Large-scale geographic variation in distribution and abundance of Australian deep-water kelp forests

Assessing how restoration can facilitate 30×30 goals for climate-resilient coastal ecosystems in the United States

Ecosystems globally have reached critical tipping points because of climate change, urbanization, unsustainable resource consumption, and pollution. In response, international agreements have set targets for conserving 30% of global ecosystems and restoring 30% of degraded lands and waters by 2030 (30×30). In 2021, the United States set a target to jointly conserve and restore 30% of US lands and waters by 2030, with a specific goal to restore coastal ecosystems, namely wetlands, seagrasses, coral and oyster reefs, and mangrove and kelp forests, to increase resilience to climate change. Although US efforts to conserve and restore coastal ecosystems have increased in recent decades, critical knowledge gaps about the effectiveness of past and current efforts remain. To address key knowledge gaps, we first collated information on current and historic extent and drivers of change for wetlands, seagrasses, coral and oyster reefs, and mangrove and kelp forests in the United States. We then synthesized guiding principles from the literature for restoration practitioners to evaluate ecosystem trade-offs, sustain and enhance ecosystem connectivity, bolster climate resilience, and promote social equity. Significant investment in standardized ecosystem mapping and monitoring and multispecies, landscape-scale restoration efforts can improve resilience of coastal ecosystems to climate change and help the United States achieve its 30×30 target.

Geomorphological drivers of benthic community distribution on high energy temperate mesophotic and rariphotic reefs

Current knowledge of mesophotic benthic reef communities has predominantly focused on the distribution of sessile assemblages along the depth gradient. However, the influence of geomorphology on exposure to hydrodynamic processes may independently shape community assemblages, in addition to depth. We examined the distribution of sessile invertebrates at 50-150 m depths on exposed continental shelf reefs within a Marine Park in southwest Tasmania. Using marine still imagery and bathymetric mapping derivatives, we described the spatial response of biota to the prevailing hydrodynamic regime and geomorphology in this region, based on the growth forms of dominant morphospecies. The biota is exposed to large oceanic swells where high-wave energy mobilises sediments at depths of up to 140 m. As expected, the encrusting sponge morphospecies group was most prevalent but showed a niche habitat preference. Unlike wave-exposed reefs elsewhere, we observed a high cover of dominant morphospecies with three-dimensional growth forms alongside encrusting sponges over a wide range of depths. Notably, whip octocorals, cup-like, and tube sponge morphospecies groups had high cover on the most exposed slopes, while other groups such as encrusting and simple massive sponges were absent. However, this baseline assessment suggests there may be high species turnover due to the severe conditions during ocean storms, which may influence population dynamics. We recommend conducting future monitoring at ecologically relevant intervals to assess the natural variability in distribution due to local habitat effects.

Strong Environmental and Genome-Wide Population Differentiation Underpins Adaptation and High Genomic Vulnerability in the Dominant Australian Kelp (Ecklonia radiata)

Ongoing and predicted range loss of kelp forests in response to climatic stressors is pressing marine managers to look into the adaptive capacity of populations to inform conservation strategies. Characterising how adaptive genetic diversity and structure relate to present and future environmental variation represents an emerging approach to quantifying kelp vulnerability to environmental change and identifying populations with genotypes that potentially confer an adaptive advantage in future ocean conditions. The dominant Australian kelp, Ecklonia radiata, was genotyped from 10 locations spanning 2000 km of coastline and a 9.5°C average temperature gradient along the east coast of Australia, a global warming hotspot. ddRAD sequencing generated 10,700 high-quality single nucleotide polymorphisms (SNPs) and characterized levels of neutral and adaptive genomic diversity and structure. The adaptive dataset, reflecting portions of the genome putatively under selection, was used to infer genomic vulnerability by 2050 under the RCP 8.5 scenario. There was strong neutral genetic differentiation between Australia mainland and Tasmanian populations, but only weak genetic structure among mainland populations within the main path of the East Australian Current. Genetic diversity was highest in the center of the range and lowest in the warm-edge population. The adaptive SNP candidates revealed similar genetic structure patterns, with a spread of adaptive alleles across most warm (northern) populations. The lowest, but most unique, adaptive genetic diversity values were found in both warm and cool population edges, suggesting local adaptation but low evolutionary potential. Critically, genomic vulnerability modeling identified high levels of vulnerability to future environmental conditions in Tasmanian populations. Populations of kelp at range edges are unlikely to adapt and keep pace with predicted climate change. Ensuring the persistence of these kelp forests, by boosting resilience to climate change, may require active management strategies with assisted adaptation in warm-edge (northern) populations and assisted gene flow in cool-edge (Tasmania) populations.

