Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic pro...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-02-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/2/531 |
| _version_ | 1797619196148842496 |
|---|---|
| author | Nazima Habibi Saif Uddin Hanan Al-Sarawi Ahmed Aldhameer Anisha Shajan Farhana Zakir Nasreem Abdul Razzack Faiz Alam |
| author_facet | Nazima Habibi Saif Uddin Hanan Al-Sarawi Ahmed Aldhameer Anisha Shajan Farhana Zakir Nasreem Abdul Razzack Faiz Alam |
| author_sort | Nazima Habibi |
| collection | DOAJ |
| description | Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were <i>Woeseia, Nitrosopumilus</i>, and <i>Rhizophagus</i>, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA <i>p</i> > 0.05; ANOSIM-0.05, <i>p</i> > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs. |
| first_indexed | 2024-03-11T08:23:40Z |
| format | Article |
| id | doaj.art-f0bd8803746f4659bf943da88196169f |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T08:23:40Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-f0bd8803746f4659bf943da88196169f2023-11-16T22:17:11ZengMDPI AGMicroorganisms2076-26072023-02-0111253110.3390/microorganisms11020531Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and ResistomeNazima Habibi0Saif Uddin1Hanan Al-Sarawi2Ahmed Aldhameer3Anisha Shajan4Farhana Zakir5Nasreem Abdul Razzack6Faiz Alam7Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitEnvironment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, KuwaitCoastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were <i>Woeseia, Nitrosopumilus</i>, and <i>Rhizophagus</i>, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA <i>p</i> > 0.05; ANOSIM-0.05, <i>p</i> > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.https://www.mdpi.com/2076-2607/11/2/531shotgun sequencingenvironmental DNAbacteriafunctional annotationbiomonitoringarchaea |
| spellingShingle | Nazima Habibi Saif Uddin Hanan Al-Sarawi Ahmed Aldhameer Anisha Shajan Farhana Zakir Nasreem Abdul Razzack Faiz Alam Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome Microorganisms shotgun sequencing environmental DNA bacteria functional annotation biomonitoring archaea |
| title | Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome |
| title_full | Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome |
| title_fullStr | Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome |
| title_full_unstemmed | Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome |
| title_short | Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome |
| title_sort | metagenomes from coastal sediments of kuwait insights into the microbiome metabolic functions and resistome |
| topic | shotgun sequencing environmental DNA bacteria functional annotation biomonitoring archaea |
| url | https://www.mdpi.com/2076-2607/11/2/531 |
| work_keys_str_mv | AT nazimahabibi metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT saifuddin metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT hananalsarawi metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT ahmedaldhameer metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT anishashajan metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT farhanazakir metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT nasreemabdulrazzack metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome AT faizalam metagenomesfromcoastalsedimentsofkuwaitinsightsintothemicrobiomemetabolicfunctionsandresistome |