A hyperspectral deep learning attention model for predicting lettuce chlorophyll content.

BACKGROUND: The phenotypic traits of leaves are the direct reflection of the agronomic traits in the growth process of leafy vegetables, which plays a vital role in the selection of high-quality leafy vegetable varieties. The current image-based phenotypic traits extraction research mainly focuses on the morphological and structural traits of plants or leaves, and there are few studies on the phenotypes of physiological traits of leaves. The current research has developed a deep learning model aimed at predicting the total chlorophyll of greenhouse lettuce directly from the full spectrum of hyperspectral images. RESULTS: A CNN-based one-dimensional deep learning model with spectral attention module was utilized for the estimate of the total chlorophyll of greenhouse lettuce from the full spectrum of hyperspectral images. Experimental results demonstrate that the deep neural network with spectral attention module outperformed the existing standard approaches, including partial least squares regression (PLSR) and random forest (RF), with an average R2 of 0.746 and an average RMSE of 2.018. CONCLUSIONS: This study unveils the capability of leveraging deep attention networks and hyperspectral imaging for estimating lettuce chlorophyll levels. This approach offers a convenient, non-destructive, and effective estimation method for the automatic monitoring and production management of leafy vegetables.

Characterization of simultaneous ammonium and nitrate removal and microbial communities in airlift reactor using 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) as carbon source and biofilm carrier.

As a novel trend, solid carbon sources are applied to act as electron donors and biofilm carrier in biological denitrification process. In this study, simultaneous nitrate and ammonium removal process in an airlift sequencing batch reactor using 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) as carbon source and biofilm carrier under intermittent aeration conditions was established to treat effluent of synthetic marine recirculating aquaculture system. The results showed that maximum nitrate and ammonia nitrogen removal rates of 0.45 and 0.09 kg m-3 d-1 were achieved. No significant nitrite accumulation was found during 200-day operation, while effluent dissolved organic carbon accumulation and particle size reduction significantly increased. Microbial community analysis and batch tests illuminate that the generated sludge and attached biofilm played important roles in nitrogen removal. This study demonstrates the potential mechanism for the nitrogen removal process mediated by 3-hydroxybutyrate-co-3-hydroxyvalerate and provide a new idea for the alternative solutions of solid carbon sources.

Effects of Ion Combinations and Their Concentrations on Denitrification Performance and Gene Expressions of an Aerobic Strain Marinobacter Hydrocarbonoclasticus RAD-2.

Salinity is one of the most important factors affecting the nitrogen-removal efficiency of denitrifying bacteria. A series of different ion combinations and salinity gradients were carried out to clarify the effects of ion types and concentrations on nitrogen removal by halophilic aerobic denitrifying bacteria RAD-2. Nitrate concentrations, nitrite concentrations, TAN concentrations, and OD600 were monitored to investigate their effects on denitrification in each group. The results showed that Na+, K+, and Cl- accelerated the denitrification process and improved nitrogen-removal efficiency at moderate additions, while Ca2+ and Mg2+ showed no significant effect. Na+ was effective alone, while K+ or Cl- needed to be combined with at least one of Na+, K+, or Cl- to achieve similar efficiency. The batch tests of salinity confirmed that the addition of a moderate concentration of NaCl/Na2SO4 could effectively improve nitrogen-removal efficiency, while excessive salinity might hinder denitrification metabolism. In the salinity range of 5~40‱, a 5‱ dosage might be the most economical method for strain RAD-2. Real-time PCR experiments on 17 key nitrogen metabolism-related genes revealed that chloride was widely involved in the nitrogen and carbon metabolism of microorganisms by altering cell osmotic pressure and opening ion channel proteins, thereby affecting the efficiency of denitrification. The results of this study may contribute to a better understanding of the different roles of various ions in aerobic denitrification and highlight the importance of salinity control in highly salted wastewater treatment.

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

Estimation of rice seedling growth traits with an end-to-end multi-objective deep learning framework.

