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Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gb of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669.0 Mb, a scaffold N50 of 288.6 kb, and predicted 18,545 genes. We also established a robust phylogenetic tree from 14 representative algae species. With additional transcriptome data, we revealed some novel potential genes that are involved in the synthesis, accumulation, and regulation of astaxanthin production. In addition, we generated an isoform-level reference transcriptome set of 18,483 transcripts with high confidence. Alternative splicing analysis demonstrated that intron retention is the most frequent mode. In summary, we report the first draft genome of H. pluvialis. These genomic resources along with transcriptomic data provide a solid foundation for the discovery of the genetic basis for theoretical and commercial astaxanthin enrichment. [ABSTRACT FROM AUTHOR]

Soil microbial communities play a key role in the biochemical processes and nutrient cycles of the soil ecosystem and their byproducts, including greenhouse gases (GHGs). Organic fertilization influences bacterial soil biodiversity and is an essential emission source of GHGs in paddy soil ecosystems. However, the impact of organic fertilization on the functional microorganisms associated with the GHGs methane and nitrous oxide remains unknown. We conducted paddy soil field experiments under three different treatments (no fertilization, base fertilization, and organic fertilization) to investigate the contribution of organic fertilization to soil nutrients and the functional microorganisms associated with GHG emissions. We found that organic fertilization effectively increased the soil organic matter (P < 0.001), soil organic carbon (P < 0.001), and total nitrogen (P < 0.05) as well as the richness (operational taxonomic units and abundance-based coverage estimators) of the methanogenic communities. Correlation analyses showed that methanogenic communities that were present in abundance were more vulnerable to perturbations in soil properties compared to nitrifying bacterial communities. Partial least squares path model analyses elucidated that organic fertilization directly affected both methanogenic communities and nitrifying bacterial communities (P < 0.05), thereby accelerating methane emissions. Strong co-occurrence networks were observed within the soil-dominant phyla Acidobacteria, Bacteroidetes , and Proteobacteria. Our findings highlight the impact of organic fertilization on soil nutrients and functional microorganisms and guide mitigating GHG emissions from paddy soil agroecosystems. [Display omitted] • Organic fertilization effectively increased SOM, SOC and TN in paddy soils. • Methanogenic microbes are more vulnerable to changes in soil than nitrifying bacteria. • Organic fertilization substantially enhanced the richness of methanogenic communities. • Organic fertilization affects methanogenic and nitrifying bacterial communities. • Short-term fertilization did not change the co-occurrence network among soil microbes. [ABSTRACT FROM AUTHOR]

Vibrio natriegens has massive biotechnological potential owing to its fast growth rate. However, this bacterium rapidly loses its culturability during low-temperature preservation (LTP), the reason for which is still unknown. To reveal the metabolic responses of V. natriegens during LTP, we analyzed and compared the transcriptome before and after 8 days of preservation at 4 or 25 °C (room-temperature preservation (RTP)) in liquid culture medium. Most genes exhibited significant transcriptional responses to LTP. Using gene set enrichment analysis, we compared the transcriptional responses of different V. natriegens Gene Ontology (GO) sets during LTP or RTP. The enrichment of the GO set "SOS response" during LTP, but not RTP, indicated the occurrence of DNA damage during LTP. The GO set "respiratory electron transport chain" was suppressed during LTP and RTP. Although the GO set "response to oxidative stress" was not significantly altered, we observed an increase in reactive oxygen species (ROS) during LTP, suggesting a relationship between ROS and cold-induced loss of culturability (CILC) in V. natriegens. The faster loss of culturability and accumulation of ROS in 20 mL compared to 100 mL of liquid culture medium further suggested a relationship between CILC and oxygen availability. Furthermore, we showed that the deletion of Na+-translocating NADH-ubiquinone oxidoreductase, but not type-II NADH dehydrogenase, accelerated CILC and increased intracellular ROS levels in V. natriegens. These findings will help to understand the cause of CILC which may lead to improving the stability of V. natriegens at low temperatures. Key points: • V. natriegens transcriptome was analyzed before and after storage at 4 or 25 °C. • V. natriegens SOS response was induced by 4 °C storage. • Medium volume, NaCl concentration, and nqr deletion affect the CILC of V. natriegens. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have been extensively applied to genetics and breeding in the aquaculture industry. To date, many aquaculture animal genomes have been sequenced, and single nucleotide polymorphisms (SNPs) have become the most popular genetic markers. SNP applications include high-density genetic linkage map construction, quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic selection (GS). In this review, we assess the availability of complete genomes of aquaculture animals and then briefly discuss the sequencing technologies and SNP array for SNPs genotyping. Finally, we summarize the current status of genetic linkage map construction, QTL mapping, GWAS, and GS in aquatic animals. As the overall research programs and aims are similar across aquaculture animals, successful practices in some species might act as reference frameworks for in-depth investigations in other species. • Assess the availability of complete genomes of aquaculture animals; • Discuss the sequencing technologies for discovery of SNPs; • Summarize the current status of genetic linkage map construction, QTL mapping, GWAS, and GS in aquatic animals. [ABSTRACT FROM AUTHOR]