Using predictive models to identify kelp refuges in marine protected areas for management prioritization

Kelp forests serve as the foundation for shallow marine ecosystems in many temperate areas of the world but are under threat from various stressors, including climate change. To better manage these ecosystems now and into the future, understanding the impacts of climate change and identifying potential refuges will help to prioritize management actions. In this study, we use a long-term dataset of observations of kelp percentage cover for two dominant canopy-forming species off the coast of Victoria, Australia: Ecklonia radiata and Phyllospora comosa. These observations were collected across three scuba sampling programs that extend from 1998 to 2019. We then associated those observations with habitat and environmental variables including depth, seafloor structure, wave climate, currents, temperature, and population connectivity in generalized additive mixed-effects models and used these models to develop predictive maps of kelp cover across the Victorian marine protected areas (MPAs). These models were also used to project kelp coverage into the future by replacing wave climate and temperature with future projections (2090, Representative Concentration Pathways [RCPs] 4.5 and 8.5). Once the spatial predictions were compiled, we calculated percent cover change from 1998 to 2019, stability over the same period, and future predicted change in percent cover (2019-2090) to understand the dynamics for each species across the MPAs. We also used the current percentage cover, stability, and future percentage cover to develop a ranking system for classifying the maps into very unlikely refugia, unlikely refugia, neutral, potential refugia, and likely refugia. A management framework was then developed to use those refugia ranking values to inform management actions, and we applied this framework across three case studies: one at the scale of the MPA network and two at the scale of individual MPAs, one where management decisions were the same for both species, and one where the actions were species-specific. This study shows how species distribution models, both contemporary and with future projections, can help to identify potential refugia areas that can be used to prioritize management decisions and future-proof restoration actions.

Environmental and social framework to protect marine bivalves under extreme weather events

Rising ocean temperatures, a consequence of anthropogenic climate change, are increasing the frequency, intensity, and magnitude of extreme marine heatwaves (MHWs). These persistent anomalous warming events can have severe ecological and socioeconomic impacts, threatening ecologically and economically vital organisms such as bivalves and the ecosystems they support. Developing robust environmental and social frameworks to enhance the resilience and adaptability of bivalve aquaculture is critical to ensuring the sustainability of this crucial food source. This review synthesizes the current understanding of the physiological and ecological impacts of MHWs on commercially important bivalve species farmed globally. We propose an integrated risk assessment framework that encompasses environmental monitoring, farm-level preparedness planning, and community-level social support systems to safeguard bivalve aquaculture. Specifically, we examine heatwave prediction models, local mitigation strategies, and social programs that could mitigate the impacts on bivalve farms and vulnerable coastal communities economically dependent on this fishery. At the farm level, adaptation strategies such as selective breeding for heat-tolerant strains, optimized site selection, and adjustments to culture practices can improve survival outcomes during MHWs. Robust disease surveillance and management programs are essential for early detection and rapid response. Furthermore, we highlight the importance of stakeholder engagement, knowledge exchange, and collaborative governance in developing context-specific, inclusive, and equitable safeguard systems. Proactive measures, such as advanced forecasting tools like the California Current Marine Heat Wave Tracker developed by NOAA's Southwest Fisheries Science Center, enable preemptive action before losses occur. Coordinated preparation and response, underpinned by continuous monitoring and adaptive management, promise to protect these climate-vulnerable food systems and coastal communities. However, sustained research, innovation, and cross-sector collaboration are imperative to navigate the challenges posed by our rapidly changing oceans.

Cryptic diversity in southern African kelp

The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution ~ 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.

Temperature sensitivity of detrital photosynthesis

BACKGROUND AND AIMS

Kelp forests are increasingly considered blue carbon habitats for ocean-based biological carbon dioxide removal, but knowledge gaps remain in our understanding of their carbon cycle. Of particular interest is the remineralization of detritus, which can remain photosynthetically active. Here, we study a widespread, thermotolerant kelp (Ecklonia radiata) to explore detrital photosynthesis as a mechanism underlying temperature and light as two key drivers of remineralization.

