Assessment of genetic and phenotypic diversity of the giant kelp, Macrocystis pyrifera, to support breeding programs

Past climate-driven range shifts structuring intraspecific biodiversity levels of the giant kelp (Macrocystis pyrifera) at global scales

The paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp (Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species' population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found (particularly in the Channel Islands of California and in Peru), while post-glacial expansions following ~ 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants-or "ecomorphs"-in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis "pyrifera" and M. "integrifolia" are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. "pyrifera" and M. "integrifolia" across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. "pyrifera" and M. "integrifolia" are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent "integrifolia" morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics

Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.

Reproductive phenology and morphology of Macrocystis pyrifera (Laminariales, Ochrophyta) from southern New Zealand in relation to wave exposure1

Macrocystis pyrifera is a major habitat forming kelp in coastal ecosystems of temperate regions of the northern and southern hemispheres. We investigated the seasonal occurrence of adult sporophytes, morphological characteristics, and reproductive phenology at two sites within a wave-protected harbour and two wave-exposed sites in southern New Zealand every 3-4 months between 2012 and 2013. Seasonality in reproduction was assessed via the number of sporophylls, the occurrence of sori on sporophylls, and non-sporophyllous laminae (fertile pneumatocyst-bearing blades and fertile apical scimitars), meiospore release, and germination. We found that M. pyrifera was present and reproductive year-round in three of the four sites, and patterns were similar for the wave-exposure conditions. Sori were found on pneumatocyst-bearing blades and apical scimitars in addition to the sporophylls, and viable meiospores were released from all three types of laminae. Morphological variations between sites with different wave exposure indicate that sporophytes from wave-protected sites have bigger blades and holdfasts and are longer than those from wave-exposed sites. We discuss the implications of these biological variables for the ecology of M. pyrifera inhabiting different wave exposure environments in southern New Zealand.

Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operational taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from 106 samples of benthic habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained differences of abundance across locations for 15 species, and marked aggregation from sample to sample for most of the common species of plants and animals. Previous analyses could not distinguish these patterns from artefacts of amplification or sequence bias. Our haplotype data also reveal strong population genetic differentiation over small spatial scales for 48 species of red algae, sponges and Bryozoa. Last, phylogenetic analysis of mismatch frequencies among haplotypes show a wide variety of demographic histories from recent expansions to long, stable population sizes. These analyses show that abundant, small-bodied marine species that are often overlooked in ecological surveys can have strikingly different patterns of ecological and genetic structure leading to population, ecological and perhaps adaptive differences between habitats. MOTU diversity data from the same sequencing efforts that generate species-level analyses can greatly increase the scope and value of metabarcoding studies.

Mates Matter: Gametophyte Kinship Recognition and Inbreeding in the Giant Kelp, Macrocystis pyrifera (Laminariales, Phaeophyceae)

Inbreeding, the mating between genetically related individuals, often results in reduced survival and fecundity of offspring, relative to outcrossing. Yet, high inbreeding rates are commonly observed in seaweeds, suggesting compensatory reproductive traits may affect the costs and benefits of the mating system. We experimentally manipulated inbreeding levels in controlled crossing experiments, using gametophytes from 19 populations of Macrocystis pyrifera along its Eastern Pacific coastal distribution (EPC). The objective was to investigate the effects of male-female kinship on female fecundity and fertility, to estimate inbreeding depression in the F1 progeny, and to assess the variability of these effects among different regions and habitats of the EPC. Results revealed that the presence and kinship of males had a significant effect on fecundity and fertility of female gametophytes. Females left alone or in the presence of sibling males express the highest gametophyte size, number, and size of oogonia, suggesting they were able to sense the presence and the identity of their mates before gamete contact. The opposite trend was observed for the production of embryos per female gametes, indicating higher costs of selfing and parthenogenesis than outcrossing on fertility. However, the increased fecundity compensated for the reduced fertility, leading to a stable overall reproductive output. Inbreeding also affected morphological traits of juvenile sporophytes, but not their heatwave tolerance. The male-female kinship effect was stronger in high-latitude populations, suggesting that females from low-latitude marginal populations might have evolved to mate with any male gamete to guarantee reproductive success.

