Biology subjects

Hernandez-Lopez, A.

Publications and source records attributed to Hernandez-Lopez, A..

4 recordsLinked to original sources

bioRxiv2025

Evaluating Stock Status and Biological Reference Points for a Data-Limited Brown Shrimp Fishery in the Gulf of California

The state of exploitation of the brown shrimp, Penaeus californiensis, fishery in the northeastern region of the Gulf of California was evaluated using landed catch and fishing efforts from 2010 to 2020. The annual catchability coefficient, , was estimated through the Leslie model; the monthly biomass, , was estimated from the catch per unit effort; via the relationship = /; and through a biomass accumulation model throughout the fishing season, an approach to the biomass corresponding to the carrying capacity, {infty},, was obtained. The harvest rate, , for each month and year was obtained and the annual maximum sustainable yield, , derived as , = 0.50, which represents the target biological reference point, . The decrease in population abundance allows for estimates of the recruitment rate, , at the beginning of the fishing season and the survival rate, , at the end of the fishing season, which represent the remaining reproductive population. From these estimates, a limit biological reference point was computed, described as [Formula], which corresponds to the population replacement level. With these estimates, the Kobe diagram was constructed, in which the biological reference points and , were incorporated. The diagnosis of the state of exploitation indicates, considering a precautionary criterion regarding recruitment, that the fishery has been operating at acceptable levels of sustainability, near the maximum production capacity.

ecology↗

bioRxiv2024

Microbial communities thriving in agave fermentations are locally influenced across diverse biogeographic regions

The production of traditional agave spirits in Mexico is a deeply rooted traditional process that relies on environmental microorganisms to ferment the cooked must from agave plants. Analysis of these microorganisms provides the opportunity to understand the dynamics of the microbial communities in the interface of natural and human-associated environments in a biologically and culturally rich region of the world. Here, we performed 16S and ITS amplicon sequencing of close to 100 fermentation tanks from 42 distilleries throughout Mexico. The Agave species used, production practices, climatic conditions, and biogeographic characteristics varied considerably among sites. Yet, we did find taxa present in most fermentations suggesting that there is a core of microorganisms that are hallmarks of these communities. These core taxa are represented by hundreds of OTUs showing large intra-specific variation. The only variable that was consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that microbial composition is determined by the local production practices and unique attributes of each site. Fermentation stage, climate and producing region were also associated with the community composition, but only for prokaryotes. Analysis of microbial composition in several tanks within three distilleries also revealed taxa that were enriched in specific fermentation stages or agave species. Our work provides a comprehensive analysis of the microbiome of agave fermentations, contributing key knowledge for its management and conservation.

microbiology↗

bioRxiv2023

Yeast diversity in open agave fermentations across Mexico

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX.1.0 culture collection by isolating 4,524 strains from 68 sites in diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and a subset of the strains was verified by ITS and D1/D2 sequencing. The most abundant species isolated from all producing regions were Saccharomyces cerevisiae, Pichia kudriavzevii, Pichia manshurica, and Kluyveromyces marxianus. Despite the great diversity of environmental conditions and production practices the composition of yeast communities remained largely homogeneous throughout locations and fermentation stages, even if less abundant but commonly occurring yeasts were considered. Furthermore, ITS and D1/D2 sequencing revealed two candidate new species of Saccharomycetales. To explore the intraspecific variation of the yeasts from agave fermentations, we conducted genome sequencing on four isolates of the non-conventional yeast Kazachstania humilis. The genomes of these four strains were considerably distinct from other genomes of the same species, suggesting that they belong to a different population. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments. TAKE AWAYO_LIWe isolated and identified 4,524 yeast strains from open agave fermentations in Mexico. C_LIO_LIYeast communities remained largely homogeneous throughout diverse locations. C_LIO_LIKazachstania humilis genomes differed significantly from isolates in other regions of the world. C_LIO_LIWe report two candidate new species related to the Pichia clade. C_LI

microbiology↗

bioRxiv2019

Toward a dynamic threshold for quality-score distortion in reference-based alignment

The intrinsic high entropy sequence metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collateral side effects. In this paper we leverage on the penalty functions of HISAT2 aligner to rebin the quality score scale in such a way as to avoid any impact on sequence alignment, identifying alongside a distortion threshold for \"safe\" quality score representation. We tested our findings on whole-genome and RNA-seq data, and contrasted the results with three methods for lossy compression of the quality scores.

bioinformatics↗