Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats.

Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.

Genomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique.

Routine sampling of pregnant women at first antenatal care (ANC) visits could make Plasmodium falciparum genomic surveillance more cost-efficient and convenient in sub-Saharan Africa. We compare the genetic structure of parasite populations sampled from 289 first ANC users and 93 children from the community in Mozambique between 2015 and 2019. Samples are amplicon sequenced targeting 165 microhaplotypes and 15 drug resistance genes. Metrics of genetic diversity and relatedness, as well as the prevalence of drug resistance markers, are consistent between the two populations. In an area targeted for elimination, intra-host genetic diversity declines in both populations (p = 0.002-0.007), while for the ANC population, population genetic diversity is also lower (p = 0.0004), and genetic relatedness between infections is higher (p = 0.002) than control areas, indicating a recent reduction in the parasite population size. These results highlight the added value of genomic surveillance at ANC clinics to inform about changes in transmission beyond epidemiological data.

Extraction methods and nutritional characterization of protein concentrates obtained from bean, chickpea, and corn discard grains.

Protein concentrates obtained from discarded grain flours of white chickpea Sinaloa (Cicer arietinum) (CC), "Azufrazin" bean (Phaseolus vulgaris) (BC), and white corn (Zea mays) (MC), were characterized biochemically through bromatological analyses (protein, lipid, fiber, moisture, ashes, and nitrogen free extract), HPLC techniques (amino acids content), and spectrophotometry (anti-nutrients: phytic acid, trypsin inhibitors, and saponins). The percentage of protein obtained from CC, BC, and MC was 71.23, 81.10, and 55.69%, respectively. Most peptides in the BC and CC flours had a molecular weight of <1.35 kDa, meanwhile, MC peptides were heavier (1.35 to 17 kDa). The amino acids (AA) profile of flours and protein concentrates were similar; however, all the protein concentrates showed an increased AA accumulation (300 to -400%) compared with their flours. The protein concentrates from BC registered the highest AA accumulation (77.4 g of AA/100 g of protein concentrates). Except for the phytic acid in CC and trypsin inhibitor in CC and MC, respectively, the rest of the protein concentrates exhibited higher amounts of the anti-nutrients compared with their flours; however, these levels do not exceed the reported toxicity for some animals, mainly when used in combination with other ingredients for feed formulations. It is concluded that CC and BC protein concentrates showed better nutritional characteristics than MC (level of protein, size of peptides, and AA profile). After biochemical characterization, protein concentrates derived from by-products have nutritional potential for the animal feed industry.

Mercury and selenium in oysters Saccostrea palmula and Crassostrea corteziensis from coastal lagoons of the southeastern Gulf of California: molar ratio and risk assessment on human health.

Total mercury (Hg) and selenium (Se) contents were determined in oysters Saccostrea palmula and Crassostrea corteziensis soft tissues from four coastal lagoons of the southeastern Gulf of California. The annual Hg mean concentrations for S. palmula (0.09 ± 0.04 µg g- 1, wet weight) and C. corteziensis (0.08 ± 0.04 µg g- 1) were similar (p ˃ 0.05) among the lagoons and did not exceed the limit established by the Norma Oficial Mexicana and World Health Organization (< 1.0 µg g- 1 Hg). On the other hand, the annual mean concentrations of Se for S. palmula (3.34 ± 0.96 µg g- 1) and C. corteziensis (2.79 ± 0.89 µg g- 1) were higher (p < 0.05) in El Colorado lagoon. The Se/Hg molar ratios were above 1; the positive selenium health benefit value index suggested that Se load in oysters could reduce the Hg potential toxic effect. The hazard quotient for Hg in both species was below 1. Therefore, the consumption of oysters does not represent a risk due to Hg ingestion.

Histopathological alterations in the gonads of wild white clams Dosinia ponderosa inhabiting a former copper mine locality in the Gulf of California.

OBJECTIVE: Prolonged exposure to heavy metals, such as Pb, Hg, or Cu, has multiple adverse effects on marine organisms at the cellular, physiological, and population levels. Bivalves' histopathology provides a sensitive biomarker of pollutant-induced stress and environmental health. Gonad tissue deterioration is of particular concern, as it affects the reproductive success of a species. This study aimed to examine the histopathological alterations caused by metal exposure in the gonad of the white clam Dosinia ponderosa. METHODS: Organisms were sampled from three locations in the Gulf of California: Santa Rosalia (SR), a former Cu mining town; San Lucas beach (SL), a nearby site influenced by pollution; and Escondida beach (EB), which served as a control site. Histological and histochemical stains were used, and the prevalence and intensity level of each alteration were calculated. RESULT: The prevalence of alterations was higher in the ovaries of SR clams (92% compared to 60% in SL clams and 32.7% in EB clams), during spawning (91.4% compared to 20% in SL clams and 4.7% in EB clams), and in winter (93.5% compared to 30% in SL clams and 17.4% in EB clams). CONCLUSION: These findings suggest a significant deterioration in the gonads of white clams from SR, probably linked to the chronic exposure to high concentrations of Cu and possibly other heavy metals; hence, the reproductive health of the clams is likely compromised.

