the name Flammeovirga agarivorans sp. nov. is proposed. The type strain is SR4T (=KCTC 82075T=MCCC 1A17137T).

Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics.

Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.

Complete mitochondrial genome of Echinophylliaaspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning.

Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophylliaaspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E.aspera clustered closely with Sclerophylliamaxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E.aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

Benefits of soil biochar amendments to tomato growth under saline water irrigation.

Biochar amendments have been used in agriculture to improve soil fertility and enhance crop productivity. A greenhouse experiment was conducted to test the hypothesis that biochar amendment could also enhance the productivity of salt-affected soils. The trial was conducted over two consecutive growing seasons to investigate the effect of biochar amendment (four application rates as: B1 = 0%, B2 = 2%, B3 = 4%, and B4 = 8% by mass of soil) on yield and quality of tomatoes grown in a silt loam soil using non-saline water (I0 = 0.7 dS m-1) and saline water (I1 = 1 dS m-1; I2 = 3 dS m-1) irrigation. Furthermore, the study investigated the mechanism by which biochar addresses the salt stress on plant. The results showed that soil productivity as indicated by the vegetative growth and tomato yield components was adversely and significantly affected by saline water irrigation (P < 0.05). Tomato yield decreased from 689 ± 35.6 to 533 ± 79.0 g per plant as salinity of irrigation water increased from I0 to I2. Then, biochar amendment increased vegetative growth, yield, and quality parameters under saline irrigation water regimes, and ameliorated the salt stresses on crop growth. The highest (8.73 ± 0.15 and 4.10 ± 0.82 g kg-1) and the lowest (8.33 ± 0.08 and 2.42 ± 0.76 g kg-1) values of soil pH and soil organic matter were measured at B4I0 and B1I2 treatments, respectively. Also, the highest rate of biochar amendment combining with non-saline water irrigation (B4I0) produced tomato with the highest plant photosynthetic (17.08 ± 0.19 µmol m-2 s-1) and transpiration rate (8.16 ± 0.18 mmol H2O m-2 s-1). Mechanically, biochar amendment reduced transient sodium ions by adsorption and released mineral nutrients such as potassium, calcium, and magnesium into the soil solution. Therefore, biochar amendments have the potential in ameliorating salt stress and enhancing tomato production.

The complete mitochondrial genome of the Montipora peltiformi (Scleractinia: Acroporidae).

In this study, the complete mitogenome sequence of stony coral, Montipora peltiformi (Scleractinia), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,884 bp, has unique 13 protein coding genes (PCGs), three transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome of Montipora peltiformi showing 99% identities to Montipora cactus. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for coral phylogeny.

The complete mitochondrial genome of the Cyphastrea serailia.

In this study, the complete mitogenome sequence of stony coral, Cyphastrea serailia (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,138 bp, has unique 13 protein-coding genes (PCGs), 3 transfer RNAs, and 2 ribosomal RNAs genes. The complete mitogenome of Cyphastrea serailia showed 97% identity to Montastraea annularis. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for coral phylogeny.

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita).

In this study, the complete mitogenome sequence of stony coral, Favites abdita (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,825 bp, has unique 13 protein-coding genes (PCGs), 2 transfer RNAs and 3 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral phylogeny.

Characterizing scale-specific environmental factors affecting soil organic carbon along two landscape transects.

Soil organic carbon (SOC) is one of the most important soil properties affecting many other soil and environmental properties and processes. In order to understand and manage SOC effectively, it is important to identify the scale-specific main factors affecting SOC distributions, which in this study occurred in a watershed on the Loess Plateau. Two transects were selected that passed along the upper slopes on each side of the main gully of the Liudaogou watershed. Transect 1 (3411-m length) had 27 sampling sites at 131-m intervals; transect 2 (3597 m length) had 30 sampling sites at 124-m intervals. The two transects were chosen in order to compare landscape patterns of differing complexity that were in close proximity, which reduced the effects of factors that would be caused by different locations. The landscape of transect 1 was more complex due to the greater diversity in cultivation. Multivariate empirical mode decomposition (MEMD) decomposed the total variation in SOC and five selected environmental factors into four intrinsic mode functions (IMFs) and a residual according to the scale of occurrence. Scale-specific correlation analysis was used to identify significant relationships between SOC and the environmental factors. The dominant scales were those that were the largest contributors to the total SOC variance; for transect 1, this was the IMF 1 (scale of 403 m), whereas for transect 2, it was the medium scale of the IMF 2 (scale of 688 m). For both transects, vegetation properties (vegetation cover and aboveground biomass) were the main factors affecting SOC distributions at their respective dominant scales. At each scale, the main effective factors could be identified although at the larger scales, their contributions to the overall variance were almost negligible. The distributions of SOC and the factors affecting it were found to be scale dependent. The results of this study highlighted the suitability of the MEMD method in revealing the main scale-specific factors that affect SOC distributions, which is necessary in understanding and managing this important soil property.

Predicted infiltration for sodic/saline soils from reclaimed coastal areas: sensitivity to model parameters.

This study was conducted to assess the influences of soil surface conditions and initial soil water content on water movement in unsaturated sodic soils of reclaimed coastal areas. Data was collected from column experiments in which two soils from a Chinese coastal area reclaimed in 2007 (Soil A, saline) and 1960 (Soil B, nonsaline) were used, with bulk densities of 1.4 or 1.5 g/cm(3). A 1D-infiltration model was created using a finite difference method and its sensitivity to hydraulic related parameters was tested. The model well simulated the measured data. The results revealed that soil compaction notably affected the water retention of both soils. Model simulations showed that increasing the ponded water depth had little effect on the infiltration process, since the increases in cumulative infiltration and wetting front advancement rate were small. However, the wetting front advancement rate increased and the cumulative infiltration decreased to a greater extent when θ0 was increased. Soil physical quality was described better by the S parameter than by the saturated hydraulic conductivity since the latter was also affected by the physical chemical effects on clay swelling occurring in the presence of different levels of electrolytes in the soil solutions of the two soils.