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Scientific Reports Mar 2024Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still...
Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.
Topics: Animals; Porifera; Antarctic Regions; Ammonia; Archaea; Bacteria; Microbiota; Phylogeny; RNA, Ribosomal, 16S
PubMed: 38493232
DOI: 10.1038/s41598-024-56480-w -
Antonie Van Leeuwenhoek Mar 2024A new member of the family Flavobacteriaceae (termed Hal144) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018...
A new member of the family Flavobacteriaceae (termed Hal144) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018 at Schilksee which is located in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the full-length Hal144 16S rRNA gene sequence revealed similarities from 94.3 to 96.6% to the nearest type strains of the genus Maribacter. The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain Hal144 with its closest relatives Maribacter aestuarii GY20 (96.6%) and Maribacter thermophilus HT7-2 (96.3%). Genome phylogeny showed that Maribacter halichondriae Hal144 branched from a cluster consisting of Maribacter arenosus, Maribacter luteus, and Maribacter polysiphoniae. Genome comparisons of strain Maribacter halichondriae Hal144 with Maribacter sp. type strains exhibited average nucleotide identities in the range of 75-76% and digital DNA-DNA hybridisation values in the range of 13.1-13.4%. Compared to the next related type strains, strain Hal144 revealed unique genomic features such as phosphoenolpyruvate-dependent phosphotransferase system pathway, serine-glyoxylate cycle, lipid A 3-O-deacylase, 3-hexulose-6-phosphate synthase, enrichment of pseudogenes and of genes involved in cell wall and envelope biogenesis, indicating an adaptation to the host. Strain Hal144 was determined to be Gram-negative, mesophilic, strictly aerobic, flexirubin positive, resistant to aminoglycoside antibiotics, and able to utilize N-acetyl-β-D-glucosamine. Optimal growth occurred at 25-30 °C, within a salinity range of 2-6% sea salt, and a pH range between 5 and 8. The major fatty acids identified were C 3-OH, iso-C, and iso-C G. The DNA G + C content of strain Hal144 was 41.4 mol%. Based on the polyphasic approach, strain Hal144 represents a novel species of the genus Maribacter, and we propose the name Maribacter halichondriae sp. nov. The type strain is Hal144 (= DSM 114563 = LMG 32744).
Topics: Animals; Seawater; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Porifera; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Vitamin K 2; Fatty Acids; Flavobacteriaceae
PubMed: 38489089
DOI: 10.1007/s10482-024-01950-4 -
Chembiochem : a European Journal of... May 2024This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized... (Review)
Review
This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.
Topics: Biological Products; Amino Acids; Bacteria; Fungi; Animals; Porifera
PubMed: 38487927
DOI: 10.1002/cbic.202300822 -
Zootaxa Jan 2024The South Orkney Islands (SOI) is a poorly studied Antarctic archipelago located in the Scotia Arc. In this study, we added 25 Demospongiae species to the SOI known...
The South Orkney Islands (SOI) is a poorly studied Antarctic archipelago located in the Scotia Arc. In this study, we added 25 Demospongiae species to the SOI known sponge richness, which was previously represented by only 16 species. Of these, 22 species represent new records for SOI region, although they were previously recorded from other Antarctic sectors. Samples were collected during two Argentinean Antarctic Research Cruises onboard RV Puerto Deseado. The most frequently collected species were Artemisina apollinis, Iophon gaussi, I. unicorne, Lissodendoryx (E.) ramilobosa, Myxodoryx hanitschi and Tedania (T.) tantula. Data and illustrations of some rare or uncommon species are provided: Iophon gaussi, Lissodendoryx (E.) anacantha, Microxina charcoti, Raspailia (H.) hentscheli, Haliclona spongiosissima, Haliclona (G.) cf. cucurbitiformis. Although the present results increase substantially the previously known information on sponge species, this is still an underestimation of total richness because certain orders (Tetractinellida, Suberitida, Biemnida, Polymastiida) and classes were not studied during the current investigation, although previous records were included.
Topics: Animals; Antarctic Regions; Haliclona; Porifera
PubMed: 38480427
DOI: 10.11646/zootaxa.5403.4.1 -
Zootaxa Feb 2024Acanthotetilla is a genus of tetillid sponges diagnosed by the presence of medium-sized, heavily spined oxeas, which are known as megacanthoxeas (or simply acanthoxeas)....
A new Acanthotetilla sponge from the Southwest Atlantic (Tetillidae, Spirophorina, Tetractinellida, Demospongiae), with an updated discussion on the diversity, distribution and morphologic characters of Acanthotetilla spp.