METHODS

We used meta-analysis to constrain the thermal optimum (Topt) of E. radiata. Temperature and light were subsequently controlled over a 119-day ex situ decomposition experiment. Flow-through experimental tanks were kept in darkness at 15 °C or under a subcompensating maximal irradiance of 8 µmol photons m-2 s-1 at 15, 20 or 25 °C. Photosynthesis of laterals (analogues to leaves) was estimated using closed-chamber oxygen evolution in darkness and under a saturating irradiance of 420 µmol photons m-2 s-1.

KEY RESULTS

T opt of E. radiata is 18 °C across performance variables (photosynthesis, growth, abundance, size, mass and fertility), life stages (gametophyte and sporophyte) and populations. Our models predict that a temperature of >15 °C reduces the potential for E. radiata detritus to be photosynthetically viable, hence detrital Topt ≤ 15 °C. Detritus is viable under subcompensating irradiance, where it performs better than in darkness. Comparison of net and gross photosynthesis indicates that elevated temperature primarily decreases detrital photosynthesis, whereas darkness primarily increases detrital respiration compared with optimal experimental conditions, in which detrital photosynthesis can persist for ≥119 days.

CONCLUSIONS

T opt of kelp detritus is ≥3 °C colder than that of the intact plant. Given that E. radiata is one of the most temperature-tolerant kelps, this suggests that photosynthesis is generally more thermosensitive in the detrital phase, which partly explains the enhancing effect of temperature on remineralization. In contrast to darkness, even subcompensating irradiance maintains detrital viability, elucidating the accelerating effect of depth and its concomitant light reduction on remineralization to some extent. Detrital photosynthesis is a meaningful mechanism underlying at least two drivers of remineralization, even below the photoenvironment inhabited by the attached alga.

Climate change threatens unique evolutionary diversity in Australian kelp refugia

Climate change has driven contemporary decline and loss of kelp forests globally with an accompanying loss of their ecological and economic values. Kelp populations at equatorward-range edges are particularly vulnerable to climate change as these locations are undergoing warming at or beyond thermal tolerance thresholds. Concerningly, these range-edge populations may contain unique adaptive or evolutionary genetic diversity that is vulnerable to warming. We explore haplotype diversity by generating a Templeton-Crandall-Sing (TCS) network analysis of 119 Cytochrome C Oxidase (COI) sequences among four major population groupings for extant and putatively extinct populations only known from herbarium specimens of the dominant Laminarian kelp Ecklonia radiata in the south-western Pacific, a region warming at 2-4 times the global average. Six haplotypes occurred across the region with one being widespread across most populations. Three unique haplotypes were found in a deep-water range-edge population off Moreton Island, Queensland, which likely represents both a contemporary and historic refuge during periods of climatic change. Hindcasting E. radiata cover estimates using extant data, we reveal that this region likely supported the highest kelp cover in eastern Australia during the last glacial maximum. The equatorward range edge, deep-water kelp populations off Moreton Island represent a genetically diverse evolutionary refuge that is currently threatened by warming and requires prompt ex-situ conservation measures.

Loss of a globally unique kelp forest from Oman

Kelp forests are declining in many regions globally with climatic perturbations causing shifts to alternate communities and significant ecological and economic loss. Range edge populations are often at most risk and are often only sustained through localised areas of upwelling or on deeper reefs. Here we document the loss of kelp forests (Ecklonia radiata) from the Sultanate of Oman, the only confirmed northern hemisphere population of this species. Contemporary surveys failed to find any kelp in its only known historical northern hemisphere location, Sadah on the Dhofar coast. Genetic analyses of historical herbarium specimens from Oman confirmed the species to be E. radiata and revealed the lost population contained a common CO1 haplotype found across South Africa, Australia and New Zealand suggesting it once established through rapid colonisation throughout its range. However, the Omani population also contained a haplotype that is found nowhere else in the extant southern hemisphere distribution of E. radiata. The loss of the Oman population could be due to significant increases in the Arabian Sea temperature over the past 40 years punctuated by suppression of coastal upwelling. Climate-mediated warming is threatening the persistence of temperate species and precipitating loss of unique genetic diversity at lower latitudes.

