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Microbial Biotechnology Jun 2024Carboxylic ester hydrolases with the capacity to degrade polyesters are currently highly sought after for their potential use in the biological degradation of PET and...
Carboxylic ester hydrolases with the capacity to degrade polyesters are currently highly sought after for their potential use in the biological degradation of PET and other chemically synthesized polymers. Here, we describe MarCE, a carboxylesterase family protein identified via genome mining of a Maribacter sp. isolate from the marine sponge Stelligera stuposa. Based on phylogenetic analysis, MarCE and its closest relatives belong to marine-associated genera from the Cytophaga-Flavobacterium-Bacteroides taxonomic group and appear evolutionarily distinct to any homologous carboxylesterases that have been studied to date in terms of structure or function. Molecular docking revealed putative binding of BHET, a short-chain PET derivative, onto the predicted MarCE three-dimensional structure. The synthetic ester-degrading activity of MarCE was subsequently confirmed by MarCE-mediated hydrolysis of 2 mM BHET substrate, indicated by the release of its breakdown products MHET and TPA, which were measured, respectively, as 1.28 and 0.12 mM following 2-h incubation at 30°C. The findings of this study provide further insight into marine carboxylic ester hydrolases, which have the potential to display unique functional plasticity resulting from their adaptation to complex and fluctuating marine environmentsw.
Topics: Carboxylesterase; Phylogeny; Animals; Porifera; Esters; Gene Expression; Molecular Docking Simulation; Aquatic Organisms
PubMed: 38881500
DOI: 10.1111/1751-7915.14479 -
Marine Drugs Sep 2023The adamantane structure of arsenicin A and nor-adamantane structures of arsenicins B-D have gained attention as unique natural polyarsenicals, as well as hits showing...
The adamantane structure of arsenicin A and nor-adamantane structures of arsenicins B-D have gained attention as unique natural polyarsenicals, as well as hits showing promising anticancer activity. The purpose of this study is to apply the predictive power of NMR DFT calculations in order to identify a valid tool to be used in the structural elucidation of similar molecules. H- and C-NMR chemical shifts of twelve natural and synthetic polyarsenical analogs were calculated and validated by comparison with experimental data acquired in CDCl solutions, in regard to mean absolute error (MAE) values under various combinations of two methods (GIAO and CSGT), four functionals and five basis sets, also considering relativistic effects. The best computational approaches are highlighted for predicting the chemical shifts of H and C nuclei and (H,H) coupling constants in the series of O- and S-polyarsenicals. This comprehensive analysis contributes to making NMR spectroscopy appealing for the structural elucidation of such molecules, contrary to the first structural elucidation of natural arsenicin A, in which the experimental NMR analysis was limited by the poor presence of proton and carbon atoms in its structure and by the shortage of reference data.
Topics: Animals; Magnetic Resonance Spectroscopy; Arsenicals; Porifera; Protons; Adamantane
PubMed: 37888446
DOI: 10.3390/md21100511 -
The Science of the Total Environment Mar 2024Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the...
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V-V 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
Topics: Humans; Seawater; Carbon Dioxide; RNA, Ribosomal, 16S; Dysbiosis; Hydrogen-Ion Concentration; Microbiota; Phylogeny
PubMed: 38246375
DOI: 10.1016/j.scitotenv.2024.170171 -
Environmental Microbiome Mar 2024Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal...
BACKGROUND
Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding.
RESULTS
Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics.
CONCLUSIONS
These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.
PubMed: 38468324
DOI: 10.1186/s40793-024-00556-7 -
BMC Microbiology Dec 2023Malaria is a persistent illness that is still a public health issue. On the other hand, marine organisms are considered a rich source of anti‑infective drugs and other...
Malaria is a persistent illness that is still a public health issue. On the other hand, marine organisms are considered a rich source of anti‑infective drugs and other medically significant compounds. Herein, we reported the isolation of the actinomycete associated with the Red Sea sponge Callyspongia siphonella. Using "one strain many compounds" (OSMAC) approach, a suitable strain was identified and then sub-cultured in three different media (M1, ISP2 and OLIGO). The extracts were evaluated for their in-vitro antimalarial activity against Plasmodium falciparum strain and subsequently analyzed by Liquid chromatography coupled with high-resolution mass spectrometry (LC-HR-MS). In addition, MetaboAnalyst 5.0 was used to statistically analyze the LC-MS data. Finally, Molecular docking was carried out for the dereplicated metabolites against lysyl-tRNA synthetase (PfKRS1). The phylogenetic study of the 16S rRNA sequence of the actinomycete isolate revealed its affiliation to Streptomyces genus. Antimalarial screening revealed that ISP2 media is the most active against Plasmodium falciparum strain. Based on LC-HR-MS based metabolomics and multivariate analyses, the static cultures of the media, ISP2 (ISP2-S) and M1 (M1-S), are the optimal media for metabolites production. OPLS-DA suggested that quinone derivatives are abundant in the extracts with the highest antimalarial activity. Fifteen compounds were identified where eight of these metabolites were correlated to the observed antimalarial activity of the active extracts. According to molecular docking experiments, saframycin Y3 and juglomycin E showed the greatest binding energy scores (-6.2 and -5.13) to lysyl-tRNA synthetase (PfKRS1), respectively. Using metabolomics and molecular docking investigation, the quinones, saframycin Y3 (5) and juglomycin E (1) were identified as promising antimalarial therapeutic candidates. Our approach can be used as a first evaluation stage in natural product drug development, facilitating the separation of chosen metabolites, particularly biologically active ones.
