Spatial and temporal anoxia in single-osculum Halichondria panicea demosponge explants studied with planar optodes

The water flow through sponges is regulated by their contractile behaviour including contraction and expansion of the aquiferous system, which leads to shifting oxygen levels in the sponge interior. Still, knowledge of spatial and temporal anoxia in sponges is lacking, but important in elucidating interactions between sponge hosts and their microbiomes. We combined 2-D luminescence lifetime imaging of oxygen with simultaneous time-lapse recordings of the sponge exhalant opening (osculum) to unveil temporal as well as spatial oxygen dynamics caused by contractile behaviour in single-osculum explants of the demosponge Halichondria panicea. The present study reveals an intrinsic concentric deoxygenation pattern in explants during episodes of osculum contraction generating an oxygen gradient with increasing concentrations towards the explant periphery. Four sponge explants faced 25 episodes with substantial changes in internal oxygen and anoxia which prevailed for 4.4 h of the total 92.0 h observation period. The 2-D images revealed that the total area of the explant experiencing anoxia during periods of osculum contraction–expansion varied between 0.01 and 13.22% and was on average 7.4 ± 4.4% for all sponge explants. Furthermore, oxygen respiration, as approximated by the rate of change of oxygen concentration during deoxygenation of the explant interior, was similar throughout the oxic parts of the explant base. The resolved 2-D dynamics provide an unprecedented insight into the internal O2 distribution of sponges and complement the traditional point measurements of oxygen sensors.

Antibiotic treatment of the breadcrumb sponge Halichondria panicea and subsequent recolonization v1

This protocol generates sponges (Halichondria panicea) with a disturbed microbiome under controlled experimental conditions, in order to study bacterial recolonization dynamics. Bacteria-bacteria interactions can be analysed with this set-up within the host environment aiming at a better understanding of sponge-microbe symbiosis in vivo. It is divided into the sections 1) preparation, 2) antibiotic treatment and recovery phase, 3) recolonization with the natural microbiome and 4) sampling.

Metagenomic data for Halichondria panicea from Illumina and Nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.

Objectives: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses. Data description: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of H. panicea - one Illumina MiSeq (2x300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the best assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3,084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.

DNA/RNA extraction and qPCR protocol to assess bacterial abundance in the spongeHalichondria panicea v1

This protocol summarizes experience and recommendations regarding DNA and RNA extractions from the sponge Halichondria panicea and qPCR to quantify bacterial abundance. We have used both bacterial and sponge DNA and RNA for subsequent qPCR. Further, bacterial 16S rRNA amplicon sequencing was performed on DNA and sponge transcriptomes were sequenced successfully from extracted RNA.

Optimasi Kondisi Fermentasi pada Produksi Metabolit Antibakteri dari Bacillus tequilensis BSMF Simbiotik Halichondria panicea

Pendahuluan: Resistensi antibakteri merupakan masalah kesehatan global yang dialami hampir di seluruh negara. Eksplorasi antibakteri dari sumber baru seperti tumbuhan, hewan, dan mikroorganisme baik yang hidup bebas maupun bersimbiosis menjadi solusi alternatif untuk mengatasi resistensi antibakteri. Mikroorganisme berupa bakteri ditargetkan sebagai sumber antibakteri yang berkelanjutan karena jumlahnya melimpah dan mudah dalam proses pembiakan. Bakteri yang hidup bersimbiosis diketahui dapat memproduksi metabolit antibakteri berspektrum lebih luas dibandingkan bakteri yang hidup bebas. Bakteri dapat bersimbiosis dengan berbagai makhluk hidup termasuk organisme multiseluler seperti spons. Isolat Bacillus tequilensis BSMF yang bersimbiosis dengan Halichondria panicea dari Perairan Cabbiya Madura menunjukkan adanya produksi metabolit yang memiliki aktivitas antibakteri. Tujuan: Menentukan pH dan suhu optimum untuk produksi metabolit antibakteri dari Bacillus tequilensis BSMF simbiotik Halichondria panicea. Metode: Produksi metabolit antibakteri dilakukan dengan metode fermentasi padat pada media Potato Dextrose Agar (PDA) yang telah diatur pH dan suhu inkubasinya, sedangkan uji aktivitas antibakteri terhadap Staphylococcus aureus ATCC 25923 dan Eschericia coli ATCC 25922 dilakukan menggunakan metode difusi agar. Penentuan aktivitas antibakteri dilakukan melalui pengukuran diameter zona hambat. Hasil: pH media yang menunjukkan aktivitas antibakteri optimum Bacillus tequilensis BSMF terhadap Staphylococcus aureus ATCC 25923 dan Eschericia coli ATCC 25922 adalah 8 ± 0,5 pada suhu inkubasi 32 ± 1oC dengan rata- rata indeks aktivitas antibakteri berturut- turut 2,74 ± 0,07 dan 3,39 ± 0,07. Kesimpulan: pH dan suhu optimum yang diperoleh adalah pH 8 ± 0,5 dan suhu 32 ± 1oC.

Comparative efficiency of Mytilus edulis as engineering species for shallow-water fouling communities on artificial structures in the White Sea

Currently, there is little comparative data on ‘efficiency’ of different engineering species, i.e. species richness, density and biomass of the associated organisms that have been supported by engineering species. The use of fouling communities makes it possible to compare the efficiency of different engineering species under the same conditions, which is necessary to obtain correct estimates and difficult to do when studying natural bottom communities. In this study, we have analysed the fouling communities in four different mussel culture farms in the White Sea to test the following hypotheses. (1) Different engineering species (mussel Mytilus edulis, solitary ascidian Styela rustica, sponge Halichondria panicea) have different assemblages of the associated vagile fauna. (2) Mytilus edulis is the most efficient engineering species, i.e. species richness, species diversity, density and biomass of the associated vagile fauna is higher in the mussel communities than in those dominated by Styela rustica or Halichondria panicea. The first hypothesis was confirmed, while the second was rejected. In all the culture farms studied, all parameters of the mussel-associated vagile fauna were not higher and in most cases were even lower than those of the fauna associated with ascidians or sponges. The reason for this seems to be the very dense packing of mussels in patches. Therefore, Mytilus edulis is not the most efficient engineering species among fouling organisms, at least in the conditions of the subarctic White Sea. The data obtained are particularly important in view of the ever-increasing volume of anthropogenic substrate and fouling communities in coastal marine ecosystems.

Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea

The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.