Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California.

This study presents a comprehensive taxonomic revision of the family Suberitidae (Porifera: Demospongiae) for California, USA. We include the three species previously known from the region, document two additional species previously known from other regions, and formally describe four new species as Pseudosuberites latke sp. nov.

Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera).

Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies.

Novel trends of genome evolution in highly complex tropical sponge microbiomes.

Background: Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.

New shallow water species of Caribbean Ircinia Nardo, 1833 (Porifera: Irciniidae).

Seven Ircinia morphospecies were collected from three sites in the Caribbean (Bocas del Toro, Panama; the Mesoamerican Barrier Reef, Belize; and the Florida Keys, United States of America). Previous research used an integrative taxonomic framework (genome-wide SNP sampling and microbiome profiling) to delimit species boundaries among these Ircinia. Here, we present morphological descriptions for these species, six of which are new to science (Ircinia lowi sp.

The Relationship Between Microbiomes and Selective Regimes in the Sponge Genus .

Sponges are often densely populated by microbes that benefit their hosts through nutrition and bioactive secondary metabolites; however, sponges must simultaneously contend with the toxicity of microbes and thwart microbial overgrowth. Despite these fundamental tenets of sponge biology, the patterns of selection in the host sponges' genomes that underlie tolerance and control of their microbiomes are still poorly understood. To elucidate these patterns of selection, we performed a population genetic analysis on multiple species of from Belize, Florida, and Panama using an -outlier approach on transcriptome-annotated RADseq loci.

Microbial symbionts and ecological divergence of Caribbean sponges: A new perspective on an ancient association.

Marine sponges host diverse communities of microbial symbionts that expand the metabolic capabilities of their host, but the abundance and structure of these communities is highly variable across sponge species. Specificity in these interactions may fuel host niche partitioning on crowded coral reefs by allowing individual sponge species to exploit unique sources of carbon and nitrogen, but this hypothesis is yet to be tested. Given the presence of high sponge biomass and the coexistence of diverse sponge species, the Caribbean Sea provides a unique system in which to investigate this hypothesis.

Host population genetics and biogeography structure the microbiome of the sponge .

Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted by the excavating sponge .

The sponge microbiome project.

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales.

How a collaborative integrated taxonomic effort has trained new spongiologists and improved knowledge of Martinique Island (French Antilles, eastern Caribbean Sea) marine biodiversity.

Although sponges are important components of benthic ecosystems of the Caribbean Sea, their diversity remained poorly investigated in the Lesser Antilles. By organizing a training course in Martinique, we wanted both to promote taxonomy and to provide a first inventory of the sponge diversity on this island. The course was like a naturalist expedition, with a field laboratory and a classroom nearby.

TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

Background: Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information.

Diversity, structure and convergent evolution of the global sponge microbiome.

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans.

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama.

Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama.

Vansoestia caribensis gen. nov., sp. nov.: first report of the family Ianthellidae (Verongida, Demospongiae) in the Caribbean.

A thin fiber-less sponge from Caribbean reefs (Bocas del Toro, Panama) with close genetic affinities (based on 18S and 28S nuclear ribosomal RNA gene sequences) to large fan-shaped fiber-bearing sponges (Ianthella and Anomoianthella) from the Indo-Pacific Ocean is here presented. We describe its overall external morphology, histological features, and ultrastructure. Its genetic distance from the only previously known fiber-less verongid genus, Hexadella, prompted the need to erect a new genus to classify this species.

Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses.

Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes.

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges.

Sponges (Porifera) can host diverse and abundant communities of microbial symbionts that make crucial contributions to host metabolism. Although these communities are often host-specific and hypothesized to co-evolve with their hosts, correlations between host phylogeny and microbiome community structure are rarely tested. As part of the Earth Microbiome Project (EMP), we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range.

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

Background: Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications.

Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).

The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments.

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.

Exploring individual- to population-level impacts of disease on coral reef sponges: using spatial analysis to assess the fate, dynamics, and transmission of Aplysina Red Band Syndrome (ARBS).

Background: Marine diseases are of increasing concern for coral reef ecosystems, but often their causes, dynamics and impacts are unknown. The current study investigated the epidemiology of Aplysina Red Band Syndrome (ARBS), a disease affecting the Caribbean sponge Aplysina cauliformis, at both the individual and population levels. The fates of marked healthy and ARBS-infected sponges were examined over the course of a year.

Molecular community profiling reveals impacts of time, space, and disease status on the bacterial community associated with the Caribbean sponge Aplysina cauliformis.

Reports of marine sponge diseases have increased in recent years, but few etiologic agents have been identified. Aplysina red band syndrome (ARBS), a condition observed in the Caribbean sponge Aplysina cauliformis, is characterized by a rust-colored leading margin. Culture-independent methods (terminal restriction fragment length polymorphism and clone library analyses) were used to assess bacterial communities associated with healthy and ARBS-affected sponges from two locations over 2 years.

Next-generation phenomics for the Tree of Life.

The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life.