In recent years, rice seedling raising factories have gradually been promoted in China. The seedlings bred in the factory need to be selected manually and then transplanted to the field. Growth-related traits such as height and biomass are important indicators for quantifying the growth of rice seedlings. Nowadays, the development of image-based plant phenotyping has received increasing attention, however, there is still room for improvement in plant phenotyping methods to meet the demand for rapid, robust and low-cost extraction of phenotypic measurements from images in environmentally-controlled plant factories. In this study, a method based on convolutional neural networks (CNNs) and digital images was applied to estimate the growth of rice seedlings in a controlled environment. Specifically, an end-to-end framework consisting of hybrid CNNs took color images, scaling factor and image acquisition distance as input and directly predicted the shoot height (SH) and shoot fresh weight (SFW) after image segmentation. The results on the rice seedlings dataset collected by different optical sensors demonstrated that the proposed model outperformed compared random forest (RF) and regression CNN models (RCNN). The model achieved R2 values of 0.980 and 0.717, and normalized root mean square error (NRMSE) values of 2.64% and 17.23%, respectively. The hybrid CNNs method can learn the relationship between digital images and seedling growth traits, promising to provide a convenient and flexible estimation tool for the non-destructive monitoring of seedling growth in controlled environments.

Optimization of Extraction Process, Structure Characterization, and Antioxidant Activity of Polysaccharides from Different Parts of Camellia oleifera Abel.

The flowers, leaves, seed cakes and fruit shells of Camellia oleifera are rich in bioactive polysaccharides, which can be used as additives in food and other industries. In this study, a Box-Behnken design was used to optimize the extraction conditions of polysaccharides from C. oleifera flowers (P-CF), leaves (P-CL), seed cakes (P-CC), and fruit shells (P-CS). Under the optimized extraction conditions, the polysaccharide yields of the four polysaccharides were 9.32% ± 0.11 (P-CF), 7.57% ± 0.11 (P-CL), 8.69% ± 0.16 (P-CC), and 7.25% ± 0.07 (P-CS), respectively. Polysaccharides were mainly composed of mannose, rhamnose, galacturonic acid, glucose, galactose, and xylose, of which the molecular weights ranged from 3.31 kDa to 128.06 kDa. P-CC had a triple helix structure. The antioxidant activities of the four polysaccharides were determined by Fe2+ chelating and free radical scavenging abilities. The results showed that all polysaccharides had antioxidant effects. Among them, P-CF had the strongest antioxidant activity, of which the highest scavenging ability of DPPH•, ABTS•+, and hydroxyl radical could reach 84.19% ± 2.65, 94.8% ± 0.22, and 79.97% ± 3.04, respectively, and the best chelating ability of Fe2+ could reach 44.67% ± 1.04. Overall, polysaccharides extracted from different parts of C. oleifera showed a certain antioxidant effect, and could be developed as a new type of pure natural antioxidant for food.

Performance of Aerobic Denitrification by the Strain Pseudomonas balearica RAD-17 in the Presence of Antibiotics.

Aerobic denitrification, one of the important nitrate metabolic pathways in biological denitrification, has been attracting increasing interest recently due to its functional advantages. In order to evaluate the effect of antibiotics on aerobic denitrification and guide practical engineering application of aerobic denitrification techniques, we evaluated the performance of aerobic denitrification by the strain Pseudomonas balearica RAD-17 in the presence of ciprofloxacin (CFX) and oxytetracycline (OTC). No significant negative impact on the performance of aerobic denitrification in the presence of CFX or OTC within the range of 50 to 300 µg L-1 was found. Significant degradation of OTC was found within the range of 50 µg L-1 to 300 µg L-1 under aerobic denitrification conditions, while no degradation was found for CFX. Stimulation of cell growth occurred within the investigated range of antibiotics. Under anoxic or aerobic conditions, the addition of CFX or OTC changed the N2O production trend. The results in the present study may play an important role in informing the use of aerobic denitrification techniques in the presence of antibiotics within environmentally relevant concentrations (<1 mg/L).

Characterization of a novel marine aerobic denitrifier Vibrio spp. AD2 for efficient nitrate reduction without nitrite accumulation.

