Dissertations / Theses on the topic 'CCA Crustose Coralline Algae'

2010/2011
The recent and steady CO2 increase, mainly due to human activities, causes a shift in the chemical equilibrium of the carbonates dissolved in sea-water, which results in a lowering of pH level. This phenomenon, known as ocean acidification, interacts with many physiological processes, including, calcification due to biological factors. Plenty of consequences can affect both the ecosystem and the human society; the latter benefits from goods and services produced by the ecosystem itself, such as fishing, shoreline protection, landscape, tourist and recreational activities. It seems there isn’t much awareness of all of this. The study of the effect of acidification on coralline algae (Corallinales) is of primary importance for the comprehension of the consequences at ecosystem level, since the Corallinales represent one of the key groups in the formation of submerged habitats, but also because they’ve proven to be some of the most responsive to acidification. The question that was tried to answer is whether the calcareous algae can be resilient towards acidification and, if that is so, which is the threshold value beyond which that ability expires. In this analysis, particular attention has been paid to reproductive phases, that represent a de facto sensitive point in the life cycle.
Il recente e costante aumento della CO2 dovuto principalmente alle attività antropiche provoca un’alterazione dell’equilibrio chimico dei carbonati disciolti nell’acqua marina, che si traduce in un abbassamento del pH. Questo fenomeno, noto come ocean acidification, interagisce con numerosi processi fisiologici fra cui, in primis, la calcificazione di origine biologica. Numerose potrebbero essere le conseguenze sugli ecosistemi, e quindi anche sulla società umana, che usufruisce di beni e servizi prodotti dagli ecosistemi stessi, come la pesca, la protezione della linea di costa, il paesaggio e le attività turistico - ricreative. Di tutto questo non sembra esserci in realtà grande consapevolezza. Lo studio degli effetti dell’acidificazione sulle alghe rosse calcaree (Corallinales) è di primaria importanza nella comprensione delle conseguenze a livello di ecosistema, in quanto le Corallinales rappresentano uno dei gruppi chiave nella formazione di habitat sommersi, ma anche perché esse si sono rivelate fra gli organismi più sensibili all’acidificazione. Il quesito di fondo a cui si è cercato quindi di dare una risposta è quale sia la resilienza da parte delle alghe calcaree nei confronti dell’acidificazione e quale possa essere il valore soglia al di là del quale tale capacità venga meno. In questa analisi, particolare attenzione è stata rivolta alle fasi riproduttive, che potrebbero rappresentare la fase più sensibile nel ciclo vitale.
XXIV Ciclo
1969

Over the past few decades, coral cover has declined worldwide due to overfishing, disease, and storms, and these effects have been exacerbated by ocean warming and acidification. Corals are extremely susceptible to these changes because they are already living close to their thermal and aragonite saturation thresholds. Ocean warming and acidification (OAW) may also impact coral survival and growth by impacting their settlement cues. Coral larvae use crustose coralline algae (CCA) and their associated biofilms as cues for settlement, i.e., habitat selection. Settlement cues can also be negatively affected by increased water temperature and acidity. It was hypothesized that the impacts of OAW on settlement substrate can further threaten coral persistence by altering/inhibiting larval settlement and potentially decreasing the post-settlement survival and growth of coral recruits. In this study, we 1) assessed the effect of substrate quality (substrate conditioned in ambient or OAW conditions) on settlement of A. agaricites larvae, 2) determined the effect of substrate quality on post-settlement survival and growth of A. agaricites recruits, and 3) determined the effect of ocean warming and acidification on the post-settlement survival and growth of A. agaricites recruits. Aragonite settlement tiles were placed offshore for one month to accrue CCA and associated biofilms, and were then conditioned in either ambient (29°C, 8.2 pH) or predicted future oceanic conditions (31°C, 7.9 pH) conditions for 7 – 10 days. Agaricia agaricites larvae were then introduced to the settlement tiles, and their settlement percentage was calculated. Once a week for 12 weeks after larval settlement, the size, survival, and pigmentation of A. agaricites recruits was recorded. Larvae settled marginally more on optimally conditioned tiles than on tiles previously exposed to OAW conditions (p=0.053). The survival of coral recruits in OAW conditions was greatly reduced, their growth was very limited, and they became paler over time. When reared in ambient conditions, recruits on OAW treated substrate initially displayed higher survival rates than recruits on ambient treated substrate. After 3 weeks in ambient conditions, however, survival rates were similar for recruits on ambient and OAW treated substrate; their growth curves were very similar, and coral recruits became more pigmented over time. Ocean warming and acidification conditions not only directly impacted the growth, survival, and pigmentation of A. agaricites recruits, but it also indirectly affected larval 5 settlement by likely altering microbial composition in bacterial biofilms on the settlement tiles. These results indicate that future conditions of ocean warming and acidification can be deleterious for A. agaricites, particularly after settlement. If the early life stages of scleractinian corals are negatively affected by OAW conditions, successful recruitment throughout the Caribbean and Florida Reef Tract could decrease. As a result, recovery from disturbances could be hindered, thus compromising the sustainability of many coral species and other marine ecosystems that depend on coral reefs for protection, habitat, and food.

