Genomics, Phylogeny, and in Silico Phenotyping of Nitrosopumilus Genus.

The present study reports the first genome of Nitrosopumilus extracted from the marine sponge Thoosa mismalolli. The genomic study of Nitrosopumilus genus using seven genomes type strains (N. maritimus, N. piranensis, N. zosterae, N. ureiphilus, N. adriaticus, N. oxyclinae and N. cobalaminigenes), four genomes Candidatus species (Ca. N. koreensis, Ca. N. sp. AR2, Ca. N. salaria BD31, and SZUA-335), and six reference genomes (SI075, SI0036, SI0060, SI0034, SI0048, and bin36o) isolated from marine sponge, a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, near-surface sediment, and MAG N. sp NMAG03 isolated from Thoosa mismalolli was performed. These genomes were characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA) of 139 single-copy genes (SCG), core-pangenome, ANI, and in silico phenotypic characterization. We found that the genomes of the Nitrosopumilus genus formed three separate clusters (A, B, and C) based in 139 SCG sequence similarity. The genomes showed values between 75.2 and 99.5% for ANI, the core genome consisted of 168 gene families and the pangenome of 6,011 gene families. Based on the genomic analyses performed, the cluster A may contain a potential new species (NMAG03), and the cluster C could be represented by three new species of the genus. Finally, based on the results shown in this polyphasic approach, we support the use of the integrated approach for genomic analysis of poorly studied genera.

Genomics and phylogeny of the proposed phylum 'Candidatus Poribacteria' associated with the excavating sponge Thoosa mismalolli.

Members of the proposed phylum 'Candidatus Poribacteria' are among the most abundant microorganisms in the highly diverse microbiome of the sponge mesohyl. Genomic and phylogenetic characteristics of this proposed phylum are barely known. In this study, we analyzed metagenome-assembled genomes (MAGs) obtained from the coral reef excavating sponge Thoosa mismalolli from the Mexican Pacific Ocean. Two MAGs were extracted and analyzed together with 32 MAGs and single-amplified genomes (SAGs) obtained from NCBI. The phylogenetic tree based on the sequences of 139 single-copy genes (SCG) showed two clades. Clade A (23 genomes) represented 67.7% of the total of the genomes, while clade B (11 genomes) comprised 32.3% of the genomes. The Average Nucleotide Identity (ANI) showed values between 66 and 99% for the genomes of the proposed phylum, and the pangenome of genomes revealed a total of 37,234 genes that included 1722 core gene. The number of genes used in the phylogenetic analysis increased from 28 (previous studies) to 139 (this study), which allowed a better resolution of the phylogeny of the proposed phylum. The results supported the two previously described classes, 'Candidatus Entoporibacteria' and 'Candidatus Pelagiporibacteria', and the genomes SB0101 and SB0202 obtained in this study belong to two new species of the class 'Candidatus Entoporibacteria'. This is the first comparative study that includes MAGs from a non-sponge host (Porites lutea) to elucidate the taxonomy of the poorly known Candidatus phylum in a polyphasic approach. Finally, our study also contributes to the sponge microbiome project by reporting the first MAGs of the proposed phylum 'Candidatus Poribacteria' isolated from the excavating sponge T. mismalolli.

Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs.

Thoosa mismalolli is one of the most abundant and common excavating sponges along Mexican and Central America shallow reefs. This sponge harbors a microbiome unknown so far. In the present study, the metagenome of T. mismalolli was sequenced, and total reads obtained were classified, and contigs were assembled to analyze the microbiota. The results showed that the highest number of contigs was assigned to the phylum 'Candidatus Poribacteria' (8848), followed by the phylum Proteobacteria (6415), and Chloroflexi (3972). 22 MAGs with <8.5% redundancy using MaxBin 2 were detected: 'Candidatus Poribacteria' (5), Proteobacteria (5), Chloroflexi (6), Gemmatimonadetes (2), Actinobacteria (2), and Thaumarchaeota (2). The phylogenetic tree based on the 139 single-copy gene (SCG) suggested a subdivision into two clades of the phylum Proteobacteria. The presence Thaumarchaeota is also interesting to highlight because contains ammonia-oxidizing archaea considered key members of the global nitrogen and carbon biogeochemical cycles. In addition, shotgun metagenomic analysis revealed that protein sequences associated for amino acids (13.0%) and carbohydrate metabolism (12.4%) predominated. In this study, the first microbiome and functional potential of T. mismalolli is reported, which also represents the first investigation of a microbiota sponge in the Mexican Pacific reefs.

The complete mitogenome of excavating sponge Thoosa mismalolli (Demospongiae, Tetractinellida, Thoosidae) from Northeastern Tropical Pacific.

