Influence of climate extremes on long-term changes in cyanobacterial blooms in a eutrophic and shallow lake.

Climate change and human activities have crucial effects on the variations in phytoplankton blooms in lakes worldwide. A record-breaking heatwave and drought event was reported in the middle and lower reaches of the Yangtze River during the summer of 2022, but only little is known about how cyanobacterial blooms in lakes respond to such climate extremes. Here, we utilized MODIS images to generate the area, occurrence, and initial blooming date (IBD) of cyanobacterial blooms in Lake Chaohu from 2000 to 2022. We found that the area and occurrence of cyanobacterial blooms were largely reduced. At the same time, the IBD was delayed in 2022 compared with the previous 20 years. The annual occurrence and mean area of cyanobacterial blooms in 2022 were 17 % and 23.1 km2, respectively, which were the lowest reported levels since the 21st century. The IBD in 2022 was four months late compared with the IBD in 2020. The high wind speed in spring delayed the spring blooms in 2022. The record-breaking heatwaves and drought from June to August reduced the blooms by influencing the growth of cyanobacteria and reducing the flow of nutrients from the watershed into the lake. This study highlights the compound impact of heatwave and drought climate events on reducing cyanobacterial blooms in a long-term period, enhancing additional understanding of the changes in phytoplankton blooms in lakes.

Coordinated dynamics of aquaculture ponds and water eutrophication owing to policy: A case of Jiangsu province, China.

Aquaculture ponds (APs) are rapidly expanding globally and are considered crucial for guaranteeing the supply of food, population growth, and economic development. However, the rapid expansion of aquaculture not only brought benefits but also a series of eco-environmental issues, such as water eutrophication. To achieve sustainable development, it is essential to gain a profound understanding of the spatiotemporal evolution of APs, the drivers behind their dynamics, and their relationship with the aquatic environment. Jiangsu Province (JS) in China, a historically significant aquaculture region, encompasses two prominent river basins: the Huai River Basin (HRB) and the Yangtze River Basin (YRB). In light of the construction of an ecological civilization, JS serves as a demonstration and pioneering area for basin protection and development. Therefore, this study focuses on JS, aiming to elucidate the spatiotemporal dynamics of APs, the corresponding relationship with basin management policies, and the impact on water eutrophication. The results revealed that: (1) in 2022, APs in JS were unevenly distributed, with a total area of 3278.78 km2, of which 79 % was located in the HRB. (2) During 2016-2022, APs exhibited an initial growth trend before 2019, followed by a decrease. (3) Due to policy interventions, AP changes within different basins showed opposite trends, and the corresponding water eutrophic state aligned with AP dynamics. The findings of this study can serve as a typical case to provide scientific evidence for the formulation and implementation of policies to improve the water environment in eutrophic basins.

Characteristics and potential biomarkers of flavor compounds in four Chinese indigenous chicken breeds.

Chinese indigenous chickens have a long history of natural and artificial selection and are popular for their excellent meat quality and unique flavor. This study investigated six meat quality-related traits in Ningdu yellow, Baier yellow, Kangle, and Shengze 901 chickens. Two-dimensional gas chromatography-time-of-flight mass spectrometry was used to detect unique flavors in 24 breast muscle samples from the same phenotyped chickens. Overall, 685, 618, 502, and 487 volatile organic compounds were identified in Ningdu yellow, Baier yellow, Kangle, and Shengze 901 chickens, respectively. The flavor components were separated into eight categories, including hydrocarbons and aldehydes. Multivariate analyses of the identified flavor components revealed some outstanding features of these breeds. For example, the hydrocarbons (22.09%) and aldehydes (14.76%) were higher in Ningdu yellow chickens and the highest content of N, N-dimethyl-methylamine was in Ningdu yellow, Baier yellow, and Shengze 901 chickens, indicating the maximum attribution to the overall flavor (ROAV = 439.57, 289.21, and 422.80). Furthermore, we found that 27 flavor compounds differed significantly among the four Chinese breeds, including 20 (e.g., 1-octen-3-ol), two (e.g., 2-methyl-naphthalene), four (e.g., 2,6-lutidine), and one (benzophenone) flavor components were showed significant enrichment in Ningdu yellow, Baier yellow, Kangle, and Shengze 901 chickens, respectively. The flavor components enriched in each breed were key biomarkers distinguishing breeds and most were significantly correlated with meat quality trait phenotypes. These results provide novel insights into indigenous Chinese chicken meat flavors.