Coral reefs are amongst the most biologically diverse ecosystems on our planet, supporting the livelihoods of millions of people globally. Despite their economic and ecological importance, human-driven global change is posing a major threat to the integrity of coral reefs worldwide. Ocean warming (OW) and ocean acidification (OA), both brought on by increased atmospheric CO2, are adversely affecting coral reefs and the organisms that inhabit them, particularly those organisms that calcify. Crustose coralline algae (CCA) are calcifying red macroalgae that provide essential ecosystem functions to coral reefs worldwide. CCA help to build and stabilise the coral reef framework and contribute to reef resilience and recovery by inducing the settlement of coral larvae to the reef. Previous research has shown CCA to be vulnerable to OW and OA, with resulting changes to their physiology and biology (i.e., reductions in calcification, abundance, survival). However, research on CCA lags behind other coral reef organisms, particularly in terms of their acclimatisation potential and knowledge of molecular, cellular, and metabolic processes. Given the known vulnerability of CCA, urgent research is required to understand how CCA will respond across molecular and physiological levels to global change drivers and this could directly aid in reef restoration efforts. The first data chapter of my thesis (Chapter 2) provides previously missing molecular information for CCA. De novo transcriptomes were compiled for four species, Porolithon cf. onkodes, Sporolithon cf. durum, Lithophyllum cf. insipidum, and Lithothamnion proliferum, that commonly occur in Australia’s Great Barrier Reef (GBR). Analyses of orthologous genes were conducted between CCA species and two noncalcifiying red algae, Chondrus crispus and Gracilariopsis chorda. Functional enrichment analysis of CCA orthologous proteins revealed a higher-than-expected number of sequences in categories relating to regulation of biological and cellular processes, such as actin related proteins, heat shock proteins, and adhesion proteins. This study allowed me to create reference transcriptomes that can be used in future studies investigating molecular responses of CCA to OW and OA and offered insight into the evolution of coralline algae. In Chapter 3 I investigated the differential physiological and transcriptomic responses of two species of CCA, P. cf. onkodes and S. cf. durum, to global change drivers (OW and OA). Previous literature investigating the responses of CCA species to global change drivers found variable results and these have been largely speciesspecific. The two species used in this study have been documented to have contrasting responses to OW and OA. Species-specific responses were seen in both the metabolic rate measurements and in the number of differentially expressed genes (DEGs) detected, indicating resilience in one species and not in the other. This study was also the first to reveal pathways and proteins that are differentially regulated in response to global change drivers. This work will help to predict the fate and functioning of different CCA species in future ocean conditions. Early life history stages of organisms are thought to be more impacted by climatic stressors than their adult stages, therefore, I investigated the responses across different life history stages of the CCA species S. cf. durum to varying levels of temperature and pCO2 (Chapter 4). In this study, I used adults and germlings of their first generation (F1). The findings suggest that adult stages of S. cf. durum are largely robust to end of century levels of temperature and pH, in terms of their survival and metabolic rates, and indicate that adult stages may be able to acclimatise to global change. On the other hand, the data show early life history stages of this species are highly sensitive to global change stressors with reductions in their survival and growth. This could impact the persistence of this species in future oceans. How an acclimation history to predicted, future levels of temperature and/or pH affects the physiological responses to chronic and acute thermal stress was investigated in the last chapter of my thesis (Chapter 5). P. cf. onkodes was acclimated to chronic, varying levels of temperature and pH for 6 weeks and then subjected to an acute, increasing temperature experiment (+ 4 – 6 ºC). The findings from this study suggest that an acclimation history to elevated temperature will reduce the thermal tolerance of P. cf. onkodes to withstand anomalous temperature events, which are projected to increase in number and severity within this century. Overall, the findings of the work described in this thesis have: 1) Made available the first comprehensive and annotated de novo transcriptomes for any species of CCA; 2) shown that physiological and transcriptomic response to global change drivers is species specific, with some CCA being more resilient and others not, and identified proteins relating to physiological processes that are differentially expressed in response to stress; 3) supported the hypothesis that early life history stages of CCA will be more impacted by global change drivers than adults of the same species, with possible plasticity being seen in adults in response to sustained exposure to stress; and 4) determined an acclimation history of elevated temperature will reduce thermal tolerance and productivity in CCA. My thesis also provides evidence that more anciently diverged genera (e.g., Sporolithon) are physiologically more robust and molecularly less responsive to global change drivers. My thesis demonstrates the strength of incorporating molecular, life history stage, and acclimation type approaches to more holistically understand the future of a critical group of reef-building organisms under global climate change and will ultimately contribute to conservation efforts that are currently being made into saving coral reefs worldwide.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

Ocean acidification (OA) and warming are both threats to the physiological and demographic processes of crustose coralline algae (CCA). This group of algae is one of the most abundant in tropical and temperate reefs where they play essential roles including reef building and induction of invertebrate settlement. Despite their importance, little is known about the effects of OA on early stages of CCA and on population and community dynamics. In addition, CCA are widely distributed around the world and are especially abundant in coral reef ecosystems. They can occupy different habitats due to their variation in life history characteristics. However, there is a gap in the knowledge about their temporal variation (in adult and recruits) and demographic relationships among reproduction, recruitment and adult abundance. Therefore, this PhD thesis aimed to assess the supply-side ecology of crustose coralline algae in the reef and their responses to future anthropogenic impacts.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

As algas calcárias crostosas ou CCA (do inglês Crustose Coralline Algae) têm como principal característica a impregnação de carbonato de cálcio em suas paredes celulares. Este grupo é formado atualmente por três ordens, Corallinales, Hapalidiales e Sporolithales, cuja taxonomia é historicamente problemática por se basear na fase tetrasporofítica, fundamental para qualquer identificação até mesmo em nível de ordem. Em virtude disso, diversos estudos, principalmente nos últimos 10 anos, têm incluído ferramentas moleculares como auxílio à taxonomia morfoanatômica deste grupo. O objetivo deste estudo foi investigar a diversidade e a distribuição das CCA ao longo da costa Brasileira, através de dados moleculares e morfoanatômicos. Para isso, foram utilizados quatro marcadores moleculares, UPA, rbcL-3P, COI-5P e psbA, aliados à imagens de microscopia óptica e microscopia eletrônica de varredura, que resultaram na identificação de pelo menos 37 espécies entre Corallinales, Hapalidiales e Sporolithales. Os resultados obtidos a partir das análises de agrupamento dos quatro marcadores demonstraram que as ordens Corallinales e Sporolithales são monofiléticas, e Hapalidiales constitui um grupo não-monofilético (com exceção do marcador psbA, que resolveu a ordem como grupo monofilético). Os resultados também revelaram existência de uma grande diversidade de espécies e gêneros destas ordens no Brasil, além de espécies novas e ao menos um potencial gênero novo para ciência. O estudo também revelou relações filogeográficas entre espécies do Brasil e do Golfo do México e do Indo-Pacífico. Considerando as três ordens de CCA (Corallinales, Hapalidiales e Sporolithales), este estudo representa a primeira tentativa de desvendar de forma mais ampla a diversidade de espécies CCA encontradas ao longo da costa brasileira, utilizando dados moleculares
