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Gupta RK, Tikariha H, Purohit HJ, Khardenavis AA. Pangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal. Arch Microbiol 2023; 205:270. [PMID: 37356030 DOI: 10.1007/s00203-023-03597-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/27/2023]
Abstract
Nitrogen metabolism in the genus Citrobacter is very poorly studied despite its several implications in wastewater treatment. In the current study, Citrobacter portucalensis strain AAK_AS5 was assessed for remediation of simulated wastewater supplemented with different inorganic nitrogen sources. Combination of (NH4)2SO4 with KNO3 was the most preferred for achieving high growth density followed by (NH4)2SO4 and KNO3 alone. This was in agreement with highest ammonical nitrogen removal of 92.9% in the presence of combined nitrogen sources and the corresponding nitrate nitrogen removal of 93% in the presence of KNO3. Furthermore, these removal capacities were validated by investigating the uniqueness and the spread of metabolic features through pan-genomic approach that revealed the largest number of unique genes (2097) and accessory genes (705) in strain AAK_AS5. Of the total 44 different types of nitrogen metabolism-related genes, 39 genes were associated with the core genome, while 5 genes such as gltI, nasA, nasR, nrtA, and ntrC uniquely belonged to the accessory genome. Strain AAK_AS5 possessed three major nitrate removal pathways viz., assimilatory and dissimilatory nitrate reduction to ammonia (ANRA & DNRA), and denitrification; however, the absence of nitrification was compensated by ammonia assimilation catalyzed by gene products of the GDH and GS-GOGAT pathways. narGHIJ encoding the respiratory nitrate reductase was commonly identified in all the studied genomes, while genes such as nirK, norB, and nosZ were uniquely present in the strain AAK_AS5 only. A markedly different genetic content and metabolic diversity between the strains reflected their adaptive evolution in the environment thus highlighting the significance of C. portucalensis AAK_AS5 for potential application in nitrogen removal from wastewater.
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Affiliation(s)
- Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hitesh Tikariha
- NUS Environmental Research Institute, National University of Singapore, Singapore, 117411, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Arumugaperumal A, Sudalaimani DK, Arumugaswami V, Sivasubramaniam S. Draft Genome Sequence of the Earthworm Eudrilus eugeniae. Curr Genomics 2022; 23:118-125. [PMID: 36778974 PMCID: PMC9878837 DOI: 10.2174/1389202923666220401095626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Earthworms are annelids. They play a major role in agriculture and soil fertility. Vermicompost is the best organic manure for plant crops. Eudrilus eugeniae is an earthworm well suited for efficient vermicompost production. The worm is also used to study the cell and molecular biology of regeneration, molecular toxicology, developmental biology, etc., because of its abilities like high growth rate, rapid reproduction, tolerability toward wide temperature range, and less cost of maintenance. Objective: The whole genome has been revealed only for Eisenia andrei and Eisenia fetida. Methods: In the present work, we sequenced the genome of E. eugeniae using the Illumina platform and generated 160,684,383 paired-end reads. Results: The reads were assembled into a draft genome of size 488 Mb with 743,870 contigs and successfully annotated 24,599 genes. Further, 208 stem cell-specific genes and 3,432 non-coding genes were identified. Conclusion: The sequence and annotation details were hosted in a web application available at https://sudhakar-sivasubramaniam-labs.shinyapps.io/eudrilus_genome/.
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Affiliation(s)
| | | | | | - Sudhakar Sivasubramaniam
- Address correspondence to this author at the Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu- 627012, India; Tel: +91 9940998936; E-mail:
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Paul S, Balakrishnan S, Arumugaperumal A, Lathakumari S, Syamala SS, Vijayan V, Durairaj SCJ, Arumugaswami V, Sivasubramaniam S. Importance of clitellar tissue in the regeneration ability of earthworm Eudrilus eugeniae. Funct Integr Genomics 2022; 22:1-32. [PMID: 35416560 DOI: 10.1007/s10142-022-00849-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost segments. The adult earthworm Eudrilus eugeniae contains 120 segments and the body segments of the earthworm are divided into pre-clitellar, clitellar and post-clitellar segments. The present study denoted that clitellum plays vital role in the successful regeneration of the species. We have performed histological studies to identify among the three skin layers of the earthworm, which cellular layer supports the blastema formation and regeneration of the species. The histological evidences denoted that the proliferation of the longitudinal cell layer at the amputation site is crucial for the successful regeneration of the earthworm and it takes place only in the presence of an intact clitellum. Besides we have performed clitellar transcriptome analysis of the earthworm Eudrilus eugeniae to monitor the key differentially expressed genes and their associated functions and pathways controlling the clitellar tissue changes during both anterior and posterior regeneration of the earthworm. A total of 4707 differentially expressed genes (DEGs) were identified between the control clitellum and clitellum of anterior regenerated earthworms and 4343 DEGs were detected between the control clitellum and clitellum of posterior regenerated earthworms. The functional enrichment analysis confirmed the genes regulating the muscle mass shape and structure were significantly downregulated and the genes associated with response to starvation and anterior-posterior axis specification were significantly upregulated in the clitellar tissue during both anterior and posterior regeneration of the earthworm. The RNA sequencing data of clitellum and the comparative transcriptomic analysis were helpful to understand the complex regeneration process of the earthworm.
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Affiliation(s)
- Sayan Paul
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.,Centre for Cardiovascular Biology and Disease, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | | | - Arun Arumugaperumal
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Saranya Lathakumari
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Sandhya Soman Syamala
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Vijithkumar Vijayan
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India
| | - Selvan Christyraj Jackson Durairaj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.,Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600 119, India
| | | | - Sudhakar Sivasubramaniam
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, 627012, India.
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