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Sefrji FO, Abulfaraj AA, Alshehrei FM, Al-Andal A, Alnahari AA, Tashkandi M, Baz L, Barqawi AA, Almutrafy AM, Alshareef SA, Alkhatib SN, Abuauf HW, Jalal RS, Aloufi AS. Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera. Funct Integr Genomics 2025; 25:82. [PMID: 40195156 PMCID: PMC11976380 DOI: 10.1007/s10142-025-01580-7] [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: 01/19/2025] [Revised: 03/07/2025] [Accepted: 03/13/2025] [Indexed: 04/09/2025]
Abstract
Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.
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Affiliation(s)
- Fatmah O Sefrji
- Department of Biology, College of Science, Taibah University, Madinah, 42353, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
| | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, Makkah, 21955, Saudi Arabia
| | - Abeer Al-Andal
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Alaa A Alnahari
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, 21493, Saudi Arabia
| | - Manal Tashkandi
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, 21493, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Aminah A Barqawi
- Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
| | - Abeer M Almutrafy
- Department of Biology, College of Science, Taibah University, Madinah, 42353, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, 21493, Saudi Arabia
| | - Shaza N Alkhatib
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, 21493, Saudi Arabia
| | - Haneen W Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, 24381, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, 21493, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
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Ma J, Yang W, Li S, Yang Z, Qiao C, Liu D, Wang M. Comprehensive effects of tea branch biochar on antibiotic resistance profiles and C/N/S cycling in the compost microbiota of animal manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177457. [PMID: 39536864 DOI: 10.1016/j.scitotenv.2024.177457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 11/05/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
The comprehensive effects of exogenous additives on microbial-driven antibiotic resistance profiles and C/N/S conversion in animal manure composting remains uncertain. This study examined whether tea branch biochar could regulate the microflora involved in antibiotic resistance and C/N/S conversion during pig and chicken manure composting. Compared with the control treatment, biochar addition prolonged the high-temperature period (>55 °C) for 1-2 days and raised the maximum temperature in chicken manure composting. Moreover, biochar addition reduced the prevalence of antibiotic resistance genes (ARGs) in both pig and chicken manure composting by up to 30 %, targeting various types of ARGs such as peptide, phenicol, and diaminopyrimidines. Additionally, the compost microbiota exhibited the overlaps of C/N/S conversion functions. Luteimonas (Xanthomonadaceae) was identified as a dominant bacterium responsible for C/N/S conversion in both pig and chicken manure composting, while also acting as a potential ARG carrier. Thus, Luteimonas is crucial in shaping antibiotic resistance profiles and C/N/S cycling in animal manure composting, indicating its role as a keystone genus. These findings suggest that tea branch biochar can mitigate the spread of ARGs from animal manure, as well as enhance nutrient cycling and compost quality.
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Affiliation(s)
- Jiawei Ma
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wenyan Yang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuai Li
- Key Laboratory of Soil Pollution Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhenyu Yang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China
| | - Chen Qiao
- Key Laboratory of Soil Pollution Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Dan Liu
- Key Laboratory of Soil Pollution Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Mei Wang
- Key Laboratory of Applied Biotechnology on Animal Science & Veterinary Medicine of Zhejiang Province, Zhejiang Engineering Research Center for Veterinary Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, Belt and Road International Joint Laboratory for One Health and Food Safety, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China.
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Wen X, Xu J, Wang Y, Yang X, Peng G, Li S, Ma B, Zou Y, Liao X, Wang Y, Worrich A, Wu Y. Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system. Microbiol Res 2024; 284:127734. [PMID: 38670037 DOI: 10.1016/j.micres.2024.127734] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/27/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yiting Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xin Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guoliang Peng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China
| | - Siming Li
- Shimadzu (China) Co., LTD. Guangzhou Branch, Guangzhou 510656, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Ashy RA. Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum. Saudi J Biol Sci 2023; 30:103789. [PMID: 37680975 PMCID: PMC10480775 DOI: 10.1016/j.sjbs.2023.103789] [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: 08/02/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.
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Affiliation(s)
- Ruba Abdulrahman Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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