Yan Zhao

While intensive aquaculture has developed rapidly, the consequent buildup of nitrogenous compounds, poses a critical threat to aquatic organisms. Microbial degradation offers an environmentally sustainable solution. We investigated the metabolic regulatory capacity of Priestia megaterium BZ-95 under four nitrogen regimes—ammonium (NH₄⁺-N), nitrite (NO₂⁻-N), nitrate (NO₃⁻-N), and a mixture of them (Mix)—using comparative transcriptomics. We revealed that BZ-95 in NH₄⁺-N activated a direct assimilation program prioritizing branched-chain amino acid biosynthesis. Conversely, under nitrate, BZ-95 enhanced membrane transport and 2-oxocarboxylic acid metabolism to facilitate the rapid incorporation of nitrate-derived ammonium into biomass. Nitrite stress triggered a coordinated response involving the assimilatory nir module (nirC-nirB-nirD) and enhanced energy metabolism to meet the heightened demand for reducing power during its rapid reduction. Under mixed nitrogen sources, BZ-95 established a highly synergistic carbon-nitrogen network, simultaneously processing multiple nitrogen inputs without a hierarchical preference, highlighting its remarkable metabolic plasticity. Intersection analysis defined a refined core of 692 nitrite-specific DEGs and revealed broad transcriptional activation under nitrite stress. Analysis of the NO₂⁻-specific core identified enhanced transmembrane transport capacity, coupled with auxiliary metabolic tuning, as central adaptive strategies for nitrite processing. Collectively, these findings provide crucial insights into the molecular basis of nitrogen coordination in P. megaterium BZ-95.

In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise F_ST values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.

Nile tilapia is a GSD + TE (Genetic Sex Determination + Temperature Effect) fish, and high-temperature treatment during critical thermosensitive periods (TSP) can induce the sex reversal of Nile tilapia genetic females, and brain transcriptomes have revealed the upregulation of Jarid2 (Jumonji and AT-rich domain containing 2) expression after 36 °C high-temperature treatment for 12 days during TSP. It was shown that JARID2 forms a complex with polycomb repressive complex 2 (PRC2) that catalyzed H3K27me3, which was strongly associated with transcriptional repression. In this study, Jarid2b was cloned and characterized in Nile tilapia, which was highly conserved among the analyzed fish species. The expression of Jarid2b was upregulated in the gonad of 21 dpf XX genetic females after 12-day high-temperature treatment and reached a similar level to that of males. Similar responses to high-temperature treatment also appeared in the brain, heart, liver, muscle, eye, and skin tissues. Interestingly, Jarid2b expression was only in response to high-temperature treatment, and not to 17α-methyltestosterone (MT) or letrozole treatments; although, these treatments can also induce the sex reversal of genetic Nile tilapia females. Further studies revealed that Jarid2b responded rapidly at the 8th hour after high-temperature treatment. Considering that JARID2 can recruit PRC2 and establish H3K27me3, we speculated that it might be an upstream gene participating in the regulation of Nile tilapia GSD + TE through regulating the H3K27 methylation level at the locus of many sex differentiation-related genes.

Fish sex-determining mechanisms can be classified as genotypic (GSD), temperature (TSD), or genotypic plus temperature effects (GSD+TE). Previous studies have shown that culturing water temperature during thermosensitive periods (TSP) could affect the expression of many genes in the gonad in some fish. However, few studies have focused on gene expression changes in the brain after temperature treatment during TSP in fish species. In this study, three families were developed by crossing XX neomales with XX females and one of them was used for transcriptome analysis. The results showed that a total of 105, 3164 and 4666 DEGs were respectively obtained in FC (female control) vs FT (high temperature treated females at TSP), FC vs MC (male control) and MC vs FT comparison groups. By profiling analysis, we identified that the mRNA expression levels of sixteen DEGs exhibited significant downregulation or upregulation after high temperature treatment and reached a similar level as that in MC. Among the 16 DEGs, LOC100699848 (lysine specific demethylase 6A) and Jarid2 contained JmjC domain, showing the possible important role of JmjC domain in response to temperature treatment in Nile tilapia. Kdm6b (lysine demethylase 6B) and Jarid2 have been shown to play important roles in reptile TSD, showing the relative conservation of regulation mechanisms underlying between TSD in reptile and TSD or GSD+TE in fish species. Finally, the transcriptome profiling was validated using quantitative real time PCR in 9 selected genes. These results will give a hint for investigating the GSD+TE molecular mechanism in fish species.

Background: Nowadays, the molecular mechanisms governing TSD (temperature-dependent sex determination) or GSD + TE (genotypic sex determination + temperature effects) remain a mystery in fish. Methods: We developed three all-female families of Nile tilapia (Oreochromis niloticus), and the family with the highest male ratio after high-temperature treatment was used for transcriptome analysis. Results: First, gonadal histology analysis indicated that the histological morphology of control females (CF) was not significantly different from that of high-temperature-treated females (TF) at various development stages. However, the high-temperature treatment caused a lag of spermatogenesis in high-temperature-induced neomales (IM). Next, we sequenced the transcriptome of CF, TF, and IM Nile tilapia. 79, 11,117, and 11,000 differentially expressed genes (DEGs) were detected in the CF–TF, CF–IM, and TF–IM comparisons, respectively, and 44 DEGs showed identical expression changes in the CF–TF and CF–IM comparisons. Principal component analysis (PCA) indicated that three individuals in CF and three individuals in TF formed a cluster, and three individuals in IM formed a distinct cluster, which confirmed that the gonad transcriptome profile of TF was similar to that of CF and different from that of IM. Finally, six sex-related genes were validated by qRT-PCR. Conclusions: This study identifies a number of genes that may be involved in GSD + TE, which will be useful for investigating the molecular mechanisms of TSD or GSD + TE in fish.