Improving the assessment of ecosystem and wildlife health: microbiome as an early indicator.

Human activities are causing dramatic declines in ecosystem health, compromising the functioning of the life-support system, economic activity, and animal and human health. In this context, monitoring the health of ecosystems and wildlife populations is crucial for determining ecological dynamics and assessing management interventions. A growing body of evidence indicates that microbiome provides a meaningful early indicator of ecosystem and wildlife health. Microbiome is ubiquitous and both environmental and host-associated microbiomes rapidly reflect anthropogenic disturbances. However, we still need to overcome current limitations such as nucleic acid degradation, sequencing depth, and the establishment of baseline data to maximize the potential of microbiome studies.

The fecal bacterial microbiome of the Kuhl's pipistrelle bat (Pipistrellus kuhlii) reflects landscape anthropogenic pressure.

BACKGROUND: Anthropogenic disturbance has the potential to negatively affect wildlife health by altering food availability and diet composition, increasing the exposure to agrochemicals, and intensifying the contact with humans, domestic animals, and their pathogens. However, the impact of these factors on the fecal microbiome composition of wildlife hosts and its link to host health modulation remains barely explored. Here we investigated the composition of the fecal bacterial microbiome of the insectivorous bat Kuhl's pipistrelle (Pipistrellus kuhlii) dwelling in four environmental contexts with different levels of anthropogenic pressure. We analyzed their microbiome composition, structure and diversity through full-length 16S rRNA metabarcoding using the nanopore long-read sequencer MinION™. We hypothesized that the bacterial community structure of fecal samples would vary across the different scenarios, showing a decreased diversity and richness in samples from disturbed ecosystems. RESULTS: The fecal microbiomes of 31 bats from 4 scenarios were sequenced. A total of 4,829,302 reads were obtained with a taxonomic assignment percentage of 99.9% at genus level. Most abundant genera across all scenarios were Enterococcus, Escherichia/Shigella, Bacillus and Enterobacter. Alpha diversity varied significantly between the four scenarios (p < 0.05), showing the lowest Shannon index in bats from urban and intensive agriculture landscapes, while the highest alpha diversity value was found in near pristine landscapes. Beta diversity obtained by Bray-Curtis distance showed weak statistical differentiation of bacterial taxonomic profiles among scenarios. Furthermore, core community analysis showed that 1,293 genera were shared among localities. Differential abundance analyses showed that the highest differentially abundant taxa were found in near pristine landscapes, with the exception of the family Alcaligenaceae, which was also overrepresented in urban and intensive agriculture landscapes. CONCLUSIONS: This study suggests that near pristine and undisturbed landscapes could promote a more resilient gut microbiome in wild populations of P. kuhlii. These results highlight the potential of the fecal microbiome as a non-invasive bioindicator to assess insectivorous bats' health and as a key element of landscape conservation strategies.

Biomonitoring of potentially toxic elements through oysters (Saccostrea palmula and Crassostrea corteziensis) from coastal lagoons of Southeast Gulf of California, Mexico: health risk assessment.

The coastal lagoons of the Gulf of California support important traditional fisheries and mollusc cultures (generally oysters) and receive important volumes of agricultural, industrial and urban effluents, consumption of the oysters could pose risk to human health. The concentrations of arsenic (As), cadmium (Cd), copper (Cu), iron (Fe), lead (Pb), and zinc (Zn) in the oysters Saccostrea palmula and Crassostrea corteziensis, from four coastal lagoons (Altata, AL; Macapule, ML; Navachiste, NL; El Colorado, ECL) in the Southeast Gulf of California, were seasonally evaluated (summer 2019-spring 2020). The order of magnitude of potentially toxic elements concentrations in the soft tissue in both oyster species and at all sites was Zn > Fe > Cu > As > Cd > Pb. Cadmium, Cu, Pb, and Zn exceeded the maximum permissible limits in more than one sampling site. The highest concentrations (mg kg-1, wet weight) of As (4.2 ± 1.1, spring) and Cd (3.3 ± 0.7, autumn) were registered in S. palmula et al. and NL sampling sites, respectively. Crassostrea corteziensis presented higher levels of Cu (40.5 ± 6.7, spring), Pb (2.0 ± 0.4, spring), and Zn (96.9 ± 20.4, spring) in ECL and Fe (62.2 ± 25.4, autumn) in ML. The hazard quotient (HQ) values exceeded the safe level of 1 for Cd in S. palmula and C. corteziensis in NL for children (~ 16 kg weight). In addition, in children, the hazard index (HI) values in both species of oysters ranged from 0.7 to 2.1 and 0.6 to 1.9, respectively. On the other hand, the intake of the studied elements through the consumption of oysters would not induce adverse effects to human health (men and women weighing 70 and 60 kg, respectively); HQ and HI values were < 1.

