Digital RNA-seq analysis of the cardiac transcriptome response to thermal stress in turbot Scophthalmus maximus.

The hearts of fish play a major role in their physiological plasticity and acclimation to different thermal conditions. To understand the precise mechanism and the pathways activated by thermal cardiac stress in fish, we sampled cardiac tissue from juvenile turbot (Scophthalmus maximus) exposed to control (14°C) and test (20°C, 24°C, and 28°C) conditions, and performed digital RNA sequencing (RNA-seq). A total of 3359 differentially expressed genes (DEGs) were identified. The results of an expression tendency analysis and KEGG annotation analysis of the DEGs demonstrated that energy metabolism played a core role in thermal stress in turbot for the majority of the up-regulated genes. This was followed by lipid metabolism, mitochondrial function, glycolysis, and carbohydrate metabolism. RNA modifications are gaining the interest of biologists worldwide. In this study, at the transcriptome level, our results showed that 246 m6A-containing genes were detected in the DEGs, which were related to EIF3C, EIF3D, EIF3J, METTL16, RBM15B, VIRMA, and YTHDC1. This indicates that m6A is involved in the regulation of heat stress in turbot. This study is an important step towards understanding the cardiac adaptive response to thermal stress. Importantly, the plasticity of cardiac tissue could predict the adaptability of fish species to environmental temperature.

Transcriptome analysis reveals that high temperatures alter modes of lipid metabolism in juvenile turbot (Scophthalmus maximus) liver.

With the increase in farming density and the continuously high summer temperatures against the background of global warming, high temperature stress has become a major challenge in fish farming. In this study, we simulated the high temperature environments (20 °C, 24 °C, and 28 °C) that may occur during turbot culture. High-throughput sequencing was used to investigate the lipid metabolism response patterns in juvenile turbot liver under high temperature stress. A total of 2067 differentially expressed genes (DEGs) were identified. KEGG analysis revealed that the DEGs were mainly associated with glycerophospholipid metabolism, steroid biosynthesis, glycerolipid metabolism, fatty acid metabolic pathways, and the PPAR signaling pathway. A regulatory network was constructed to further elucidate the transcriptional regulation of lipid metabolism. We speculated that high temperature activates PPAR signaling pathway through interaction with ligands such as fatty acids. On the one hand, the HMGCS1 gene in this pathway can inhibit sterol synthesis by down-regulating the expression of key genes in steroid biosynthesis pathway (SQLE, EBP, and DHCR24). On the other hand, the expression of ACSL1 in this pathway is significantly increased under high temperature, which may play an important role in regulating fatty acid metabolism. Moreover, we collected blood and detected changes in serum lipid parameters; the variation patterns were also consistent with our results. These findings reveal that lipid metabolism has an important regulatory role in stress resistance when turbot is exposed to high temperatures.

Correction: Climatic and topographic variables control soil nitrogen, phosphorus, and nitrogen: Phosphorus ratios in a Picea schrenkiana forest of the Tianshan Mountains.

[This corrects the article DOI: 10.1371/journal.pone.0204130.].

Climatic and topographic variables control soil nitrogen, phosphorus, and nitrogen: Phosphorus ratios in a Picea schrenkiana forest of the Tianshan Mountains.

Knowledge about soil nitrogen (N) and phosphorus (P) concentrations, stocks, and stoichiometric ratios is crucial for understanding the biogeochemical cycles and ecosystem function in arid mountainous forests. However, the corresponding information is scarce, particularly in arid mountainous forests. To fill this gap, we investigated the depth and elevational patterns of the soil N and P concentrations and the N: P ratios in a Picea schrenkiana forest using data from soil profiles collected during 2012-2017. Our results showed that the soil N and P concentrations and the N: P ratios varied from 0.15 g kg-1 to 0.56 g kg-1 (average of 0.31 g kg-1), from 0.09 g kg-1 to 0.16 g kg-1 (average of 0.12 g kg-1), and from 2.42 g kg-1 to 4.36 g kg-1 (average of 3.42 g kg-1), respectively; additionally, values significantly and linearly decreased with soil depth. We did not observe a significant variation in the soil N and P concentrations and the N: P ratios with the elevational gradient. In contrast, our results revealed that the mean annual temperature and mean annual precipitation exhibited a more significant influence on the soil N and P concentrations and the N: P ratios than did elevation. This finding indicated that climatic variables might have a more direct impact on soil nutrient status than elevation. The observed relationship among the soil N and P concentrations and the N: P ratios demonstrated that the soil N was closely coupled with the soil P in the P. schrenkiana forest.

