Marine sponges are filter-feeding metazoans that can host complex microbial communities which comprise as much as 35% of total sponge biomass. In this thesis I have employed high-throughput, next-generation sequencing technologies to study the sponge microbiota at two different scales. Firstly, I studied complex communities associated with different sponge assemblages, then subsequently conducted an in-depth investigation of an enigmatic sponge symbiont which has largely escaped attention until now. Analysis of the marine sponge microbiota poses unique conceptual and analytical challenges, as microbial species may number in the thousands. One way to overcome this issue is to consider only the persistent and/or abundant species, i.e. the „core‟ community. While this approach has been widely used to analyse diverse biological systems, including sponge microbiota, to date its robustness has not been rigorously evaluated. Thus, in this thesis I systematically evaluated the applicability of the core microbiota approach for the complex microbial communities of three Xestospongia species from southeast Sulawesi (Indonesia), using 16S rRNA gene-based amplicon sequencing (Illumina MiSeq). Different factors for OTU selection were then considered to generate a set of different core communities, including percentage occurrence, minimum abundance threshold and sample set selection. Alpha- and beta- diversity analyses conducted on the core communities were largely insensitive to major changes in core microbiota definition, thus revealing the robustness of this approach when considering closely related sponge species. Furthermore, none of the applied core definitions altered ecological network structure summarising interactions among bacteria within the sponges. Sponge reefs often comprise an array of different and sometimes phylogenetically distant sponge species, with most of them hosting distinct microbial communities. Thus, to further assess the strength and sensitivity of the core microbiota approach in complex sponge assemblages, I analysed the associated bacterial communities of 20 co-occurring sponge species from the south coast of Wellington (New Zealand), using the same 16S rRNA genebased amplicon sequencing approach described above. The application of different core definitions resulted in a marked (and uneven at sponge species level) decrease in bacterial OTU and phylum richness. As a consequence of this decrease in richness, alpha- and betadiversity patterns changed significantly. Therefore, although the application of a core microbiota approach may seem appropriate in closely related systems (e.g. congeneric sponges), I showed that this approach can have a profound influence on the results obtained when studying complex host species assemblages. While sponge microbiota surveys have tended to focus on the study of a few dominant symbionts, other, less prominent members of these diverse communities remain poorly understood. To shed light on one abundant but under-studied community member, I investigated the distribution and phylogenetic status of the sponge symbiont SAUL (spongeassociated unclassified lineage). A meta-analysis of the available literature revealed the ubiquitous distribution of this clade and its association with taxonomically different sponge species. Additionally, the phylogeny of SAUL was revisited using both a 16S rRNA genebased phylogeny and a concatenated set of single-copy marker genes. Phylogenetic analyses revealed the monophyletic nature of this clade and, consequently, I suggest its status as a novel putative candidate phylum. To provide the first information on the putative function of SAUL clade members, I conducted a comprehensive analysis of two draft genomes assembled from sponge metagenome data, revealing novel insights into the physiology of this ubiquitous symbiont. This included the identification of genes encoding several symbiosis factors such as eukaryotic-like repeats (involved in symbiont recognition) and the presence of a CRISPR-Cas defense system, as well as the genomic capability of secondary metabolite production. This thesis represents the first systematic evaluation of the widely applied core microbiota approach, and highlights the importance of testing data sensitivity before its implementation. Moreover, the phylogenetic and genomic analyses of the SAUL lineage conducted here have contributed to expand the knowledge of less prominent and poorly understood sponge-associated microorganisms.