Recent Differentiation of Aquatic Bacterial Communities in a Hydrological System in the Cuatro Ciénegas Basin, After a Natural Perturbation.

Pozas Rojas is a hydrological system comprising nine isolated shallow ponds and a deep lagoon, which were temporally merged in 2010 by increased rainfall due to a tropical cyclone. In this work, we assess which components, biotic interactions, or environment filtering effects, drive the assembly of microbial communities after a natural perturbation. Arsenic, pH, and temperature are among the most significant environmental variables between each pond, clustering the samples in two main groups, whereas microbial composition is diverse and unique to each site, with no core at the operational taxonomic unit level and only 150 core genera when studied at the genus level. Los Hundidos lagoon has the most differentiated community, which is highly similar to the epipelagic Mediterranean Sea communities. On the other hand, the shallow ponds at the Pozas Rojas system resemble more to epicontinental hydrological systems, such as some cold rivers of the world and the phreatic mantle from Iowa. Overall, despite being a sole of water body 2 years prior to the sampling, interspecific interactions, rather than environmental selection, seem to play a more important role in Pozas Rojas, bolstered by founder effects on each poza and subsequent isolation of each water body.

Reporte de presuntas hipnosporas de Perkinsus sp, en Megapitaria squalida del Golfo de California con la técnica de tinción con tioglicolato / Report of presumptive Perkinsus sp hypnospores in Megapitaria squalida of the Gulf of California with the thioglycollate staining technique

RESUMEN Objetivo. Detectar la presencia de presuntas hipnosporas del protozoario Perkinsus sp. en una población silvestre de la almeja chocolata mexicana (Megapitaria squalida) del sureste del Golfo de California, usando el medio fluido de tioglicolato de Ray (RFTM). Materiales y métodos. Cada mes durante un ciclo anual, se capturaron 30 especímenes con una longitud entre 56.17 y 69.04 mm. La prevalencia e intensidad de la infección y los parámetros del agua se registraron mensualmente desde septiembre 2012 a septiembre 2013. Resultados. Se detectó la presencia de presuntas hipnosporas de Perkinsus sp. en muestras de tejido de la almeja chocolata mexicana usando la prueba RFTM, por la presencia de corpúsculos redondos y oscuros que representan hipnosporas del parásito. Los muestreos mensuales revelaron un rango de prevalencia e intensidad de la infección de 0-43.33% y 1-4 (infección negativa = 0 hipnosporas/preparación, a moderada = 34 hipnosporas/ preparación), respectivamente. Conclusiones. Perkinsus sp. es reportado por primera vez en una población silvestre de M. squalida en la parte más al sureste del Golfo de California. Los resultados indican que el parásito está disperso intraespecíficamente y, potencialmente, parasitaría un nuevo huésped en la región.

ABSTRACT Objective. To detect the presence of presumptive hypnospores of the protozoan Perkinsus sp. in a wild population of the Mexican chocolata clam Megapitaria squalida in the southeastern Gulf of California, using Ray's fluid thioglycollate medium (RFTM). Material and methods. Thirty specimens with size between 56.17 and 69.04 mm were captured each month, during an annual cycle. Infection prevalence and intensity and water parameters were recorded monthly from September 2012 to September 2013. Results. Perkinsus sp. was detected in tissue samples from the Mexican chocolate clam using the RFTM test by the presence of dark round corpuscles that represent parasite's hypnospores. Monthly samplings revealed a prevalence of 0-43.33% and an infection intensity ranging from 1 to 4 (no infection = 0 hypnospores/entire preparation, to moderate = 34 hypnospores/entire preparation). Conclusions. Perkinsus sp. is reported for the first time in a wild population of M. squalida in the southesternmost Gulf of California. The results indicate that this protozoan is dispersed intraspecifically and would now, potentially, parasiting a new host in the region.

Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation.

Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima's D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.

Desove y desarrollo intracapsular del caracol marino Hexaplexnigritus (Neogastropoda: Muricidae) en laboratorio / Spawning and intracapsular development of the marine snail Hexaplex nigritus (Neograstropoda: Muricidae) in the laboratory

Introducción: El caracol marino Hexaplex nigritus es un murícido fuertemente explotado en el Golfo de California para consumo y artesanías. Cuando se reproducen, los adultos se agregan en forma de arrecifes artificiales facilitando su identificación y extracción, lo cual, ha mermado su población en dicha zona. Objetivo: Investigar el desove y desarrollo intracapsular y larvario de esta especie como herramientas para su producción en cautiverio con fines de repoblamiento. Métodos: Se recolectaron 18 progenitores que fueron mantenidos en un sistema cerrado con parámetros y alimentación controladas durante abril 2017 hasta septiembre 2018. Se registró: crecimiento de progenitores, desove de masas ovígeras, cantidad de cápsulas y número de embriones y larvas dentro de las cápsulas. La temperatura de incubación fue de 28.2 ± 1.5 °C. Las principales estructuras morfológicas de embriones y larvas fueron documentadas conforme su desarrollo. Resultados: El desarrollo embrionario intracapsular y de la larva velígera hasta su asentamiento tuvieron una duración de 14-15 y 31-32 días, respectivamente. Cada hembra de 80-88 mm de longitud produjo alrededor de 4 masas ovígeras, 627 cápsulas y 663 993 larvas velígeras extracapsulares por año. Conclusiones: La fácil adaptación y el potencial reproductivo mostrado por H. nigritus en laboratorio se presentan como estrategias promisorias para su repoblación y conservación.

Introduction: The marine snail Hexaplex nigritus is a heavily exploited muricid in the Gulf of California for consumption and handcrafts. When they reproduce, adults aggregated in the form of artificial reefs facilitating their identification and extraction, situation that has reduced their population in that area. Objective: In order to investigate the spawning and intracapsular and larval development of this species as tools for its production in captivity for repopulation purposes. Methods: Eighteen brooders were collected and kept in a closed system with controlled parameters and feeding from April 2017 to September 2018. Growth of parents, spawning of ovigerous masses, number of capsules, and number of embryos and larvae within the capsules, were registered. The main morphological structures of embryos and larvae were documented according to their development. Results: Intracapsular embryonic development and veliger larva until its establishment lasted 14-15 and 31-32 days, respectively. Each 80-88 mm length female produced around 4 ovigerous masses, 627 capsules and 663 993 extracapsular veliger larvae per year. Conclusions: Easy adaptation and reproductive potential shown by H. nigritus in the laboratory are presented as promising strategies for its repopulation and conservation.

Two Pseudomonas aeruginosa clonal groups belonging to the PA14 clade are indigenous to the Churince system in Cuatro Ciénegas Coahuila, México.

Pseudomonas aeruginosa is a widely distributed environmental bacterium but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequences shows the existence of three clades, one of which (PA7 clade) has a higher genetic diversity. These three clades include clinical and environmental isolates that are very diverse in terms of geographical origins and isolation date. Here, we report the characterization of two distinct clonal P. aeruginosa groups that form a part of the PA14 clade (clade 2) sampled from the Churince system in Cuatro Ciénegas Basin (CCB). One of the clonal groups that we report here was isolated in 2011 (group 2A) and was displaced by the other clonal group (2B) in 2015. Both Churince groups are unable to produce pyoverdine but can produce other virulence-associated traits. The existence of these unique P. aeruginosa clonal groups in the Churince system is of ecological and evolutionary significance since the microbiota of this site is generally very distinct from other lineages, and this is the first time that a population of P. aeruginosa has been found in CCB.

Heavy metal concentrations in diploid and triploid oysters (Crassostrea gigas) from three farms on the north-central coast of Sinaloa, Mexico.