The Crustose Coralline Algae (CCA) has as a main distinguishing characteristic the calcium carbonate impregnation in their cell walls. This group currently encompasses three orders, the Corallinales, Hapalidiales and Sporolithales, whose taxonomy is historically problematic because it is based on the tetrasporophytic phase, fundamental to any classification, even at the ordinal level. Therefore, many studies, especially in the last 10 years, have included molecular tools to assist the morphological taxonomy of this group. This study aims to investigate the diversity and distribution of the CCA along the Brazilian coast, through molecular and morphoanatomical data. In order to achieve this aim, four markers were used, UPA, rbcL-3P, COI-5P and psbA, allied to light and scanning electron microscopy, that resulted in the identification of at least 37 species between Corallinales, Hapalidiales and Sporolithales. The results of the cluster analyses of the four markers showed that Corallinales and Sporolithales are monophyletic, and Hapalidiales comprises a non-monophyletic group (with the exception of psbA, which resolved the order as a monophyly). Our results also revealed a great diversity of species and genera of these three orders in Brazil, as well as putative new species and at least a new genus. This study also revealed phylogeographic relationships between Brazilian species and species from Gulf of Mexico and from Indo-Pacific oceans. Considering all the three orders of CCA, this study represents the first broad attempt and effort to unveil the diversity of CCA species found on the Brazilian coast using molecular data

Crustose coralline algae (CCA) are calcifying marine red macroalgae that play key ecological roles in building and cementing reef structures, and contribute significantly to the coastal marine carbon cycle. Anthropogenic global change is advancing rapidly and its two main threats in the marine realm, ocean acidification (OA) and ocean warming, have been empirically shown to impair the physiology of CCA. However, the presence of CCA in the geological record dates back to more than 180 million years ago, indicating that CCA have endured periods of substantial fluctuation in oceanic temperature and pCO2. CCA taxa comprise three lineages: Corallinales (most recently evolved), Hapalidiales (intermediate/more basal), and Sporolithales (most basal). Yet, it is still not well understood how their distinct evolutionary histories may have affected selection for certain physiological strategies and how this may shape trends in their responses to OA and warming. Two key carbon physiological processes in CCA are photosynthesis and calcification, and due to their variable and interdependent nature, the observation of a singular physiological response may not suffice in predicting the long-term survival of these reef-building macroalgae. Gaps exist in the knowledge of mechanisms that underpin carbon fixation and biomineralisation across lineages that would ultimately elucidate the fate of CCA taxa under global threats. Thus, I aimed to identify the strategies that exist across various carbon physiological processes: inorganic carbon uptake, carbon partitioning, carbon release, and cell wall organic matrix composition, which allow the movement of carbon into, within, and out of the CCA thallus. I examined six common CCA species from the northern Great Barrier Reef that belong to lineages with distinct evolutionary histories (time and environmental conditions endured). I chose three dominant taxa that pertain to the more basal lineages and occupy low-light habitats, and three dominant taxa that belong to the most recently evolved lineage and occupy high-light environments. I conducted experiments where OA and warming scenarios (largely IPCC 8.5) were simulated in a flow-through mesocosm system, CCA fragments were subjected to treatment for 1-2 months, and physiological strategies and their responses to treatment were quantified. First, to establish the extent of diffusive CO2 and/or HCO3- use, inorganic carbon uptake was characterised by measuring the stable carbon isotope ratio of surficial CCA tissue (Chapter 2). Second, I determined patterns in the quantity of carbon partitioned to surficial organic tissue and inorganic skeleton, as well as the amount of carbon released as dissolved organic carbon (DOC) (Chapter 3). Finally, I examined strategies of the monosaccharide composition of polysaccharides that compose the cell wall in surficial organic tissue, and its relationship with biomineralisation capacity (Chapter 4). The results indicated that CCA possess a range of strategies within each physiological process. In Chapters 2 and 3, I found that CCA from basal lineages that evolved to occupy low-light environments largely possess strategies of greater diffusive CO2 uptake, lower organic:inorganic biomass ratios, and from a zero to positive net efflux of DOC. On the other hand, CCA from the more recently-evolved lineage that occupy high-light environments largely possess greater HCO3- uptake, higher organic:inorganic biomass ratios, and a net DOC influx. Results from Chapter 4 suggest variability in abundance of cellulose, mannan, alginate, and galactan across taxa. Patterns in the abundance of a monomer of alginate indicate a positive correlation between alginate abundance and biomineralisation potential. However, composition is largely not predicted by evolutionary history. In response to OA and warming, Chapter 2 results indicate that CCA largely increase HCO3- uptake across strategies, which is associated with maintained or increased metabolic performance. Chapter 3 results suggest that while low-light CCA tend to retain carbon content in their surficial thallus and switch to a net influx of DOC under global change, high-light taxa largely decrease surficial carbon content and release more DOC. Chapter 4 results demonstrate that monosaccharides were differentially modulated across CCA taxa under OA and warming. Changes in the monosaccharides of the important reef-builder P. cf. onkodes were correlated with lower biomineralisation capacity. Overall, these findings provide a framework for characterising the distinct strategies of carbon acquisition, partitioning, release, and organic matrix composition across dominant reef-building CCA of the Great Barrier Reef. The data suggest that some physiological strategies may be specific to high- or low-light reef environments, showing the importance of the relationship between light availability and carbon fluxes. The data also indicate that the distinct environmental conditions during which each CCA lineage evolved may have played a role in the diversity of carbon physiologies across CCA. Ultimately, the carbon physiological responses of some species were more suitable to maintain metabolic performance, and may potentially be more adaptable to global change than others. These findings suggest that if less robust CCA are not capable of acclimating/adapting relatively quickly, there may be serious repercussions for the integrity and ecology of certain reef environments into the Anthropocene.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

