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Benzo[a]pyrene (BaP) is a highly toxic and carcinogenic polycyclic aromatic hydrocarbon (PAH) whose toxicological effects in the gut microbiota of aquatic organisms have not yet been fully revealed. Therefore, in this study, we used high-throughput 16S rRNA gene sequencing to evaluate the effects of BaP in the gut microbiome of Oreochromis niloticus, including its possible participation in the process of detoxification and its ability to recover. The fish were injected with a single intraperitoneal dose of 20 mg kg−1 of BaP, and the effects in the microbiome were evaluated at 24, 72, and 120 h post-injection. The results indicate a clear dysbiosis (in composition, relative abundance, diversity, and interaction networks) of the gut microbiota during 24 h post-injection, dominated by Fusobacteria and Bacteroidetes and a decrease in Proteobacteria and Spirochaetae. Interestingly, a slight recovery of the microbiome begins at 72 h and stabilises at 120 h post-injection. Pathway analysis revealed the participation of the gut microbiome in PAH degradation mainly at 24 h post-injection. This study provides new insights in the toxicology of BaP in O. niloticus and the first evidence of the ability of the gut microbiome to recovery after a chemical disturbance. • Benzo[a]pyrene caused a dysbiosis in the gut microbiota of Oreochromis niloticus. • We observed an enrichment of bacteria involved in the metabolism of xenobiotics. • The gut microbiota was recovered after exposure to benzo[a]pyrene.

In this study, we report molecular and metabolic responses of Sciaenops ocellatus during an acute oil exposure bioassay (100, 800 and 8000 mg 1–1 of crude oil). The global DNA methylation and expression profiles of key genes of the xenobiotic biotransformation system (cytochrome P450 1A [cyp1a] and glutathione S-tranferase [gst]), oxidative stress system (glutathione peroxidase [gpx], catalase [cat], aldehyde dehydrogenase [aldh]) and reproductive system (vitellogenin [vtg]) were evaluated. At the metabolic level, we evaluated the concentration of four polycyclic aromatic hydrocarbon (PAH) metabolites -hydroxybenzo[a]pyrene, hydroxypyrene, hydroxynaphthalene and hydroxyphenanthrene- in fish bile. The results of this study revealed that fish exposed to crude oil exhibited hypomethylation of DNA, up-regulation of cyp1a and gst and down-regulation of gpx, cat, aldh and vtg and high concentrations of PAH metabolites with respect to the control.

We report the chemical characterisation and toxic effects of municipal solid waste landfill leachates on the embryonic development of Danio rerio. The results of the Fourier transform infrared spectroscopy (FTIR) revealed the presence of nitrogen-containing groups and aromatic functional groups associated with highly toxic pollutants such as ammonia and heavy metal–humic complexes. Mortalities of up to 93 and 100% were observed in 1:64 and 1:32 landfill leachate dilutions, v/v, respectively. The hatching percentages of the fish were also severely affected, with very low percentages ranging from 0 to 33.3% for 1:32, 1:64 and 1:128 dilutions, v/v. Morphologically, a developmental arrest was evident for all treatments. This study reveals the high toxicity of landfill leachates that could contaminate the aquifer of the Yucatan Peninsula and threaten the health of living organisms.

WRKY transcription factors (TFs) play key roles in plant defense responses through phytohormone signaling pathways. However, their functions in tropical fruit crops, especially in banana, remain largely unknown. Several

The health status of Sciaenops ocellatus was studied by qualitative and quantitative histopathological analysis through histological damage prevalence and degree of tissue change (DTC) in response to 96 h and 9 days of exposure to 0.1, 0.8, and 8 g/L of light crude oil in seawater. The histology of the liver, spleen, kidney, and gills of the fish were analyzed and compared between treatments. Our results showed that the exposed fish developed lesions associated with degenerative and necrotic changes. The highest frequency of damage and DTC scores were observed in the liver and kidney from 96 h to 9-days post-exposure. Generalized additive models of location, scale, and shape, showed that the DTC was strongly associated with crude oil compounds such as napthalene, Cd, Ni, Pb, and bile polycyclic aromatic hydrocarbon metabolites. Our findings suggest that exposure to crude oil affects fish health, producing irreversible histological damage.

