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Nutrient acquisition through heterotrophy is critical for the health of reef-building corals. The optimization of exogenous nutrition protocols to support a diversity of aquaculture corals requires improved techniques to assess feeding rates. Here, we compared the feeding rates of three coral species (Acropora millepora, Pocillopora acuta and Galaxea fascicularis) fed Artemia salina through capture rate (indirect) and dissection (direct) approaches, with direct detection and enumeration within dissected polyps facilitated by fluorescent microbeads ingested by the Artemia. When A. millepora was provided Artemia at 3 individuals ml−1 for one hour, the calculated capture rates (0.7 ind. polyp−1 h−1) overestimated prey ingested compared to prey detected directly within polyps (0.2 ind. polyp−1 h−1), and ingestion varied significantly between genotypes. In contrast, for P. acuta, capture rate calculations (1 ind. polyp−1 h−1) underestimated prey detected within polyps (3.5 ind. polyp−1 h−1) and ingestion did not vary between genotypes. For G. fascicularis, the feeding rates were similar as calculated by both capture rates (59 ind. polyp−1 h−1) and by polyp dissections (75 ind. polyp−1 h−1). Results from this study provide valuable insights into coral feeding rates of different coral species that can improve prey enrichment and feeding strategies for nutritional supplementation of corals in captivity.

Highly nutritional microalgal species are extensively used in aquaculture as live feedstock. Due to difficulties in maintaining microalgae in axenic conditions, they represent a potential pathogen carrier and disease vector in aquaculture ponds. Photodynamic therapy (PDT) via singlet oxygen (1O2) production is a promising sterilization technique in aquaculture. Here, we report on the sensitivity of aquaculture-relevant microalgae towards 1O2 generated by the cationic photosensitizer TMPyP. Possible PDT sterilization protocols of contaminated microalgae cultures were evaluated using the luminescent bacterium Vibrio campbellii ISO7 as a model aquaculture pathogen. Species-specific sensitivity of microalgae to TMPyP-mediated PDT was demonstrated and found to be strongly influenced by the nature and architecture of their respective cell wall. While cytotoxicity was not evident against Nannochloropsis oculata, toxicity of 1O2 was dose-, time- and light activation-dependent against Tisochrysis lutea, Tetraselmis chui, Chaetoceros muelleri and Picochlorum atomus. The 1O2-resilient N. oculata was sterilized when incubated under light in the presence of V. campbellii ISO7 (up to 107 CFU mL−1) and 20 μM TMPyP; hence, TMPyP-based PDT sterilization of N. oculata could be suitable for aquaculture hatcheries. This study also suggests that PDT using cationic porphyrins such as TMPyP holds potential as an algicidal treatment in aquaria and aquaculture systems (but more research using opportunistic and toxic species is needed for confirmation).

Archaeal populations are abundant in cold and temperate environments, but little is known about their potential response to climate change-induced temperature changes. The effects of temperature on archaeal communities in unamended slurries of weakly acidic peat from Spitsbergen were studied using a combination of fluorescent in situ hybridization (FISH), 16S rRNA gene clone libraries and denaturing gradient gel electrophoresis (DGGE). A high relative abundance of active archaeal cells (11–12% of total count) was seen at low temperatures (1 and 5 °C), and this community was dominated by Group 1.3b Crenarchaeota and the euryarchaeal clusters rice cluster V (RC-V), and Lake Dagow sediment (LDS). Increasing temperature reduced the diversity and relative abundance of these clusters. The methanogenic community in the slurries was diverse and included representatives of Methanomicrobiales , Methanobacterium , Methanosarcina and Methanosaeta . The overall relative abundance and diversity of the methanogenic archaea increased with increasing temperature, in accordance with a strong stimulation of methane production rates. However, DGGE profiling showed that the structure of this community changed with temperature and time. While the relative abundance of some populations was affected directly by temperature, the relative abundance of other populations was controlled by indirect effects or did not respond to temperature.

Background The bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience. Results Using long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes , genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), the latter of which suggests involvement of Endozoicomonas in host ‘sex-type’ steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses. Conclusions This study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning.

Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.

