isolated from deep-water marine sponge Theonella swinhoei

A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).

Theonellamides J and K and 5-cis-Apoa-theopalauamide, Bicyclic Glycopeptides of the Red Sea Sponge Theonella swinhoei

Theonella swinhoei is a fairly common inhabitant of reefs throughout the Indian and Pacific Oceans. Metabolomic analyses of samples of T. swinhoei collected in different depths in the Gulf of Aqaba revealed two chemotypes differing in the profiles of the theonellamides they produce, some of which seem to be unknown. Driven by this finding, we examined a sample of T. swinhoei collected more than 40 years ago in the southern part of the Gulf of Aqaba. Large-scale extract of this sample yielded four theonellamides, the known theopalauamide (4), as the major component, and three new metabolites, theonellamide J (1), 5-cis-Apoa-theopalauamide (2), and theonellamide K (3), as the minor components. The planar structure of these complex cyclic glycopeptides was elucidated by combination of 1D and 2D NMR techniques and HRESIMS. The absolute configuration of the amino acids was established by Marfey's and advanced Marfey's methods, and the absolute configuration of its galactose unit using "Tanaka's method" for monosaccharides. The biological activity of the pure compounds was tested for antibacterial activity and for cytotoxicity to HTC-116 cell line. The compounds presented significant cytotoxicity against the HTC-116 cell line, illuminating the importance of the Apoa subunit for the activity.

Arsenate reducing bacteria isolated from the marine sponge Theonella swinhoei: Bioremediation potential

Arsenic (As) contamination of freshwater resources constitutes a major environmental issue affecting over 200 million people worldwide. Although the use of microorganisms for the bioremediation of As has been well studied, only very few candidates have been identified to date. Here, we investigated bacteria associated with the Red Sea sponge Theonella swinhoei and their potential to reduce As in a low-salinity liquid medium. This Indo-Pacific common sponge has been shown to hyper-accumulate As, at an average concentration of 8600 mg/g^-1 in an environment uncontaminated by arsenic or barium. Four isolated strains of bacteria exhibited arsenic reduction potential by transforming inorganic As in the form of arsenate (iAs^V) to arsenite (iAs^III). Two of these isolates were identified as Alteromonas macleodii and Pseudovibrio ascidisceicola, and the other two isolates, both belonging to the same species, were identified as Pseudovibrio denitrificans. The four isolates were then cultured in a low-salinity iAs^V-rich medium (5 mM) and As concentration was measured over time using a specifically designed high-performance liquid chromatograph coupled to a mass spectrometer (HPLC-MS). Out of the four isolates, A. macleodii and P. ascidisceicola grew successfully in a low-salinity liquid medium and reduced As^V to As^III at an average rate of 0.094 and 0.083 mM/h, respectively, thereby demonstrating great potential for the bioremediation of As-contaminated groundwater.

Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges

Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.

Oxygenated Theonellastrols: Interpretation of Unusual Chemical Behaviors Using Quantum Mechanical Calculations and Stereochemical Reassignment of 7α-Hydroxytheonellasterol

A total of eight new oxygenated 4-exo-methylene sterols, 1–8, together with one artifact 9 and six known sterols 11–16, were isolated from the marine sponge Theonella swinhoei collected from the Bohol province in Philippines. Structures of sterols 1–8 were determined from 1D and 2D NMR data. Among the sterols, 8α-hydroxytheonellasterol (4) spontaneously underwent an allylic 1,3-hydroxyl shift to produce 15α-hydroxytheonellasterol (9) as an artifact; this was rationalized by quantum mechanical calculations of the transition state. In addition, the 1,2-epoxy alcohol subunit of 8α-hydroxy-14,15-β-epoxytheonellasterol (5) was assigned using the Gauge-Independent Atomic Orbital (GIAO) NMR chemical shift calculations and subsequent DP4+ analysis. Finally, comparison of the ¹³C chemical shifts of isolated 7α-hydroxytheonellasterol (6) with the reported values revealed significant discrepancies at C-6, C-7, C-8, and C-14, leading to reassignment of the C-7 stereochemistry in the known structure.

New 4-methylidene sterols from the marine sponge Theonella swinhoei

A series of 4-methylidene sterols including three new compounds 1-3, were isolated from the marine sponge Theonella swinhoei. The structures of new compounds were determined on the basis of spectroscopic analyses. Compounds 3, 5, and 6 showed cytotoxicities against U937, MCF-7, and PC-9 cancer cells with IC₅₀ in the range of 1.6-8.8 μM. The new compound 3 exhibited remarkable proapoptotic activity in breast cancer cells. Mechanically, 3 significantly triggered reactive oxygen species (ROS) accumulation resulting in apoptosis and DNA damage in breast cancer cells.

Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium

Theonella swinhoei is an arsenic hyper-accumulator sponge, harboring a multitude of associated bacteria. These bacteria reside in the mesohyl, the dense extracellular matrix of the sponge. Previous elemental analysis of separated cell fractions from the sponge had determined that arsenic is localized to the associated bacteria. Subsequently, sponge-associated arsenic-tolerant bacteria were isolated here and grouped into 15 operational taxonomic units (OTUs, 97% similarity). Both culture-dependent and culture-independent work had revealed that T. swinhoei harbors a highly diverse bacterial community. It was thus hypothesized the acclimation of bacteria in the presence of a sponge skeleton, better mimicking its natural environment, would increase the yield of isolation of sponge-associated bacteria. Using seven modularly designed media, 380 bacteria isolates were grown and grouped into 22 OTUs. Inclusion of sponge skeleton in the growth medium promoted bacterial growth in all seven media, accounting for 20 of the 22 identified OTUs (the other two in a medium without skeleton). Diversity and richness indices were calculated for each treatment or combination of treatments with shared growth parameters. Integrating data inherent in the modularly designed media with the ecological indices led to the formation of new hypotheses regarding the aeration conditions and expected arsenic form in situ. Both aerobic and anoxic conditions are expected to occur in the sponge (temporally and/or spatially). Arsenate is expected to be the dominant (or even the only) arsenic form in the sponge.

Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations

Sponges are potent filter feeders and as such are exposed to high fluxes of toxic trace elements, which can accumulate in their body over time. Such is the case of the Red Sea sponge Theonella swinhoei, which has been shown to accumulate up to 8500 mg/Kg of the highly toxicelement arsenic. T. swinhoei is known to harbor a multitude of sponge-associated bacteria, so it is hypothesized that the associated-bacteria will be tolerant to high arsenic concentration. This study also investigates the fate of the arsenic accumulated in the sponge to test if the associated-bacteria have an important role in the arsenic accumulation process of their host, since bacteria are key players in the natural arsenic cycle. Separation of the sponge to sponge cells and bacteria enriched fractions showed that arsenic is accumulated by the bacteria. Sponge-associated, arsenic-tolerant bacteria were cultured in the presence of 5 mM of either arsenate or arsenite (equivalent to 6150 mg/Kg arsenic, dry weight). The 54 isolated bacteria were grouped to 15 operational taxonomic units (OTUs) and isolates belonging to 12 OTUs were assessed for tolerance to arsenate at increased concentrations up to 100 mM. Eight of the 12 OTUs tolerated an order of magnitude increase in the concentration of arsenate, and some exhibited external biomineralization of arsenic-magnesium salts. The biomineralization of this unique mineral was directly observed in bacteria for the first time. These results may provide an explanation for the ability of the sponge to accumulate considerable amounts of arsenic. Furthermore arsenic-mineralizing bacteria can potentially be used for the study of bioremediation, as arsenic toxicity affects millions of people worldwide.

Isoswinholide B and swinholide K, potently cytotoxic dimeric macrolides from Theonella swinhoei

Chemical investigation of an Indonesian specimen of Theonella swinhoei afforded the new dimeric macrolides isoswinholide B (5) and swinholide K (6), along with the known swinholides A (1), B (2) and D (3) and isoswinholide A (4). Isoswinholide B showed an unprecedented 21/19' lactonization pattern, while swinholide K included an sp(2) methylene attached at C-4 and an additional oxymethine group at C-5, whose configuration has been determined through application of J-based configuration analysis. The isolated swinholides (1-6), with the exception of isoswinholide B, showed a cytotoxic activity on HepG2 (hepatocarcinoma cell line) in the nanomolar range.

Swinholide J, a potent cytotoxin from the marine sponge Theonella swinhoei

In our ongoing search for new pharmacologically active leads from Solomon organisms, we have examined the sponge Theonella swinhoei. Herein we report the isolation and structure elucidation of swinholide A (1) and one new macrolide, swinholide J (2). Swinholide J is an unprecedented asymmetric 44-membered dilactone with an epoxide functionality in half of the molecule. The structural determination was based on extensive interpretation of high-field NMR spectra and HRESIMS data. Swinholide J displayed potent in vitro cytotoxicity against KB cells (human nasopharynx cancer) with an IC₅₀ value of 6 nM.