Molecular biodiversity of Iranian shallow water sponges

Erpenbeck, Dirk; Gholami, A; Hesni, Majid Askari; Ranjbar, Mohammad Sharif; Galitz, Adrian; Eickhoff, Benjamin; Namuth, Leonard; Schumacher, Tatjana; Esmaeili, Hamid Reza; Wörheide, Gert; Teimori, Azad

doi:10.1080/14772000.2020.1737978

Cited by 11 publications

(7 citation statements)

References 64 publications

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“…Initial UPLC-HRMS/MS profiling of the crude organic extract from C. celata revealed the presence of diverse new DKPH analogues. The fractionation of the crude extract by semi-preparative RP-HPLC guided by molecular networking analyses yielded nine fractions (F1-F9), of which F3 and F4 were found to be the main reservoirs of DKPH analogues, which was also supported by 1 H NMR analyses (Supplementary Figure S3). Further RP-HPLC purification of F3 and F4 afforded DKPHs 1-3 (Figure 6).…”

Section: Purification and Structure Elucidation Of Dkphsmentioning

confidence: 58%

“…The hot and dry nature of the geographical area, where evaporation of water exceeds the freshwater input tenfold, as well as the separation from open waters by the Strait of Hormuz, makes the Persian Gulf a hypersaline environment. The Persian Gulf is a shallow sea with high temperature fluctuations, ranging from 12 to 35 °C, representing a significant stress factor for marine flora and fauna [ 1 , 2 ]. Despite all these harsh environmental conditions, plus additional anthropogenic pressures, such as busy shipping lines, the Persian Gulf has a highly diverse fauna dominated by coral and sponge communities [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Networking-Guided Isolation of New Etzionin-Type Diketopiperazine Hydroxamates from the Persian Gulf Sponge Cliona celata

Kouchaksaraee

Nazemi

et al. 2021

Marine Drugs

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The Persian Gulf is a unique and biologically diverse marine environment dominated by invertebrates. In continuation of our research interest in the chemistry and biological activity of marine sponges from the Persian Gulf, we selected the excavating sponge Cliona celata for detailed metabolome analyses, in vitro bioactivity screening, and chemical isolation studies. A UPLC-MS/MS (MS2) molecular-networking-based dereplication strategy allowed annotation and structural prediction of various diketopiperazines (DKPs) and etzionin-type diketopiperazine hydroxamates (DKPHs) in the crude sponge extract. The molecular-networking-guided isolation approach applied to the crude extract afforded the DKPH etzionin (1) and its two new derivatives, clioetzionin A (2) and clioetzionin B (3). Another new modified DKP (4) was identified by MS/MS analyses but could not be isolated in sufficient quantities to confirm its structure. The chemical characterization of the purified DKPHs 1–3 was performed by a combination of 1D and 2D NMR spectroscopy, HRMS, HRMS/MS, and [α]D analyses. Compounds 1 and 2 exhibited broad antibacterial, antifungal, and anticancer activities, with IC50 values ranging from 19.6 to 159.1 µM. This is the first study investigating the chemical constituents of a C. celata specimen from the Persian Gulf. It is also the first report of full spectroscopic data of etzionin based on extensive spectroscopic analyses.

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Section: Purification and Structure Elucidation Of Dkphsmentioning

confidence: 58%

Section: Introductionmentioning

confidence: 99%

Molecular Networking-Guided Isolation of New Etzionin-Type Diketopiperazine Hydroxamates from the Persian Gulf Sponge Cliona celata

Kouchaksaraee

Nazemi

et al. 2021

Marine Drugs

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“…The compounds 1-2 were isolated and their structures were elucidated. 1 H NMR profiling allowed us to observe the presence of DKPs (7, 8), small cyclic peptide compounds, which did not appear on the MN of both crude and CHCl 3 extracts of A. sinoxea. The first DKP ( 7) was previously purified from the sponge-associated yeast Aureobasidium pullulans [21], and from the endophytic bacterium Nocardiopsis sp.…”

Section: Discussionmentioning

confidence: 99%

“…By employing a state-of-the-art automated dereplication strategy such as MN in combination with a traditional chemical profiling method, 1 H NMR spectroscopy, we were able to unravel the chemical machinery of the Persian Gulf sponge A. sinoxea. This approach, together with antimicrobial activity assessments, enabled the purification and characterization of eight compounds from four different natural product classes, which have never been reported from A. sinoxea before.…”

Section: Discussionmentioning

confidence: 99%

“…The Persian Gulf is an extension of the Indian Ocean and is connected to the GO by the Strait of Hormuz. The average depth of the Persian Gulf is around 35 m, and the maximum depth can reach 100 m. Due to extreme aridity and high summer temperatures up to 48 °C, water surface temperature fluctuates between 12 to 35 °C [ 1 , 2 ]. The evaporation of the Persian Gulf exceeds freshwater input tenfold (commonly measured at 40–50 ppt and up to 70 ppt in shallow, enclosed bays) leading to high salinity.…”

