Coral endosymbiont growth is enhanced by metabolic interactions with bacteria.

Bacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overlooked. Here, we show that altering the bacterial composition of two widespread Symbiodiniaceae species, during their free-living stage, results in a significant shift in their cellular metabolism. Indeed, the abundance of monosaccharides and the key phytohormone indole-3-acetic acid (IAA) were correlated with the presence of specific bacteria, including members of the Labrenzia (Roseibium) and Marinobacter genera. Single-cell stable isotope tracking revealed that these two bacterial genera are involved in reciprocal exchanges of carbon and nitrogen with Symbiodiniaceae. We identified the provision of IAA by Labrenzia and Marinobacter, and this metabolite caused a significant growth enhancement of Symbiodiniaceae. By unravelling these interkingdom interactions, our work demonstrates how specific bacterial associates fundamentally govern Symbiodiniaceae fitness.

Identification and quantification of Acanthamoeba spp. within seawater at four coastal lagoons on the east coast of Australia.

Acanthamoeba is an opportunistic free-living heterotrophic protist that is the most predominant amoeba in diverse ecological habitats. Acanthamoeba causes amoebic keratitis (AK), a painful and potentially blinding corneal infection. Major risk factors for AK have been linked to non-optimal contact lens hygiene practices and Acanthamoeba contamination of domestic and recreational water. This study investigated the incidence and seasonal variation of Acanthamoeba spp. within coastal lagoons located on the eastern coast of Australia and then examined the association between Acanthamoeba and water abiotic factors and bacterial species within the water. Water samples were collected from four intermittently closed and open lagoons (ICOLLs) (Wamberal, Terrigal, Avoca and Cockrone) every month between August 2019 to July 2020 except March and April. qPCR was used to target the Acanthamoeba 18S rRNA gene, validated by Sanger sequencing. Water abiotic factors were measured in situ using a multiprobe metre and 16S rRNA sequencing (V3-V4) was performed to characterise bacterial community composition. Network analysis was used to gauge putative associations between Acanthamoeba incidence and bacterial amplicon sequence variants (ASVs). Among 206 water samples analysed, 79 (38.3%) were Acanthamoeba positive and Acanthamoeba level was significantly higher in summer compared with winter, spring, or autumn (p = 0.008). More than 50% (23/45) water samples of Terrigal were positive for Acanthamoeba which is a highly urbanised area with extensive recreational activities while about 32% (16/49) samples were positive from Cockrone that is the least impacted lagoon by urban development. All sequenced strains belonged to the pathogenic genotype T4 clade except two which were of genotype clades T2 and T5. Water turbidity, temperature, intl1 gene concentration, and dissolved O2 were significantly associated with Acanthamoeba incidence (p < 0.05). The ASVs level of cyanobacteria, Pseudomonas spp., Candidatus spp., and marine bacteria of the Actinobacteria phylum and Acanthamoeba 18S rRNA genes were positively correlated (Pearson's r ≥ 0.14). The presence of Acanthamoeba spp. in all lagoons, except Wamberal, was associated with significant differences in the composition of bacterial communities (beta diversity). The results of this study suggest that coastal lagoons, particularly those in urbanised regions with extensive water recreational activities, may pose an elevated risk to human health due to the relatively high incidence of pathogenic Acanthamoeba in the summer. These findings underscore the importance of educating the public about the rare yet devastating impact of AK on vision and quality of life, highlighting the need for collaborative efforts between public health officials and educators to promote awareness and preventive measures, especially focusing lagoons residents and travellers.

Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation.

Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.

Acclimation in intertidal animals reduces potential pathogen load and increases survival following a heatwave.

Intertidal animals can experience intense heat during a heatwave, leading to mortality. The causes of death for intertidal animals following heatwaves have often been attributed to a breakdown in physiological processes. This, however, contrasts with research in other animals where heatwave mortality is attributed to existing or opportunistic diseases. We acclimated intertidal oysters to four treatment levels, including an antibiotic treatment, and then exposed all treatments to a 50°C heatwave for 2 h, replicating what can be experienced on Australian shorelines. We found that both acclimation and antibiotics increased survival and reduced the presence of potential pathogens. Non-acclimated oysters had a significant shift in their microbiome, with increasing abundances of bacteria from the Vibrio genera, including known potential pathogens. Our results demonstrate that bacterial infection plays a pivotal role in post-heatwave mortality. We anticipate these findings to inform the management of aquaculture and intertidal habitats as climate change intensifies.

