4-Deoxy-l-erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate

4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery.

Metabolic strategies of sharing pioneer bacteria mediating fresh macroalgae breakdown

Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of pioneer bacteria within the flavobacterial genus Zobellia to initiate the degradation of fresh brown macroalgae, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT could use macroalgae as a sole carbon source and extensively degrade algal tissues without requiring physical contact, via the secretion of extracellular enzymes. This indicated a sharing behaviour, whereby pioneers release public goods that can fuel other bacteria. Comparisons of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include stress resistance proteins, type IX secretion system proteins and novel uncharacterized Polysaccharide Utilization Loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the niche, metabolism and evolution of pioneer degraders, as well as their cooperative interactions within microbial communities, as key players in macroalgal biomass turnover.

Effects of Macroalgal Habitats on the Community and Population Structure of Temperate Reef Fishes

<p>Two families of brown macroalgae that occur in sympatry dominate temperate subtidal rocky coasts: the Laminareales, and the Fucales. Both of these families are habitat-forming species for a wide variety of invertebrates and fishes. Variation in the presence, density, and composition of brown macroalgae can have large influences on the evolution and ecology of associated organisms. Here, using a series of observational and experimental studies, I evaluated the effects of heterogeneity in the composition of brown macroalgal stands at the population and community levels for reef fishes. A central ecological challenge is the description of patterns that occur at local scales, and how these are manifested at larger ones. I conducted further sampling across a set of sites nested within locations over three regions, Juan Fernandez Islands (Chile), Northern New Zealand, and Tasmania (Australia), to evaluate patterns of variation in the diversity and composition of fish assemblages. Specifically, I explored spatial variation in fish assemblages as a function of rocky reef habitats (dominated by brown-macroalgae) and other sources of variation (abiotic and biotic factors) that potentially mediate the relationship between fishes and reef habitats. Analyses suggest that spatial variation in diversity (e.g., species and trophic) may be explained by spatial variation in depth, temperature, and composition of macroalgal habitats. At each location, only 2-3 families dominated the composition of fish assemblages, but species identities varied among locations. In a subsequent study, I assessed the fish-habitat associations from sites within the Juan Fernandez Islands, an isolated eastern Pacific Island that lack large brown macroalgae. I found that, despite the close proximity of these Islands to the South American continent, fish assemblages were mostly composed of endemic representatives from families that dominate the fish assemblages in New Zealand and Australia. Spatial variation in depth and temperature did not contribute to the observed variation in fish abundance. Instead, I found that benthic habitat-forming species (particularly foliose brown macroalgae) appeared to limit the abundance of some reef fishes. These results suggest that a mixture of large-scale (e.g., stochastic recruitment) and small-scale processes (i.e., relating to habitat heterogeneity) influence the diversity, composition and abundance of fish assemblages. Subsequently, I evaluated relationships between reef fishes and macroalgae composition across multiple sites, surveyed repeatedly over four seasons. I found that fishes were associated with different components of heterogeneity in macroalgal habitats, potentially indicating interspecific partitioning of resources that may arise from differential feeding habits and sizesusceptibility to predation. Seasonal variation in the fish-habitat associations was detected, and site differences in macroalgal composition explained significant variation in the local diversity of fishes. Using a series of small-scale lab and field-based manipulative experiments, I determined the demographic and behavioural responses of reefassociated fishes to heterogeneity in the composition of brown macroalgal habitats. I found that (i) different fish species distinguished between monospecific macroalgae stands (macroalgal identity affected the abundance of 7 of 15 reef fish species); (ii) there is within-species variation in the response of fishes to macroalgal composition (suggesting ontogenetic habitat shifts); and (iii) the abundance of 5 of 7 reef fish species, and the overall structure of the local fish assemblage, varied with the composition of mixed-species macroalgal stands. Lastly, I evaluated the potential for fishes to provision demographic feedbacks to macroalgae. Specifically, I conducted a mesocosm experiment to evaluate the effects of fishes on grazing amphipods, and therefore, the potential indirect-effects of fishes on large-brown macroalgae. I found that only one of the two fish species studied reduced grazer abundance. Although the second fish species did not consume grazing amphipods, its presence altered amphipod behaviour to significantly reduce grazing efficiency on the macroalgal-host. This study illustrates how density and trait-mediated indirect interactions can have similar effects on primary producers. Overall, my observational and experimental components of this thesis emphasize the influence of heterogeneity in macroalgal structures on the breadth of habitat use for reef fishes at multiple locations. I found strong behaviourally mediated linkages between the abundance of reef fishes and composition of macroalgal stand. I also provide some evidence that mutualistic relationships may exist between kelp and associated fishes.</p>