Aerobic denitrifiers have the potential to reduce nitrate in polluted water under aerobic conditions. A salt-tolerant aerobic denitrifier was newly isolated and identified as Vibrio spp. AD2 from a marine recirculating aquaculture system, in which denitrification performance was investigated via single-factor experiment, Box-Behnken experiment, and nitrogen balance analysis. Nitrate reductase genes were identified by polymerase chain reaction. Results showed that strain AD2 removed 98.9% of nitrate-nitrogen (NO3--N) with an initial concentration about 100 mg·L-1 in 48 h without nitrite-nitrogen (NO2--N) accumulation. Nitrogen balance indicated that approximately 17.5% of the initial NO3--N was utilized for bacteria synthesis themselves, 4.02% was converted to organic nitrogen, 39.8% was converted to nitrous oxide (N2O), and 31.1% was converted to nitrogen (N2). Response surface methodology experiment showed that the maximum removal of total nitrogen (TN) occurred under the condition of C/N ratio 11.5, shaking speed 127.9 rpm, and temperature 30.8 °C. Sequence amplification indicated that the denitrification genes, napA and nirS, were present in strain AD2. These results indicated that the strain AD2 has potential applications for removing NO3--N from high-salinity (3%) wastewater.

Carbon availability shifts the nitrogen removal pathway and microbial community in biofilm airlift reactor.

This study investigated the response of nitrogen removal performance and microbial community to different carbon composites in biofilm airlift reactors for wastewater treatment. Three reactors were filled with poly (butylene succinate) and bamboo powder composite at the blending ratio of 9:1, 1:1 and 1:9. Increasing the component of bamboo powder in the carrier reduced the carbon availability and had an adverse effect on nitrate removal efficiency. However, bamboo powder improved the ammonia removal rate which mainly through autotrophic nitrification. Three reactors exhibited distinct microbial compositions in both bacterial and fungal diversity. High inclusion of bamboo power decreased the relative abundance of denitrifiers Denitromonas and increased the relative abundance of nitrifiers, including Nitromonas, Nitrospina and Nitrospira. Moreover, correlation network revealed a competitive interaction between the taxa responsible for ammonia removal and nitrate removal processes. Those results indicated the feasibility of steering nitrogen removal pathway through carrier formulation in wastewater treatment.

Interrelationships between tetracyclines and nitrogen cycling processes mediated by microorganisms: A review.

Due to their broad-spectrum antibacterial activity and low cost, tetracyclines (TCs) are a class of antibiotics widely used for human and veterinary medical purposes and as a growth-promoting agent for aquaculture. Interrelationships between TCs and nitrogen cycling have attracted scientific attention due to the complicated processes mediated by microorganisms. TCs negatively impact the nitrogen cycling; however, simultaneous degradation of TCs during nitrogen cycling mediated by microorganisms can be achieved. This review encapsulates the background and distribution of TCs in the environment. Additionally, the main nitrogen cycling process mediated by microorganisms were retrospectively examined. Furthermore, effects of TCs on the nitrogen cycling processes, namely nitrification, denitrification, and anammox, have been summarized. Finally, the pathway and microbial mechanism of degradation of TCs accompanied by nitrogen cycling processes were reviewed, along with the scope for prospective studies.

Simultaneous aerobic denitrification and antibiotics degradation by strain Marinobacter hydrocarbonoclasticus RAD-2.

Simultaneous denitrification and antibiotics (oxytetracycline, OTC and ciprofloxacin, CFX) degradation was evaluated using a typical aerobic denitrifying strain Marinobacter hydrocarbonoclasticus RAD-2. There was no significant influence on the aerobic nitrate removal efficiency of strain RAD-2 in the presence of these two antibiotics. Along with denitrification, the average degradation rate of 2.92 µg OTC L-1h-1 was achieved, while no degradation was observed for CFX. The growth behavior indicated that an insignificant inhibition effect could have occurred at an antibiotics dosage lower than 300 µg/L. The transcriptional results revealed that antibiotics exposure caused (<2h) down-regulation of the denitrifying related genes, but triggered a significant subsequent up-regulation (4 h). Less nitrous oxide productions were observed in both aerobic and anoxic denitrification processes with antibiotics. Overall, the hormesis effect caused by antibiotics exposure indicated a potential approach to enhance the co-metabolism degradation performance for nitrate and antibiotics in aerobic denitrification.

Kinetic affinity index informs the divisions of nitrate flux in aerobic denitrification.