The impacts of selective logging on arbuscular mycorrhiza and bacteria of tropical forests are little known globally. In this study, we analysed and compared the composition and diversity of bacteria and arbuscular mycorrhizal fungi (AMF) in a forest with sustainable management (stands with 6-years-old after selective logging) compared with a conserved forest and secondary vegetation recovered from agriculture (20-years-old) in Nuevo Becal, Campeche, Mexico. The analyses were based on environmental DNA sequences using Illumina miseq platform and morphological diversity of AMF glomerospores. We found 30 species of virtual AMF taxa (10 potential new virtual taxa) based on DNA sequences, 22 AMF species based on morphology, and 3,963 amplicon sequence variants (ASVs) for bacteria. For AMF, the most abundant order (in the whole study) were the Glomerales (with higher significant abundance in secondary vegetation), followed by Gigasporales and Diversisporales, while for bacterial phylum, Proteobacteria and Actinobacteria were highly represented, followed by Acidobacteria, Planctomycetes, Nitrospirae, Bacteroidetes, and Gemmationonadetes. Actinobacteria showed significantly higher relative abundance in conserved forests, Chloroflexi in managed forests, and Verrucomicrobia in secondary vegetation. Bacterial and glomerospores community composition did not showed significant differences among the three sites analysed. However, AMF VT community composition were significant different between the conserved forest and secondary vegetation. Forest management showed higher bacteria and glomerospores diversity (Shannon index) compared to the conserved forest and secondary vegetation. Our study showed that stands 6 years after selective logging and old secondary vegetation conserved an important bacteria and AMF species compared with conserved forests.

Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (

Coconut (Cocos nucifera L.) encounters many problems due to the lethal diseases that severely affect its growth and development. Over the last decades, plant breeders have realized that certain genes are directly involved in disease resistance, known as resistance genes (R genes). Most of them encode for proteins (R proteins) with a nucleotide-binding site and a leucine-rich repeat domain (NBS-LRR). However, there are certain sequences of unknown function that code for these motifs and have been linked to known R genes and have been denominated as ‘resistance gene candidates’ (RGC). Currently, 340 RGCs have been identified in the genome of C. nucifera, and 231 sequences have been well characterized phylogenetically indicating the existence of specific clades of genes in C. nucifera. Other clades also comprise a mixture of NBS sequences from C. nucifera, E. guineensis, and P. dactylifera, indicating that similar resistance genes are still shared in different genera of the Arecales. The identification of RGCs in plants is a valuable resource for the discovery of new resistance genes. It has great potential in breeding programs using marker-assisted selection, with special emphasis on the resistance to phytoplasma, a pathogen that causes a high mortality on the plantations of this species.

The health status of Sciaenops ocellatus was studied by qualitative and quantitative histopathological analysis through histological damage prevalence and degree of tissue change (DTC) in response to 96 h and 9 days of exposure to 0.1, 0.8, and 8 g/L of light crude oil in seawater. The histology of the liver, spleen, kidney, and gills of the fish were analyzed and compared between treatments. Our results showed that the exposed fish developed lesions associated with degenerative and necrotic changes. The highest frequency of damage and DTC scores were observed in the liver and kidney from 96 h to 9-days post-exposure. Generalized additive models of location, scale, and shape, showed that the DTC was strongly associated with crude oil compounds such as napthalene, Cd, Ni, Pb, and bile polycyclic aromatic hydrocarbon metabolites. Our findings suggest that exposure to crude oil affects fish health, producing irreversible histological damage.

We report the chemical characterisation and toxic effects of municipal solid waste landfill leachates on the embryonic development of Danio rerio. The results of the Fourier transform infrared spectroscopy (FTIR) revealed the presence of nitrogen-containing groups and aromatic functional groups associated with highly toxic pollutants such as ammonia and heavy metal-humic complexes. Mortalities of up to 93 and 100% were observed in 1:64 and 1:32 landfill leachate dilutions, v/v, respectively. The hatching percentages of the fish were also severely affected, with very low percentages ranging from 0 to 33.3% for 1:32, 1:64 and 1:128 dilutions, v/v. Morphologically, a developmental arrest was evident for all treatments. This study reveals the high toxicity of landfill leachates that could contaminate the aquifer of the Yucatan Peninsula and threaten the health of living organisms.