Effect of environmental history on the habitat-forming kelp Macrocystis pyrifera responses to ocean acidification and warming: a physiological and molecular approach

The capacity of marine organisms to adapt and/or acclimate to climate change might differ among distinct populations, depending on their local environmental history and phenotypic plasticity. Kelp forests create some of the most productive habitats in the world, but globally, many populations have been negatively impacted by multiple anthropogenic stressors. Here, we compare the physiological and molecular responses to ocean acidification (OA) and warming (OW) of two populations of the giant kelp Macrocystis pyrifera from distinct upwelling conditions (weak vs strong). Using laboratory mesocosm experiments, we found that juvenile Macrocystis sporophyte responses to OW and OA did not differ among populations: elevated temperature reduced growth while OA had no effect on growth and photosynthesis. However, we observed higher growth rates and NO₃^- assimilation, and enhanced expression of metabolic-genes involved in the NO₃^- and CO₂ assimilation in individuals from the strong upwelling site. Our results suggest that despite no inter-population differences in response to OA and OW, intrinsic differences among populations might be related to their natural variability in CO₂, NO₃^- and seawater temperatures driven by coastal upwelling. Further work including additional populations and fluctuating climate change conditions rather than static values are needed to precisely determine how natural variability in environmental conditions might influence a species' response to climate change.

Photoacclimation and Photoprotection of Juvenile Sporophytes of Macrocystis pyrifera (Laminariales, Phaeophyceae) Under High-light Conditions During Short-term Shallow-water Cultivation1

This study was designed to understand better if and how juvenile sporophytes of Macrocystis pyrifera can photoacclimate to high-light conditions when transplanted from 10 to 3 meters over 7 d. Acclimation of adult sporophytes to light regimes in the bathymetric gradient has been extensively documented. It primarily depends on photoacclimation and translocation of resources among blades. Among other physiological differences, juvenile sporophytes of M. pyrifera lack the structural complexity shown by adults. As such, juveniles may primarily depend on their photoacclimation capacities to maintain productivity and even avoid mortality under changing light regimes. However, little is known about how these mechanisms operate in young individuals. The capacity of sporophytes to photoacclimate was assessed by examining changes in their photosynthetic performance, pigment content, and bio-optical properties of the blade. Sporophytes nutritional status and oxidative damage were also determined. Results showed that juvenile sporophytes transplanted to shallow water were able to regulate light harvesting by reducing pigment concentration, and thus, absorptance and photosynthetic efficiency. Also, shallow-water sporophytes notably enhanced the dissipation of light energy as heat (NPQ) as a photoprotective mechanism. Generally, these adjustments allowed sporophytes to manage the absorption and utilization of light energy, hence reducing the potential for photo-oxidative damage. Furthermore, no substantial changes were found in the internal reserves (i.e., soluble carbohydrates and nitrogen) of these sporophytes. To our knowledge, these results are the first to provide robust evidence of photoprotective and photoacclimation strategies in juveniles of M. pyrifera, allowing them to restrict or avoid photodamage during shallow-water cultivation.

Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae

Genetic diversity is considered a key factor of population survival and evolution, especially in changing environments. Genetic diversity arises from mutations in the DNA sequence of cell lines and from there it reaches the level of organisms, populations, and regions. However, many previous studies have not considered the organism architecture or pattern of thallus construction, ignoring the potential genetic complexities that intraorganismal genetic heterogeneity could generate in modular organisms. In seaweeds, modularity and clonality exist in many species. Modular organization has been related to advantages in terms of rapid construction and recovery after the loss of individual modules, which have their own demographic properties as they generate, mature, senesce, and die. Based on recent evidence from the literature, we suggest that modules also have their own genetic properties. Specifically, modular seaweeds have two possible sources of genetic diversity at the individual level: the heterozygosity of the genotypes composing the genet, and genetic heterogeneity among the modules within a genet (i.e., intraclonal genetic variability). Both sources of genetic diversity can have ecological and evolutionary consequences, and most of them must be considered in research on modular seaweeds. Linking intraorganismal genetic diversity with clonal architecture and propagation styles may help us to understand important ecological and evolutionary processes such as speciation modes, invasive capacities, or farming potential.