Curcumin, a natural phenolic compound with various bioactivities, is easily decomposed into stability ferulic acid and vanillin molecules. Whether the functional equivalence of decomposition products can match that of curcumin is a matter worth attention. In this work, the inhibition and interaction of curcumin and its decomposition products on pepsin were studied. The inhibition by curcumin and ferulic acid belonged to competitive inhibition, the quenching types were static quenching with spontaneous process. Binding energies of curcumin, ferulic acid and vanillin were −8.33 ± 0.14, −7.88 ± 0.09 and −6.12 ± 0.08 kcal/mol, respectively, through H-bonds and hydrophobic interactions. All molecules significantly changed the secondary structure of pepsin and reduced the deformation temperature about 15 °C. The results show that better inhibition on pepsin from curcumin than ferulic acid, whereas vanillin did not show inhibition. The results provided the experimental basis for curcumin as potential inhibitors of pepsin in special diets. [Display omitted] • Curcumin shows the best inhibitory effect on pepsin than its decomposition products. • Inhibition of pepsin by curcumin and ferulic acid is based on competitive inhibition. • Curcumin improves stability and inhibition through more binding sites. • Vanillin does not exhibit pepsin inhibition due to the absence of a "-CH 2 COOH" structure. [ABSTRACT FROM AUTHOR]

Lined seahorse (Hippocampus erectus), the most widely cultivated seahorse in China, has been in short supply because of its important medicinal value; meanwhile, unnatural deaths caused by various diseases (especially enteritis) have limited their practical large-scale aquaculture. Antimicrobial peptides (AMPs), as the best alternative to antibiotics, have been extensively applied in agricultural practices. In this study, we identified 290 putative AMP sequences from our previously published genome and transcriptome data of the lined seahorse. Among them, 267 are novel, and 118 were validated by our proteome data generated in the present study. It seems that there is a tissue preference in the distribution of AMP/AMP precursor transcripts, such as lectins in the male pouch. In addition, their transcription levels usually varied during development. Interestingly, the representative lectins kept extremely high levels at the pre-pregnancy stage while at relatively lower levels at other stages. Especially Lectin25, with the highest transcription levels and significant developmental changes, has been reported to be involved in seahorse and human pregnancy. The comparison of transcriptome data between one-day and three-month juveniles indicated that Hemoglobin2 (Hemo2) was significantly upregulated in the body, haslet, and brain. Our proteome data of female and male individuals revealed three putative AMP precursors with sexual specificity, including two male-biased cyclin-dependent kinases (CDK-like16 and CDK-like23) and one female-biased bovine pancreatic trypsin inhibitor 2 (BPTI2). In conclusion, our present high-throughput identification of putative AMP sequences from multi-omics (including genomics, transcriptomics, and proteomics) data provides an overview of AMPs in the popular lined seahorse, which lays a solid foundation for further development of AMP-based fish food additives and human drugs. [ABSTRACT FROM AUTHOR]

Antibiotics, heavy metals and related antibiotic resistance genes (ARGs) in municipal solid waste (MSW) landfills have aroused more attentions due to their potential risk toward the ecosystems and public healthcare, but the contents and relationships of them have yet to be systematically understood during landfilling process. In this study, we selected refuse samples with different ages from two representative landfills and leachate samples from three major landfills. The total contents of measured antibiotics and metals respectively ranged from 157.22 to 1752.01 μg/kg and 19624.62–30624.01 mg/kg in refuse, while 3961.59–4497.12 ng/L and 9.16–10.82 mg/L in detected leachates. Among them, Ten of fourteen antibiotics were relatively higher in aged refuse, and contrary results were presented in most detected metals. Three ARGs (sul1 , ermB and sul2) and intl1 were found with a higher abundance across all detected samples. Network analysis indicated that the abundance of tetM and tetQ in refuse were positively correlated with corresponding antibiotics doxycycline (DC) and oxytetracycline (OTC), respectively (P < 0.05). Similarly, ermB and bla CTX-M in leachates were respectively related with corresponding roxithromycin (RTM) and cefalexin (CEF), (P < 0.01). Moreover, Cu exhibited positive and significant correlations with sul1 , mexF and intl1 in all refuse and leachates (P < 0.05). Mantel test indicated that the quantified intl1 was closely correlated with detected contents of ARGs (Mantel test, R = 0.48, P < 0.05), and the highly abundant intl1 were correlated with sul1 (P < 0.001) and bla CTX-M (P < 0.05) across all samples. Image 1 • Antibiotics, heavy metals and ARGs were investigated in MSW landfill systems. • Most antibiotics and ARGs in refuse exhibited decreased trends with landfill ages. • Cu exhibited positive correlated with sul1 , mexF and intl1 in landfill systems. • Mantel test showed intl1 was closely correlated with ARGs in landfill systems. • intl1 were significantly correlated with sul1 and bla CTX-M across all samples. Summarizes: (1) Most antibiotics and ARGs in refuse exhibited relatively decreased trends with landfill ages, while opposite results were presented in most heavy metals; (2) sul1 , ermB and sul2 were dominant ARGs during landfill process in MSW landfills; (3) Mantel test indicated that intl1 was closely correlated with detected contents of ARGs in landfill systems. [ABSTRACT FROM AUTHOR]

The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies. [ABSTRACT FROM AUTHOR]