Lethal yellowing (LY) represents a serious threat to coconut in Mexico, Central America and the Caribbean islands. It is caused by a phytoplasma of group 16SrIV, and particularly subgroups -A and -D have been the major phytoplasmas affecting coconut palms grown in the southeast of Mexico. Therefore, is important to reliably detect the 16SrIV group of phytoplasmas not only for diagnosis purposes but also to improve the understanding of pathogen-plant-vector pathosystems. The 16S ribosomal operon genes have been particularly used as the targets for probes and primers for universal phytoplasma detection. However, its conservative nature has imposed the search of non-ribosomal genes to support a finer characterization and differentiation of phytoplasmas, particularly those closely related and one alternative has been the GroEL gene for the specific detection of subgroups 16SrIV-A and 16SrIV-D. Sensitive, rapid and reliable singleplex and duplex assays were developed based on real-time PCR (TaqMan) targeting both the GroEL gene and 16S rRNA. The assay performed with higher sensitivity compared to conventional nested-PCR when analysing DNA extracts obtained from LY symptom bearing palms. The LY 16S TaqMan probe assays amplified DNA from both subgroups, while the LY GroEL TaqMan probe assay only amplified DNA from subgroup 16SrIV-A. The duplex TaqMan probe assay is a novel option for the simultaneous detection and quantification of LY phytoplasmas of 16Sr subgroups -A and -D, which are the phytoplasmas that predominantly affect palms in Mexico.

Isostichopus badionotus is a sea cucumber species of great ecological and economic relevance for Mexico and Central American and Caribbean countries; however, the protocols for the extraction of the nucleic acids have not yet been published. In this study, we describe the first protocols to obtain DNA and RNA from different tissues of I. badionotus, which include the respiratory tree, gonad, longitudinal muscle bands, anterior intestine and cloaca. The extraction of high-quality DNA was performed using the DNeasy Blood & Tissue kit (Qiagen, Valencia, CA, USA) with minor modifications in different points of the protocol.Concerning the RNA, the method of TRIzol was used. This method is particularly advantageous in situations where cells or tissues are enriched for endogenous RNases or when the separation of cytoplasmic RNA from nuclear RNA is impractical. The methodologies used in this study allowed us to obtain DNA and RNA of high quality and integrity in the different tissues of I. badionotus, which will be the basis for future genomic and transcriptomic studies. • The successful extraction of DNA and RNA was achieved in the different tissues of I. badionotus. • The concentrations of DNA and RNA obtained were adequate for a diversity of analyses at a molecular level. Method name: I. badionotus DNA and RNA isolation, Keywords: Holothuroid, Molecular biology, Genetics, Nucleic acid

The present study reports partial sequences of a group of genes used as exposure and effect biomarkers of organic contaminants and/or heavy metals in Syacium gunteri. In order to isolate these sequences, cDNA was used to amplify fragments between 200 and 800 bp, which were then cloned and sequenced. The sequences presented high percentages of identity with genes involved in the metabolism of xenobiotic biotransformation (cytochrome P4501A and glutathione S-transferase), oxidative stress (catalase, glutathione reductase, glutathione peroxidase and superoxide dismutase), reproductive system (vitellogenin) and with the tumor suppressor protein p53 reported in the GenBank database. Subsequently, from the deduced sequence of amino acids of each fragment, their tridimensional structure was predicted, using homologous proteins from the Protein Data Base. This study generates an important base of molecular biomarkers for the monitoring of environmental health in the Gulf of Mexico.