Elevated estuary water temperature drives fish gut dysbiosis and increased loads of pathogenic vibrionaceae.

Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of coastal waters is increasing the abundance and virulence of pathogenic members of the Vibrionaceae, posing a significant health risk to both humans and aquatic organisms. Fish disease, notably outbreaks of emerging pathogens in response to environmental perturbations such as heatwaves, have been recognised in aquaculture settings. Considerably less is known about how rising sea surface temperatures will impact the microbiology of wild fish populations, particularly those within estuarine systems that are more vulnerable to warming. We used a combination of Vibrio-specific quantitative PCR and amplicon sequencing of the 16S rRNA and hsp60 genes to examine seawater and fish (Pelates sexlineatus) gut microbial communities across a quasi-natural experimental system, where thermal pollution from coal-fired power stations creates a temperature gradient of up to 6 °C, compatible with future predicted temperature increases. At the warmest site, fish hindgut microbial communities were in a state of dysbiosis characterised by shifts in beta diversity and a proliferation (71.5% relative abundance) of the potential fish pathogen Photobacterium damselae subsp. damselae. Comparable patterns were not identified in the surrounding seawater, indicating opportunistic proliferation within estuarine fish guts under thermal stress. A subsequent evaluation of predicted future warming-related risk due to pathogenic Vibrionaceae in temperate estuarine fish demonstrated that warming is likely to drive opportunistic pathogen increases in the upper latitudinal range of this estuarine fish, potentially impacting adaptations to future warming. These findings represent a breakthrough in our understanding of the dynamics of emerging pathogens in populations of wild aquatic organisms within environments likely to experience rapid warming under future climate change.

The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters.

The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 µm and >2 µm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.

Rainfall leads to elevated levels of antibiotic resistance genes within seawater at an Australian beach.

Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following significant rainfall events.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment.

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

Chemotaxis shapes the microscale organization of the ocean's microbiome.

The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.

Can seagrass modify the effects of ocean acidification on oysters?

Solutions are being sought to ameliorate the impacts of anthropogenic climate change. Seagrass may be a solution to provide refugia from climate change for marine organisms. This study aimed to determine if the seagrass Zostera muelleri sub spp. capricorni benefits the Sydney rock oyster Saccostrea glomerata, and if these benefits can modify any anticipated negative impacts of ocean acidification. Future and ambient ocean acidification conditions were simulated in 52 L mesocosms at control (381 µatm) and elevated (848 µatm) CO2 with and without Z. muelleri. Oyster growth, physiology and microbiomes of oysters and seagrass were measured. Seagrass was beneficial to oyster growth at ambient pCO2, but did not positively modify the impacts of ocean acidification on oysters at elevated pCO2. Oyster microbiomes were altered by the presence of seagrass but not by elevated pCO2. Our results indicate seagrasses may not be a panacea for the impacts of climate change.

Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton.

Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.

Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.

Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.

Rapid Shifts in Bacterial Communities and Homogeneity of Symbiodiniaceae in Colonies of Pocillopora acuta Transplanted Between Reef and Mangrove Environments.

It has been proposed that an effective approach for predicting whether and how reef-forming corals persist under future climate change is to examine populations thriving in present day extreme environments, such as mangrove lagoons, where water temperatures can exceed those of reef environments by more than 3°C, pH levels are more acidic (pH < 7.9, often below 7.6) and O2 concentrations are regularly considered hypoxic (<2 mg/L). Defining the physiological features of these "extreme" corals, as well as their relationships with the, often symbiotic, organisms within their microbiome, could increase our understanding of how corals will persist into the future. To better understand coral-microbe relationships that potentially underpin coral persistence within extreme mangrove environments, we therefore conducted a 9-month reciprocal transplant experiment, whereby specimens of the coral Pocillopora acuta were transplanted between adjacent mangrove and reef sites on the northern Great Barrier Reef. Bacterial communities associated with P. acuta specimens native to the reef environment were dominated by Endozoicomonas, while Symbiodiniaceae communities were dominated by members of the Cladocopium genus. In contrast, P. acuta colonies native to the mangrove site exhibited highly diverse bacterial communities with no dominating members, and Symbiodiniaceae communities dominated by Durusdinium. All corals survived for 9 months after being transplanted from reef-to-mangrove, mangrove-to-reef environments (as well as control within environment transplants), and during this time there were significant changes in the bacterial communities, but not in the Symbiodiniaceae communities or their photo-physiological functioning. In reef-to-mangrove transplanted corals, there were varied, but sometimes rapid shifts in the associated bacterial communities, including a loss of "core" bacterial members after 9 months where coral bacterial communities began to resemble those of the native mangrove corals. Bacterial communities associated with mangrove-to-reef P. acuta colonies also changed from their original composition, but remained different to the native reef corals. Our data demonstrates that P. acuta associated bacterial communities are strongly influenced by changes in environmental conditions, whereas Symbiodiniaceae associated communities remain highly stable.

