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 Halichondria panicea-one Illumina MiSeq (2 × 300 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: 3084). 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.

Effects of Seasonal Anoxia on the Microbial Community Structure in Demosponges in a Marine Lake in Lough Hyne, Ireland.

Climate change is expanding marine oxygen minimum zones (OMZs), while anthropogenic nutrient input depletes oxygen concentrations locally. The effects of deoxygenation on animals are generally detrimental; however, some sponges (Porifera) exhibit hypoxic and anoxic tolerance through currently unknown mechanisms. Sponges harbor highly specific microbiomes, which can include microbes with anaerobic capabilities. Sponge-microbe symbioses must also have persisted through multiple anoxic/hypoxic periods throughout Earth's history. Since sponges lack key components of the hypoxia-inducible factor (HIF) pathway responsible for hypoxic responses in other animals, it was hypothesized that sponge tolerance to deoxygenation may be facilitated by its microbiome. To test this hypothesis, we determined the microbial composition of sponge species tolerating seasonal anoxia and hypoxia in situ in a semienclosed marine lake, using 16S rRNA amplicon sequencing. We discovered a high degree of cryptic diversity among sponge species tolerating seasonal deoxygenation, including at least nine encrusting species of the orders Axinellida and Poecilosclerida. Despite significant changes in microbial community structure in the water, sponge microbiomes were species specific and remarkably stable under varied oxygen conditions, which was further explored for Eurypon spp. 2 and Hymeraphia stellifera However, some symbiont sharing occurred under anoxia. At least three symbiont combinations, all including large populations of Thaumarchaeota, corresponded with deoxygenation tolerance, and some combinations were shared between some distantly related hosts. We propose hypothetical host-symbiont interactions following deoxygenation that could confer deoxygenation tolerance.IMPORTANCE The oceans have an uncertain future due to anthropogenic stressors and an uncertain past that is becoming clearer with advances in biogeochemistry. Both past and future oceans were, or will be, deoxygenated in comparison to present conditions. Studying how sponges and their associated microbes tolerate deoxygenation provides insights into future marine ecosystems. Moreover, sponges form the earliest branch of the animal evolutionary tree, and they likely resemble some of the first animals. We determined the effects of variable environmental oxygen concentrations on the microbial communities of several demosponge species during seasonal anoxia in the field. Our results indicate that anoxic tolerance in some sponges may depend on their symbionts, but anoxic tolerance was not universal in sponges. Therefore, some sponge species could likely outcompete benthic organisms like corals in future, reduced-oxygen ecosystems. Our results support the molecular evidence that sponges and other animals have a Neoproterozoic origin and that animal evolution was not limited by low-oxygen conditions.

Sediment tolerance mechanisms identified in sponges using advanced imaging techniques.

Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events.

Effects of suspended sediments on the sponge holobiont with implications for dredging management.

Dredging can cause high suspended sediment concentrations (SSC) in the water column, posing a hazard to filter feeding organisms like sponges as sediment may clog their aquiferous systems and reduce feeding. In order to provide pressure-response values for sponges to SSC and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were experimentally exposed to a range of dredging-relevant SSC of up to 100 mg L-1, with light compensation across treatments to ensure that SSC was the primary physical parameter. This study shows that some sponge species exposed to high SSC (≥23 mg L-1) for extended periods (28 d) have lower survival, increased necrosis and depletion of energy reserves. In contrast, SSC of ≤10 mg L-1 caused few, if any, negative effects and is thus suggested as a prudent sub-lethal threshold for sponges. Microbial communities did not change significantly among SSC treatments, although a nutritional shift from mixotrophy towards increased phototrophy was detected for some sponge species exposed to high SSC. Importantly however, it is expected that the combined effect of SSC with low light availability and sediment smothering as occurs during dredging operations will increase the negative effects on sponges.

Effects of combined dredging-related stressors on sponges: a laboratory approach using realistic scenarios.

Dredging can cause increased suspended sediment concentrations (SSCs), light attenuation and sedimentation in marine communities. In order to determine the combined effects of dredging-related pressures on adult sponges, three species spanning different nutritional modes and morphologies were exposed to 5 treatment levels representing realistic dredging scenarios. Most sponges survived under low to moderate turbidity scenarios (SSCs of ≤ 33 mg L-1, and a daily light integral of ≥0.5 mol photons m-2 d-1) for up to 28 d. However, under the highest turbidity scenario (76 mg L-1, 0.1 mol photons m-2 d-1) there was 20% and 90% mortality of the phototrophic sponges Cliona orientalis and Carteriospongia foliascens respectively, and tissue regression in the heterotrophic Ianthella basta. All three sponge species exhibited mechanisms to effectively tolerate dredging-related pressures in the short term (e.g. oscula closure, mucus production and tissue regression), although reduced lipids and deterioration of sponge health suggest that longer term exposure to similar conditions is likely to result in higher mortality. These results suggest that the combination of high SSCs and low light availability can accelerate mortality, increasing the probability of biological effects, although there is considerable interspecies variability in how adult sponges respond to dredging pressures.

Effects of sediment smothering on the sponge holobiont with implications for dredging management.