Acanthotetilla is a genus of tetillid sponges diagnosed by the presence of medium-sized, heavily spined oxeas, which are known as megacanthoxeas (or simply acanthoxeas). Currently, seven species are known worldwide: three from the Western Atlantic (A. gorgonosclera, A. rocasensis and A. walteri), three from the Western Indian (A. hemisphaerica, A. enigmatica and A. seychellensis) and one from the Western Pacific (A. celebensis). A megacanthoxea-bearing specimen was obtained from the Fernando de Noronha Archipelago, Southwest Atlantic, in 2016. It is described here as a new Acanthotetilla, namely, A. noronhensis sp. nov. This new species has two categories of megacanthoxeas, like A. celebensis from Celebes/Sulawesi Sea, Indonesia. However, the former differs from the latter, as well as from other congeners, by the combination of endolithic habit and spiculation. Acanthotetilla noronhensis sp. nov. is known on the basis of a single specimen from a large collection of sponges from Fernando de Noronha. Besides, the species was not found in other sponge collections from different areas of Brazil, including oceanic areas. Thus, the new species has probably a low abundance and restricted distribution, alike all other known Acanthotetilla species, aside A. celebensis, which (regardless its low abundance) occurs in a large sector of the western Pacific. Despite A. noronhensis sp. nov. and A. celebensis being separated by a wide geographic distance, the unique occurrence of two categories of megacanthoxeas might suggest closer phylogenetic relationship and biogeographic history as well. A wider discussion on the diversity, distribution and morphologic characters of Acanthotetilla spp. is supplied in this study. A comparative taxonomic table and a taxonomic identification key to Acanthotetilla spp. is supplied as well.
Topics: Animals; Phylogeny; Porifera
PubMed: 38480256
DOI: 10.11646/zootaxa.5410.1.4 -
Zootaxa Feb 2024The demosponge genus Placospongia includes 13 valid species, of which six occur in the Brazilian Exclusive Economic Zone. In the present study, we describe two new...
The demosponge genus Placospongia includes 13 valid species, of which six occur in the Brazilian Exclusive Economic Zone. In the present study, we describe two new species of Placospongia from Northern (off the Amazon River mouth) and Northeastern Brazilian continental shelf and oceanic islands (i.e., Fernando de Noronha Archipelago), viz., Placospongia beatrizae sp. nov. and Placospongia amphinolastra sp. nov., and redescribe the holotype of Placospongia cristata Boury-Esnault, 1973, a poorly known species. In addition, we revise the Brazilian records of the allegedly cosmopolitan species P. carinata, P. melobesioides and P. intermedia, and provide new records of P. colombiensis and P. ruetzleri from Brazil. We demonstrate that P. carinata sensu Coelho & Mello-Leito and P. intermedia sensu Muricy & Moraes and Jimenez et al. belong in fact to P. ruetzleri, and that P. melobesioides sensu Mothes et al. and Gonzlez-Faras is a new species, described here as Placospongia beatrizae sp. nov. With the description of the two new species and synonymyzation of previous records, six species of Placospongia are currently known in Brazilian waters, two of which are endemic. A key to Placospongia species is also provided.
Topics: Animals; Brazil; Porifera
PubMed: 38480173
DOI: 10.11646/zootaxa.5405.4.2 -
Frontiers in Microbiology 2024Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is...
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of and , which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
PubMed: 38476944
DOI: 10.3389/fmicb.2024.1347422 -
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 -
Proceedings of the National Academy of... Mar 2024Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established...
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
Topics: Animals; Peptides; Peptides, Cyclic; Amino Acid Sequence; Bandages; Protein Sorting Signals
PubMed: 38442178
DOI: 10.1073/pnas.2314383121 -
Marine Biotechnology (New York, N.Y.) Apr 2024The present study aims to characterize and to evaluate the biological effects of a skin dressing manufactured with the organic part of the Chondrilla caribensis marine...
The present study aims to characterize and to evaluate the biological effects of a skin dressing manufactured with the organic part of the Chondrilla caribensis marine sponge (called spongin-like collagen (SC)) associated or not to photobiomodulation (PBM) on the skin wound healing of rats. Skin dressings were manufactured with SC and it was characterized using scanning electron microscopy (SEM) and a tensile assay. In order to evaluate its biological effects, an experimental model of cutaneous wounds was surgically performed. Eighteen rats were randomly distributed into three experimental groups: control group (CG): animals with skin wounds but without any treatment; marine collagen dressing group (DG): animals with skin wounds treated with marine collagen dressing; and the marine collagen dressing + PBM group (DPG): animals with skin wounds treated with marine collagen dressing and PBM. Histopathological, histomorphometric, and immunohistochemical evaluations (qualitative and semiquantitative) of COX2, TGFβ, FGF, and VEGF were done. SEM demonstrates that the marine collagen dressing presented pores and interconnected fibers and adequate mechanical strength. Furthermore, in the microscopic analysis, an incomplete reepithelialization and the presence of granulation tissue with inflammatory infiltrate were observed in all experimental groups. In addition, foreign body was identified in the DG and DPG. COX2, TGFβ, FGF, and VEGF immunostaining was observed predominantly in the wound area of all experimental groups, with a statistically significant difference for FGF immunostaining score of DPG in relation to CG. The marine collagen dressing presented adequate physical characteristics and its association with PBM presented favorable biological effects to the skin repair process.
Topics: Animals; Wound Healing; Rats; Porifera; Collagen; Skin; Bandages; Low-Level Light Therapy; Male; Vascular Endothelial Growth Factor A; Cyclooxygenase 2; Disease Models, Animal; Rats, Wistar; Transforming Growth Factor beta; Tensile Strength; Fibroblast Growth Factors; Microscopy, Electron, Scanning
PubMed: 38441733
DOI: 10.1007/s10126-024-10295-y