Aerobic denitrification is attracting increasing attention since its advantage of complete nitrogen removal in a single aerobic reactor with simplified configurations. This study investigated the nitrate kinetic affinity (half-saturation index, Km) by an isolated aerobic denitrifier named P. balearica strain RAD-17. It turned out that strain RAD-17 had a high Km of 162.5 mg-N/L and maximum nitrate reduction rate of 21.7 mg-N/(L•h), enabling it to treat high-strength nitrogen wastewater with high efficiency. Further analysis illustrated that Km was the critical value for the change of growth yield rate along initial nitrate concentrations. Nitrogen balance results elucidated an opposite nitrogen flux to cell synthesis and nitrogen loss during aerobic denitrification. Moreover, the expression of functional genes provided proofs for these phenotypic results at transcriptional level. Consequently, Km could be an indicator for nitrate flux division directing to respiration and assimilation in aerobic denitrifiers, shedding light on its regulation for wastewater treatment.

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite.

This study explored the denitrification performance of solid-phase denitrification (SPD) systems packed with poly (butylene succinate)/bamboo powder composite to treat synthetic aquaculture wastewater under different salinity conditions (0‰ Vs. 25‰). The results showed composite could achieve the maximum denitrification rates of 0.22 kg (salinity, 0‰) and 0.34 kg NO3--N m-3 d-1 (salinity, 25‰) over 200-day operation. No significant nitrite accumulation and less dissolved organic carbon (DOC) release (<15 mg/L) were found. The morphological and spectroscopic analyses demonstrated the mixture composites degradation. Microbial community analysis showed that Acidovorax, Simplicispira, Denitromonas, SM1A02, Marinicella and Formosa were the dominant genera for denitrifying bacteria, while Aspergillus was the major genus for denitrifying fungus. The co-network analysis also indicated the interactions between bacterial and fungal community played an important role in composite degradation and denitrification. The outcomes provided a potential strategy of DOC control and cost reduction for aquaculture nitrate removal by SPD.

Nitrogen Removal Performance and Metabolic Pathways Analysis of a Novel Aerobic Denitrifying Halotolerant Pseudomonas balearica strain RAD-17.

An aerobic denitrification strain, Pseudomonas balearica RAD-17, was identified and showed efficient inorganic nitrogen removal ability. The average NO3--N, NO2--N, and total ammonium nitrogen (TAN) removal rate (>95% removal efficiency) in a batch test was 6.22 mg/(L∙h), 6.30 mg/(L∙h), and 1.56 mg/(L∙h), respectively. Meanwhile, optimal incubate conditions were obtained through single factor experiments. For nitrogen removal pathways, the transcriptional results proved that respiratory nitrate reductases encoded by napA, which was primarily performed in aerobic denitrification and cell assimilation, were conducted by gluS and gluD genes for ammonium metabolism. In addition, adding the strain RAD-17 into actual wastewater showed obvious higher denitrification performance than in the no inoculum group (84.22% vs. 22.54%), and the maximum cell abundance achieved 28.5 ± 4.5% in a ratio of total cell numbers. Overall, the efficient nitrogen removal performance plus strong environmental fitness makes the strain RAD-17 a potential alternative for RAS (recirculating aquaculture system) effluent treatment.

Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations.

Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.

Biofloc technology is an efficient approach for intensive shrimp culture. However, the extent to which this process can influence the composition of intestinal microbial community is still unknown. Here, we surveyed the shrimp intestinal bacteria as well as the floc water from three biofloc systems with different stock densities. Our study revealed a similar variation trend in phylum taxonomy level between floc bacteria and gut microbiota. Microbial community varied notably in floc water from different stock densities, while a core genus with dominating relative abundance was detected in gut samples. Extensive variation was discovered in gut microbiota, but still clustered into groups according to stock density. Our results indicated that shrimp intestinal microbiota as well as bacteria aggregated in flocs assembled into distinct communities from different stock densities, and the intestinal communities were more similar with the surrounding environment as the increase of stock density and resulting high floc biomass. The high stock density changed the core gut microbiota by reducing the relative abundance of Paracoccus and increasing that of Nocardioides, which may negatively influence shrimp performance. Therefore, this study helps us to understand further bacteria and host interactions in biofloc system.

Effect of magnetic nanoparticles plus microwave or far-infrared thawing on protein conformation changes and moisture migration of red seabream (Pagrus Major) fillets.