Space use by the endemic common (weedy) seadragon (Phyllopteryx taeniolatus): influence of habitat and prey

The weedy seadragon (Phyllopteryx taeniolatus: Syngnathidae) is an iconic fish endemic to the southern coastal waters of Australia. The authors of this study analysed the habitat preferences and factors influencing microhabitat selection by P. taeniolatus in a population from Kurnell, NSW, Australia. Using field surveys and the resource selection probability function, the authors determined that P. taeniolatus significantly preferred kelp (Ecklonia radiata)-dominated habitat and avoided rock-dominated habitat. They showed P. taeniolatus preferred habitat of between 40% and 80% coverage of Ecklonia, while avoiding areas of <20% cover. Furthermore, across all habitats, mysid prey availability significantly influenced P. taeniolatus habitat selection. The strong dependence of P. taeniolatus on Ecklonia habitat shown in this study was previously untested and highlights that reductions in Ecklonia cover under climate change, or impacts from increasing urbanisation, may render seadragon populations vulnerable to declines.

Molecular analysis of a fungal disease in the habitat-forming brown macroalga Phyllospora comosa (Fucales) along a latitudinal gradient

Infectious diseases affecting habitat-forming species can have significant impacts on population dynamics and alter the structure and functioning of marine ecosystems. Recently, a fungal infection was described as the causative agent of necrotic lesions on the stipe of the forest-forming macroalga Phyllospora comosa, a disease named "stipe rot" (SR). Here, we developed a quantitative PCR (qPCR) method for rapid detection and quantification of this pathogen, which was applied to evaluate the level of SR infection in eight P. comosa populations spanning the entire latitudinal distribution of this species along southeastern Australia. We also investigated the relationship between the abundance and prevalence of Stipe Rot Fungus (SRF) and potential host chemical defenses as well as its relationship with morphological and ecophysiological traits of P. comosa. qPCR estimates of SRF abundance reflected the levels of infection estimated by visual assessment, with higher numbers of SRF copies being observed in individuals showing high or intermediate levels of visual symptoms of SR. Concordance of conventional PCR and visual assessments was 92 and 94%, respectively, compared to qPCR detection. SRF prevalence was positively related to fucoxanthin content and herbivory, but not significant related to other traits measured (phlorotannin content, total length, thallus diameter, stipe width, number of branches, frond width, fouling, bleaching, gender, and photosynthetic efficiency). These results provide confidence for previous reports of this disease based upon visual assessments only, contribute to the development of monitoring and conservation strategies for safeguarding P. comosa forests, and generate insights into potential factors influencing host-pathogen interactions in this system.

Testing the efficacy of sea urchin exclusion methods for restoring kelp

Kelps are ecosystem engineers, which collectively form forests that provide a variety of important ecosystem services for humans and other organisms. Kelp forests are threatened by multiple local and global stressors, one of the most notable is herbivory. Overabundant sea; urchins can consume kelp, leading to a phase shift from productive forests to unproductive; rocky barrens. Reducing sea urchin densities by directly removing them can reverse this; phase shift. However, maintaining low densities of sea urchins, is logistically and financially; challenging. Following a review of herbivore exclusion methods to date, we tested the efficacy of three different methods for excluding sea urchins from kelp in the laboratory: flexible fences; electricity; and copper anti-fouling paint. The results from the laboratory; experiment showed that flexible fencing was the most successful method for excluding sea urchins. To test the efficacy of this method in the field, sea urchins were removed from 1m2 patches in barrens and intact kelp beds, and the effectiveness of flexible fences of two different heights (30 cm and 60 cm) at excluding sea urchins were tested. The results from the field study demonstrated that flexible fences of both heights were effective at maintaining low sea urchin densities in barrens but not in intact kelp beds, relative to unmanipulated; rocky barrens. These findings suggest that flexible fencing could be an important tool in restoring kelp in barrens, however the costs of fencing are likely to place limits on the scale at which this management strategy can be implemented.

Shifts in biomass and structure of habitat-formers across a latitudinal gradient

Global patterns of plant biomass drive the distribution of much of the marine and terrestrial life on Earth. This is because their biomass and physical structure have important consequences for the communities they support by providing food and habitat. In terrestrial ecosystems, temperature is one of the major determinants of plant biomass and can influence plant and leaf morphology. In temperate marine systems, macroalgae are major habitat-formers and commonly display highly variable morphology in response to local environmental conditions. Variation in their morphology, and thus habitat structure on temperate reefs, however, is poorly understood across large scales. In this study, we used a trait-based approach to quantify morphological variability in subtidal rocky reefs dominated by the algal genus Sargassum along a latitudinal gradient, in southeastern Australia (~900 km). We tested whether large-scale variation in sea surface temperature (SST), site exposure, and nutrient availability can predict algal biomass and individual morphology. We found Sargassum biomass declined with increasing maximum SST. We also found that individual morphology varied with abiotic ocean variables. Frond size and intraindividual variability in frond size decreased with increasing with distance from the equator, as SST decreased and nitrate concentration increased. The shape of fronds displayed no clear relationship with any of the abiotic variables measured. These results suggest climate change will cause significant changes to the structure of Sargassum habitats along the southeastern coast of Australia, resulting in an overall reduction in biomass and increase in the prevalence of thalli with large, highly variable fronds. Using a space-for-time approach means shifts in morphological trait values can be used as early warning signs of impending species declines and regime shifts. Consequently, by studying traits and how they change across large scales we can potentially predict and anticipate the impacts of environmental change on these communities.