Microbiomes of an oyster are shaped by metabolism and environment.

Microbiomes can both influence and be influenced by metabolism, but this relationship remains unexplored for invertebrates. We examined the relationship between microbiome and metabolism in response to climate change using oysters as a model marine invertebrate. Oysters form economies and ecosystems across the globe, yet are vulnerable to climate change. Nine genetic lineages of the oyster Saccostrea glomerata were exposed to ambient and elevated temperature and PCO2 treatments. The metabolic rate (MR) and metabolic by-products of extracellular pH and CO2 were measured. The oyster-associated bacterial community in haemolymph was characterised using 16 s rRNA gene sequencing. We found a significant negative relationship between MR and bacterial richness. Bacterial community composition was also significantly influenced by MR, extracellular CO2 and extracellular pH. The effects of extracellular CO2 depended on genotype, and the effects of extracellular pH depended on CO2 and temperature treatments. Changes in MR aligned with a shift in the relative abundance of 152 Amplicon Sequencing Variants (ASVs), with 113 negatively correlated with MR. Some spirochaete ASVs showed positive relationships with MR. We have identified a clear relationship between host metabolism and the microbiome in oysters. Altering this relationship will likely have consequences for the 12 billion USD oyster economy.

Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia.

Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3-8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44-115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.

Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues.

Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, suggests that the haemolymph and inside shell environment is a source of microbial spillover into the oyster tissues, and a potentially useful tool for non-destructive routine disease testing and early warning surveillance. These data provide important foundational information for future studies identifying the factors that drive microbial assembly in a valuable aquaculture species.

Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia.

Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanobacteria. These observations highlight the dynamic nature of Vibrio communities and expands current understanding of the processes governing the occurrence of potentially pathogenic Vibrio spp. in tropical coastal ecosystems.

Microbiome response differs among selected lines of Sydney rock oysters to ocean warming and acidification.

Oyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed to predicted warming (ambient = 24°C, elevated = 28°C) and ocean acidification (ambient pCO2 = 400, elevated pCO2 = 1000 µatm) for 4 weeks. The haemolymph bacterial microbiome was characterized using 16S rRNA (V3-V4) gene sequencing and varied among oyster lines in the control (ambient pCO2, 24°C) treatment. Microbiomes were also altered by climate change dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial ß-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Climate change treatments caused shifts in the abundance of multiple amplicon sequence variants driving change in the microbiome of some selected lines. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future assisted evolution breeding programs to enhance resilience should consider the oyster microbiome.

Climate change alters the haemolymph microbiome of oysters.

The wellbeing of marine organisms is connected to their microbiome. Oysters are a vital food source and provide ecological services, yet little is known about how climate change such as ocean acidification and warming will affect their microbiome. We exposed the Sydney rock oyster, Saccostrea glomerata, to orthogonal combinations of temperature (24, 28 °C) and pCO2 (400 and 1000 µatm) for eight weeks and used amplicon sequencing of the 16S rRNA (V3-V4) gene to characterise the bacterial community in haemolymph. Overall, elevated pCO2 and temperature interacted to alter the microbiome of oysters, with a clear partitioning of treatments in CAP ordinations. Elevated pCO2 was the strongest driver of species diversity and richness and elevated temperature also increased species richness. Climate change, both ocean acidification and warming, will alter the microbiome of S. glomerata which may increase the susceptibility of oysters to disease.

Unlocking the phylogenetic diversity, primary habitats, and abundances of free-living Symbiodiniaceae on a coral reef.

Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef-building corals, but also inhabit reef environments as free-living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free-living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus-specific qPCR to resolve the community structure and cell abundances of free-living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free-living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera-equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment-associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free-living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.