Microcystins risk assessment in lakes from space: Implications for SDG 6.1 evaluation.

Cyanobacterial blooms release a large number of algal toxins (e.g., Microcystins, MCs) and seriously threaten the safety of drinking water sources what the SDG 6.1 pursues (to provide universal access to safe drinking water by 2030, United Nations Sustainable Development Goal). Nevertheless, algal toxins in lake water have not been routinely monitored and evaluated well and frequently so far. In this study, a total of 100 large lakes (>25 km2) in densely populated eastern China were studied, and a remote sensing scheme of human health risks from MCs based on Sentinel-3 OLCI data was developed. The spatial and temporal dynamics of MCs risk in eastern China lakes since OLCI satellite observation data (2016-2021) were first mapped. The results showed that most of the large lakes in eastern China (80 out of 100) were detected with the occurrence of a high risk of more than 1 pixel (300×300 m) at least once. Fortunately, in terms of lake areas, the frequency of high human health risks in most waters (70.93% of total lake areas) was as less as 1%. This indicates that drinking water intakes can be set in most waters from the perspective of MCs, yet the management departments are required to reduce cyanobacterial blooms. This study highlights the potential of satellite in monitoring and assessing the risk of algal toxins and ensuring drinking water safety. It is also an important reference for SDG 6.1 reporting for lakes that lack routine monitoring.

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.

The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.

Can the establishment of a protected area improve the lacustrine environment? A case study of Lake Chaohu, China.

Eutrophication of lacustrine environments with frequent cyanobacterial blooms has become a serious problem. Overpopulation and runoff into groundwater and lakes from fertilizers with too much nitrogen and phosphorous have caused most of the problems. Here, we first devised a land use and cover classification system based on the local characteristics of the first-level protected area of Lake Chaohu (FPALC). Lake Chaohu is the fifth largest freshwater lake in China. The land use and cover change (LUCC) products were produced using sub-meter resolution satellite data from 2019 to 2021 in the FPALC. This study presents an evaluation of the effectiveness of the established protected areas. The results show the most impactful type was the reduction in cropland with an area that declined from 7446.4 hm2 to 6433.3 hm2 from 2019 to 2021. Most of the reduced cropland was converted into wetlands, with 460.2 hm2 and 152.0 hm2 of cropland restored to wetlands from 2019 to 2020 and 2020-2021, respectively. The area of cyanobacterial blooms in Lake Chaohu showed a downward trend, and the lacustrine environment was greatly improved after the establishment of the FPALC. These quantified data can inform decision-making related to Lake Chaohu conservation and provide a reference for managing the aquatic environment in other watersheds.

Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails.

Increasing evidence indicates that the gut microbiome plays an important role in host aging and sexual maturity. However, the gut microbial taxa associated with sexual maturity in quails are unknown. This study used shotgun metagenomic sequencing to identify bacterial taxa associated with sexual maturity in d 20 and d 70 quails. We found that 17 bacterial species and 67 metagenome-assembled genomes (e.g., Bacteroides spp. and Enterococcus spp.) significantly differed between the d 20 and d 70 groups, including 5 bacterial species (e.g., Enterococcus faecalis) enriched in the d 20 group and 12 bacterial species (e.g., Christensenella massiliensis, Clostridium sp. CAG:217, and Bacteroides neonati) which had high abundances in the d 70 group. The bacterial species enriched in d 20 or d 70 were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. Untargeted serum metabolome analysis revealed that 5 metabolites (e.g., nicotinamide riboside) were enriched in the d 20 group, and 6 metabolites (e.g., D-ribose, stevioside, and barbituric acid) were enriched in the d 70 group. Furthermore, metabolites with high abundances in the d 20 group were significantly enriched for the KEGG pathways of arginine biosynthesis, nicotinate and nicotinamide metabolism, and lysine degradation. However, glutathione metabolism and valine, leucine and isoleucine biosynthesis were enriched in high-abundance metabolites from the d 70 group. These results provide important insights into the effects of gut microbiome and host metabolism on quail sexual maturity.