Section: Introductionmentioning

confidence: 99%

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Integrating Molecular Networking and 1H NMR Spectroscopy for Isolation of Bioactive Metabolites from the Persian Gulf Sponge Axinella sinoxea

Kouchaksaraee

Farimani

et al. 2020

Marine Drugs

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The geographic position, highly fluctuating sea temperatures and hypersalinity make Persian Gulf an extreme environment. Although this unique environment has high biodiversity dominated by invertebrates, its potential in marine biodiscovery has largely remained untapped. Herein, we aimed at a detailed analysis of the metabolome and bioactivity profiles of the marine sponge Axinella sinoxea collected from the northeast coast of the Persian Gulf in Iran. The crude extract and its Kupchan subextracts were tested in multiple in-house bioassays, and the crude extract and its CHCl3-soluble portion showed in vitro antibacterial activity against Methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium (Efm). A molecular networking (MN)-based dereplication strategy by UPLC-MS/MS revealed the presence of phospholipids and steroids, while 1H NMR spectroscopy indicated the presence of additional metabolites, such as diketopiperazines (DKPs). Integrated MN and 1H NMR analyses on both the crude and CHCl3 extracts combined with an antibacterial activity-guided isolation approach afforded eight metabolites: a new diketopiperazine, (-)-cyclo(L-trans-Hyp-L-Ile) (8); a known diketopiperazine, cyclo(L-trans-Hyp-L-Phe) (7); two known phospholipids, 1-O-hexadecyl-sn-glycero-3-phosphocholine (1) and 1-O-octadecanoyl-sn-glycero-3-phosphocholine (2); two known steroids, 3β-hydroxycholest-5-ene-7,24-dione (3) and (22E)-3β-hydroxycholesta-5,22-diene-7,24-dione (4); two known monoterpenes, loliolide (5) and 5-epi-loliolide (6). The chemical structures of the isolates were elucidated by a combination of NMR spectroscopy, HRMS and [α]D analyses. All compounds were tested against MRSA and Efm, and compound 3 showed moderate antibacterial activity against MRSA (IC50 value 70 μg/mL). This is the first study that has dealt with chemical and bioactivity profiling of A. sinoxea leading to isolation and characterization of pure sponge metabolites.

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Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community

et al. 2020

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Despite their ecological importance, sponges are often avoided in biodiversity studies and monitoring programs because they are notoriously difficult to identify using morphological or molecular methods. Here, we investigate the metabarcoding performance of universal degenerate cytochrome c oxidase subunit I (COI) primers in detecting species from this challenging phylum in a cryptobenthic community. Twenty‐two modified Autonomous Reef Monitoring Structures (ARMS) were deployed for 2 years in mesocosms receiving unfiltered seawater from an adjacent reef slope. Upon recovery, each unit was inspected by a marine sponge taxonomist who used a combination of taxonomy, imagery, and DNA barcoding (28S rRNA and COI) to identify sponges and generate a validated taxonomic richness value for each ARMS unit. A total of 69 unique sponge barcoded morphologies (BMs) were identified from the classes Calcarea, Demospongiae, and Homoscleromorpha. Metabarcoding identified 41 unique sponge molecular operational taxonomic units (MOTUs) from Demospongiae and Homoscleromorpha but the primers failed to amplify any species from the class Calcarea which comprised 22% of the BMs. Sponge richness did not differ between BMs and MOTUs assigned to the classes Demospongiae and Homoscleromorpha. However, assignments at the order and family level in Demospongiae underscore known limitations in sponge taxonomic resolution using the COI gene. The prevalence of false positives within the order Suberitida and the pervasiveness of false negatives within the order Haplosclerida highlighted both technical and biological constraints in the metabarcoding method. Overall, these results confirm the need for discretion in sponge MOTU assignments using universal degenerate barcoding primers that target a short fragment of the COI gene. However, they also demonstrate that COI metabarcoding is capable of capturing sponge richness from a complex natural community.

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Molecular biodiversity of Iranian shallow water sponges

Cited by 11 publications

References 64 publications

Molecular Networking-Guided Isolation of New Etzionin-Type Diketopiperazine Hydroxamates from the Persian Gulf Sponge Cliona celata

Molecular Networking-Guided Isolation of New Etzionin-Type Diketopiperazine Hydroxamates from the Persian Gulf Sponge Cliona celata

Integrating Molecular Networking and 1H NMR Spectroscopy for Isolation of Bioactive Metabolites from the Persian Gulf Sponge Axinella sinoxea

Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community

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