Biodistribution of a Promising Probiotic, Bifidobacterium longum subsp. longum Strain BBMN68, in the Rat Gut.

Bifidobacterium longum subsp. longum BBMN68, isolated from centenarians in Guangxi, China, has been proved to be a promising probiotic strain for its health benefits. In this study, the biodistribution of this strain in the rat gut was first investigated using the quantitative realtime PCR assay and propidium monoazide. Strain-specific primers were originally designed based on the BBMN68 genome sequence. Healthy rats were orally inoculated with either a single dose of BBMN68 (10(10) colony-forming units/kg), or with one dose per day for 7 days and bacterial concentrations were analyzed in detail from the intestinal contents and feces of four different gut locations, including stomach, small intestine, colon, and rectum. Results indicated that strain BBMN68 could overcome the rigors of passage through the upper gastrointestinal tract and transiently accumulate in the colon, even though survival in the stomach and small intestine was not high. A good level of BBMN8 could stay in vivo for 72 h following a 7-day oral administration, and a daily administration is suggested for a considerable and continuous population of BBMN68 to be maintained in the host intestine.

Lactobacillus salivarius REN counteracted unfavorable 4-nitroquinoline-1-oxide-induced changes in colonic microflora of rats.

Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1-Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. salivarius REN significantly altered the bacterial communities of rat colons. A total of 27 bacterial strains were identified as being affected by treatment with 4-Nitroquinoline-1-Oxide or L. salivarius REN using a t-value biplot combined with band sequencing. 4-Nitroquinoline-1-Oxide treatment increased the abundance of two potential pathogens (one Helicobacter strain and one Desulfovibrio strain), as well as reducing the abundance of two potentially beneficial strains (one Ruminococcaceae strain and one Rumen bacteria). The Helicobacter strain was initally detected in carcinogen-treated rat intestinal microflora, but L. salivarius REN treatment effectively suppressed the growth of the Helicobacter strain. These results suggested that L. salivarius REN may be a potential probiotic, efficiently acting against the initial infection with, and the growth of pathogenic bacteria.

Correlations of fecal bacterial communities with age and living region for the elderly living in Bama, Guangxi, China.

Bama County (Guangxi, China) is famous for its longevous population. In this study, intestinal microflora of 17 healthy elderly subjects of different ages and from different regions (rural and urban) in Bama, were analyzed by denaturing gradient gel electrophoresis (DGGE). Significant effects of age and living region on the whole intestinal bacterial communities were observed by redundancy analysis (RDA). A total of 11 bacterial strains that were correlated with age and living region were identified using a t-value biplot combined with band sequencing. Four bacterial strains were correlated with both age and living region of the elderly in Bama. Two Bacteroides strains and one Ruminococcaceae strain were abundant in the rural, younger elderly; conversely, one Desulfovibrio strain was high in the urban, older elderly. Another Bacteroidetes strain was only correlated with the participant's age, and its abundance increased with the age of the elderly. The richness of one Clostridium sordellii strain, which was only correlated with the elderly living region, was high in the urban elderly. The study also found five other novel bacterial strains that were correlated with the age or living region of the elderly in Bama. These results expand our understanding of age- and region-effects on the intestinal microflora of the elderly and raise the possibility of developing probiotics originating from centenarians.

Complete genomic sequence analysis of the temperate bacteriophage phiSASD1 of Streptomyces avermitilis.

The bacteriophage phiSASD1, isolated from a failed industrial avermectin fermentation, belongs to the Siphoviridae family. Its four predominant structural proteins, which include the major capsid, portal and two tail-related proteins, were separated and identified by SDS-PAGE and N-terminal sequence analysis. The entire double-stranded DNA genome of phiSASD1 consists of 37,068 bp, with 3'-protruding cohesive ends of nine nucleotides. Putative biological functions have been assigned to 24 of the 43 potential open reading frames. Comparative analysis shows perfect assembly of three "core" gene modules: the morphogenesis and head module, the tail module and the right arm gene module, which displays obvious similarity to the right arm genes of Streptomyces phage phiC31 in function and arrangement. Meanwhile, structural module flexibility within phiSASD1 suggests that assignment of phage taxonomy based on comparative genomics of structural genes will be more complex than expected due to the exchangeability of functional genetic elements.