Les algues corallines encroûtantes (CCA) sont communément associées à des récifs sains et jouent un rôle important dans les systèmes benthiques en guidant la colonisation de nombreux organismes, comme les coraux. Cependant, la capacité des CCA à induire l’implantation des coraux ne fonctionne pas pour toutes les espèces de CCA. Les larves de coraux sélectionnent certaines espèces d’algues, ce qui pose la question des mécanismes sous-jacents. Malgré l’énorme variété d’espèces de CCA dans les récifs, on en sait peu sur leur diversité chimique et microbienne et sur le rôle écologique de ces deux composants pour le recrutement des coraux. Le chapitre 2 étudie la composition microbienne et chimique de 6 espèces de CCA sur les récifs coralliens de Moorea, et comment ces deux compartiments sont liés au succès d’implantation des larves d’Acropora cytherea. Les résultats ont révélé que le taux d’implantation était le plus élevé sur l’espèce cryptique Titanoderma prototypum. Alors que toutes les espèces de CCA avaient des empreintes métaboliques distinctes et contenaient une grande diversité métabolomique, la diversité et la richesse métabolomiques de T. prototypum étaient plus élevées que celles des autres espèces. T. prototypum hébergeait également une diversité bactérienne plus élevée, et contenait une plus grande abondance de bactéries susceptibles de produire des composés antibactériens. Ces bactéries pourraient inhiber les agents pathogènes des coraux, ce qui pourrait à son tour améliorer la survie des larves. Ainsi, le recrutement corallien est un processus complexe de communications biochimiques entre les CCA, leurs communautés de surface microbiennes associées et les larves de coraux. Malgré la large acceptation que certaines espèces de CCA influencent positivement le recrutement corallien, il n’y a pas de données expérimentales sur les effets des espèces de CCA sur la survie et la croissance post-implantation tardive des coraux. Le chapitre 3 teste l’impact de 4 espèces de CCA, de deux types d’habitats (exposés et subcryptiques), sur la survie et la croissance des recrues de Pocillopora. Les CCA ont eu un effet contrasté sur la survie des recrues coralliennes suivant l’habitat et de la taille des recrues. Dans les habitats subcryptiques, les CCA réduisaient la survie et/ou la croissance des recrues coralliennes via la compétition directe, tandis que, dans les habitats exposés, elles amélioraient le recrutement des coraux en atténuant la concurrence avec le gazon algal. Cette étude a démontré que toutes les espèces de CCA ne sont pas bénéfiques à la survie et à la croissance des recrues coralliennes et qu’il existe une variabilité considérable dans l’issue et le processus de compétition entre les CCA et les coraux. Chapitres 4 et 5 déterminent si deux facteurs de stress environnementaux, respectivement l’acidification des océans (AO) et l’hypoxie, affectent l’association corail-CCA en perturbant le comportement et l’implantation des larves des deux espèces de coraux (A. cythera et A. pulchra), ainsi que leur recrutement, sur une espèce de CCA appropriée. Les larves des deux espèces évitaient l’exploration et l’implantation dans des environnements à faible pH ou à oxygène réduit. Ces résultats indiquent que les zones à faible teneur en oxygène et pH peuvent influencer négativement le succès d’implantation des larves de coraux et que l’oxygène et le pH peuvent être des signaux chimiques pour l’orientation et l’implantation des larves de coraux. Cette thèse aide à mieux comprendre le rôle des CCA, des micro-organismes et des composés chimiques dans la dynamique à petite échelle du recrutement des coraux maintenant et dans les conditions océaniques futures. Les résultats soulignent que les interactions CCA-corail sont des processus complexes qui sont probablement médiés par des composés chimiques et microbiens et que ces interactions peuvent être affectées par des environnements changeants
Crustose coralline algae (CCA) are commonly associated with healthy reefs and play an important role in benthic systems by guiding settlement of many habitat forming or ecologically important organisms, including corals. However, the ability of CCA to induce coral settlement is not ubiquitous among CCA species. Corals exhibit settlement preferences for certain CCA species. These preferences demonstrate the capacity of coral larvae to discriminate among CCA species and raise the question of the mechanisms involved. Despite the enormous variety of CCA species on coral reefs, little is known about the diversity of their associated chemicals and microbes and the ecological role of these compartments, notably for coral recruitment. Chapter 2 of this thesis investigated the microbial and chemical composition of six CCA species, which occupy different ecological niches on the coral reefs of Moorea (French Polynesia), and how these two compartments (i.e., microbial and chemical) relate to successful settlement success of Acropora cytherea larvae. Results showed settlement was highest on the cryptic CCA species Titanoderma prototypum and that practically no larvae settled on exposed CCA species. While all CCA species had distinct metabolic fingerprints and contained high metabolic diversity, the metabolomic diversity and richness of T. prototypum were significantly higher than those of the other CCA species. T. prototypum also hosted a significantly higher bacterial diversity than the other CCA species, and contained a higher abundance of bacteria that potentially produce antibacterial compounds. The presence of these bacteria could inhibit coral pathogens, which in turn could enhance the survival of coral settlers. Thus, coral settlement is a complex process of biochemical communications between CCA, their associated microbial surface communities and coral larvae. Despite widespread acceptance that CCA positively influence coral recruitment success, there are no experimental data on the effects of CCA species on late post-settlement survival and growth of corals. Chapter 3 tested the impact of four CCA species from two habitats (exposed and subcryptic) on the survival and growth of Pocillopora recruits. CCA had a contrasting effect on the survival of coral recruits depending on habitat and recruit size. In subcryptic habitats, CCA can reduce the survival and/or growth of coral recruits via direct competitive overgrowth, while, in exposed habitats, they can enhance coral recruitment by alleviating competition with turf algae. Importantly, this study demonstrated that not all CCA species are beneficial to the survival and growth of coral recruits and that there is considerable variability in both the outcome and process of competition between CCA and corals. Chapter 4 and 5 focused on investigating whether two environmental stressors, ocean acidification (OA) and hypoxia, respectively, impact the coral-CCA association by disrupting larval settlement behavior and recruitment of two coral species (A. cytherea and A. pulchra) on an otherwise preferred and beneficial CCA species (T. prototypum). Larvae of both coral species avoided bottom exploration and settlement in low pH environments. They avoided bottom exploration in reduced oxygen environments and settled on T. prototypum fragments only in oxygen rich environments, with settlement rates increasing exponentially with oxygen concentrations. These results indicate that low oxygen and low pH areas can negatively influence coral settlement success and that oxygen and pH act as chemical cues for coral larval orientation and settlement. This thesis aids to better understand the role of CCA, micro-organisms and chemicals in the fine-scale dynamics of coral recruitment now and under future ocean conditions. It highlights that CCA-coral interactions are complex processes that are likely mediated by chemicals and microbes and these interactions can be affected by changing environments

