A revision of the genus Wrangelia (Wrangeliaceae, Ceramiales) in Bermuda resolves six new species including W. ryancraigii from the mesophotic zone.

Four species of the genus Wrangelia are presently known from the western Atlantic Ocean: W. argus, W. bicuspidata, W. penicillata, and W. gordoniae, with the first three historically being reported from Bermuda. Morphological and molecular barcode (COI-5P) and phylogenetic analyses used in this study (SSU, LSU, rbcL) indicated eight species groupings of Wrangelia in Bermuda, excluding two of the historically recognized species, retaining only W. argus while adding seven new species, of which six are formally described. What had been historically reported as W. penicillata from Bermuda was shown to be distinct from Mediterranean Sea specimens (type locality) and was shown to be a mixture of W. hesperia sp. nov. and W. incrassata sp. nov. Along with these two, three other new species (W. laxa sp. nov., W. ryancraigii sp. nov., and W. secundiramea sp. nov.) have complete rhizoidal cortication tightly covering axial cells of indeterminate axes below the apices, distinguishing them from the two local incompletely corticated congeners W. argus and W. abscondita sp. nov., the latter a morphologically cryptic sister species with W. bicuspidata from the Caribbean Sea. Only one of the new species, W. ryancraigii, has thus far been observed in the mesophotic zone off the Bermuda platform, and it is morphologically cryptic with the euphotic zone's W. laxa.

Surface currents shape protist community structure across the Indo-Pacific.

Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.

Rubble fields shape planktonic protist communities in Indonesia at a local scale.

The Coral Triangle encompasses nearly 30% of the world's coral reefs and is widely considered the epicenter of marine biodiversity. Destructive fishing practices and natural disturbances common to this region damage reefs leaving behind fields of coral rubble. While the impacts of disturbances in these ecosystems are well documented on metazoans, we have a poor understanding of their impact on microbial communities at the base of the food web. We use metabarcoding to characterize protist community composition in sites of varying fisheries management schemes and benthic profiles across the island of Lombok, Indonesia. Our study shows that rubble coverage and net primary productivity are the strongest explainers of variation in protist communities across Lombok. More specifically, rubble fields are characterized by increases in small heterotrophic protists, including ciliates and cercozoans. In addition to shifts in heterotrophic protist communities, we also observed increases in diatom relative abundance in rubble fields, which corresponded to sites with higher net primary productivity. These results are the first to characterize protist communities in tropical marine rubble fields and provide insight on environmental factors potentially driving these shifts on a local scale.

Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans.

BACKGROUND: Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria. RESULTS: Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines. CONCLUSIONS: Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.

Response to Preuss and Zuccarello (2020): biological definitions that can be unambiguously applied for red algal parasites.

In response to a comment in this issue on our proposal of new terminology to distinguish red algal parasites, we clarify a few key issues. The terms adelphoparasite and alloparasite were previously used to identify parasites that infected close or distant relatives. However, most red algal parasites have only been studied morphologically, and molecular tools have shown that these binary terms do a poor job at representing the range of parasite-host relationships. We recognize the need to clarify inferred misconceptions that appear to be drawing from historical terminology to contaminate our new definitions. We did not intend to replace the term adelphoparasite with neoplastic parasites and the term alloparasites with archaeplastic parasites. Rather, we seek to establish new terms for discussing red algal parasites, based on the retention of a native plastid, a binary biological trait that is relatively easy to identify using modern methods and has biological implications for the interactions between a parasite and its host. The new terminology can better account for the spectrum of relationships and developmental patterns found among the many independently evolved red algal parasites, and it is intended to inspire new research, particularly the role of plastids in the survival and evolution of red algal parasites.

Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data.

Despite their diversity and ecological importance, many areas of the SAR-Stramenopila, Alveolata, and Rhizaria-clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the "dark area" of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and "non-vertebrate" hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. See also the video abstract here: https://youtu.be/_VUXqaX19Rw.

Recruitment tolerance to increased temperature present across multiple kelp clades.

