Transcriptomic responses to pollution in natural riverine environment in Rita rita

Tandrima Mitra; Arabinda Mahanty; Satabdi Ganguly; Bimal Prasanna Mohanty

doi:10.1016/j.envres.2020.109508

Transcriptomic responses to pollution in natural riverine environment in Rita rita

Environ Res. 2020 Jul:186:109508. doi: 10.1016/j.envres.2020.109508. Epub 2020 Apr 14.

Authors

Tandrima Mitra¹, Arabinda Mahanty², Satabdi Ganguly³, Bimal Prasanna Mohanty⁴

Affiliations

¹ ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; School of Biotechnology, KIIT-Deemed to be University, Patia, Bhubaneswar, 751024, India.
² ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; ICAR-National Rice Research Institute, Crop Protection Division, Cuttack, 753006, India.
³ ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India.
⁴ ICAR- Central Inland Fisheries Research Institute, Fishery Resource and Environmental Management Division, Biochemistry Laboratory, Barrackpore, Kolkata, 700 120, India; ICAR-Fisheries Science Division, Krishi Anusandhan Bhawan II, Pusa, New Delhi, 110 012, India. Electronic address: bimal.mohanty@icar.gov.in.

PMID: 32325295
DOI: 10.1016/j.envres.2020.109508

Abstract

Aquatic pollution is one of the most common threats to the ecological health of aquatic ecosystems and its biota. Fish as lower vertebrates are excellent model to study the impact and responses of aquatic pollution. In fish, gill is the main organ indicator of whole animal health as it comes in contact with the surrounding water and absorbs many pollutants and contaminants; therefore, investigations on alterations in fish gill at transcriptome level could provide newer insights to the stress response mechanism(s) and pathways. For comprehensive evaluation of the impacts of pollutants (joint toxicity) prevalent in the riverine environment, comparative transcriptome analysis, by Next Generation Sequencing under Illumina HiSeq 2500 platform, was carried out in gill tissues of Rita rita collected from two stretches of river Ganga (Kanpur and Farakka) and results were validated by RT-qPCR. Out of 154,077 unigenes (Accession SRR548008), a total of 2024 differentially expressed genes (DEGs) including 942 up-regulated and 1082 down-regulated genes were identified by DESeq program. Further, Gene Ontology (GO) of DEGs showed that ribosomal large subunit biogenesis, mitochondrial ribosome and box H/ACA SnoRNA binding categories are highly affected by pollution. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed the involvement of the DEGs in energy metabolism, translational and transcriptional machinery, protein folding and degradation suggesting that these signalling pathways are highly affected by aquatic pollution. Among the DEGs, up-regulation of cytochrome c oxidase subunit (cox) 7a2 (69.47 fold), hsp70 subunit 14 (hsp70-14, 5.27 fold), muscle related coiled-coil protein (MURC, 21.55 fold), lysozyme G (40.14 fold), cox17 (29.36 fold) were the conspicuous ones which showed similar trends in expression when analysed by RT-qPCR. Based on fold change, perturbation values, correlation analysis by PCA and RT-qPCR validation, up-regulation of cox7a2, MURC and hsp70-14 appeared to be the most promising biomarker responses and could be useful in the evaluation of gill health and possibly be extended towards aquatic ecosystem health assessment.

Keywords: Aquatic pollution; Biomarker; Gill; Rita rita; Riverine environment; Transcriptomic responses.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Catfishes*
Ecosystem
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Transcriptome*