Crustose coralline algae (CCA) are considered a key functional group in coral reef ecosystems. Changes in the abundances of certain CCA species can directly regulate the abundance of other components of reefs, in particular corals, and can therefore result in changes in structure and function of this marine ecosystem. This thesis assesses important questions on what controls distribution and abundance patterns of tropical CCA species along environmental gradients, their responses to sedimentation and the herbicide diuron, and species-specific differences in their roles in inducing or inhibiting coral recruitment, hence contributing to the structuring of coral reefs. The taxonomic composition of CCA is described for the inshore and offshore reefs within the central and northern Great Barrier Reef (GBR). Twenty-three species from twelve genera and three subfamilies of Corallinaceae were identified to species level using reproductive and vegetative morphology and anatomical features as diagnostic characters. Distribution and relative abundance of the species were compared along gradients in depth and across the shelf, and along a set of environmental variables such as slope angle and sedimentation. Changes across the continental shelf were observed in CCA cover and CCA community composition, as well as in the environmental variables slope angle, sediment deposits, and water clarity. Percent cover of CCA increased more than four-fold across the shelf. Inshore reefs were dominated by thin leafy non-adherent corallines (i.e. Mastophora pacifica), whereas offshore reefs were dominated by thick adherent species (i.e. Porolithon onkodes and Neogoniolithon fosliei). Abundances of several species were significantly related to cross-shelf distance, depth and sedimentation. For example, the most abundant CCA, Porolithon onkodes was 4 times more abundant on offshore reefs compared to inshore reefs, and preferred shallow depths (2 to 5 m) and low sediment deposits. Conversely, the most abundant species on the inshore reefs, Hydrolithon reinboldii, decreased in abundance across the shelf, preferred deeper depths (8 to 12 m) and was not affected by high levels of sediment. Differences in CCA communities between inshore and offshore reefs may however be additionally related to the factors of wave force, grazing and water clarity. On the inshore reefs, the reduced cover of CCA, the dominance of thin and leafy species and the reduced abundance of thick consolidators have profound implications for differences in the ecosystem structure. At present, the degree to which human activity can affect abundance and species composition of CCA on reefs is poorly understood. The herbicide diuron (N’-(3,4-dichlorophenyl)-N, N-dimethylurea) is detectible in many inshore sediment samples along the central Queensland coast. Organisms living on some of the inshore coral reefs of the GBR are regularly exposed to river plumes transporting this herbicide. This study compares physiological responses and survival of CCA that were exposed to diuron and to sedimentation, separately and in combination, in controlled time course laboratory experiments, using pulse-amplitude modulation chlorophyll fluorometry. The results demonstrate that sediment deposition and exposure to diuron when applied in isolation can negatively affect the photosynthetic activity of CCA, but were often reversible depending on diuron concentration and sediment type. Significant reductions in effective quantum yields (DF/Fm’) of photosystem II in CCA species were observed at nominal diuron concentrations greater than 1 mg L-1. Exposure to fine (<63 mm grain size) nutrient-rich estuarine sediments reduced DF/Fm’ more than exposure to the same amount of fine (<63 mm grain size) calcareous sediments. There are clear differences in sedimentation tolerance between species, with an inshore species (H. reinboldii) being more sediment tolerant than two offshore species (P. onkodes and N. fosliei). Sedimentation stress is however significantly enhanced by trace concentrations of diuron, and recovery from a combined sediment and diuron exposure was still incomplete after 9 days. The finding of synergistic effects of simultaneous exposure to sedimentation and diuron on CCA has implications for the recruitment of the vast number of reef organisms specialized to settle on CCA. The ability of coral larvae to identify an appropriate site for settlement and metamorphosis is critical for recruitment. Crustose coralline algae are known to induce metamorphosis of coral larvae in the laboratory. The aim of this field study was to determine what types of substrata (namely reef-dwelling species of CCA) coral recruits settle on and at what orientation (i.e. upper, lower or vertical surfaces). This study was conducted in 3 regions: in the GBR on inshore and offshore reefs, and in the Caribbean. After one year, the amount of unoccupied substrata (bare), and the space occupancy of CCA, Peyssonnelia sp., invertebrates and turf algae on the settlement tiles varied between the 3 regions. On offshore reefs in the GBR the percent of CCA on the tiles was greatest (26%) and turf algae lowest (5%). On average, 89% of coral recruits were found on the bottoms and sides of the settlement tiles. Most coral recruits in the GBR and in the Caribbean attached to a widespread but rare CCA, Titanoderma prototypum, that overall comprised less the 5% of the coralline flora on natural reef surfaces, but as a pioneer species, nevertheless covered 2.5% of the settlement tiles. Most other reef-dwelling organisms, such as other encrusting algae (i.e. the CCA species H. reinboldii and Porolithon sp. and the non-coralline crust Peyssonnelia sp., which induce metamorphosis under laboratory conditions), and some invertebrates (specifically polychaetes, foraminifera and attached bivalves), supported significantly lower coral recruit densities. In all regions combined, only 0.1% of the coral recruits settled onto turf algae despite it covering 14% of the tiles, and 0% settled on sediment-covered surfaces, macroalgae and certain species of dominant CCA. Titanoderma prototypum may provide a good attachment surface in microhabitats where competition and grazing from other reef organisms is low. This research identifies the available settlement substrata for coral settlement in the GBR and Caribbean and highlights the critical role a single species can play in the structure and function of a highly complex ecosystem. Several species of CCA are known to induce coral settlement, however CCA also employ physical and biological anti-settlement defence strategies at varying effectiveness. This study describes the chemical and physical recognition and ranking of five CCA species and inert settlement substrata by coral larvae, and the subsequent survival of these larvae on the varying substrata. Settlement on the most preferred substratum, T. prototypum, was 15 times higher than on the least preferred substratum, N. fosliei. The rates of post-settlement survival of the corals also varied among CCA species in response to their anti-settlement strategies (shedding of surface cell layers, overgrowth and potential chemical deterrents). Rates of larval settlement, post-settlement survival and the sensitivity of larvae to chemical extracts of CCA were all positively correlated across the five species of CCA. Non-living settlement substrata on coral reefs are sparse, consequently the presence of only a few CCA species that facilitate coral recruitment has important implications for structuring the reef ecosystem. These four studies have extended our knowledge of basic ecology of CCA and their important role in structuring coral reefs. They have also advanced our knowledge of how the mosaic of benthic organisms, influenced by human disturbances, affect coral settlement. A small and inconspicuous species of CCA that strongly facilitates and catalyzes coral recruitment on reefs has been identified. The information gained from these studies assists in the understanding of reef recovery, and therefore may contribute to the management and conservation of reef ecosystems.