Vibrio owensii DY05 is a serious pathogen causing epizootics in the larviculture of ornate spiny lobster Panulirus ornatus. In the present study a multi-tiered probiotic screening strategy was used to identify a probiotic combination capable of protecting P. ornatus larvae (phyllosomas) from experimental V. owensii DY05 infection. From a pool of more than 500 marine bacterial isolates, 91 showed definitive in vitro antagonistic activity towards the pathogen. Antagonistic candidates were shortlisted based on phylogeny, strength of antagonistic activity, and isolate origin. Miniaturized assays used a green fluorescent protein labelled transconjugant of V. owensii DY05 to assess pathogen growth and biofilm formation in the presence of shortlisted candidates. This approach enabled rapid processing and selection of candidates to be tested in a phyllosoma infection model. When used in combination, strains Vibrio sp. PP05 and Pseudoalteromonas sp. PP107 significantly and reproducibly protected P. ornatus phyllosomas during vectored challenge with V. owensii DY05, with survival not differing significantly from unchallenged controls. The present study has shown the value of multispecies probiotic treatment and demonstrated that natural microbial communities associated with wild phyllosomas and zooplankton prey support antagonistic bacteria capable of in vivo suppression of a pathogen causing epizootics in phyllosoma culture systems.

Bacterial Quorum Sensing (QS), the indirect regulation of gene expression through production and detection of small diffusible molecules, has emerged as a point of interaction between eukaryotic host organisms and their associated microbial communities. The extracellular nature of QS molecules enables interference in QS systems, in many cases via mimicry. This study targeted QS induction and inhibition in soft coral holobionts, as many soft coral species commonly contain compounds with structural similarities to the well-studied bacterial QS molecules acyl homoserine lactones. Screening with two bacterial biosensors, Agrobacterium tumefaciens A136 and Chromobacterium violaceum CV026, demonstrated that QS interference differed between the two biosensor strains and extended across the soft coral families Alcyoniidae, Clavulariidae, Nephtheidae, and Xeniidae. Bioassay-guided fractionation revealed chemical activity patterns, particularly in the induction of QS. Cembranoid diterpenes from active fractions were purified and tested for QS interference activity. Interestingly, the type of QS activity (induction or inhibition) in A. tumefaciens A136 correlated with structural variability of the secondary oxygen ring; cembranoid diterpenes with a furan ring or five-membered lactone induced QS, while compounds with larger (six or seven membered) lactone rings inhibited QS. Addition of the dominant cembranoid diterpene in the soft coral Lobophytum compactum, isolobophytolide, to bacterial culture media increased the number and morphological diversity of bacteria recovered from the mucosal layer of this soft coral, demonstrating a selective effect on certain members of the soft coral bacterial community. The identity and QS activity of recovered isolates differed between the mucosal layers of L. compactum and Sinularia flexibilis. In conclusion, this study provides information on the complexity of the interaction between soft corals and their associated bacteria, as well as, a structural understanding of how QS mimic compounds are able to interfere with a bacterial communication system.

Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building coral, Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribed Endozoicomonas strains isolated from A. loripes. Subsequent 16S rRNA gene amplicon sequencing revealed their classification into two distinct phylogenetic clades. To resolve their spatial distribution in hospite, clade-specific fluorescence in situ hybridization probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed by Endozoicomonas from both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These morphological differences highlight the importance of further investigations into the mechanisms governing bacterial aggregate formation in corals.

Two bacterial strains (DY05T and 47666-1) were isolated in Queensland, Australia, from diseased cultured crustaceans Panulirus ornatus and Penaeus monodon, respectively. On the basis of 16S rRNA gene sequence identity, the strains were shown to belong to the Harveyi clade of the genus Vibrio. Multilocus sequence analysis using five housekeeping genes (rpoA, pyrH, topA, ftsZ and mreB) showed that the strains form a monophyletic group with 94.4% concatenated sequence identity to the closest species. DNA-DNA hybridization experiments showed that strains DY05T and 47666-1 had 76% DNA similarity to each other, but <70% to their closest neighbours Vibrio harveyi LMG 4044T ([less-than or equal to]55%), Vibrio campbellii LMG 11216T ([less-than or equal to]52%) and Vibrio rotiferianus LMG 21460T ([less-than or equal to]46%). Strains DY05T and 47666-1 could be differentiated from their relatives on the basis of several phenotypic characteristics. The major fatty acids were C₁₅:₀ iso 2-OH and/or C₁₆:₁ω7, C₁₆:₀, C₁₈:₁ω7 and C₁₄:₀. Based on the polyphasic evidence presented here, it can be concluded that strains DY05T and 47666-1 belong to the same novel species of the genus Vibrio, for which the name Vibrio owensii sp. nov. is proposed. The type strain is DY05T (=JCM 16517T=ACM 5300T).