Climate refugia for kelp within an ocean warming hotspot revealed by stacked species distribution modelling

Canopy forming macroalgae are declining globally due to climate change and the identification of refuges for these habitats is crucial for their conservation. This is particularly pertinent in ocean warming hotspots where significant range contractions of kelp have occurred and are projected to continue. We developed a stacked urchin-kelp species distribution model (SDM) to predict climate refugia for kelp (Ecklonia radiata) in an ocean warming hotspot, south-eastern Australia. The optimal stacked-SDM incorporated biotic and abiotic explanatory covariates and was validated using an independent dataset. Density of the urchin Centrostephanus rodgersii, summer bottom temperature and photosynthetically available radiation at the seabed were significant predictors of kelp cover, highlighting the physiological and ecological influence of these variables on the distribution of kelp. Our optimal stacked-SDM predicted three spatially distinct refuge areas, where kelp occurs in deeper waters than surrounding seascapes. The presence of kelp at two of these refuge areas was confirmed using independent data. The identification of these refuge areas is crucial for conservation, as they are likely to facilitate the persistence of ecologically and economically important kelp forests as waters warm in shallow areas and kelp retreat to depth under climate change. Furthermore, identification of refugia will enable proactive spatial planning that prioritises new locations for protection to ensure that key kelp habitats can persist in a future of increasing stress.

Reproductive Output, Synchrony across Depth and Influence of Source Depth in the Development of Early Life stages of Kelp

Ecklonia radiata is the main foundation species in Australian temperate reefs, yet little has been published on its reproduction and how this may change across its depth range (1-50+ m). In this study, we examined differences in sporophyte morphology and zoospore production during a reproductive season and across four depths (7, 15, 25, and 40 m). Additionally, we examined differences in germination rate, survival, and morphological traits of gametophytes obtained from these four depths, cultured under the same light and temperature conditions. Multivariate morphology of sporophytes differed significantly between deep (~40 m) and shallow sites (7 and 15 m), but individual morphological traits were not significantly different across depths. Total spore production was similar across depths but the peak of zoospore release was observed in February at 15 m of depth (6,154 zoospores · mm-2 of tissue) and the minimum observed in January at 7, 25, and 40 m (1,141, 987, and 214 zoospores · mm-2 of tissue, respectively). The source depth of zoospores did not have an influence in the germination rate or the survival of gametophytes, and only gametophytes sourced from 40 m sites presented significantly less surface area and number of branches. Overall, these results indicate that E. radiata's reproductive performance does not change across its depth range and that kelp beds reproducing in deeper areas may contribute to the replenishment of their shallow counterparts. We propose that deep kelps may constitute a mechanism of resilience against climate change and anthropogenic disturbances.

Substantial blue carbon in overlooked Australian kelp forests

Recognition of the potential for vegetated coastal ecosystems to store and sequester carbon has led to their increasing inclusion into global carbon budgets and carbon offset schemes. However, kelp forests have been overlooked in evaluations of this 'blue carbon', which have been limited to tidal marshes, mangrove forests, and seagrass beds. We determined the continental-scale contribution to blue carbon from kelp forests in Australia using areal extent, biomass, and productivity measures from across the entire Great Southern Reef. We reveal that these kelp forests represent 10.3-22.7 Tg C and contribute 1.3-2.8 Tg C year^-1 in sequestered production, amounting to more than 30% of total blue carbon stored and sequestered around the Australian continent, and ~ 3% of the total global blue carbon. We conclude that the omission of kelp forests from blue carbon assessments significantly underestimates the carbon storage and sequestration potential from vegetated coastal ecosystems globally.