Crustose coralline algae (CCA) are considered a key functional group in coral reef ecosystems. Changes in the abundances of certain CCA species can directly regulate the abundance of other components of reefs, in particular corals, and can therefore result in changes in structure and function of this marine ecosystem. This thesis assesses important questions on what controls distribution and abundance patterns of tropical CCA species along environmental gradients, their responses to sedimentation and the herbicide diuron, and species-specific differences in their roles in inducing or inhibiting coral recruitment, hence contributing to the structuring of coral reefs. The taxonomic composition of CCA is described for the inshore and offshore reefs within the central and northern Great Barrier Reef (GBR). Twenty-three species from twelve genera and three subfamilies of Corallinaceae were identified to species level using reproductive and vegetative morphology and anatomical features as diagnostic characters. Distribution and relative abundance of the species were compared along gradients in depth and across the shelf, and along a set of environmental variables such as slope angle and sedimentation. Changes across the continental shelf were observed in CCA cover and CCA community composition, as well as in the environmental variables slope angle, sediment deposits, and water clarity. Percent cover of CCA increased more than four-fold across the shelf. Inshore reefs were dominated by thin leafy non-adherent corallines (i.e. Mastophora pacifica), whereas offshore reefs were dominated by thick adherent species (i.e. Porolithon onkodes and Neogoniolithon fosliei). Abundances of several species were significantly related to cross-shelf distance, depth and sedimentation. For example, the most abundant CCA, Porolithon onkodes was 4 times more abundant on offshore reefs compared to inshore reefs, and preferred shallow depths (2 to 5 m) and low sediment deposits. Conversely, the most abundant species on the inshore reefs, Hydrolithon reinboldii, decreased in abundance across the shelf, preferred deeper depths (8 to 12 m) and was not affected by high levels of sediment. Differences in CCA communities between inshore and offshore reefs may however be additionally related to the factors of wave force, grazing and water clarity. On the inshore reefs, the reduced cover of CCA, the dominance of thin and leafy species and the reduced abundance of thick consolidators have profound implications for differences in the ecosystem structure. At present, the degree to which human activity can affect abundance and species composition of CCA on reefs is poorly understood. The herbicide diuron (N’-(3,4-dichlorophenyl)-N, N-dimethylurea) is detectible in many inshore sediment samples along the central Queensland coast. Organisms living on some of the inshore coral reefs of the GBR are regularly exposed to river plumes transporting this herbicide. This study compares physiological responses and survival of CCA that were exposed to diuron and to sedimentation, separately and in combination, in controlled time course laboratory experiments, using pulse-amplitude modulation chlorophyll fluorometry. The results demonstrate that sediment deposition and exposure to diuron when applied in isolation can negatively affect the photosynthetic activity of CCA, but were often reversible depending on diuron concentration and sediment type. Significant reductions in effective quantum yields (DF/Fm’) of photosystem II in CCA species were observed at nominal diuron concentrations greater than 1 mg L-1. Exposure to fine (<63 mm grain size) nutrient-rich estuarine sediments reduced DF/Fm’ more than exposure to the same amount of fine (<63 mm grain size) calcareous sediments. There are clear differences in sedimentation tolerance between species, with an inshore species (H. reinboldii) being more sediment tolerant than two offshore species (P. onkodes and N. fosliei). Sedimentation stress is however significantly enhanced by trace concentrations of diuron, and recovery from a combined sediment and diuron exposure was still incomplete after 9 days. The finding of synergistic effects of simultaneous exposure to sedimentation and diuron on CCA has implications for the recruitment of the vast number of reef organisms specialized to settle on CCA. The ability of coral larvae to identify an appropriate site for settlement and metamorphosis is critical for recruitment. Crustose coralline algae are known to induce metamorphosis of coral larvae in the laboratory. The aim of this field study was to determine what types of substrata (namely reef-dwelling species of CCA) coral recruits settle on and at what orientation (i.e. upper, lower or vertical surfaces). This study was conducted in 3 regions: in the GBR on inshore and offshore reefs, and in the Caribbean. After one year, the amount of unoccupied substrata (bare), and the space occupancy of CCA, Peyssonnelia sp., invertebrates and turf algae on the settlement tiles varied between the 3 regions. On offshore reefs in the GBR the percent of CCA on the tiles was greatest (26%) and turf algae lowest (5%). On average, 89% of coral recruits were found on the bottoms and sides of the settlement tiles. Most coral recruits in the GBR and in the Caribbean attached to a widespread but rare CCA, Titanoderma prototypum, that overall comprised less the 5% of the coralline flora on natural reef surfaces, but as a pioneer species, nevertheless covered 2.5% of the settlement tiles. Most other reef-dwelling organisms, such as other encrusting algae (i.e. the CCA species H. reinboldii and Porolithon sp. and the non-coralline crust Peyssonnelia sp., which induce metamorphosis under laboratory conditions), and some invertebrates (specifically polychaetes, foraminifera and attached bivalves), supported significantly lower coral recruit densities. In all regions combined, only 0.1% of the coral recruits settled onto turf algae despite it covering 14% of the tiles, and 0% settled on sediment-covered surfaces, macroalgae and certain species of dominant CCA. Titanoderma prototypum may provide a good attachment surface in microhabitats where competition and grazing from other reef organisms is low. This research identifies the available settlement substrata for coral settlement in the GBR and Caribbean and highlights the critical role a single species can play in the structure and function of a highly complex ecosystem. Several species of CCA are known to induce coral