Topics: Animals; Antimalarials; Actinobacteria; Callyspongia; Actinomyces; Indian Ocean; Phylogeny; RNA, Ribosomal, 16S; Molecular Docking Simulation; Lysine-tRNA Ligase; Plasmodium falciparum
PubMed: 38087203
DOI: 10.1186/s12866-023-03094-3 -
Biology Dec 2023As a result of climate change, the Mediterranean Sea has been exposed to an increase in the frequency and intensity of marine heat waves in the last decades, some of...
As a result of climate change, the Mediterranean Sea has been exposed to an increase in the frequency and intensity of marine heat waves in the last decades, some of which caused mass mortality events of benthic invertebrates, including sponges. Sponges are an important component of benthic ecosystems and can be the dominant group in some rocky shallow-water areas in the Mediterranean Sea. In this study, we exposed the common shallow-water Mediterranean sponge (Demospongiae: Chondrillidae) to six different temperatures for 24 h, ranging from temperatures experienced in the field during the year (15, 19, 22, 26, and 28 °C) to above normal temperatures (32 °C) and metabolic traits (respiration and clearance rate) were measured. Both respiration and clearance rates were affected by temperature. Respiration rates increased at higher temperatures but were similar between the 26 and 32 °C treatments. Clearance rates decreased at temperatures >26 °C, indicating a drop in food intake that was not reflected by respiration rates. This decline in feeding, while maintaining high respiration rates, may indicate a negative energy balance that could affect this species under chronic or repeated thermal stress exposure. will probably be a vulnerable species under climate change conditions, affecting its metabolic performance, ecological functioning and the ecosystem services it provides.
PubMed: 38248440
DOI: 10.3390/biology13010009 -
PeerJ 2023The Messinian Salinity Crisis is considered as one of the most influential Cenozoic events that impacted negatively on the benthic fauna of the Mediterranean area....
The Messinian Salinity Crisis is considered as one of the most influential Cenozoic events that impacted negatively on the benthic fauna of the Mediterranean area. Changing environmental conditions, including a sharp reduction of water exchange between the Mediterranean Sea and the Atlantic Ocean, altered the geographical ranges of many organisms, including sponges (Porifera). Here, we report a unique assemblage of isolated sponge spicules from the upper Miocene of southwestern Spain. The newly recognized sponge fauna was inhabiting the Guadalquivir Basin-the corridor between the Mediterranean and the Atlantic Ocean at that time. It represents a taxonomically rich sponge community that consisted of members of "soft" and "lithistid" demosponges and hexactinellids. Demosponges are represented by at least thirty-four taxa, while hexactinellids are significantly rarer; only six taxa have been identified. From among eighteen taxa recognized to the species level, at least eight seem to be inhabiting this area to these days; six are recorded from adjacent areas, such as the Western Mediterranean, South European Atlantic Shelf, and the Azores, and three are present in the Red Sea and/or the Northern Atlantic. Intriguingly, some taxa seem to have their closest relatives in distant areas, such as the Indo-Pacific and Japanese waters which suggests that the range of some once widely-distributed populations shrunk after the isolation of the Mediterranean and the Messinian Salinity Crisis, surviving to the present day only in refugia.
Topics: Salinity; Mediterranean Sea; Geography; Spain; Atlantic Ocean
PubMed: 38025719
DOI: 10.7717/peerj.16277 -
Marine Drugs Apr 2024Two new meroterpenoids, hyrtamide A () and hyrfarnediol A (), along with two known ones, 3-farnesyl-4-hydroxybenzoic acid methyl ester () and dictyoceratin C (), were...
Two new meroterpenoids, hyrtamide A () and hyrfarnediol A (), along with two known ones, 3-farnesyl-4-hydroxybenzoic acid methyl ester () and dictyoceratin C (), were isolated from a South China Sea sponge sp. Their structures were elucidated by NMR and MS data. Compounds - exhibited weak cytotoxicity against human colorectal cancer cells (HCT-116), showing IC values of 41.6, 45.0, and 37.3 μM, respectively. Furthermore, compounds and significantly suppressed the invasion of HCT-116 cells while also downregulating the expression of vascular endothelial growth factor receptor 1 (VEGFR-1) and vimentin proteins, which are key markers associated with angiogenesis and epithelial-mesenchymal transition (EMT). Our findings suggest that compounds and may exert their anti-invasive effects on tumor cells by inhibiting the expression of VEGFR-1 and impeding the process of EMT.
Topics: Humans; Animals; Antineoplastic Agents; Porifera; Colorectal Neoplasms; Terpenes; Epithelial-Mesenchymal Transition; HCT116 Cells; Vascular Endothelial Growth Factor Receptor-1; Vimentin; Cell Line, Tumor; China
PubMed: 38667800
DOI: 10.3390/md22040183 -
Frontiers in Cell and Developmental... 2023
PubMed: 38125877
DOI: 10.3389/fcell.2023.1320209 -
Vavilovskii Zhurnal Genetiki I Selektsii Oct 2023The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina...
The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p<0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius gregarius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring.
PubMed: 38213463
DOI: 10.18699/VJGB-23-80