Kelp beds as coastal protection: wave attenuation of Ecklonia radiata in a shallow coastal bay

BACKGROUND AND AIMS

Coastal protection from erosion and flooding is a significant ecosystem service provided by vegetated marine systems. Kelp beds are a dominant habitat-forming species on temperate reefs worldwide. While they are valued as hotspots of biodiversity, there is a paucity of information that supports their use in nature-based coastal defence. This includes the effectiveness of kelp beds in attenuating waves approaching the shore and how this influences sediment transport.

METHODS

Wave loggers were deployed at paired kelp bed and control (urchin barren) treatments at four sites in Port Phillip Bay, Australia. The significant wave height offshore (exposed side) to onshore (sheltered side) of the treatment were compared to determine wave attenuation.

KEY RESULTS

At three sites, the wave attenuation of kelp beds was significantly less than that of the control. This result was consistent across the environmental conditions recorded in this study. At the fourth site, on average there was no significant difference in wave transmission between kelp and control. However, wave attenuation at kelp beds was 10 % greater than the control during periods of northerly winds. We highlight the importance of disentangling the effects of the reef substratum and kelp when evaluating the efficacy of kelp at providing coastal protection.

CONCLUSIONS

We have highlighted a significant gap in the research on ecosystem services provided by kelp beds. A greater understanding is needed on which kelp species are able to provide coastal protection, and under what conditions. Such future research is essential for providing managers and policy makers with actionable information on sustainable and cost-effective solutions for coastal defence when faced with a changing climate.

Automatic Hierarchical Classification of Kelps Using Deep Residual Features

Across the globe, remote image data is rapidly being collected for the assessment of benthic communities from shallow to extremely deep waters on continental slopes to the abyssal seas. Exploiting this data is presently limited by the time it takes for experts to identify organisms found in these images. With this limitation in mind, a large effort has been made globally to introduce automation and machine learning algorithms to accelerate both classification and assessment of marine benthic biota. One major issue lies with organisms that move with swell and currents, such as kelps. This paper presents an automatic hierarchical classification method local binary classification as opposed to the conventional flat classification to classify kelps in images collected by autonomous underwater vehicles. The proposed kelp classification approach exploits learned feature representations extracted from deep residual networks. We show that these generic features outperform the traditional off-the-shelf CNN features and the conventional hand-crafted features. Experiments also demonstrate that the hierarchical classification method outperforms the traditional parallel multi-class classifications by a significant margin (90.0% vs. 57.6% and 77.2% vs. 59.0%) on Benthoz15 and Rottnest datasets respectively. Furthermore, we compare different hierarchical classification approaches and experimentally show that the sibling hierarchical training approach outperforms the inclusive hierarchical approach by a significant margin. We also report an application of our proposed method to study the change in kelp cover over time for annually repeated AUV surveys.

Ocean warming compresses the three-dimensional habitat of marine life

Vertical migration to reach cooler waters is a suitable strategy for some marine organisms to adapt to ocean warming. Here, we calculate that realized vertical isotherm migration rates averaged -6.6 + 18.8 m dec^-1 across the global ocean between 1980 and 2015. Throughout this century (2006-2100), surface isotherms are projected to deepen at an increasing rate across the globe, averaging -32.3 m dec^-1 under the representative concentration pathway (RCP)8.5 'business as usual' emissions scenario, and -18.7 m dec^-1 under the more moderate RCP4.5 scenario. The vertical redistribution required by organisms to follow surface isotherms over this century is three to four orders of magnitude less than the equivalent horizontal redistribution distance. However, the seafloor depth and the depth of the photic layer pose ultimate limits to the vertical migration possible by species. Both limits will be reached by the end of this century across much of the ocean, leading to a rapid global compression of the three-dimensional (3D) habitat of many marine organisms. Phytoplankton diversity may be maintained but displaced toward the base of the photic layer, whereas highly productive benthic habitats, especially corals, will have their suitable 3D habitat rapidly reduced.