Adonidia merrillii is a palm species native to the Philippines and commonly known as the manila palm. Lethal yellowing-type symptoms were first observed for the manila palm in Florida, USA. Manila palms in Mexico have not been reported to carry the lethal yellowing-type phytoplasma and moreover we have documented other symptoms that are not commonly associated to lethal yellowing (LY) disease. Therefore, our objective was to use molecular techniques to identify and characterize the presence of phytoplasmas in manila palms from southeastern Mexico. Thirty-three manila palm plants were analyzed. In general, three syndromes were observed: mature leaf browning, spear leaf necrosis and spear leaf opening. The presence of phytoplasma DNA was detected by nested-PCR using universal and LY-specific primers. Of the 33 palms analyzed, 24 (73%) were positive for the presence of phytoplasmas using universal primers, and 18 (55%) were positive for phytoplasma DNA using the LY-specific primers. By a TaqMan/real-time PCR assay for LY detection, 82% of palms tested were positive for LY-specific phytoplasma DNA. The restriction enzyme profiles of the DNA tested showed two clear patterns. One pattern was similar to that of the phytoplasma 16SrIV-A strain associated with coconut LY, and the other corresponded to the Pritchardia pacifica 16SrIV-D strain. The 16SrIV-A strain is associated with mature leaf-browning syndrome. The palms infected with the 16Sr-IV-D phytoplasma exhibited spear leaf necrosis and opening. This is the first report of two phytoplasma strains belonging to the subgroups 16SrIV-A and 16SrIV-D in manila palms.

Pterois volitans venom induces muscular fibrillation, which results from nerve transmission caused by the presence of acetylcholine (ACh). It also has cardiovascular effects that are due to its actions on muscarinic and nicotinic cholinergic receptors. In this study, we characterized the effects of P. volitans venom on nicotinic acetylcholine receptors (nAChRs) and dopaminergic neurons. After exposure to P. volitans venom, acetylcholinesterase (AChE) mRNA levels and the expression of the α2 subunit of nAChR increased in zebrafish embryos (15-20 somites). In addition, the lionfish venom blocked zebrafish α2 nAChR subunit functional expression and the ACh-induced response of human neuronal α3β2 receptors. The latter receptor was blocked by a protein fraction named F2, which was isolated from P. volitans venom using reversed phase high performance liquid chromatography (RP-HPLC). This venom causes death in dopaminergic neurons, and affects the cholinergic system. The effect of these two systems may result in retarded embryonic development of zebrafish, since the two systems function in a related manner to control growth hormone secretion.

Phytases are phosphatases employed in monogastric animal feed to improve animal growth rates and protect the environment by reducing phosphorous in manure. In this study, the highly active phytase PhyAsr of the protein tyrosine phosphatase class, which was derived from the ruminal bacterium Selenomonas ruminantium, was successfully produced for the first time in the chloroplast of the green microalga Chlamydomonas reinhardtii. Two homoplasmic lines (C1 and C3) exhibited the highest level of PhyAsr expression, while the highest phytase activity was detected in the C1 line at 34 U/g dry weight. The results of this study indicate that C. reinhardtii is a suitable host for producing the phytase PhyAsr, which may be utilized as a supplement in the monogastric animal diet.

Lethal yellowing (LY) is a disease caused by 16SrIV phytoplasmas that has devastated coconut plantations in the Americas. An alternative means of phytoplasma spread is through seeds. Therefore, we used a novel approach based on plumules from the embryos of LY-diseased coconut palms. We cultured the plumules in vitro to determine the presence of phytoplasma DNA in the plantlets. In the first assay, 185 embryos were obtained. The results showed positive detection in 20 samples (11%) with the nested PCR and in 59 samples (32%) with the TaqMan real-time PCR. A second assay was designed to trace plumules to their respective embryos and haustorial tissues to determine whether they had derived from an embryo with positive LY detection; a total of 124 embryos were obtained. The results showed no positive detection with the nested PCR and positive detection in 42 of the haustorial tissue samples (32%) with the TaqMan real-time PCR. The 124 plumules isolated from the embryos were cultivated under in vitro conditions and divided into two groups. Group A was followed for shoot formation and Group B was followed to the plantlet stage. After 3 months of cultivation, 33 cultures (50%) within Group A became necrotic; the rest were analysed to evaluate LY phytoplasma DNA with the TaqMan real-time PCR assay and 14 (42%) tested positive. After 18 months of cultivation, 20 cultures (34%) within Group B became necrotic. The rest were analysed for the detection of the LY phytoplasma DNA, and 15 and 11 (39% and 29%) of the samples tested positive with the TaqMan real-time PCR and nested PCR assays, respectively. Blast analysis of the sequenced products revealed that the sequences showed 99% homology with LY-phytoplasma subgroup 16SrIV-A. The results presented here demonstrate, for the first time, the occurrence of the transmission of LY phytoplasmas from coconut embryos to plantlets.

