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Transcriptome sequencing of Macrobrachium nipponense hepatopancreas at different nitrite concentrations

ABSTRACT: Macrobrachium nipponense is one of the commonest species threatened by ambient superfluous nitrite. The mechanism of nitrite stress at the molecular level was studied using de novo RNA-Seq to explore the molecular pathways in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24h and the chronic nitrite stress (6.58 mg/L nitrite-N) for 21d. A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1,028.7 bp and N50 of 1,294bp. 2,824 and 2,610 unigenes in the acute and chronic nitrite stress were significantly differentially expressed respectively. Based on the change in GO analysis and KEGG pathway analysis, pathways both in the acute and chronic nitrite stress were glycosphingolipid biosynthesis - ganglio series, alanine aspartate and glutamate metabolism, biotin metabolism and amino sugar and nucleotide sugar metabolism which revealed the commonly functional pathways in acute and chronic nitrite stress. The markedly altered pathways were divided into four sections of immunity, metabolism, cell and others. Immunity section contained the most pathways among the classifications as phagosome, folate biosynthesis, glycerolipid metabolism, glycine, serine and threonine metabolism, selenoamino acid metabolism, cysteine and methionine metabolism, amino sugar and nucleotide sugar metabolism and taurine and hypotaurine metabolism in the acute nitrite stress and lysosome, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, glycosaminoglycan degradation and amino sugar and nucleotide sugar metabolism in the chronic nitrite stress. This is the first report of whole molecular responses of M. nipponense under acute and chronic nitrite stress through de novo transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanisms of the nitrite stress for crustacean species.

ORGANISM(S): Macrobrachium nipponense

PROVIDER: GSE74684 | GEO | 2016/11/04

SECONDARY ACCESSION(S): PRJNA301151

REPOSITORIES: GEO

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Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.

Project description:Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 hours of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.

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Transcriptome sequencing of Macrobrachium nipponense hepatopancreas at different nitrite concentrations

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