settlement, however CCA also employ physical and biological anti-settlement defence strategies at varying effectiveness. This study describes the chemical and physical recognition and ranking of five CCA species and inert settlement substrata by coral larvae, and the subsequent survival of these larvae on the varying substrata. Settlement on the most preferred substratum, T. prototypum, was 15 times higher than on the least preferred substratum, N. fosliei. The rates of post-settlement survival of the corals also varied among CCA species in response to their anti-settlement strategies (shedding of surface cell layers, overgrowth and potential chemical deterrents). Rates of larval settlement, post-settlement survival and the sensitivity of larvae to chemical extracts of CCA were all positively correlated across the five species of CCA. Non-living settlement substrata on coral reefs are sparse, consequently the presence of only a few CCA species that facilitate coral recruitment has important implications for structuring the reef ecosystem. These four studies have extended our knowledge of basic ecology of CCA and their important role in structuring coral reefs. They have also advanced our knowledge of how the mosaic of benthic organisms, influenced by human disturbances, affect coral settlement. A small and inconspicuous species of CCA that strongly facilitates and catalyzes coral recruitment on reefs has been identified. The information gained from these studies assists in the understanding of reef recovery, and therefore may contribute to the management and conservation of reef ecosystems.

Crustose coralline algae (CCA), and in particular Porolithon onkodes, play an important reef-building role in modern tropical coral reefs. CCA form thick crusts of Mg-calcite and grow over corals and loose substrate to bind these together. This binding and cementing process is fundamental to the development of structural reefs that are capable of withstanding the high-energy waves in the shallow to inter-tidal areas of the reef. As anthropogenic CO2 emissions continue to increase, the oceans absorb part of this extra CO2 and become more acidic, a process known as Ocean Acidification (OA). There are concerns that OA will have a negative affect on the reef-building capacity of coral reef organisms, in particular on CCA. This is because Mg-calcite is meta-stable and more susceptible to dissolution than aragonite, the mineral used by corals to build skeletons. The goal of this thesis work was to firstly understand the physical and mechanical properties that enable the CCA to cement the reef and withstand damage from high-energy waves, bioerosion and chemical dissolution. Secondly, to anticipate how OA may interfere with these reef-building properties. These goals were pursued by setting clear aims with associated specific objectives designed to elucidate information relevant to these questions. Methods were developed for X-ray diffraction to identify the mineral composition of CCA. Nanoindentation was investigated as a tool for determining the mechanical properties of CCA and the measurement of fracture toughness was found to return physically meaningful information relevant to structural reef development. Study of CCA calcification showed that cell wall Mg-calcite exhibited radial crystal morphology in agreement with published studies on temperate species. However, high-resolution imaging showed the radial crystals were made of banded stacked sub-micron grains within an organic framework. Dolomite was found not only as cell lining by submicron rhombs, but also as the primary calcification of hypothallial cell walls. Dolomite is shown to be resistant to bacterial erosion. A model is developed whereby it is proposed that dolomite formation is dependent on polysaccharide accumulation. Using nanoindentation, P. onkodes are found to be extraordinarily tough, on par with the measured fracture toughness for metamorphic minerals quartz and corundum. The fracture toughness is enabled by the presence of dolomite cell lining. Contrary to the literature, bacterial erosion is found to be a constructive, not destructive, process. A survey of P. onkodes from Heron Island fore reef and reef flat showed that dolomite was present in all the fore reef crusts but none of the reef flat crusts. The reef flat crusts did not have fracture resistance except where remineralised. The presence of dolomite cell lining was shown to decrease skeletal dissolution rates by an order of magnitude. OA experiments showed that skeletal dissolution rates increased with elevated pCO2, but dolomite continued to confer resistance to dissolution. pCO2 levels did not affect the skeletal Mg content or dolomite formation in living CCA. Of concern, and in agreement with the literature, bacterial erosion is accelerated under a combination of elevated pCO2 and temperatures, suggesting this may be the main threat to CCA reef-building in the future. The experimental findings were corroborated by results of a field survey along a natural pCO2 gradient. In summary, dolomite was found to be an essential component of modern reef development via its contribution to enabling CCA P. onkodes thick crust development and persistence. Reef building by CCA P. onkodes is likely to continue as pCO2 rises up until a tipping point is reached whereby bacterial erosion switches from constructive to destructive.

Climate variability in the North Atlantic has been linked in part to the North Atlantic Oscillation (NAO). The NAO influences marine ecosystems in the northwestern Atlantic and the transport variability of the cold Labrador Current (LC). Understanding historic patterns and predicting future changes in LC transport require long-term and high-resolution climate records that are not available from instrumental data sets. This thesis presents the first century-scale sea surface temperature (SST)reconstructions from the Northwestern Atlantic using Mg/Ca ratios in the long-lived crustose coralline algae Clathromorphum compactum. which is characterized by a high Mg-calcite skeleton exhibiting annual growth increments. Results indicate strong correlations between interannual variations in Mg/Ca ratios and instrumental SST. The 131-year algal Mg/Ca record reveals NAO-type periodicities and evidence of past cold events and warming periods associated with basin-wide ecosystem shifts. Negative correlations between LC volume transport and algal Mg/Ca reflect the cooling influence of the LC on eastern Canadian shelf ecosystems.