Unbalanced impacts of nature and nurture factors on the phenology, area and intensity of algal blooms in global large lakes: MODIS observations.

Under the influence of climate warming and human activities, many large lakes have experienced an increase in eutrophication and algal blooms. Although these trends have been identified using low temporal resolution (~16 days) satellites such as those of the Landsat missions, the opportunity to compare high-frequency spatiotemporal variations of algal bloom characteristics between lakes has not been explored. In the present study, we explore daily satellite observations by developing a universal, practical, and robust algorithm to identify the spatiotemporal distribution of algal bloom dynamics in large lakes (>500 km2) across the globe. Data from 161 lakes, taken from 2000 to 2020 showed an average accuracy of 79.9 %. Algal blooms were detected in 44 % of all lakes, with a higher incidence in temperate lakes (67 % of all temperate lakes), followed by tropical lakes (59 %) compared to lakes in arid climates (23 %). We found positive trends in bloom area and frequency (p < 0.05), as well as an earlier bloom time (p < 0.05). Climate factors were found to be linked to changes in annual initial bloom time (44 %); while an increase in human activities was associated to bloom duration (49 %), area (max percent: 53 %, mean percent: 45 %), and frequency (46 %). The study shows the evolution of daily algal blooms and their phenology in global large lakes for the first time. Such information enhances our understanding of algal bloom dynamics and their drivers, with important considerations to improve the management of large lake ecosystems.

Additive Manufacturing of Polyhydroxyalkanoate-Based Blends Using Fused Deposition Modelling for the Development of Biomedical Devices.

In the last few decades Additive Manufacturing has advanced and is becoming important for biomedical applications. In this study we look at a variety of biomedical devices including, bone implants, tooth implants, osteochondral tissue repair patches, general tissue repair patches, nerve guidance conduits (NGCs) and coronary artery stents to which fused deposition modelling (FDM) can be applied. We have proposed CAD designs for these devices and employed a cost-effective 3D printer to fabricate proof-of-concept prototypes. We highlight issues with current CAD design and slicing and suggest optimisations of more complex designs targeted towards biomedical applications. We demonstrate the ability to print patient specific implants from real CT scans and reconstruct missing structures by means of mirroring and mesh mixing. A blend of Polyhydroxyalkanoates (PHAs), a family of biocompatible and bioresorbable natural polymers and Poly(L-lactic acid) (PLLA), a known bioresorbable medical polymer is used. Our characterisation of the PLA/PHA filament suggest that its tensile properties might be useful to applications such as stents, NGCs, and bone scaffolds. In addition to this, the proof-of-concept work for other applications shows that FDM is very useful for a large variety of other soft tissue applications, however other more elastomeric MCL-PHAs need to be used.

An Improved POD Model for Fast Semi-Quantitative Analysis of Carbendazim in Fruit by Surface Enhanced Raman Spectroscopy.

The current detection method of carbendazim suffers from the disadvantages of complicated preprocessing and long cycle time. In order to solve the problem of rapid quantitative screening of finite contaminants, this article proposed a qualitative method based on characteristic peaks and a semi-quantitative method based on threshold to detect carbendazim in apple, and finally the method is evaluated by a validation system based on binary output. The results showed that the detection limit for carbendazim was 0.5 mg/kg, and the detection probability was 100% when the concentration was no less than 1 mg/kg. The semi-quantitative analysis method had a false positive rate of 0% and 5% at 0.5 mg/kg and 2.5 mg/kg, respectively. The results of method evaluation showed that when the added concentration was greater than 2.5 mg/kg, the qualitative detection method was consistent with the reference method. When the concentration was no less than 5 mg/kg, the semi-quantitative method is consistent between different labs. The semi-quantitative method proposed in this study can achieve the screening of finite contaminants in blind samples and simplify the test validation process through the detection probability model, which can meet the needs of rapid on-site detection and has a good application prospect.

Rapid Detection of Nonprotein Nitrogen Adulterants in Milk Powder Using Point-Scan Raman Hyperspectral Imaging Technology.

