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

Feed types driven differentiation of microbial community and functionality in marine integrated multitrophic aquaculture system

Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system. Preferable water quality, higher animal yields and higher cost efficiency were achieved in the FD pond. Feed types changed the pond bacterial community distribution, especially in the rearing water. The FFD pond was dominated with Cyanobacteria in the water, which played an important role in nitrogen fixation through photosynthesis due to the high nitrogen input of the frozen fish diet. The high carbohydrate composition in the formulated diet triggered higher metabolic pathways related to carbon and lipid metabolism in the water of the FD pond. Sediment had significantly higher microbial diversity than the rearing water. In sediment, the dominating genus, Sulfurovum and Desulfobulbus, were found to be positively correlated by network analysis, which had similar functionality in sulfur transformation. The relatively higher rates of antibiotic biosynthesis in the FFD sediment might be related to the pathogenic bacteria introduced by the trash fish diet. The difference in microbial community composition and metabolic pathways may be associated with the different pathways for nutrient cycling and animal growth performance. The formulated diet was determined to be more ecologically and economically sustainable than the frozen fish diet for marine IMTA pond systems.</p

Preparation of a Novel Resin Based Covalent Framework Material and Its Application in the Determination of Phenolic Endocrine Disruptors in Beverages by SPE-HPLC

A new type of economical covalent organic framework material(COF), namely resin based covalent organic framework material, was prepared by combining resin and covalent organic framework material by hydrothermal synthesis, which was based on the preparation of traditional COF material(TpBD COF). The properties of the material and covalent organic framework material were compared in the way of characterization, and the possible reaction mechanism was analyzed. The solid phase extraction separation (SPE) ability of this material for four kinds of phenolic endocrine disrupting compounds (bisphenol F, bisphenol A, octylphenol and nonylphenol) in beverage samples was investigated. The results showed that the prepared COF materials had abundant internal channels, ordered structure, large specific surface area (TpBD COF: 814.6 m2/g and resin based COF: 623.9 m2/g) and good thermal stability (pyrolysis temperature was 443 °C and 437 °C, respectively). Solid phase extraction experiments demonstrated that the two COF materials as adsorbent of solid phase extraction column had ideal adsorption separation effect and good anti-interference ability, and had strong anti-interference ability. The SPE effect was superior to the traditional solid phase extraction column. The precision RSD of this method was less than 3%. This SPE method had high recovery and could be reused (carbonated beverage: 98.18–102.18% and beverage: 98.52–101.79%), In addition, the recovery of the material did not change significantly in the 50 cycles of solid phase extraction, indicating that the material had good stability and could be reused, which could meet the requirements for the detection and analysis of trace pollutants in environmental samples. The resin based COF material prepared in this study could reduce the cost of monomer uses and provide a possibility for its industrial production. At the same time, as an efficient SPE adsorbent, it also provided a new research scheme for the enrichment of trace phenolic endocrine disruptors in beverage samples

Denitrification-potential evaluation and nitrate-removal-pathway analysis of aerobic denitrifier strain Marinobacter hydrocarbonoclasticus RAD-2

An aerobic denitrifier was isolated from a long-term poly (3-hydroxybutyrate-co-3- hydroxyvalerate) PHBV-supported denitrification reactor that operated under alternate aerobic/anoxic conditions. The strain was identified as Marinobacter hydrocarbonoclasticus RAD-2 based on 16S rRNA-sequence phylogenetic analysis. Morphology was observed by scanning electron microscopy (SEM), and phylogenetic characteristics were analyzed with the API 20NE test. Strain RAD-2 showed efficient aerobic denitrification ability when using NO3 - -N or NO2 --N as its only nitrogen source, while heterotrophic nitrification was not detected. The average NO3 --N and NO2 --N removal rates were 6.47 mg/(L·h)and 6.32 mg/(L·h), respectively. Single-factor experiments indicated that a 5:10 C/N ratio, 25-40 °C temperature, and 100-150 rpm rotation speed were the optimal conditions for aerobic denitrification. Furthermore, the denitrifying gene napA had the highest expression on a transcriptional level, followed by the denitrifying genes nirS and nosZ. The norB gene was found to have significantly low expression during the experiment. Overall, great aerobic denitrification ability makes the RAD-2 strain a potential alternative in enhancing nitrate management for marine recirculating aquaculture system (RAS) practices.</p

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.</p

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.</p

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, K) by an isolated aerobic denitrifier named P. balearica strain RAD-17. It turned out that strain RAD-17 had a high K 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 K 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, K 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.</p

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.</p