Monitoring mosaic biotopes in a marine conservation zone by autonomous underwater vehicle

The number of marine protected areas (MPAs) has increased dramatically in the last decade and poses a major logistic challenge for conservation practitioners in terms of spatial extent and the multiplicity of habitats and biotopes that now require assessment. Photographic assessment by autonomous underwater vehicle (AUV) enables the consistent description of multiple habitats, in our case including mosaics of rock and sediment. As a case study, we used this method to survey the Greater Haig Fras marine conservation zone (Celtic Sea, northeast Atlantic). We distinguished 7 biotopes, detected statistically significant variations in standing stocks, species density, species diversity, and faunal composition, and identified significant indicator species for each habitat. Our results demonstrate that AUV-based photography can produce robust data for ecological research and practical marine conservation. Standardizing to a minimum number of individuals per sampling unit, rather than to a fixed seafloor area, may be a valuable means of defining an ecologically appropriate sampling unit. Although composite sampling represents a change in standard practice, other users should consider the potential benefits of this approach in conservation studies. It is broadly applicable in the marine environment and has been successfully implemented in deep-sea conservation and environmental impact studies. Without a cost-effective method, applicable across habitats, it will be difficult to further a coherent classification of biotopes or to routinely assess their conservation status in the rapidly expanding global extent of MPAs.

Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp

Climate change is driving global declines of marine habitat-forming species through physiological effects and through changes to ecological interactions, with projected trajectories for ocean warming and acidification likely to exacerbate such impacts in coming decades. Interactions between habitat-formers and their microbiomes are fundamental for host functioning and resilience, but how such relationships will change in future conditions is largely unknown. We investigated independent and interactive effects of warming and acidification on a large brown seaweed, the kelp Ecklonia radiata, and its associated microbiome in experimental mesocosms. Microbial communities were affected by warming and, during the first week, by acidification. During the second week, kelp developed disease-like symptoms previously observed in the field. The tissue of some kelp blistered, bleached and eventually degraded, particularly under the acidification treatments, affecting photosynthetic efficiency. Microbial communities differed between blistered and healthy kelp for all treatments, except for those under future conditions of warming and acidification, which after two weeks resembled assemblages associated with healthy hosts. This indicates that changes in the microbiome were not easily predictable as the severity of future climate scenarios increased. Future ocean conditions can change kelp microbiomes and may lead to host disease, with potentially cascading impacts on associated ecosystems.

Artificial structures alter kelp functioning across an urbanised estuary

Assessments of human impacts on natural habitats often focus on the abundance of component species, yet physiological and/or sub-lethal effects of stressors on functional attributes may be equally important to consider. Here we evaluated how artificial structures, an integral part of urbanisation in the marine environment, affects key functional properties of the habitat-forming kelp Ecklonia radiata. Given that stressors rarely occur in isolation, we assessed the effects of infrastructure across an urbanised estuary. Estuaries are ideal for studying how multiple anthropogenic and natural stressors influence potential impacts of infrastructure on habitat-forming species because these habitats usually face a wide range and levels of stressors. Here, we compared the abundance of habitat-forming macro-algae as well as the growth, erosion and photosynthetic activity of kelp in artificial and natural habitats across one of the largest urbanised estuaries in the word - Sydney Harbour. We predicted that effects of artificial structures on functional attributes of kelps would be stronger in the inner area of the Harbour, characterised by higher levels of human impacts and low flushing. Contrary to our predictions, we found that effects of infrastructure were consistent across the estuary, regardless of the ecological footprint caused by human activities or natural environmental gradients. When differences were observed between areas of the estuary, they mostly occurred independently of impacts of substrate type. Importantly, we found lower erosion rates of kelp on pilings than on reefs, likely resulting in lower production of detritus in estuaries where natural reefs are degraded or lost and pilings added. Such impacts have important implications for the connectivity among coastal habitats and secondary productivity in adjacent and remote habitats, which are highly dependent on the exportation of kelp detritus. Our study is the first to assess potential functional consequences of urbanisation through physiological and/or biomechanical effects on habitat-formers, an often overlooked mechanism of environmental impact on ecosystem functioning.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate ‘no-take’ and ‘general-use’ (fishing allowed) zones within three MPAs along 7^o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5–10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales.

Coastal urbanisation affects microbial communities on a dominant marine holobiont

Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host–microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour—pier-pilings and seawalls—and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia. There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.

Artificial structures in the marine coastal environment, such as piers and seawalls can alter microbial interactions with seaweed hosts. Researchers in Australia, led by Ezequiel Marzinelli at the University of New South Wales, studied the microbial communities growing on kelps in Sydney Harbour. They compared this altered environment with neighbouring natural rocky reefs. The work illustrates the “holobiont” concept, which treats communities of microbes and hosts as holistic entities. Significant findings included an increase in microbes associated with algal diseases in pier piling structures. This study shows that urbanisation of the coastal environment can have ecological consequences on major habitat-forming species such as kelp. The researchers argue that the combination of abiotic factors, such as shade, and biotic factors, such as altered grazing patterns, might be involved.