Kelp systems dominate nearshore marine environments in upwelling zones characterized by cold temperatures and high nutrients. Worldwide, kelp population persistence and recruitment success generally decreases with rising water temperatures coupled with low nutrients, making kelp populations vulnerable to impending warming of the oceans. This response to climate change at a global scale, however, may vary due to regional differences in temperature variability, acclimation, and differential responses of kelp species to changing conditions. Culture experiments were conducted on 12 eastern Pacific kelp taxa across geographic regions (British Columbia, central California, and southern California) under three nitrate levels (1, 5, and 10 µmol/L) and two temperatures (12°C and 18°C) to determine sporophyte production (i.e., recruitment success). For all taxa from all locations, sporophytes were always present in the 12°C treatment and when recruitment failure was observed, it always occurred at 18°C, regardless of nitrate level, indicating that temperature is the driving factor limiting recruitment, not nitrate. Rising ocean temperatures will undoubtedly cause recruitment failure for many kelp species; however, the ability of species to acclimatize or adapt to increased temperatures at the warmer edge of their species range may promote a resiliency of kelp systems to climate change at a global scale.

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Molecular phylogenetics supports a clade of red algal parasites retaining native plastids: taxonomy and terminology revised.

Parasitism is a life strategy that has repeatedly evolved within the Florideophyceae. Historically, the terms adelphoparasite and alloparasite have been used to distinguish parasites based on the relative phylogenetic relationship of host and parasite. However, analyses using molecular phylogenetics indicate that nearly all red algal parasites infect within their taxonomic family, and a range of relationships exist between host and parasite. To date, all investigated adelphoparasites have lost their plastid, and instead, incorporate a host-derived plastid when packaging spores. In contrast, a highly reduced plastid lacking photosynthesis genes was sequenced from the alloparasite Choreocolax polysiphoniae. Here we present the complete Harveyella mirabilis plastid genome, which has also lost genes involved in photosynthesis, and a partial plastid genome from Leachiella pacifica. The H. mirabilis plastid shares more synteny with free-living red algal plastids than that of C. polysiphoniae. Phylogenetic analysis demonstrates that C. polysiphoniae, H. mirabilis, and L. pacifica form a robustly supported clade of parasites, which retain their own plastid genomes, within the Rhodomelaceae. We therefore transfer all three genera from the exclusively parasitic family, Choreocolacaceae, to the Rhodomelaceae. Additionally, we recommend applying the terms archaeplastic parasites (formerly alloparasites), and neoplastic parasites (formerly adelphoparasites) to distinguish red algal parasites using a biological framework rather than taxonomic affiliation with their hosts.

Kelp transcriptomes provide robust support for interfamilial relationships and revision of the little known Arthrothamnaceae (Laminariales).

If ever there were "charismatic megaflora" of the sea, the Laminariales (kelp) would undoubtedly meet that designation. From the Northeast Pacific kelp forests to the less diverse, but nonetheless dense, kelp beds ranging from the Arctic to the cold temperate waters of the Southern Hemisphere, kelp provide habitat structure and food for a variety of productive marine systems. Consequently, kelp are well represented in the literature, however, understanding their evolution has proven challenging. We used a 152-gene phylogenomics approach to better resolve the phylogeny of the "derived" kelp families (viz., Agaraceae, Alariaceae, Laminariaceae, and Lessoniaceae). The formerly unresolved Egregia menziesii firmly joined a significantly expanded Arthrothamnaceae including Arthrothamnus, Cymathaere, Ecklonia, Macrocystis, Nereocystis, Pelagophycus, Postelsia, Pseudolessonia, Saccharina, and Streptophyllopsis, which rendered both the Laminariaceae and Lessoniaceae monogeneric. A published eight-gene alignment, the most marker-rich prior to this study, was expanded and analyzed to facilitate inclusion of Aureophycus. Although the topology was unchanged at the family level between the transcriptome data set relative to eight-gene analyses, the superior resolving power of the former was clearly established.

The ghost plastid of Choreocolax polysiphoniae.

Parasitism has evolved innumerable times among eukaryotes. Red algal parasites alone have independently evolved over 100 times. The accepted evolutionary paradigm proposes that red algal parasites arise by first infecting a close relative and over time diversifying and infecting more distantly related species. This provides a natural evolutionary gradient of relationships between hosts and parasites that share a photosynthetic common ancestor. Upon infection, the parasite deposits its organelles into the host cell and takes over, spreading through cell-cell connections. Microscopy and molecular studies have demonstrated that the parasites do not maintain their own plastid, but rather abscond with a dedifferentiated host plastid as they pack up spores for dispersal. We sequenced a ~90 kb plastid genome from the parasite Choreocolax polysiphoniae, which has lost genes for light harvesting and photosynthesis. Furthermore, the presence of a native C. polysiphoniae plastid indicates that not all red algal parasites follow the same evolutionary pathway to parasitism. Along with the 167 kb plastid genome of its host, Vertebrata lanosa, these plastids are the first to be sequenced from the Ceramiales.