The environmental quality differences between two groups of reefs in the Veracruz Reef System were evaluated. The North group of reefs is very close to Veracruz, an urban and port zone, whereas the South group is more isolated, with minor anthropogenic disturbances. To prove the hypothesis that the North group is more affected by anthropogenic activities, the concentrations of hydrocarbons in liver, metals and metalloids such as Se, As, Ba, Cd, Hg and V in muscle, and PAH metabolites in bile were evaluated, and related to biomarkers (transcript abundance of cytochrome P4501A, Vitellogenin, and Glutathione-S-transferase) in two species of fish: Haemulon aurolineatum and Ocyurus chysurus. H. aurolineatum presents the highest concentrations for many pollutants, but O. chysurus shows the most significant differences in pollutant concentrations and biomarkers between the two reef groups, suggesting that this species could be used as a sentinel in future studies in the Gulf of Mexico.

The nucleotide binding site and leucine rich repeat (NBS–LRR) class of R genes is the most comprehensively studied in terms of sequence evolution; however, in coconut palm and, more generally, in the family of Arecaceae, our understanding of the evolution of these genes is rather limited. In this study, disease resistance gene candidates (RGCs) of the nucleotide binding site (NBS) type of coconut palm were used to investigate evolutionary relationships in Arecaceae, Poaceae and Brassicaceae species. The results indicate a species-specific evolution of RGCs in coconut palm. However, strikingly similar RGCs between species of Arecales indicate a high conservation of specific RGCs of this family, suggesting a monophyletic origin of three genera. The phylogenetic relationship between RGCs of Arecales and Brassicales suggests that these sequences possibly emerged before being divided between monocots and dicots. Finally the comparative analysis of the expression of four RGCs in healthy coconut palm and those affected with lethal yellowing disease revealed differences in their expression profiles. This study provides new insights for future efforts towards the improvement of disease resistance in coconut palm and other species of Arecaceae.

Fluctuating asymmetry (FA) and increased variation in bilateral symmetry in a sample of monogeneans can indicate disturbance in developmental stability caused by environmental and/or genomic stress. This study was conducted to determine the presence of FA in the sclerotized structures of Haliotrematoides spp. (Monogenea) collected along the continental shelf of the Yucatan Peninsula. We hypothesize the potential effect of chemical contamination on FA. Geometric morphometrics with Procrustes ANOVA was used to test FA in the ventral and dorsal anchors in Haliotrematoides spp. Then, Generalized Additive Model for Location, Scale and Shape (GAMLSS) were used to assess the statistical associations of heavy metal concentrations, Polycyclic Aromatic Hydrocarbons (PAHs), gene expression, PAHs metabolites in bile, fish morphometric measurements, physicochemical and spatial variables on FA patterns. Principal Component Analysis showed no clear group formation according to shape variability by sampling site. Evidence of FA for size and shape in ventral anchors of Haliotrematoides striatohamus was found, in contrast to dorsal anchors, which only displayed shape FA. For Haliotrematoides sp. only evidence for shape FA of ventral and dorsal anchors was found. The GAMLSS models revealed a significant positive relationship between the FA of Haliotrematoides spp. and PAHs, Pb, Naphthalene, Ni, pH, Hydroxy-Phenanthrene, Depth, DNA Methylation, Glutathione peroxydase and Condition factor (K). These results partially support our hypothesis that FA in the anchors would be produced by aquatic contamination but in association to other environmental variables and host related factors.