In order to evaluate the effects of magnetic nanoparticles plus microwave (MNPMT) or far-infrared (MNPFT) thawing on protein conformation changes and moisture migration of red seabream (Pagrus major) fillets, cold storage thawing, microwave thawing, MNPMT, far-infrared thawing and MNPFT were subjected to red seabream fillets. DSC and dynamic rheology were conducted to analyze physicochemical changes. Raman spectra before and after isotope H/D exchange, intrinsic fluorescence and UV second derivative spectra were carried out to explore myofibrillar protein structural changes. Low-field NMR was used to test water migration. SEM was performed to observe fiber microstructure. Results indicated that MNPMT and MNPFT both had a desirable thermal stability and gelation property. Besides, both showed stable protein secondary and tertiary structure. Immobilized water in them also had no significant changes compared with fresh sample. This research provided some novel thawing technologies for application in food industry.

The impact of DO and salinity on microbial community in poly(butylene succinate) denitrification reactors for recirculating aquaculture system wastewater treatment.

The interactions between environmental factors and bacterial community shift in solid-phase denitrification are crucial for optimum operation of a reactor and to achieve maximum treatment efficiency. In this study, Illumina high-throughput sequencing was applied to reveal the effects of different operational conditions on bacterial community distribution of three continuous operated poly(butylene succinate) biological denitrification reactors used for recirculating aquaculture system (RAS) wastewater treatment. The results indicated that salinity decreased OTU numbers and diversity while dissolved oxygen (DO) had no obvious influence on OTU numbers. Significant microbial community composition differences were observed among and between three denitrification reactors under varied operation conditions. This result was also demonstrated by cluster analysis (CA) and detrended correspondence analysis (DCA). Hierarchical clustering and redundancy analysis (RDA) was performed to test the relationship between environmental factors and bacterial community compositions and result indicated that salinity, DO and hydraulic retention time (HRT) were the three key factors in microbial community formation. Besides, Simplicispira was detected under all operational conditions, which worth drawing more attention for nitrate removal. Moreover, the abundance of nosZ gene and 16S rRNA were analyzed by real-time PCR, which suggested that salinity decreased the proportion of denitrifiers among whole bacterial community while DO had little influence on marine reactors. This study provides an overview of microbial community shift dynamics in solid-phase denitrification reactors when operation parameters changed and proved the feasibility to apply interval aeration for denitrification process based on microbial level, which may shed light on improving the performance of RAS treatment units.

Simultaneous ammonia and nitrate removal in an airlift reactor using poly(butylene succinate) as carbon source and biofilm carrier.

In this study, an airlift inner-loop sequencing batch reactor using poly(butylene succinate) as the biofilm carrier and carbon source was operated under an alternant aerobic/anoxic strategy for nitrogen removal in recirculating aquaculture system. The average TAN and nitrate removal rates of 47.35±15.62gNH4-Nm(-3)d(-1) and 0.64±0.14kgNO3-Nm(-3)d(-1) were achieved with no obvious nitrite accumulation (0.70±0.76mg/L) and the dissolved organic carbon in effluents was maintained at 148.38±39.06mg/L. Besides, the activities of dissimilatory nitrate reduction to ammonium and sulfate reduction activities were successfully inhibited. The proteome KEGG analysis illustrated that ammonia might be removed through heterotrophic nitrification, while the activities of nitrate and nitrite reductases were enhanced through aeration treatment. The microbial community analysis revealed that denitrifiers of Azoarcus and Simplicispira occupied the dominate abundance which accounted for the high nitrate removal performance. Overall, this study broadened our understanding of simultaneous nitrification and denitrification using biodegradable material as biofilm carrier.

The effects of different seeding ratios on nitrification performance and biofilm formation in marine recirculating aquaculture system biofilter.

Rapid start-up of biofilter is essential for intensive marine recirculating aquaculture system (RAS) production. This study evaluated the nitrifying biofilm formation using mature biofilm as an inoculum to accelerate the process in RAS practice. The effects of inoculation ratios (0-15 %) on the reactor performance and biofilm structure were investigated. Complete nitrification was achieved rapidly in reactors with inoculated mature biofilm (even in 32 days when 15 % seeding ratio was applied). However, the growth of target biofilm on blank carrier was affected by the mature biofilm inoculated through substrate competition. The analysis of extracellular polymeric substance (EPS) and nitrification rates confirmed the divergence of biofilm cultivation among reactors. Besides, three N-acyl-homoserine lactones (AHLs) were found in the process, which might regulate the activities of biofilm. Multivariate analysis based on non-metric multidimensional scaling (nMDS) also indicated the great roles of AHLs and substrate supply which might fundamentally determine varied cultivation performance on target biofilm.