To develop a rapid detection method for nonprotein nitrogen adulterants, this experiment sets up a set of point-scan Raman hyperspectral imaging systems to qualitatively distinguish and quantitatively and positionally analyze samples spiked with a single nonprotein nitrogen adulterant and samples spiked with a mixture of nine nonprotein nitrogen adulterants at different concentrations (5 × 10-3 to 2.000%, w/w). The results showed that for samples spiked with single nonprotein nitrogen adulterants, the number of pixels corresponding to the adulterant in the region of interest increased linearly with an increase in the analyte concentration, the average coefficient of determination (R 2) was above 0.99, the minimum detection concentration of nonprotein nitrogen adulterants reached 0.010%, and the relative standard deviation (RSD) of the predicted concentration was less than 6%. For the sample spiked with a mixture of nine nonprotein nitrogen adulterants, the standard curve could be used to accurately predict the additive concentration when the additive concentration was greater than 1.200%. The detection method established in this study has good accuracy, high sensitivity, and strong stability. It provides a method for technical implementation of real-time and rapid detection of adulterants in milk powder at the port site and has good application and promotion prospects.

Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail.

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear. Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail. Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

From unusual suspect to serial killer: Cyanotoxins boosted by climate change may jeopardize megafauna.

The recent mass mortality event of more than 330 African elephants in Botswana has been attributed to biotoxins produced by cyanobacteria; however, scientific evidence for this is lacking. Here, by synthesizing multiple sources of data, we show that, during the past decades, the widespread hypertrophic waters in Southern Africa have entailed an extremely high risk and frequent exposure of cyanotoxins to the wildlife within this area, which functions as a hotspot of mammal species richness. The hot and dry climatic extremes have most likely acted as the primary trigger of the recent and perhaps also of prehistoric mass mortality events. As such climate extremes are projected to become more frequent in Southern Africa in the near future, there is a risk that similar tragedies may take place, rendering African megafauna species, especially those that are already endangered, in risk of extinction. Moreover, cyanotoxin poisoning amplified by climate change may have unexpected cascading effects on human societies. Seen within this perspective, the tragic mass death of the world's largest terrestrial mammal species serves as an alarming early warning signal of future environmental catastrophes in Southern Africa. We suggest that systematic, quantitative cyanotoxin risk assessments are made and precautionary actions to mitigate the risks are taken without hesitation to ensure the health and sustainability of the megafauna and human societies within the region.

Satellite Estimation of Dissolved Carbon Dioxide Concentrations in China's Lake Taihu.

Lakes play an important role in the global carbon cycle; however, there are still large uncertainties in the estimation of global lake carbon emission due to the limitations in conducting field surveys at large geographic scales. Using long-term Moderate-Resolution Imaging Spectroradiometer (MODIS) imagery and field observation data in eutrophic Lake Taihu, we developed a novel approach to estimate the concentration of dissolved carbon dioxide (cCO2) in lakes. Based on the MODIS-derived chlorophyll-a concentration, lake surface temperature, diffuse attenuation coefficient of photosynthetically active radiation, and photosynthetically active radiation, a spatially explicit cCO2 model was developed using multivariate quadratic polynomial regression (coefficient of determination (R2) = 0.84, root-mean-square error (RMSE) = 11.81 µmol L-1, unbiased percent difference (UPD) = 22.46%). Monte Carlo simulations indicated that the model is stable with relatively small deviations in cCO2 estimates caused by input variables (UPD = 26.14%). MODIS data from 2003 to 2018 showed a significant declining trend (0.42 µmol L-1 yr-1, p < 0.05) in the annual mean cCO2. This was associated with a complex balance between the increasing algae biomass and decreasing external inputs of inorganic carbon, nutrients, and organic matter. The high spatiotemporal variabilities in cCO2 were attributed to river inputs and seasonal changes in temperature and algae biomass. The study shows that satellite remote sensing can play an important role in the field of inland water carbon cycling, providing timely much-needed insights into the drivers of the spatial and temporal changes in dissolved CO2 concentrations in inland waters.

Specific enrichment of caffeic acid from Taraxacum mon-golicum Hand.-Mazz. by pH and magnetic dual-responsive molecularly imprinted polymers.