The main focus of this book entitled is to provide an up-to-date coverage of marine sponges and their significance in the current era. This book is an attempt to compile an outline of marine sponge research to date, with specific detail on these bioactive compounds, and their pharmacological and biomedical applications. The book encompasses twenty chapters covering various topics related to Marine Sponges. Initial couple of chapters deal about the worldwide status of marine sponge research, the recent findings regarding dynamics of sponges, and several interesting research areas, that are believed to be deserving of increased attention. Variety of sponges, their toxicology, metagenomics, pharmaceutical significance and their possible applications in biomedicine has been discussed in detail. The second half of this part includes chapters on chemical ecology of marine sponges followed by the discussion on importance of bioeroding sponges in aquaculture systems. The following four chapters of the book deal majorly with the chemical molecules of marine sponges. In the fifth chapter, marine sponge-associated actinobacteria and their pysicochemical properties have been discussed followed by their bioactive potential. The biological application of marine sponges has been presented in later chapters with the classification of biologically active compounds being explored in detail. The second half of the book presents the vast repertoire of secondary metabolites from marine sponges, which include terpenoids, heterocycles, acetylenic compounds, steroids and nucleosides. Further, the bioactive potential of these compounds has also been discussed. One of the constituent chapter elaborates the bioactive alkaloids from marine sponges namely, pyridoacridine, indole, isoquinolene, piperidene, quinolizidine, steroidal and bromotyrosine alkaloids isolated from them. In the next couple of chapters, important sponge polymers and the anticancer effects of marine sponge compounds have been presented. The most interesting aspect of sponge biology is their use in biomedical arena. An effort has been made in this book, to cover the major constituents of sponges and their biomedical potentials. The major portion of sponge body is composed of collagen and silica and used in tissue engineering as scaffold material. This part of the book compiles chapters delineating the isolation of sponge biomaterials including collagen and their use in medical diagnostics. Overall, this book would be an important read for novice and experts in the field of sponge biology.

Sponges (phylum Porifera) are known to be very rich sources for bioactive compounds, mainly secondary metabolites. Main efforts are devoted to cell- and mariculture of sponges to assure a sustainable exploitation of bioactive compounds from biological starting material. These activities are flanked by improved technologies to cultivate bacteria and fungi which are associated with the sponges. It is the hope that by elucidating the strategies of interaction between microorganisms and their host (sponge), by modern cell and molecular biological methods, a more comprehensive cultivation of the symbiotic organisms will be possible. The next step in the transfer of knowledge to biotechnological applications is the isolation, characterization and structural determination of the bioactive compounds by sophisticated chemical approaches.

Microbial communities spanning nearly all evolutionary lineages of bacteria and archaea are found within many species of marine sponges. Although diverse microbial metabolic pathways may benefit sponge hosts, minimal experimental evidence exists supporting host assimilation of symbiont-derived nutrients. By coupling manipulative shading experiments with stable isotope analyses of isolated microbial and sponge cell fractions, I provide evidence that some sponge hosts assimilate a large proportion of their C and N from microbial symbionts and that these inputs are crucial to host performance. Interestingly, however, these interactions are highly variable across host species, suggesting that overall symbiont abundance alone does not drive trends across species. Instead, using light-dark bottle incubations with inorganic compounds enriched in 13C and 15N, I show that variation in the efficiency of symbiont metabolism is correlated to holobiont photosynthesis: respiration ratio (gross primary productivity [P] : respiration [R]) and the presence of specific clades of the cyanobacterial symbiont Synechococcus spongiarum. Finally, to determine if symbioses within two closely related species have fundamentally different responses to a gradient of environmental change, I conducted a shading experiment with Aplysina cauliformis and A. fulva using 6 irradiance treatments. Growth rates in A. cauliformis were variable across treatments and highest at the 2 extremes, while growth rates in A. fulva decreased with irradiance, suggesting that a gradient of environmental conditions impacts these sponges differently. These trends are especially interesting considering that both species had minimal variation in the abundance of S. spongiarum clades A, B, and C and assimilated a predominant portion of their C and N from symbiont sources across all treatments. Instead, increased symbiont carbon assimilation under the full shade in A. cauliformis may translate to added benefit to this host, while the efficiency of symbiont carbon metabolism decreased with irradiance in A. fulva , leading to a reduction in growth rate. Together, these results suggest that dense symbiont communities vary in their overall benefit to sponge hosts. Such variation may be due to multiple, complex factors including the relative presence of beneficial vs. harmful symbionts and how the benefit conferred by specific symbiont taxa differs under changing environmental conditions.

The authors "have intended to make the forefront of sponge research easily accessible to the nonspecialist, illustrating the state of the art of the field,and presenting current controversial issues. For the specialist, we wanted this monograph to be a handy, valuable update on the most recent advances in sponge science."--p. x