Graphical abstract, Isostichopus badionotus is a sea cucumber species of great ecological and economic relevance for Mexico and Central American and Caribbean countries; however, the protocols for the extraction of the nucleic acids have not yet been published. In this study, we describe the first protocols to obtain DNA and RNA from different tissues of I. badionotus, which include the respiratory tree, gonad, longitudinal muscle bands, anterior intestine and cloaca. The extraction of high-quality DNA was performed using the DNeasy Blood & Tissue kit (Qiagen, Valencia, CA, USA) with minor modifications in different points of the protocol. Concerning the RNA, the method of TRIzol was used. This method is particularly advantageous in situations where cells or tissues are enriched for endogenous RNases or when the separation of cytoplasmic RNA from nuclear RNA is impractical. The methodologies used in this study allowed us to obtain DNA and RNA of high quality and integrity in the different tissues of I. badionotus, which will be the basis for future genomic and transcriptomic studies. • The successful extraction of DNA and RNA was achieved in the different tissues of I. badionotus. • The concentrations of DNA and RNA obtained were adequate for a diversity of analyses at a molecular level.

The lethal yellowing (LY) disease and LY-type syndromes affecting several palm species are associated with 16SrIV phytoplasmas in the Americas. In Mexico, palms of the species Roystonea regia and the native Acrocomia mexicana were found to exhibit LY-type symptoms, including leaf decay, starting with mature leaves, necrosis and atrophy of inflorescences. DNA extracts obtained from these palms could be amplified by nested-PCR using phytoplasma-universal primer pair P1/P7 followed by LY-group-specific primer pair LY16Sr/LY16Sf. Blast analysis of the sequences obtained revealed an identity of 100% for R. regia and 99.27% for A. mexicana with 16SrIV-A strain associated with LY in Florida, USA (Acc. AF498309). Computer-simulated RFLP analysis showed that the patterns for the phytoplasma DNA of the two palm species were highly similar to that for 16SrIV subgroup A strain. A neighbour-joining tree was constructed, and the sequences of the two palm species clustered in the same clade of group 16SrIV subgroup A. The results therefore support that LY-type syndromes observed in palms of R. regia and A. mexicana in the Yucatan region of Mexico are associated with 16SrIV subgroup A phytoplasmas.

In this study, degenerate primers were used to amplify nucleotide-binding site (NBS)-type sequences from coconut ecotypes either resistant or susceptible to lethal yellowing. Genomic DNA fragments of approximately 500–700 bp were obtained and sequenced. Phylogenetic analysis of these fragments revealed that they clustered in seven different clades. We also found that all CnRGC sequences were grouped within the non-TIR-NBS-LRR subclass of NBS-LRR genes. The expression analysis revealed changes in expression profiles in response to salicylic acid (SA) and a constitutive expression profile in plants untreated with SA. This is the first large scale analysis of NBS-type sequences in coconut palm.

The Gulf of Mexico (GoM) is exposed to a diversity of contaminants, such as hydrocarbons and heavy metal(oid)s, either from natural sources or as a result of uncontrolled coastal urbanisation and industrialisation. To determine the effect of these contaminants on the marine biota along the Mexican GoM, the biological responses of the shoal flounder Syacium gunteri, naturally exposed, were studied. The study area included all the Mexican GoM, which was divided into three areas: West-southwest (WSW), South-southwest (SSW) and South-southeast (SSE). The biological responses included the global DNA methylation levels, the expression of biomarker genes related to contaminants (cytochrome P450 1A, glutathione S-transferase, glutathione reductase, glutathione peroxidase, catalase, and vitellogenin), histopathological lesions and PAH metabolites in bile (hydroxynaphthalene, hydroxyphenanthrene, hydroxypyrene and Benzo[a]pyrene). The correlation between the biological responses and the concentration of contaminants (hydrocarbons and metal(oid)s), present in both sediments and organisms, were studied. The shoal flounders in WSW and SSW areas presented higher DNA hypomethylation, less antioxidative response and biotransformation gene expression and a higher concentration of PAH metabolites in bile than SSE area; those responses were associated with total hydrocarbons and metals such as chromium (Cr). SSE biological responses were mainly associated with the presence of metals, such as cadmium (Cd) and copper (Cu), in the tissue of shoal flounders. The results obtained on the physiological response of the shoal flounder can be used as part of a permanent active environmental surveillance program to watch the ecosystem health of the Mexican GoM.