A molecular evaluation of the Liagoraceae sensu lato (Nemaliales, Rhodophyta) in Bermuda including Liagora nesophila sp. nov. and Yamadaella grassyi sp. nov.

We have undertaken a comprehensive, molecular-assisted alpha-taxonomic examination of the rhodophyte family Liagoraceae sensu lato, a group that has not previously been targeted for molecular studies in the western Atlantic. Sequence data from three molecular markers indicate that in Bermuda alone there are 10 species in nine different genera. These include the addition of three genera to the flora - Hommersandiophycus, Trichogloeopsis, and Yamadaella. Liagora pectinata, a species with a type locality in Bermuda, is phylogenetically allied with Indo-Pacific species of Hommersandiophycus, and the species historically reported as L. ceranoides for the islands is morphologically and genetically distinct from that taxon, and is herein described as L. nesophila sp. nov. Molecular sequence data have also uncovered the Indo-Pacific L. mannarensis in Bermuda, a long-distance new western Atlantic record. DNA sequences of Trichogloeopsis pedicellata from the type locality (Bahamas) match with local specimens demonstrating its presence in Bermuda. We described Yamadaella grassyi sp. nov. from Bermuda, a species phylogenetically and morphologically distinct from the generitype, Y. caenomyce of the Indo-Pacific. Our data also indicated a single species each of Ganonema, Gloiocallis, Helminthocladia, Titanophycus, and Trichogloea in the flora.

Etheliaceae fam. nov. (Gigartinales, Rhodophyta), with a clarification of the generitype of Ethelia and the addition of six novel species from warm waters.

Based upon COI-5P, LSU rDNA, and rbcL sequence data and morphological characteristics, six new members of the noncalcified crustose genus of red algae Ethelia are described in a new family, Etheliaceae (Gigartinales), sister to the recently described Ptilocladiopsidaceae. The novel species are described from subtropical to tropical Atlantic and Indo-Pacific Ocean basins; E. mucronata sp. nov. and E. denizotii sp. nov. from southern and northern Western Australia respectively, E. wilcei sp. nov. from the Cocos (Keeling) Islands of Australia, E. suluensis sp. nov. from the Philippines, E. umbricola sp. nov. from Bermuda and E. kraftii sp. nov. from Lord Howe Island, Australia. The generitype, Ethelia biradiata, originally reported from the Seychelles, Indian Ocean, is added to the Western Australian flora.

Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing.

DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the "good" transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.

Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata.

As a lineage, oomycetes have adapted to a wide range of lifestyles. Although the common ancestor of the group was likely a marine pathogen, extant members inhabit a spectrum from free-living saprobes to obligate biotrophs. The mitochondrial genomes of Achlya hypogyna and Thraustotheca clavata were sequenced to directly compare a facultative parasitic species (A. hypogyna) to a closely related free living saprobe (T. clavata). Both sequenced mitochondrial genomes are circular, with sizes of 46,869 bp for A. hypogyna and 47,381 bp for T. clavata. They share 63 common genes, indicating little influence of lifestyle on gene content, but small differences in total number and order of genes. Achlya hypogyna has a single copy of nad2, whereas T. clavata has one pseudogene (rps7) and two duplicated genes (nad5 and nad2), each with one full and one truncated copy. The genomes encode a total of 29 or 30 tRNAs (A. hypogyna and T. clavata, respectively) for 19 amino acids. Three unidentified open reading frames are conserved, and one is unique to T. clavata. Comparisons of these genomes with published sequences of the closely related Saprolegnia ferax mitochondrial genome, and four other more distantly related oomycetes, reveals no correlation in genome content or architecture with lifestyle.

Red algal parasites: models for a life history evolution that leaves photosynthesis behind again and again.

