Biology subjects

Suarez-Moo, P. d. J.

Publications and source records attributed to Suarez-Moo, P. d. J..

3 recordsLinked to original sources

bioRxiv2024

Species Diversity and Mitochondrial DNA Analysis of Sponges (Porifera, Demospongiae) in an Anchialine Cave on the Yucatan Peninsula

The anchialine ecosystem in the southeastern Gulf of Mexico has an unexplored fauna, among the most understudied groups is Porifera, molecular approaches to investigate their biology and evolution remain largely short. To broaden these studies, sponge individuals collected in the anchialine cave "Xcalac" in the Mexican state of Quintana-Roo were analyzed using 18S rRNA sequences from sponge metagenomes. The three individuals studied belong to the Cinachyrella, Xestospongia, and Suberites genera. The mitochondrial (mt) genomes of Cinachyrella sp. n. and Xestospongia sp. n. were 18,493 bp to 19,604 bp in length, containing 14 protein-coding genes, 2 rRNA genes (rrnS and rrnL), and 23-25 tRNA genes, respectively. The phylogenomic analysis showed that Cinachyrella sp. n. had the same gene arrangement as the members of its subclade, including sponge species of the Cinachyrella and Geodia genera. The mt genome of Xestospongia sp. n. contained the same gene arrangement as found in other sponges of the same genus and differed from other genera such as Petrosia and Haliclona by an tRNA (tyrosine, Y1). Variation in mitochondrial genomes (size, gene content, and gene order) was observed when comparing sampled sponge species from the class Demospongiae to the class Homoscleromorpha. This is the first record of Cinachyrella sp. n and Suberites sp. n. in an anchialine cave on the southeastern Yucatan peninsula, and the first report of the mitochondrial genome analysis of Cinachyrella sp. n. and Xestospongia sp. n., contributing to a better understanding of the diversity and phylogeny of sponges in this ecosystem.

evolutionary biology↗

bioRxiv2024

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations

The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea, the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among AOA. These two complete genomes were used to analyze the diversity of flexible genes (variable from strain to strain) by analyzing the long-reads located within the flexible genomic islands (fGIs) identified through their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A flexible genomic island (fGI5) previously reported as "unassigned function" in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates new third-generation sequencing metagenomics.

genomics↗

bioRxiv2018

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon

Cycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from seven Dioon species and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species of Dioon that we evaluated, suggesting a recent divergence of Dioon populations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched with Nostoc spp and Calothrix spp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

microbiology↗