An evaluation of semi-automated methods for collecting ecosystem-level data in temperate marine systems

Historically, marine ecologists have lacked efficient tools that are capable of capturing detailed species distribution data over large areas. Emerging technologies such as high-resolution imaging and associated machine-learning image-scoring software are providing new tools to map species over large areas in the ocean. Here, we combine a novel diver propulsion vehicle (DPV) imaging system with free-to-use machine-learning software to semi-automatically generate dense and widespread abundance records of a habitat-forming algae over ~5,000 m² of temperate reef. We employ replicable spatial techniques to test the effectiveness of traditional diver-based sampling, and better understand the distribution and spatial arrangement of one key algal species. We found that the effectiveness of a traditional survey depended on the level of spatial structuring, and generally 10-20 transects (50 × 1 m) were required to obtain reliable results. This represents 2-20 times greater replication than have been collected in previous studies. Furthermore, we demonstrate the usefulness of fine-resolution distribution modeling for understanding patterns in canopy algae cover at multiple spatial scales, and discuss applications to other marine habitats. Our analyses demonstrate that semi-automated methods of data gathering and processing provide more accurate results than traditional methods for describing habitat structure at seascape scales, and therefore represent vastly improved techniques for understanding and managing marine seascapes.

The effects of substratum material and surface orientation on the developing epibenthic community on a designed artificial reef

Artificial reefs provide shelter and can be an important source of food for fish depending on the epibenthic community on the structure. The growth and diversity of this community is influenced by the substratum material and the surface orientation of the reef. Settlement plates of four materials (Perspex, sandstone, wood and steel) were deployed in three orientations (upwards, downwards and vertical) at a depth of 33 m on a designed artificial reef (DAR) off the coast of Sydney, Australia. After three months, the steel surfaces had lower invertebrate species richness, total abundance and diversity compared to other surfaces. Steel was not an ideal material for the initial recruitment and growth of epibenthic invertebrates. A longer duration would be required to develop a mature epibenthic community. Surface orientation had species-specific impacts. Surface material and orientation are important factors for developing epibenthic assemblages, and are thus likely to affect the broader artificial reef assemblage, including fish.

Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.

Horizontal-Plane Trajectory-Tracking Control of an Underactuated Unmanned Marine Vehicle in the Presence of Ocean Currents

Based on an integral backstepping approach, a trajectory-tracking control algorithm is proposed for an underactuated unmanned marine vehicle (UMV) sailing in the presence of ocean-current disturbance. Taking into consideration the UMV model's fore/aft asymmetry, a nonlinear three-degree-of-freedom (3DOF) underactuated dynamic model is established for the horizontal plane. First, trajectory-tracking differences between controllers designed based on symmetric and asymmetric models of the UMV are discussed. In order to explicitly study the effect of ocean-current interference on the trajectory-tracking controller, the ocean current is integrated into the kinematic and dynamic models of the UMV. Detailed descriptions of distinct trajectory-tracking control performances in the presence of different ocean-current velocities and direction angles are presented. The well-known persistent exciting (PE) condition is completely released in the designed trajectory-tracking controller. A mild integral item of trajectory tracking error is merged into the control law, and global stability analysis of the UMV system is carried out using Lyapunov theory and Barbalat's Lemma. Simulation experiments in the semi-physical simulation platform are implemented to confirm the effectiveness and superiority of the excogitated control algorithm.

Australian sea-floor survey data, with images and expert annotations

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

Canopy interactions and physical stress gradients in subtidal communities

Species interactions are integral drivers of community structure and can change from competitive to facilitative with increasing environmental stress. In subtidal marine ecosystems, however, interactions along physical stress gradients have seldom been tested. We observed seaweed canopy interactions across depth and latitudinal gradients to test whether light and temperature stress structured interaction patterns. We also quantified interspecific and intraspecific interactions among nine subtidal canopy seaweed species across three continents to examine the general nature of interactions in subtidal systems under low consumer pressure. We reveal that positive and neutral interactions are widespread throughout global seaweed communities and the nature of interactions can change from competitive to facilitative with increasing light stress in shallow marine systems. These findings provide support for the stress gradient hypothesis within subtidal seaweed communities and highlight the importance of canopy interactions for the maintenance of subtidal marine habitats experiencing environmental stress.