Raising Awareness of the Severity of “Contactless Stings” by Cassiopea Jellyfish and Kin

Discussion around avoidance and mitigation of jellyfish stings has traditionally focused on swimmers and divers being mindful of their behavior relative to swimming medusae (pelagic jellyfish). This framework must be restructured with the inclusion of the oblique risk posed by novel autonomous stinging structures like cassiosomes from Cassiopea (a jellyfish genus of the taxonomic order Rhizostomeae). Cassiosomes are released by Cassiopea sp. into subtropical waters that can consequently sting human skin, causing varying degrees of pain and irritation; this trait extends to other rhizostome jellyfish species. Swimmers and waders may put themselves at risk simply by coming into contact with agitated water in the vicinity of Cassiopea medusae, even without touching any part of the jellyfish (medusa, tentacles, or otherwise). Herein, we highlight details provided by 46 researchers and professional aquarists reporting incidents in which they experienced “stinging water” sensations, which we also refer to as “contactless stings’’. We report these findings in order to increase the awareness of a public safety hazard the community may be unaware of in their own labs, aquariums, and sampling locations.

Feeding ecology of the catfish Ictalurus punctatus (Siluriformes: Ictaluridae) in a reservoir in Northeast Mexico

Objective: Determine the main food components of the catfish, their seasonal variability and according to the sex of the organism. Methodology: In total, 143 stomachs of catfish were examined. In the analysis of the stomach content, the detected organisms were determined until the taxonomic order rank. It was analyzed the seasonal and sex feeding variability. Results: The total annual trophic spectrum for catfish consisted of 13 items, of which only the order Ephemeroptera reached the category as a frequent food. In the winter season the catfish consumed significantly more food compared to the other seasons and there was no difference in the amount consumed by females and males (p>0.05). Implications: This information is relevant to highlight the importance of the biological integrity of the terrestrial site surrounds the reservoir, which is a source of food for the catfish. Conclusions: Catfish channel in the Venustiano Carranza Dam is a generalist species (13 alimentary items). There was a difference in the amount of food consumed between the seasons of the year; however there was no difference between the sexes.

Expanding the taxonomic range in the fecal metagenome

Background Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limited numbers of non-bacterial species in their databases compared to available genomic sequences and their methodologies do not favour classification of rare sequences which may represent only a small fraction of their parent genome. In seeking to optimise identification of non-bacterial species, we evaluated five widely-used metagenome classifier programs (BURST, Kraken2, Centrifuge, MetaPhlAn2 and CCMetagen) for their ability to correctly assign and count simulations of bacterial, viral and eukaryotic DNA sequence reads, including the effect of taxonomic order of analysis of bacteria, viruses and eukaryotes and the effect of sequencing depth. Results We found that the precision of metagenome classifiers varied significantly between programs and between taxonomic groups. When classifying viruses and eukaryotes, ordering the analysis such that bacteria were classified first significantly improved classification precision. Increasing sequencing depth decreased classification precision and did not improve recall of rare species. Conclusions Choice of metagenome classifier program can have a marked effect on results with respect to precision of species assignment in different taxonomic groups. The order of taxonomic classification can markedly improve precision. Increasing sequencing depth can decrease classification precision and yields diminishing returns in probability of species detection.

Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies

While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity “genes” varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.

Recent Changes and Corrections in the Taxonomy of Indian Pteridophytes: Part 2

Taxonomic novelties and corrections to Indian Pteridophytes are given briefly here in taxonomic order according to the forthcoming Annotated Checklist of Indian Pteridophytes vol. 3, nearing completion for January 2021. We have divided it into two parts, the present second part is from the Appendix re corrections and additions to Families treated in vols. 1-2, especially concerning relevant publications that appeared subsequently to the two volumes. Further details of the taxa and references are given in vol. 3.

New and unusual host records for North American and South American spider wasps (Hymenoptera: Pompilidae)

New and unusual host records for 133 species and subspecies of Pompilidae predominantly from the southwestern United States, Mexico, Central America, and South America are presented in modified taxonomic order. First-time species host records are given for Calopompilus Ashmead, Pepsis Fabricius, Hemipepsis Dahlbom, Priocnessus Banks, Entypus Dahlbom, Pompilocalus Roig-Alsina, Sphictostethus Kohl, Auplopus Spinola, Ageniella Banks, Eragenia Banks, Aporus Spinola, Poecilopompilus Ashmead, Tachypompilus Ashmead, Anoplius Dufour, Priochilus (Fabricius) and Notocyphus Smith. New host spider families are introduced for Calopompilus, Pepsis, Hemipepsis, Priocnessus, Entypus, Cryptocheilus Panzer, Priocnemis Schiødte, Auplopus, Ageniella, Eragenia, Aporus, Tachypompilus, Anoplius, Priochilus and Notocyphus. Eight host spider families are reported from the Western Hemisphere for the first time: Halonoproctidae (Notocyphus dorsalis dorsalis Cresson); Dipluridae (Pepsis pretiosa Dahlbom, P. montezuma Smith, P. infuscate Spinola, P. atripennis Fabricius, P. martini Vardy, Priocnessus vancei Waichert and Pitts); Nemesiidae (Pepsis pallidolimbata Lucas, P. viridis Lepeletier, P. spp., Pompilocalus hirticeps (Guérin), Sphictostethus gravesii (Haliday), S. striatulus Roig-Alsina, Priocnemis oregona Banks); Barychelidae (Eragenia sp.); Paratropididae (Pepsis stella Montet); Trechaleidae (Hemipepsis toussainti (Banks), Entypus unifasciatus cressoni (Banks), Tachypompilus ferrugineus (Say), Tachypompilus unicolor cerinus Evans, Priochilus gloriosum (Cresson); Desidae (Ageniella accepta (Cresson), Sphictostethus isodontus Roig-Alsina) and Selenopidae (Priochilus scrupulum (Fox), Tachypompilus erubescens (Taschenberg) or xanthopterus (Rohwer)). The first known host records for the rare South American pompilid genera Chirodamus (Lycosidae: Lycosa sp.) and Herbstellus (Nemesiidae: Diplothelopsis cf bonariensis Mello-Leitão) are presented.

