Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes

Martínez-Núñez, Mario Alberto; Rodríguez-Escamilla, Zuemy

doi:10.3390/toxins12060349

Cited by 10 publications

(6 citation statements)

References 87 publications

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“…Finally, our results indicate that conserved wetlands represent an invaluable source of molecules with potential applications in different industries such as pharmaceutical, cosmetic, agricultural, among others. As it has been reported in the case of the Non-ribosomal peptides synthetase (NRPSs) genes, which synthesize compounds with different biotechnological applications and whose presence is enriched in El Palmar [ 82 ]. It is important to mention that metabolic functions associated with biogeochemical processes and degradation of xenobiotics were also identified.…”

Section: Discussionmentioning

confidence: 99%

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

et al. 2021

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Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

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Section: Discussionmentioning

confidence: 99%

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

et al. 2021

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“…This microbial community analysis also highlights the different results that can be obtained when comparing metagenomics and 16S rRNA, since none of the two year sampling campaigns agree with a 2019 study describing the microbial community in El Palmar sediments, emphasizing the need for metagenomic studies to better understand the diversity of the microorganisms whose genomes are influencing the microbial processes in the environment [ 31 , 63 ].…”

Section: Discussionmentioning

confidence: 99%

“…For example, a Streptomyces strain isolated from the top sediment layer of a mangrove in Koringa, India, possessed antimicrobial activity against Candida albicans and Pectinotrichum llanense [ 27 ], while another Streptomyces strain isolated from Indian mangrove sediments was reported to possess promising antioxidant, antimicrobial, and anti-inflammatory agents [ 28 ]. However, descriptions of the biotechnological potential of mangrove microbial communities through the use of genome mining is scarce, and little research has focused on identifying genes involved in the biosynthesis of medically and industrially relevant compounds from these sediments [ 29 , 30 , 31 , 32 ]. Among these genes, polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes are the most commonly used to assess the natural product potential of a community due to their involvement in the biosynthesis of numerous bioactive compounds [ 33 , 34 , 35 ].…”

Section: Introductionmentioning

confidence: 99%

A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

et al. 2021

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Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

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“…2500 compounds [24]. Marine or terrestrial Actinobacteria utilize enzymes polyketide synthases (PKS) or non-ribosomal peptide synthetases (NRPS) for the synthesis of metabolic bioactive compounds [25]. Marine sediment sampled off the coast of San Diego, California, has a new marine actinomycete, NPS12745, associated with it.…”

Section: Antimicrobial Applications Of Actinomycetesmentioning

confidence: 99%

Microorganisms: A Potential Source of Bioactive molecules for Antioxidants and Antimicrobial Applications

Rani¹,

Saini²,

Bast³

et al. 2021

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Oxidative stress is an elevated intracellular level of free oxygen radicals that cause lipid peroxidation, protein denaturation, DNA hydroxylation, and apoptosis, ultimately negotiating cells viability. Antioxidants can scavenge such free radicals, thus reducing the oxidative stress and eventually prevent cellular damage. Medicinal plants, fruits, and spices remain the prioritized sources of antioxidants and antimicrobial properties since the time immemorial, but in contrast to plants, microorganisms can be grown at a faster rate under controlled conditions. They are non-toxic, non-carcinogenic, and biodegradable as compared to synthetic antioxidants. Microorganisms including actinomycetes, archaea, bacteria, protozoa, yeast, and fungi are auspicious source of vital bioactive compounds. The list comprises ample of bioactive components from microorganisms. One of them is bacteriocins, which are ribosomally synthesized antimicrobial peptides product of Eurotium sp., Streptomyces parvulus, S. thermophiles, Lactococcus lactis, etc. It has a great potential as next-generation antibiotics targeting the multiple-drug resistant pathogens. Pneumocandins are antifungal lipohexapeptides derived from the fungus Glarea lozoyensis, and inhibit 1,3-β-glucan synthase of the fungal cell wall and act as a precursor for the synthesis of caspofungin. It is widely used against invasive fungal infections and has been recently approved by the FDA. Taxol (paclitaxel), a chemotherapeutic drug derived from the bark of Taxus brevifolia can also be produced by endophytic fungi Taxomyces andreanae and Nodulisporium sylviforme. It is known to inhibit several fungi such as Pythium, Aphanomyces and Phytophthora. Hispidin and its derivate isolated from P. hispidus, reduce inducible nitric oxide synthase (iNOS) expression, obstruct the transcriptional activity of NF-κB, and also decrease the production of reactive oxygen species (ROS) in macrophages. Astaxanthin, known as an “aquatic” carotenoid produced by H. pluvialis, also has excellent ROS quenching activity. This study mainly focuses on fascinating antioxidant and antimicrobial compounds that have been scarcely investigated in microorganisms and discuss the promise and challenges of microorganisms as providers of health benefits.

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Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes

Cited by 10 publications

References 87 publications

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Microorganisms: A Potential Source of Bioactive molecules for Antioxidants and Antimicrobial Applications

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