Many of the most virulent and problematic eukaryotic pathogens have evolved from photosynthetic ancestors, such as apicomplexans, which are responsible for a wide range of diseases including malaria and toxoplasmosis. The primary barrier to understanding the early stages of evolution of these parasites has been the difficulty in finding parasites with closely related free-living lineages with which to make comparisons. Parasites found throughout the florideophyte red algal lineage, however, provide a unique and powerful model to investigate the genetic origins of a parasitic lifestyle. This is because they share a recent common ancestor with an extant free-living red algal species and parasitism has independently arisen over 100 times within this group. Here, we synthesize the relevant hypotheses with respect to how these parasites have proliferated. We also place red algal research in the context of recent developments in understanding the genome evolution of other eukaryotic photosynthesizers turned parasites.

The revised classification of eukaryotes.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

Codependence of individuals in the Nephromyces species swarm requires heterospecific bacterial endosymbionts.

Symbiosis is one of the most important evolutionary processes shaping the biodiversity on Earth. Symbiotic associations often bring together organisms from different domains of life, which can provide an unparalleled route to evolutionary innovation.1-4 The phylum Apicomplexa encompasses 6,000 ubiquitous animal parasites; however, species in the recently described apicomplexan family, Nephromycidae, are reportedly non-virulent.5,6 The members of the genus Nephromyces live within a specialized organ of tunicates, called the renal sac, in which they use concentrated uric acid as a primary nitrogen source.7,8 Here, we report genomic and transcriptomic data from the diverse genus Nephromyces, as well as the three bacterial symbionts that live within this species complex. We show that the diversity of Nephromyces is unexpectedly high within each renal sac, with as many as 20 different species inhabiting the renal sacs in wild populations. The many species of Nephromyces can host three different types of bacterial endosymbionts; however, FISH microscopy allowed us to demonstrate that each individual Nephromyces cell hosts only a single bacterial type. Through the reconstruction and analyses of the endosymbiont bacterial genomes, we infer that each bacterial type supplies its host with different metabolites. No individual species of Nephromyces, in combination with its endosymbiont, can produce a complete set of essential amino acids, and culture experiments demonstrate that individual Nephromyces species cannot form a viable infection. Therefore, we hypothesize that Nephromyces spp. depend on co-infection with congeners containing different bacterial symbionts in order to exchange metabolites to meet their needs.

Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida).

Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed C. glaucofraenum to be three morphologically similar species (C. glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to C. dicrus, host gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly P. tortugensis. The pharodes-coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but P. tortugensis is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether P. tortugensis is truly a widespread generalist, or instead represents a group of more specialized cryptic species.

One-Stop Serum Assay Identifies COVID-19 Disease Severity and Vaccination Responses.

SARS-CoV-2 has caused over 100,000,000 cases and almost 2,500,000 deaths globally. Comprehensive assessment of the multifaceted antiviral Ab response is critical for diagnosis, differentiation of severity, and characterization of long-term immunity, especially as COVID-19 vaccines become available. Severe disease is associated with early, massive plasmablast responses. We developed a multiplex immunoassay from serum/plasma of acutely infected and convalescent COVID-19 patients and prepandemic and postpandemic healthy adults. We measured IgA, IgG, and/or IgM against SARS-CoV-2 nucleocapsid (N), spike domain 1 (S1), S1-receptor binding domain (RBD) and S1-N-terminal domain. For diagnosis, the combined [IgA + IgG + IgM] or IgG levels measured for N, S1, and S1-RBD yielded area under the curve values ≥0.90. Virus-specific Ig levels were higher in patients with severe/critical compared with mild/moderate infections. A strong prozone effect was observed in sera from severe/critical patients-a possible source of underestimated Ab concentrations in previous studies. Mild/moderate patients displayed a slower rise and lower peak in anti-N and anti-S1 IgG levels compared with severe/critical patients, but anti-RBD IgG and neutralization responses reached similar levels at 2-4 mo after symptom onset. Measurement of the Ab responses in sera from 18 COVID-19-vaccinated patients revealed specific responses for the S1-RBD Ag and none against the N protein. This highly sensitive, SARS-CoV-2-specific, multiplex immunoassay measures the magnitude, complexity, and kinetics of the Ab response and can distinguish serum Ab responses from natural SARS-CoV-2 infections (mild or severe) and mRNA COVID-19 vaccines.