Specific recognition of caffeic acid (CA) from Taraxacum mon-golicum Hand.-Mazz. was successfully performed using a new pH responsive magnetic molecularly imprinted polymers (pH-MMIPs) by simple surface molecular imprinting polymerization. The pH-MMIPs were prepared on the surface of the Fe3O4@SiO2@MPS particles using CA as a template, 2-(dimethylamino) ethyl methacrylate (DMA) as the pH responsive functional monomer, 4-vinylpyridine (4-VP) as an assisting functional monomer, ethylene glycol dimethyl acrylate (EGDMA) as cross-linker, 2,2'-azobisisobutyronitrile (AIBN) as initiator and methanol-H2O (1:1, v/v) as the porogen. The resultant polymers were characterized by scanning electron microscope (SEM), transmission electron microscope (TEM), dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA), vibrating sample magnetometry (VSM) and x-ray diffraction (XRD). The adsorption experiments revealed that the pH-MMIPs performed high adsorption ability (11.5 mg g-1) by changing solution pH. Successful selective adsorption of CA was achieved with distribution coefficient of 0.12 and 0.21 towards ferulic acid and chlorogenic acid. Furthermore, pH-MMIPs were employed as adsorbents for extraction and enrichment of CA from Taraxacum mon-golicum Hand.-Mazz. extract. The recoveries of CA in the Taraxacum mon-golicum Hand.-Mazz. ranged from 90.47% to 98.97%. The results proved that the polymers have the potential to provide a selective recognition of CA in complex samples by simple pH regulation.

Identification of Austwickia chelonae as cause of cutaneous granuloma in endangered crocodile lizards using metataxonomics.

The crocodile lizard (Shinisaurus crocodilurus Ahl, 1930) is an endangered reptile species, and in recent years many have died from diseases, especially the rescued and breeding individuals. However, pathogens underlying these diseases are unclear. In this study, we report our effort in rapidly identifying and isolating the pathogen that causes high mortality in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. The typical symptom is cutaneous granuloma in the infected crocodile lizards. Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. In this study, 16S rDNA based mNGS was used for rapid identification of pathogens, and microscopy and microbe isolation were used to confirm the results. Austwickia chelonae was identified to be the dominant pathogen in the granuloma using 16S rDNA based mNGS. Chinese skinks were used as an animal model to verify the pathogenicity of A. chelonae to fulfill Koch's postulates. As expected, subcutaneous inoculation of A. chelonae induced granulomas in the healthy Chinese skinks and the A. chelonae was re-isolated from the induced granulomas. Therefore, A. chelonae was the primary pathogen that caused this high mortality disease, cutaneous granuloma, in crocodile lizards from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve. Antibiotics analysis demonstrated that A. chelonae was sensitive to cephalothin, minocycline and ampicillin, but not to kanamycin, gentamicin, streptomycin and clarithromycin, suggesting a possible treatment for the infected crocodile lizards. However, surgical resection of the nodules as early as possible was recommended. This study is the first report of pathogenic analysis in crocodile lizards and provides a reference for disease control and conservations of the endangered crocodile lizards and other reptiles. In addition, this study indicated that mNGS of lesions could be used to detect the pathogens in animals with benefits in speed and convenient.

Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system.

To better understand the immune system of shrimp, this study combined PacBio isoform sequencing (Iso-Seq) and Illumina paired-end short reads sequencing methods to discover full-length immune-related molecules of the Pacific white shrimp, Litopenaeus vannamei. A total of 72,648 nonredundant full-length transcripts (unigenes) were generated with an average length of 2545 bp from five main tissues, including the hepatopancreas, cardiac stomach, heart, muscle, and pyloric stomach. These unigenes exhibited a high annotation rate (62,164, 85.57%) when compared against NR, NT, Swiss-Prot, Pfam, GO, KEGG and COG databases. A total of 7544 putative long noncoding RNAs (lncRNAs) were detected and 1164 nonredundant full-length transcripts (449 UniTransModels) participated in the alternative splicing (AS) events. Importantly, a total of 5279 nonredundant full-length unigenes were successfully identified, which were involved in the innate immune system, including 9 immune-related processes, 19 immune-related pathways and 10 other immune-related systems. We also found wide transcript variants, which increased the number and function complexity of immune molecules; for example, toll-like receptors (TLRs) and interferon regulatory factors (IRFs). The 480 differentially expressed genes (DEGs) were significantly higher or tissue-specific expression patterns in the hepatopancreas compared with that in other four tested tissues (FDR <0.05). Furthermore, the expression levels of six selected immune-related DEGs and putative IRFs were validated using real-time PCR technology, substantiating the reliability of the PacBio Iso-seq results. In conclusion, our results provide new genetic resources of long-read full-length transcripts data and information for identifying immune-related genes, which are an invaluable transcriptomic resource as genomic reference, especially for further exploration of the innate immune and defense mechanisms of shrimp.

