1
|
Raghav N, Saraswat P, Kumar S, Chaurasia A, Ranjan R. Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India. World J Microbiol Biotechnol 2024; 40:113. [PMID: 38418624 DOI: 10.1007/s11274-024-03919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Yamuna River water in Agra city of India is contaminated with toxic pollutants, including heavy metals that cause damage to the environment and human health. At present, the direct use of river water for drinking purposes and household activities lead to the direct exposure of society to the contaminants. In this study, Yamuna River water samples were collected from three different sites in Agra city during the monsoon, summer, and winter seasons. The physico-chemical parameters were estimated along with heavy metals. In physico-chemical parameter, the values found were mostly above the permissible limits. The results water samples contain high levels of cadmium, chromium, lead, and nickel above the desirable levels in most cases. The metagenomic analysis revealed that Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctobacteria were the most abundant phyla with a relative abundance of 61%, 9.34%, 5.23%, 4.64%, and 4.3%, respectively. The Comamonadaceae, the most abundant family consists of the genera involved in hydrogen oxidation, iron reduction, degraders of polycyclic aromatic hydrocarbons, and fermentation. The presence of Pseudomonas, Nitrosomonas sp., Thauera humireducens and Dechloromonas denitrificans (decomposition of sewage and organic matter) and Pseudomonas aeruginosa indicates the presence of heavy metal degrading bacteria in water sample. Functional prediction showed the presence of genes responsible for different metabolic pathways that could help developing new bioremediation strategies. The study concludes the status of water contamination, the presence of complex microbial community and suggests the futuristic use and their role in bioremediation.
Collapse
Affiliation(s)
- Nupur Raghav
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Pooja Saraswat
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Sunil Kumar
- Division of Agriculture Bioinformatics, Indian Agricultural Statistical Research Institute, Pusa, New Delhi, 110012, India
| | - Anurag Chaurasia
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, 221305, India.
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India.
| |
Collapse
|
2
|
Ahmed RO, Ali A, Leeds T, Salem M. Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout. Microorganisms 2023; 11:2704. [PMID: 38004716 PMCID: PMC10673235 DOI: 10.3390/microorganisms11112704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.
Collapse
Affiliation(s)
- Ridwan O. Ahmed
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Tim Leeds
- United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV 25430, USA;
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| |
Collapse
|
3
|
Bharti M, Nagar S, Negi RK. Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758). 3 Biotech 2023; 13:320. [PMID: 37649590 PMCID: PMC10462599 DOI: 10.1007/s13205-023-03747-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. Proteobacteria dominated in both sampling sites, while Bacteroidota prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited Verrucomicrobiae and Planctomycetes, negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03747-0.
Collapse
Affiliation(s)
- Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, 110019 India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, North Campus, Delhi, 110007 India
| |
Collapse
|
4
|
Bharti M, Khurana H, Sharma M, Choksket S, Nagar S, Yadav S, Modeel S, Korpole S, Negi RK. Taxonomic and genomic characterization of Sporosarcina cyprini sp. nov., moderately tolerant of Cr +6 and Cd +2 isolated from the gut of invasive fish Cyprinus carpio var. communis (Linn., 1758). Antonie Van Leeuwenhoek 2023; 116:193-206. [PMID: 36400900 DOI: 10.1007/s10482-022-01794-w] [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: 06/28/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022]
Abstract
A Gram-stain-positive, motile, and rod-shaped bacterium, designated as strain MB25T, was isolated from the gut of Cyprinus carpio from the highly polluted river Yamuna, India. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MB25T belonged to the genus Sporosarcina, sharing the highest sequence similarity with S. luteola Y1T (98.98%) and S. koreensis S-K12T (98.91%). Digital DNA-DNA hybridization and average nucleotide identity values of strain MB25T with strain Y1T and S-K12T were 18.9, 77.69, and 18.2, 76.80 respectively. Genome analysis of strain MB25T revealed its biotechnological properties such as tolerance to potent heavy metals, genes for the production of carbohydrate-active enzymes, antimicrobial compounds, and also degradation of aromatic compounds. The G + C content of strain MB25T genome was 45%. Growth observed at 10-40 °C (optimum, 28-30 °C), pH 6.0-8.5 (optimum pH 7.5-8.0); NaCl concentrations up to 6.0% (w/v). The dominant respiratory quinone was MK-7, cell wall peptidoglycan is of the A-4 type containing amino acids Lys-Glu and the major fatty acids are anteiso-C11:0 and iso-C15: 0. The major polar lipids of strain MB25T are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of phenotypic, chemotaxonomic, phylogenetic, and phylogenomic data, strain MB25T represents a novel species of the genus Sporosarcina, for which the name Sporosarcina cyprini sp. nov. is proposed. The type strain is MB25T (= MCC 4366 T = JCM 34521 T = CCM 9113 T).
Collapse
Affiliation(s)
- Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Stanzin Choksket
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India.,Deshbandhu College, University of Delhi, Delhi, 110019, India
| | - Sheetal Yadav
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Sonakshi Modeel
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India.
| |
Collapse
|
5
|
Chen CZ, Li P, Liu L, Li ZH. Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review. ENVIRONMENTAL RESEARCH 2022; 214:114202. [PMID: 36030922 DOI: 10.1016/j.envres.2022.114202] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/10/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
The rise of "new" sequencing technologies and the development of sophisticated bioinformatics tools have dramatically increased the study of the aquaculture microbiome. Microbial communities exist in complex and dynamic communities that play a vital role in the stability of healthy ecosystems. The gut microbiome contributes to multiple aspects of the host's physiological health status, ranging from nutritional regulation to immune modulation. Although studies of the gut microbiome in aquaculture are growing rapidly, the interrelationships between the aquaculture microbiome and its aquatic environment have not been discussed and summarized. In particular, few reviews have focused on the potential mechanisms driving the alteration of the gut microbiome by surrounding aquatic environmental factors. Here, we review current knowledge on the host gut microbiome and its interrelationship with the microbiome of the surrounding environment, mainly including the main methods for characterizing the gut microbiome, the composition and function of microbial communities, the dynamics of microbial interactions, and the relationship between the gut microbiome and the surrounding water/sediment microbiome. Our review highlights two potential mechanisms for how surrounding aquatic environmental factors drive the gut microbiome. This may deepen the understanding of the interactions between the microbiome and environmental factors. Lastly, we also briefly describe the research gaps in current knowledge and prospects for the future orientation of research. This review provides a framework for studying the complex relationship between the host gut microbiome and environmental stresses to better facilitate the widespread application of microbiome technologies in fisheries and aquaculture.
Collapse
Affiliation(s)
- Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
| |
Collapse
|