The concentrations of Cu, Cd, Pb, Zn, and Hg in diploid and triploid oysters from three farms (Guasave, Ahome, and Navolato) on the north-central coast of Sinaloa, Mexico, were assessed based on samples recovered during a single culture cycle 2013-2014. Metal burdens were more strongly correlated (p < 0.05) with the location of the farm than with either the ploidy or the interaction of both variables. The metal concentration ranking for oysters of both ploidies from the three farms was Zn > Cu > Cd > Pb > Hg. For all three farms, the mean concentrations of Cd and Pb in Crassostrea gigas were high, ranging from 2.52 to 7.98 µg/g wet weight for Cd and from 0.91 to 2.83 µg/g wet weight for Pb. Diploid and triploid oysters from the Guasave farm contained high levels of Cu (76.41 and 68.97 µg/g wet weight, respectively). Cu, Cd, and Zn were highly correlated (p < 0.05), and their concentrations may be influenced by agrochemical inputs. The mean levels of Cu for the Guasave farm and of Cd and Pb for all three farms exceeded permissible limits and represented a threat to human health during the sampling period (July 2014 to July 2014).

Reproduction of Megapitaria squalida (Bivalvia: Veneridae) in the Southeast Gulf of California, Mexico / Reproducción de la almeja callista Megapitaria squalida (Bivalvia: Veneridae) en el sureste del Golfo de California, México

AbstractBivalves reproductive cycle varies according to the particular environmental conditions where they are found, and these reproductive details represent basic information for their capture, management and conservation strategies. With this objective, the reproductive cycle of the clam Megapitaria squalida, inhabiting the Southeast of the Gulf of California (Altata Bay, Sinaloa, Mexico), was studied using histology and changes in the number and size of oocytes, from June 2013 to June 2014. Histological analysis of the gonads showed spawning activity throughout the year, with two peaks. The first was registered in October and it was accompanied by the highest decrease of weight; the second was in February with the highest percentage of spawning population; besides, a resting period was observed in December. The sex-ratio (female:male) of the clam population was 1.08:1 (χ2 = 5.72, d.f. = 1, P < 0.05). Mean oocyte size and number were different (P < 0.05) among all sampling months and fluctuated from 34.6 ± 5.8 µm in June 2014, to 41.9 ± 6.8 µm in February 2014, and from 443.8 ± 424.5 in February 2014, to 1 214.4 ± 267.6 counted in April, respectively. With these results we suggest a protection season from October to November, when the most intense release of gametes occur in this population. Rev. Biol. Trop. 65 (3): 881-889. Epub 2017 September 01.

ResumenEl ciclo reproductivo de los bivalvos varía de acuerdo a las condiciones ambientales de cada lugar, y representa información importante para su conservación. Se estudió el ciclo reproductivo de la almeja Megapitaria squalida utilizando cortes histológicos de la gónada y cambios en el número y tamaño de los oocitos, en el sur del Golfo de California (Bahía Altata, Sinaloa, México), desde junio 2013 a junio 2014. El análisis histológico de las gónadas, mostró eventos de desove todo el año con dos picos: el primero fue registrado en octubre acompañado con un fuerte decremento en peso de los animales; el segundo en febrero caracterizado por un alto porcentaje de desove en la población. Se observó un periodo de reposo en diciembre. La proporción sexual (hembras:machos) de la población de almejas fue 1.08:1 (χ2 = 5.72, g.l. = 1, P < 0.05). El número y tamaño promedio de los oocitos mostró diferencias (P < 0.05) entre los muestreos mensuales, y fluctuaron de 34.6 ± 5.8 µm en junio 2014 a 41.9 ± 6.8 µm en febrero 2014, y de 443.8 ± 424.5 en febrero 2014, a 1 214.4 ± 267.6 en abril 2014. Se propone una temporada de veda desde octubre a noviembre, ya que en estos meses la liberación de gametos por la población fue más intensa.

Bioprocessing of common beans in diets for tilapia: in vivo digestibility and antinutritional factors.

BACKGROUND: Bioprocessing of ingredients by solid-state fermentation is a low-cost technique for preparing diets. It is performed by adding microorganisms such as Rhizopus oligosporus to bean grains, achieving minimal degradation of nutrients and a significant improvement in digestibility. In particular, fermentation induces favorable changes in beans by reducing enzyme inhibitors, such as phytates and tannins. RESULTS: Fermentation significantly (P < 0.05) increased the protein content and digestibility of dry matter and protein compared with whole bean grains, and decreased the content of lipids, ash and phytic acid. Hardening did not have a significant (P > 0.05) effect on the chemical content of beans and digestibility of diets. The dehulled bean meal significantly (P < 0.05) increased protein and lipid content and digestibility of dry matter and protein of beans, and decreased fiber, ash and tannin content. The chemical content of beans and digestibility of ingredients compare favorably with those reported by other authors, indicating the benefits of fermentation and dehulling. CONCLUSION: We concluded that bean meal obtained from fermentation or dehulling represents a low-cost alternative for diets for tilapia. © 2017 Society of Chemical Industry.