The complete mitogenome of Thoosa mismalolli Carballo, Cruz-Barraza & Gómez, 2004 (Tetractinellida, Thoosidae) was sequenced. This is the first complete mitogenome of the suborden Thoosina and the third Tetractinellid so far. The mitochondrial genome of T. mismalolli was assembled based on reads obtained with the Illumina HiSeq platform. The length of complete mitogenome is 19,019 bp long and contained 14 protein-coding genes and 23 tRNA, with two tRNA genes. Phylogenetic reconstruction (maximum-likelihood) based on mitogenome of Tetractinellids, supports T. mismalolli as a sister group. This result is congruent with those obtained with molecular markers (CO1, 18S, and 28S), supporting the monophyletic status of Thoosa and providing additional molecular data in favor of the suborder Thoosina.

Description and molecular phylogeny of Axinella nayaritensis n. sp. (Porifera: Axinellida) from East Pacific and remarks about the polyphyly of the genus Axinella.

Axinella nayaritensis n. sp. is a typical species of the genus Axinella in spiculation (oxeas and styles), skeletal arrangement (axial condensation from which radiate an extra-axial plumoreticulated skeleton), and external form (arborescent). The new species is orange, branching, up to 25 cm in height, and which usually live in soft bottoms. One of the most conspicuous characteristic of the new species is its aquiferous system, which is formed by a system of superficial canals and meandering ridges which run around the entire length of the branches. The species is compared with Axinella polycapella from Gulf of Mexico, which is very close in morphology, and which it shares a high similarity in the 18S ribosomal RNA region. It was also compared with Axinella aruensis, a very different species from a morphological point of view, which is distributed throughout the northern Australia, Indonesia and Papua New Guinea as both species share a high similarity in the COI mitochondrial gene region. The new species was included in the clade named Axinella by Gazave et al. (2010) for 18S and COI, where also are included eight Axinella-species. Species in this clade are typically arborescent with a choanosomal skeleton differentiated between axial and extra-axial regions. Axinella nayaritensis n. sp. constitute the first record of an Axinella for the east Pacific coast.

Internal ultrastructure of the planktonic larva of the coral Porites panamensis (Anthozoa: Scleractinia) / Ultraestructura interna de la larva planctónica del coral Porites panamensis (Anthozoa: Scleractinia)

Abstract Introduction: The scleractinian coral life cycle includes planktonic larvae that settle on the benthos, allowing the primary polyp to clone and build a sexually reproducing adult colony. The larval physiology and ecology of Eastern Tropical Pacific scleractinians needs the exploration of basic aspects such as the internal morphology of planulae. Objective: To describe histological and cytological characteristics of Porites panamensis larvae. Methods: During August-July 2019, at Islas Marias Biosphere Reserve, Central Mexican Pacific, we made 14 collections of coral larvae and identified the species with cytochrome oxidase subunit 1 gene. We used a scanning electron microscope and other techniques. Results: The ectoderm was composed by heterogeneous, mono-ciliated, columnar epithelial cells. Nematocysts were clustered at the oral pole of the ectoderm, and cells were evident in the aboral pole of the ectoderm gland. The endoderm had secretory cells, lipids and symbionts. Conclusions: The abundance of secretory cells and nematocysts in the aboral pole suggests their importance in substrate exploration and larval settlement. Our results support previous descriptions of larval ultrastructure in other coral species.

Resumen Introducción: El ciclo de vida del coral escleractinio incluye larvas planctónicas que se asientan en el bentos, lo que permite que el pólipo primario se clone y construya una colonia de adultos con reproducción sexual. La fisiología y ecología larvaria de los escleractinios del Pacífico Tropical Oriental necesita la exploración de aspectos básicos como la morfología interna de las plánulas. Objetivo: Describir las características histológicas y citológicas de las larvas de Porites panamensis. Métodos: Durante agosto-julio 2019, en la Reserva de la Biosfera Islas Marías, Pacífico Central Mexicano, realizamos 14 recolectas de larvas de coral e identificamos las especies con el gen citocromo oxidasa subunidad 1. Utilizamos un microscopio electrónico de barrido y otras técnicas. Resultados: El ectodermo está compuesto por células epiteliales columnares heterogéneas, monociliadas. Los nematocistos se agrupan en el polo oral del ectodermo, mientras que en el polo aboral son visibles células glandulares. El endodermo presentó células secretoras, lípidos y simbiontes. Conclusiones: La abundancia de células secretoras y nematocistos en el polo aboral sugiere su importancia en la exploración del sustrato y asentamiento larvario. Nuestros resultados respaldan las descripciones previas de la ultraestructura de las larvas en otras especies de coral.