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Bacteria, fungi and green algae are common inhabitants of coral skeletons. Their diversity is poorly characterized because they are difficult to identify with microscopy or environmental sequencing, as common metabarcoding markers have low phylogenetic resolution and miss a large portion of the biodiversity. We used a cost-effective protocol and a combination of markers ( tuf A, 16S rDNA, 18S rDNA and 23S rDNA) to characterize the microbiome of 132 coral skeleton samples. We identified a wide range of prokaryotic and eukaryotic organisms, many never reported in corals before. We additionally investigated the phylogenetic diversity of the green algae—the most abundant eukaryotic member of this community, for which previous literature recognizes only a handful of endolithic species. We found more than 120 taxonomic units (near species level), including six family-level lineages mostly new to science. The results suggest that the existence of lineages with an endolithic lifestyle predates the existence of modern scleractinian corals by ca . 250my and that this particular niche was independently invaded by over 20 lineages in green algae evolution. These results highlight the potential of the multi-marker approach to assist in species discovery and, when combined with a phylogenetic framework, clarify the evolutionary origins of host-microbiota associations.

The Arctic is experiencing a rapid shift toward warmer regimes, calling for a need to understand levels of biodiversity and ecosystem responses to climate cycles. This study presents genetic data for 109 Arctic marine forest species (seaweeds), which revealed contiguous populations extending from the Bering Sea to the northwest Atlantic, with high levels of genetic diversity in the east Canadian Arctic. One-fifth of the species sampled appeared restricted to Arctic waters. Further supported by hindcasted species distributions during the Last Glacial Maximum, we hypothesize that Arctic coastal systems were recolonized from many geographically disparate refugia leading to enriched diversity levels in the east Canadian Arctic, with important contributions stemming from northerly refugia likely centered along southern Greenland. Our results suggest Arctic marine biomes persisted through cycles of glaciation, leading to unique assemblages in polar waters, rather than being entirely derived from southerly (temperate) areas following glaciation. As such, Arctic marine species are potentially born from selective pressures during Cenozoic global cooling and eventual ice conditions beginning in the Pleistocene. Arctic endemic diversity was likely additionally driven by repeated isolations into globally disparate refugia during glaciation. This study highlights the need to take stock of unique Arctic marine biodiversity. Amplification of warming and loss of perennial ice cover are set to dramatically alter available Arctic coastal habitat, with the potential loss of diversity and decline in ecosystem resilience.

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j . Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Secondary plastids derived from green algae occur in chlorarachniophytes, photosynthetic euglenophytes, and the dinoflagellate genus Lepidodinium . Recent advances in understanding the origin of these plastids have been made, but analyses suffer from relatively sparse taxon sampling within the green algal groups to which they are related. In this study we aim to derive new insights into the identity of the plastid donors, and when in geological time the independent endosymbiosis events occurred. We use newly sequenced green algal chloroplast genomes from carefully chosen lineages potentially related to chlorarachniophyte and Lepidodinium plastids, combined with recently published chloroplast genomes, to present taxon-rich phylogenetic analyses to further pinpoint plastid origins. We integrate phylogenies with fossil information and relaxed molecular clock analyses. Our results indicate that the chlorarachniophyte plastid may originate from a precusor of siphonous green algae or a closely related lineage, whereas the Lepidodinium plastid originated from a pedinophyte. The euglenophyte plastid putatively originated from a lineage of prasinophytes within the order Pyramimonadales. Our molecular clock analyses narrow in on the likely timing of the secondary endosymbiosis events, suggesting that the event leading to Lepidodinium likely occurred more recently than those leading to the chlorarachniophyte and photosynthetic euglenophyte lineages.

The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach,we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, andmultiple types of giant-celled forms.

The limestone skeleton of Scleractinian corals is a complex and intricate environment consisting of an array of ecological microniches, which harbour a vast microbial community. In addition, recent studies have demonstrated that endolithic microbes play a variety of important ecological roles. Here, we use a combination of metabarcoding of the small subunit rRNA genes, microscopy and spectrophotometry to characterize the endolithic community of the coral Isopora palifera, one of the most common reef builders of the Great Barrier Reef. While a previous study suggested that the Isopora skeleton was dominated by anoxygenic phototrophs, our data show an abundance of chlorophyll a, highlighting the presence of oxygenic photosynthetic endolithic microbes. Proteobacteria, Bacteriodetes, Actinobacteria and Spirochaetes were consistently found, and the bacterial community was similar in shallow and deeper skeletal micro-samples. The micro-eukaryotic community was dominated by endolithic green algae, and the protist Labyrynthula, found at previously unreported high relative abundance.

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

Red algae are frequently dominant components of the non-native biotas in coastal areas. They often remain undetected because of morphological similarity between native and introduced species and cryptic diversity. Routine use of DNA barcodes can aid in setting baseline tabulations of native species and for detecting introduced species. We performed an extensive survey of the red algal family Rhodomelaceae in southern Australia, producing a dataset containing more than 1100 rbcL sequences. The objective of this study was to screen that dataset for introduced species of the tribes Polysiphoniaeae and Streblocladieae, and to provide morphological information of presumably introduced species that were not previously recorded in Australia. Molecular data and morphological observations confirmed the presence of five presumably introduced species: Leptosiphonia brodiei, Melanothamnus japonicus, M. strictissimus, Polysiphonia morrowii and P. delicata. Polysiphonia morrowii and M. strictissimus were detected for the first time in Australia, and M. japonicus and P. delicata were found to be more widely distributed than previously known. Somewhat unexpectedly, the distribution range of L. brodiei has apparently shrunk, with our survey suggesting it remains only in Tasmania. Four of these species have been reported as introduced species in other countries, but M. strictissimus is here recorded for the first time outside its native New Zealand. Although all five species can be considered introduced or cryptogenic, only P. morrowii, M. japonicus and M. strictissimus were locally abundant, and further work will be needed to assess their ability to spread and effect negative impacts on native biotas.

Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome. Despite this, bathymetric shifts have occurred. We inferred from ancestral reconstructions that eurybathic or intermediate distributions across both biomes were a transitional state and direct changes between shallow and deep sea did not occur. The macro-evolutionary pattern of bathome shift appeared to reflect micro-evolutionary processes of bathymetric speciation. Results suggest that most of the oldest clades have a deep-sea origin, but multiple colonization events indicate that the evolution of this group conforms neither to a simple onshore–offshore hypothesis, nor the opposite pattern. Both shallow and deep bathomes have played an important role in generating the current diversity of this major benthic class.

Abstract Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis—the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection–drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.