Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems.

Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts' distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiation degrading their virions. To better understand these complex links of phages to their hosts and the environment, we leverage the unique ecological context of the Isthmus of Panama, which narrowly disconnects the productive Tropical Eastern Pacific (EP) and nutrient-poor Tropical Western Atlantic (WA) provinces.

Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding.

Quantifying coral reef biodiversity is challenging for cryptofauna and organisms in early life stages. We demonstrate the utility of eDNA metabarcoding as a tool for comprehensively evaluating invertebrate communities on complex 3D structures for reef reformation, and the role these structures play in provisioning habitat for organisms. 3D design and printing were used to create 18 complex tiles, which were used to form artificial reef structures.

Pleistocene sea level changes and crocodile population histories on the Isthmus of Panama: A comment on Avila-Cervantes et al. (2020).

Avila-Cervantes et al. proposed that glacial-interglacial sea level changes played an important role in the evolutionary and demographic histories of the crocodile Crocodylus acutus on the Isthmus of Panama. However, the study used erroneous sea level proxy data that produced flawed paleogeographic reconstructions.

The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs.

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find significant differences in the gut microbiome composition of a facultative coral-feeding butterflyfish (Chaetodon capistratus) across Caribbean reefs that differ markedly in live coral cover (∼0-30%).

Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution.

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host's physiological capacities; however, the identity and functional role(s) of key members of the microbiome ("core microbiome") in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems' capacity to adjust to environmental changes.

Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef.

Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic community composition and microbial assemblages in a shallow tropical reef ecosystem. Conditions associated with the event precipitated coral bleaching and mass mortality, causing a 50% loss of live coral and a shift in the benthic community that persisted a year later.

Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.

In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts.

Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020).

In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view.

Two new species of emTypton/em Costa, 1844 from tropical American waters, with taxonomic notes on emT. tortugae/em McClendon, 1911 and a new record of br /emT. granulosus/em Ayón-Parente, Hendrickx amp; Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae).

Two new species of the palaemonid shrimp genus Typton Costa, 1844 are described based on material from Panama and Mexico. Both species are closely related to T. tortugae McClendon, 1911, a species originally described from the Dry Tortugas, off southern Florida, USA, and later scarcely recorded from other western Atlantic localities, from Bermuda to Mexico and Brazil.

A new species of Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from the Caribbean coast of Panama.

Alpheus viserion sp. n. is described based on the material from Bocas del Toro archipelago on the Caribbean coast of Panama.

Seabed mining could come at a high price for a unique fauna.

The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining.

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape.

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama.

New findings of the stenopodidean shrimp Microprosthema looensis Goy amp; Felder, 1988 (Decapoda: Stenopodidea: Spongicolidae).

The spongicolid genus Microprosthema Stimpson, 1860 is currently composed of 16 species inhabiting tropical and subtropical marine shallow waters worldwide, with six species found in the western Atlantic (one of them also present in the central and eastern Atlantic), one species in the eastern Pacific, and nine species in the Indo-West Pacific (Saito Okuno 2011; Goy Martin 2013; Saito Anker 2014; De Grave et al. 2016). The genus is characterised by the somewhat depressed body; the carapace more or less densely covered by spines (except in one species); the third maxilliped with a long exopod; the first pereopod with a setiferous organ on the carpus and propodus; the third pereopod greatly enlarged and elongate; and the telson with one tooth on the lateral margin (Holthuis 1946; Poore 2004; Saito Okuno 2011).

GenBank is a reliable resource for 21st century biodiversity research.

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable.

Recent and old duplications in crustaceans "Internal Transcribed Spacer 1″: structural and phylogenetic implications.

Internal Transcribed Spacer structures are important in preserving accessibility to specific enzymes for the maturation of rRNAs. ITS1 sequences reported in the literature in Crustaceans range between 182 and 820 bp and are characterized by the absence of repeats or the presence of only a limited number of microsatellites. Here, we sequenced ITS1 for a range of shrimp families (infraorder Caridea) and show that most taxa have much larger ITS1 sequences.

Dietary partitioning promotes the coexistence of planktivorous species on coral reefs.

Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co-occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved.

Five new records of marine shrimps (Decapoda: Caridea, Stenopodidea) from the Caribbean coast of Panama.

Five species of shrimps, four carideans and one stenopodidean, are recorded for the first time from the Caribbean coast of Panama: Lysmata vittata (Stimpson, 1860) [Lysmatidae Dana, 1852], Periclimenaeus ascidiarum Holthuis, 1951, P. bredini Chace, 1972, P. maxillulidens (Schmitt, 1936) [Palaemonidae Rafinesque, 1815], and Odontozona edyli Criales Lemaitre, 2017 [Stenopodidae Claus, 1872].

Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.

Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions unique to corals (competing with neighbouring colonies over benthic space).

MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database.

Summary: We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented.

Availability And Implementation: The web server is freely available at {http://reference-midori.

The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia.

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data.