Effects of Macroalgal Habitats on the Community and Population Structure of Temperate Reef Fishes

<p>Two families of brown macroalgae that occur in sympatry dominate temperate subtidal rocky coasts: the Laminareales, and the Fucales. Both of these families are habitat-forming species for a wide variety of invertebrates and fishes. Variation in the presence, density, and composition of brown macroalgae can have large influences on the evolution and ecology of associated organisms. Here, using a series of observational and experimental studies, I evaluated the effects of heterogeneity in the composition of brown macroalgal stands at the population and community levels for reef fishes. A central ecological challenge is the description of patterns that occur at local scales, and how these are manifested at larger ones. I conducted further sampling across a set of sites nested within locations over three regions, Juan Fernandez Islands (Chile), Northern New Zealand, and Tasmania (Australia), to evaluate patterns of variation in the diversity and composition of fish assemblages. Specifically, I explored spatial variation in fish assemblages as a function of rocky reef habitats (dominated by brown-macroalgae) and other sources of variation (abiotic and biotic factors) that potentially mediate the relationship between fishes and reef habitats. Analyses suggest that spatial variation in diversity (e.g., species and trophic) may be explained by spatial variation in depth, temperature, and composition of macroalgal habitats. At each location, only 2-3 families dominated the composition of fish assemblages, but species identities varied among locations. In a subsequent study, I assessed the fish-habitat associations from sites within the Juan Fernandez Islands, an isolated eastern Pacific Island that lack large brown macroalgae. I found that, despite the close proximity of these Islands to the South American continent, fish assemblages were mostly composed of endemic representatives from families that dominate the fish assemblages in New Zealand and Australia. Spatial variation in depth and temperature did not contribute to the observed variation in fish abundance. Instead, I found that benthic habitat-forming species (particularly foliose brown macroalgae) appeared to limit the abundance of some reef fishes. These results suggest that a mixture of large-scale (e.g., stochastic recruitment) and small-scale processes (i.e., relating to habitat heterogeneity) influence the diversity, composition and abundance of fish assemblages. Subsequently, I evaluated relationships between reef fishes and macroalgae composition across multiple sites, surveyed repeatedly over four seasons. I found that fishes were associated with different components of heterogeneity in macroalgal habitats, potentially indicating interspecific partitioning of resources that may arise from differential feeding habits and sizesusceptibility to predation. Seasonal variation in the fish-habitat associations was detected, and site differences in macroalgal composition explained significant variation in the local diversity of fishes. Using a series of small-scale lab and field-based manipulative experiments, I determined the demographic and behavioural responses of reefassociated fishes to heterogeneity in the composition of brown macroalgal habitats. I found that (i) different fish species distinguished between monospecific macroalgae stands (macroalgal identity affected the abundance of 7 of 15 reef fish species); (ii) there is within-species variation in the response of fishes to macroalgal composition (suggesting ontogenetic habitat shifts); and (iii) the abundance of 5 of 7 reef fish species, and the overall structure of the local fish assemblage, varied with the composition of mixed-species macroalgal stands. Lastly, I evaluated the potential for fishes to provision demographic feedbacks to macroalgae. Specifically, I conducted a mesocosm experiment to evaluate the effects of fishes on grazing amphipods, and therefore, the potential indirect-effects of fishes on large-brown macroalgae. I found that only one of the two fish species studied reduced grazer abundance. Although the second fish species did not consume grazing amphipods, its presence altered amphipod behaviour to significantly reduce grazing efficiency on the macroalgal-host. This study illustrates how density and trait-mediated indirect interactions can have similar effects on primary producers. Overall, my observational and experimental components of this thesis emphasize the influence of heterogeneity in macroalgal structures on the breadth of habitat use for reef fishes at multiple locations. I found strong behaviourally mediated linkages between the abundance of reef fishes and composition of macroalgal stand. I also provide some evidence that mutualistic relationships may exist between kelp and associated fishes.</p>