The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae–Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.

Friend or Foe? Orb-Weaver Spiders Inhabiting Ant–Acacias Capture Both Herbivorous Insects and Acacia Ant Alates

The orb-weaver spiders Eustala oblonga (Chickering) and Eustala illicita (O. Picard-Cambridge) (Araneae: Araneidae) inhabit the ant-defended acacias Vachellia melanocerus (Beurling) and Vachellia collinsii (Safford) (Fabales: Fabaceae), respectively, in Panama. These spiders do not capture patrolling Pseudomyrmex ants but exploit their plant-protection services to escape predation. What effect the spiders have on the ant-acacia mutualisms is unknown. They may provide an additional layer of plant defense by capturing flying herbivorous insects in their webs. Alternatively, the spiders may disrupt the ant–acacia mutualisms by capturing alate acacia ants during nuptial flights. We evaluated these two hypotheses by sampling insects flying through acacia foliage and by identifying prey remains in webs. The proportions of insects captured on sticky card traps and in webs varied with taxonomic order and ecological role. Herbivorous insects greatly outnumbered other groups captured on sticky cards and were captured in spiders’ webs in both acacia species but made up a minority of prey remains in webs. Instead, insect predators and parasitoids made up the majority of prey remains and were comprised primarily by alate ant mutualists of the host acacias. These results provide indirect support for both hypotheses and suggest that the spiders potentially both benefit and harm their host ant-acacia mutualisms. The net effect of spider exploitation, however, is unclear and is likely based on both the effectiveness of plant protection from herbivory provided by the spiders relative to that provided by acacia ants, as well as the overall proportion of the ant reproductive caste the spiders actually capture.

Host evolutionary history and ecology shape virome composition in fishes

Identifying the components of host ecology that promote virus diversity is crucial for our understanding of the drivers of virus evolution and disease emergence. As the most species-rich group of vertebrates that exhibit diverse ecologies, fish provide an ideal model system to study the impacts of host ecology on the composition of their viromes. To better understand the factors that shape virome composition in marine fishes, we characterised the viromes of 23 fish species (19 from this study and four that were sampled previously (Geoghegan et al 2018a)) using unbiased bulk RNA-sequencing (meta-transcriptomics) together with both sequence and protein structural homology searches to identify divergent viruses that often evade characterisation. These data revealed that fish virome composition – that is, viral richness, abundance and diversity – were predominantly shaped by the phylogenetic history of their hosts, as reflected in taxonomic order. In addition, preferred mean water temperature, climate, habitat depth, community diversity and whether fish swim in schools or are solitary were identified as important ecological features that shaped virome diversity and abundance in these fish. Our analysis also identified 25 new virus transcripts that could be assigned to 11 different viral families, including the first fish virus in the Matonaviridae. Other viruses identified fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae and Flaviviridae. Our results provide a better understanding of the ecological determinants of virome diversity and support the view that fish harbour a multitude of viruses, of which the vast majority are undescribed.

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans

Background Apicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently named corallicolids, have been detected in corals inhabiting tropical shallow reefs. These apicomplexans may represent a transitional lifestyle between free-living phototrophs and obligate parasites. To shed light on the evolutionary history of apicomplexans and to investigate their ecology in association with corals, we screened scleractinians, antipatharians, alcyonaceans, and zoantharians from shallow, mesophotic, and deep-sea communities. We detected corallicolid plastids using 16S metabarcoding, sequenced the nuclear 18S rRNA gene of corallicolids from selected samples, assembled and annotated the plastid and mitochondrial genomes from a corallicolid that associates with a deep-sea coral, and screened the metagenomes of four coral species for corallicolids. Results We detected 23 corallicolid plastotypes that were associated with 14 coral species from three orders and depths down to 1400 m. Individual plastotypes were restricted to coral hosts within a single depth zone and within a single taxonomic order of corals. Some clusters of closely related corallicolids were revealed that associated with closely related coral species. However, the presence of divergent corallicolid lineages that associated with similar coral species and depths suggests that corallicolid/coral relations are flexible over evolutionary timescales and that a large diversity of apicomplexans may remain undiscovered. The corallicolid plastid genome from a deep-sea coral contained four genes involved in chlorophyll biosynthesis: the three genes of the LIPOR complex and acsF. Conclusions The presence of corallicolid apicomplexans in corals below the photic zone demonstrates that they are not restricted to shallow-water reefs and are more general anthozoan symbionts. The presence of LIPOR genes in the deep-sea corallicolid precludes a role involving photosynthesis and suggests they may be involved in a different function. Thus, these genes may represent another set of genetic tools whose function was adapted from photosynthesis as the ancestors of apicomplexans evolved towards parasitic lifestyles.