SMRT sequencing of the full-length transcriptome of the Sunda pangolin (Manis javanica).

It is widely known that transcriptional diversity contributes greatly to biological regulation in eukaryotes. With the development of next-generation sequencing (NGS) technologies, several studies on RNA sequencing have considerably improved our understanding of transcriptome complexity. However, obtaining full-length (FL) transcripts remains a considerable challenge because of difficulties in short read-based assembly. In the present study, single-molecule real-time (SMRT) sequencing and NGS were combined to generate the complete and FL transcriptome of Manis javanica. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of the M. javanica genome. We obtained 45,530 high-confidence transcripts from 19,109 genic loci, of which 8014 genes have not yet been annotated within the M. javanica genome. Furthermore, we revealed 8824 long-chain noncoding RNAs (lncRNAs). A total of 30,199 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events were identified in the sequencing data. The structure and expression level of 59 digestive enzyme genes, including 13 carbohydrase genes, 28 lipase genes and 18 protease genes, were analyzed, which might provide original data for further research on M. javanica.

The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy.

The characteristics of flora in the intestine of an animal, including the number and abundance of different microbial species and their functions, are closely related to the diets of the animal and affect the physical condition of the host. The Malayan pangolin (Manis javanica) is an endangered species that specializes in myrmecophagy. Analyzing the microbiome in the intestine of the pangolin is imperative to protect this species. By sequencing the metagenomes of the feces of four pangolins, we constructed a non-redundant catalog of 211,868 genes representing 1,811 metagenomic species. Taxonomic annotation revealed that Bacteroidetes (49.9%), Proteobacteria (32.2%), and Firmicutes (12.6%) are the three main phyla. The annotation of gene functions identified 5,044 genes from 88 different glycoside hydrolase (GH) families in the Carbohydrate-Active enZYmes database and 114 gene modules related to chitin-degrading enzymes, corresponding to the catalytic domains of GH18 family enzymes, containing chitinase genes of classes III and V in the dataset. Fourteen gene modules corresponded to the catalytic domains of GH19 family enzymes, containing chitinase genes of classes I, II, and IV. These genes were found in 37 species belonging to four phyla: Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Moreover, when the metabolic pathways of these genes were summarized, 41,711 genes were associated with 147 unique KEGG metabolic pathways, and these genes were assigned to two Gene Ontology terms: metabolic process and catalytic activity. We also found several species that likely play roles in the digestion of cellulose and may be able to degrade chitin, including Enterobacter cloacae, Lactococcus lactis, Chitinimonas koreensis, and Chitinophaga pinensis. In addition, we identified some intestinal microflora and genes related to diseases in pangolins. Twenty-seven species were identified by STAMP analysis as differentially abundant in healthy and diseased animals: 20 species, including Cellulosilyticum lentocellum and Lactobacillus reuteri, were more abundant in healthy pangolins, while seven species, including Odoribacter splanchnicus, Marinilabilia salmonicolor, Xanthomonas citri, Xanthomonas vasicola, Oxalobacter formigenes, Prolixibacter bellariivorans, and Clostridium bolteae, were more abundant in diseased pangolins. These results will support the efforts to conserve pangolins.

Acidic mammalian chitinase gene is highly expressed in the special oxyntic glands of Manis javanica.

The Malayan pangolin (Manis javanica) is a mammal that feeds primarily on ants and termites, which contain the energy-rich carbohydrate chitin. Chitin is digestible by endogenous enzymes of the typical mammalian gastrointestinal tract, especially the acidic mammalian chitinase (AMCase). The objective of this research was to determine whether AMCase activity is expressed in the stomach of M. javanica. The stomach tissues were divided into three parts: the gastric sack, the oxyntic glands, and the pyloric musculature, which were assayed by conventional RT-PCR, quantitative reverse transcriptase-coupled PCR (qPCR) and western blot. Information regarding 3D structural models of AMCase was also obtained. In conclusion, acidic mammalian chitinase is highly expressed in the oxyntic glands of the M. javanica species.