Microbiological Food Safety of Seaweeds

The use of seaweeds in the human diet has a long history in Asia and has now been increasing also in the western world. Concurrent with this trend, there is a corresponding increase in cultivation and harvesting for commercial production. Edible seaweed is a heterogenous product category including species within the green, red, and brown macroalgae. Moreover, the species are utilized on their own or in combinatorial food products, eaten fresh or processed by a variety of technologies. The present review summarizes available literature with respect to microbiological food safety and quality of seaweed food products, including processing and other factors controlling these parameters, and emerging trends to improve on the safety, utilization, quality, and storability of seaweeds. The over- or misuse of antimicrobials and the concurrent development of antimicrobial resistance (AMR) in bacteria is a current worldwide health concern. The role of seaweeds in the development of AMR and the spread of antimicrobial resistance genes is an underexplored field of research and is discussed in that context. Legislation and guidelines relevant to edible seaweed are also discussed.

Novel and Conventional Isolation Techniques to Obtain Planctomycetes from Marine Environments

Bacteria from the distinctive Planctomycetes phylum are well spread around the globe; they are capable of colonizing many habitats, including marine, freshwater, terrestrial, and even extreme habitats such as hydrothermal vents and hot springs. They can also be found living in association with other organisms, such as macroalgae, plants, and invertebrates. While ubiquitous, only a small fraction of the known diversity includes axenic cultures. In this study, we aimed to apply conventional techniques to isolate, in diverse culture media, planctomycetes from two beaches of the Portuguese north-coast by using sediments, red, green, and brown macroalgae, the shell of the mussel Mytilus edulis, an anemone belonging to the species Actinia equina, and seawater as sources. With this approach, thirty-seven isolates closely related to seven species from the families Planctomycetaceae and Pirellulaceae (class Planctomycetia) were brought into pure culture. Moreover, we applied an iChip inspired in-situ culturing technique to successfully retrieve planctomycetes from marine sediments, which resulted in the isolation of three additional strains, two affiliated to the species Novipirellula caenicola and one to a putative novel Rubinisphaera. This work enlarges the number of isolated planctomycetal strains and shows the adequacy of a novel methodology for planctomycetes isolation.

Distinctive morphological characteristics of Fucus guiryi (Fucales, Phaeophyceae) from Canary Islands, subtropical eastern Atlantic Ocean

The brown macroalgae in the order Fucales include foundation species on rocky habitats of temperate regions. This work focused on Fucus guiryi, a recently described species segregated from F. spiralis in a molecular basis. It inhabits the upper intertidal zone from the eastern North Atlantic to the subtropical Canary Islands, where is considered its southern limit. We examined morphology and anatomy of vegetative and reproductive structures of F. guiryi from the Canary Islands. Several distinctive characteristics in habit existed between F. guiryi and other species of the genus distributed northwards, such as length and width of stipe and branches, number of branches, and morphology and number of receptacles. Anatomical features reported here for the first time exhibited subtle differences with temperate F. vesiculosus, F. spiralis and F. serratus. The morphology and arrangement of medulla, cortex and meristoderm were also distinctive for F. guiryi. Mucilage in cellular interstitial spaces constitutes good evidence that explains the presence of F. guiryi at its warmest distribution limit in the Canary Islands.