In situ rates of photosynthesis and calcification were determined for four species of reef-building crustose coralline algae on the windward crest and slope of a coral reef at Lizard Island, in the northern region of the Great Barrier Reef (GBR). The species studied were Porolithon onkodes (Heydrich) Foslie, Neogoniolithon fosliei (Heydrich) Setchell & Mason, Hydrolithon reinboldii (Weber-van Bosse & Foslie) Foslie, and Paragoniolithon conicum (Dawson) Adey, Townsend & Boykins. Rates were measured with an underwater respirometer incorporating oxygen, pH, light and temperature probes located within an ultra-violet transparent incubation chamber. Measurements of photosynthesis were also made in the laboratory using a 'Clark' type oxygen electrode and a specially constructed acrylic cell. The photosynthetic quotients (PQ) of the four species were determined from in situ measurements of oxygen, pH, and total alkalinity, with corrections for changes in seawater temperature over the period of incubation. Light-saturation curves for photosynthesis (P-I curves) and calcification (C-I curves) were constructed from each set of in situ and laboratory measurements using non-linear, least squares regression analysis. The curves were examined for evidence of photoadaptation and for estimation of the rates of maximal gross photosynthesis, absolute dark respiration, maximal light-enhanced calcification, and dark calcification. Individuals from selected habitats at depths of between 0 and 18 m were studied both in situ and in the laboratory. The specimens received from 85 to 2% of surface irradiance as measured in units of photosynthetic photon flux density (PPFD) between 400 and 700 nm. Light-saturation curves. In situ data were modelled by the hyperbolic tangent function. The less variable laboratory data revealed subtle differences in the shapes of the light-saturation curves of different species and were modelled by one of four related mathematical functions. The functions tested for accuracy of fit were the hyperbolic tangent, a simple exponential, a general exponential, and the right rectangular hyperbola. Specimens collected from 0 m exhibited slow rates of transition from light-limited to light-saturated photosynthesis. Many of these individuals were not entirely saturated at irradiance levels above those naturally occurring in the field. Rates of photosynthesis were generally lower in the laboratory than in situ. Specimens measured in situ at depths representing the lower limits of the species distributions were found to exhibit light-response curves which did not indicate saturated levels of photosynthesis or calcification. Photoadaptation. Adaptive changes were observed in the photokinetic parameters describing the shapes of the light-saturation curves of all species under both laboratory and in situ conditions as the quantity of irradiance diminished. Compensation points ((Ic), 95% saturation levels (I₀₉₅), and intercepts between the initial slopes of the curves and the horizontal asymptotes ((Ik) decreased. Rates of respiration (R), maximal gross photosynthesis (Pgm), and light-enhanced calcification (C light) based on real surface area also tended to fall. The initial slopes of the curves (α) for photosynthesis (based on projected or real surface area) and calcification (based on total protein content) increased with decreasing irradiance. The ratios of gross photosynthesis to respiration (Pᵍml-R) increased marginally with decreasing irradiance. The rates of dark calcification (C dark) and light-enhanced calcification expressed on the basis of total protein content were variable and did not vary predictably with diminishing irradiance. The natural logarithms (In) of Ic, Ik, and I₀₉₅ were directly proportional to the natural logarithms of the percentages of surface irradiance (In %SI) transmitted to the depths at which the algae were growing. Similar double logarithmic relationships were observed between Pᵍm, R,(C light)(based on real surface area) and In %SI for some species. The natural logarithms of for photosynthesis normalised on the basis of real surface area, and for calcification normalised on the basis of total protein content, were inversely proportional to In %SI for all species. Similar double logarithmic relationships were observed between Pᵍm l-R and In %SI for some species. Primary production. Photosynthetic quotients (PQ) were determined for each species. Mean PQ values for P. onkodes, N. fosliel, and H. reinboldii ranged from 1.21 to 1.33. The mean PQ for P. COM. CUM was 1.07. Mean rates of maximal net organic carbon production per hour ranged from 0.083 to 0.168 g C m⁻² (real surface area) in situ, and from 0.068 to 0.148g C m⁻² in the laboratory. Mean rates of net carbon production integrated over the course of a 24 hour day ranged from 0.180 to 1.352 g C m⁻²(real surface area) in situ, and from 0.123 to 1.206 g C m⁻² in the laboratory. Rates of gross primary production or consumption per day were directly proportional to peak noon irradiance. The rate of carbon production per day could thus be estimated for any amount of irradiance on a cloudless day. Calcification. Using an adaptation of the alkalinity anomaly technique, the precipitation or solution of calcium carbonate was estimated by subtracting the calculated change in pH resulting from photosynthesis and respiration from the measured change in pH. Mean maximal rates of in situ calcification per hour ranged from 0.156 to 0.923 g CaCO₃ m⁻² (real surface area). Mean rates of calcification integrated over a 24 hour day ranged from 0.87 to 9.86 g CaCO₃ m⁻² (real surface area). Rates of calcification per day were directly proportional to peak noon irradiance for all species except H. reinboldii. The rate of calcification per unit of surface area decreased with increasing depth and decreasing irradiance. Calcification rates were always considerably higher in the light than in the dark. Dark rates of calcification were highly variable. In several cases solution of CaCO₃ was observed in the dark. Relationships between calcification and irradiance, and photosynthesis and irradiance, were similar but not identical. In shallow water, greater irradiance was required for the saturation of calcification than for saturation of photosynthesis. These data suggest that calcification is largely controlled by photosynthesis but is probably influenced by other factors, among them tissue biomass. Conclusions. Crustose coralline algae are highly significant producers of organic and inorganic carbon on coral reefs. Their rates of photosynthesis may have been underestimated by the use of semi-artificial procedures. Their rates of calcification are comparable with corals and in certain reef zones their great abundance may result in overall calcification rates which exceed that of 98-99% of the rest of the reef. As expected crustose coralline algae photoadapt and their ability to do so influences but does not necessarily control their distributions on the reef.