One of the ways dredging can affect benthic habitats is through high levels of sediment deposition, which has the potential to smother sessile organisms such as sponges. In order to provide pressure-response values to sedimentation and tease apart the different cause-effect pathways of high turbidity, 5 sponge species, including heterotrophic and phototrophic nutritional modes, were exposed for up to 30 d to multiple sediment deposition events, each of which resulted in an initial covering of 80-100% of the surface of the sponges in a layer ~0.5 mm thick. The response of the sponges was examined using a suite of different response variables including growth, respiration, lipid content, community composition of the microbial symbionts, and maximum quantum yield and chlorophyll content of the phototrophic symbionts. Different species showed different mechanisms of sediment rejection and different patterns of sediment clearance. All species survived the treatments, were able to tolerate high levels of partial covering of their surfaces, and for most species the treatment did not alter the health of the sponge holobiont. Results from this study will guide interpretation of experiments examining the combined effects of all three dredging-related pressures, and aid the development of water quality thresholds for impact prediction purposes.

Using a thermistor flowmeter with attached video camera for monitoring sponge excurrent speed and oscular behaviour.

A digital, four-channel thermistor flowmeter integrated with time-lapse cameras was developed as an experimental tool for measuring pumping rates in marine sponges, particularly those with small excurrent openings (oscula). Combining flowmeters with time-lapse imagery yielded valuable insights into the contractile behaviour of oscula in Cliona orientalis. Osculum cross-sectional area (OSA) was positively correlated to measured excurrent speeds (ES), indicating that sponge pumping and osculum contraction are coordinated behaviours. Both OSA and ES were positively correlated to pumping rate (Q). Diel trends in pumping activity and osculum contraction were also observed, with sponges increasing their pumping activity to peak at midday and decreasing pumping and contracting oscula at night. Short-term elevation of the suspended sediment concentration (SSC) within the seawater initially decreased pumping rates by up to 90%, ultimately resulting in closure of the oscula and cessation of pumping.

Effects of light attenuation on the sponge holobiont- implications for dredging management.

Dredging and natural sediment resuspension events can cause high levels of turbidity, reducing the amount of light available for photosynthetic benthic biota. To determine how marine sponges respond to light attenuation, five species were experimentally exposed to a range of light treatments. Tolerance thresholds and capacity for recovery varied markedly amongst species. Whilst light attenuation had no effect on the heterotrophic species Stylissa flabelliformis and Ianthella basta, the phototrophic species Cliona orientalis and Carteriospongia foliascens discoloured (bleached) over a 28 day exposure period to very low light (<0.8 mol photons m-2 d-1). In darkness, both species discoloured within a few days, concomitant with reduced fluorescence yields, chlorophyll concentrations and shifts in their associated microbiomes. The phototrophic species Cymbastela coralliophila was less impacted by light reduction. C. orientalis and C. coralliophila exhibited full recovery under normal light conditions, whilst C. foliascens did not recover and showed high levels of mortality. The light treatments used in the study are directly relevant to conditions that can occur in situ during dredging projects, indicating that light attenuation poses a risk to photosynthetic marine sponges. Examining benthic light levels over temporal scales would enable dredging proponents to be aware of conditions that could impact on sponge physiology.

Transcriptomic analysis of differential host gene expression upon uptake of symbionts: a case study with Symbiodinium and the major bioeroding sponge Cliona varians.

BACKGROUND: We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbiodinium-host interactions involves cnidarian partners. To fully and broadly understand the conditions that permit Symbiodinium to procure intracellular residency, we must explore hosts from different taxa to help uncover universal cellular and genetic strategies for invading and persisting in host cells. Here, we present data from gene expression analyses involving the bioeroding sponge Cliona varians that harbors Clade G Symbiodinium. RESULTS: Patterns of differential gene expression from distinct symbiont states ("normal", "reinfected", and "aposymbiotic") of the sponge host are presented based on two comparative approaches (transcriptome sequencing and suppressive subtractive hybridization (SSH)). Transcriptomic profiles were different when reinfected tissue was compared to normal and aposymbiotic tissue. We characterized a set of 40 genes drawn from a pool of differentially expressed genes in "reinfected" tissue compared to "aposymbiotic" tissue via SSH. As proof of concept, we determined whether some of the differentially expressed genes identified above could be monitored in sponges grown under ecologically realistic field conditions. We allowed aposymbiotic sponge tissue to become re-populated by natural pools of Symbiodinium in shallow water flats in the Florida Keys, and we analyzed gene expression profiles for two genes found to be increased in expression in "reinfected" tissue in both the transcriptome and via SSH. These experiments highlighted the experimental tractability of C. varians to explore with precision the genetic events that occur upon establishment of the symbiosis. We briefly discuss lab- and field-based experimental approaches that promise to offer insights into the co-opted genetic networks that may modulate uptake and regulation of Symbiondinium populations in hospite. CONCLUSIONS: This work provides a sponge transcriptome, and a database of putative genes and genetic pathways that may be involved in Symbiodinium interactions. The relative patterns of gene expression observed in these experiments will need to be evaluated on a gene-by-gene basis in controlled and natural re-infection experiments. We argue that sponges offer particularly useful characteristics for discerning essential dimensions of the Symbiodinium niche.