Papers by Alejandra Prieto-Davo
PeerJ, Dec 14, 2021
Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic ... more Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
Marine Drugs
The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlanti... more The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically r...
Molecules, 2021
Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environment... more Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and th...
Journal of Invertebrate Pathology, 2019
moderate and severe lesions were observed in Litopenaeus vannamei reared in clear seawater while,... more moderate and severe lesions were observed in Litopenaeus vannamei reared in clear seawater while, at the same time, lesions in shrimp reared in biofloc were considerably fewer. The signs of disease included anorexia, lethargy, melanization, expanded chromatophores, luminescence and necrotic areas in the uropods, suggesting a possible vibriosis. However, lesions observed in shrimp reared in biofloc disappeared after a certain time and without mortality in tanks, whereas mortality and severe signs continued to be observed in shrimp reared in clear seawater. To treat the possible vibriosis, oxytetracycline was administered only in clear seawater tanks, but the results were not successful. Bacterial cultures from hepatopancreas tissues of shrimp from both rearing systems confirmed a vibriosis outbreak only in the clear seawater system. Subsequently, Vibrio harveyi, Vibrio rotiferianus, Photobacterium sp. and Photobacterium damselae were identified from bacterial culture previously isolated for both rearing systems by molecular methods. Shewanella sp. was isolated and identified only in biofloc. To understand the possible pathogenicity and resistance mechanisms of the Vibiro strains for both rearing systems, pathogenicity (toxR) and oxytetracycline resistance-related genes (tet (B), tet(D), tet(G)) were determined. Although these genes were expressed for both rearing systems, biofloc proved to have the ability to control the development of the disease, in comparison to clear water, where the vibriosis was evident regardless of the administration of oxytetracycline as a treatment.
Microbial Ecology, 2019
Ecology.
Journal of the World Aquaculture Society, 2018
The effectiveness of the immune defense of Litopenaeus vannamei previously reared in biofloc or i... more The effectiveness of the immune defense of Litopenaeus vannamei previously reared in biofloc or in a traditional clear seawater rearing system was assessed after a bacterial challenge with a pathogenic strain of Vibrio harveyi. The changes caused by its previous rearing system condition or the challenge were assessed in terms of metabolites (glucose, cholesterol, acylglycerides, protein), hemocyanin, the antioxidant defense system (superoxide dismutase, and catalase), and gene expression related to immune response (superoxide dismutase, alpha2 macroglobulin, prophenoloxidase, hemocyanin, and penaeidin‐3a). The biofloc rearing system was associated with a significant increase in protein, the antioxidant defense system, and the superoxide dismutase, alpha2 macroglobulin, and prophenoloxidase genes. For shrimp previously reared in biofloc, a positive interaction with the presence or absence (control) of V. harveyi significantly affected the hemocyanin concentration, and the interaction...
Environmental Microbiology, 2019
SummaryThe search for new and effective strategies to reduce bacterial biofilm formation is of ut... more SummaryThe search for new and effective strategies to reduce bacterial biofilm formation is of utmost importance as bacterial resistance to antibiotics continues to emerge. The use of anti‐biofilm agents that can disrupt recalcitrant bacterial communities can be an advantageous alternative to antimicrobials, as their use does not lead to the development of resistance mechanisms. Six MAR4 Streptomyces strains isolated from the Madeira Archipelago, at the unexplored Macaronesia Atlantic ecoregion, were used to study the chemical diversity of produced hybrid isoprenoids. These marine actinomycetes were investigated by analysing their crude extracts using LC–MS/MS and their metabolomic profiles were compared using multivariate statistical analysis (principal component analysis), showing a separation trend closely related to their phylogeny. Molecular networking unveiled the presence of a class of metabolites not previously described from MAR4 strains and new chemical derivatives belongi...
Frontiers in Marine Science, 2018
Journal of Microbiology, 2016
A computationally simplistic poly-phasic approach to explore microbial communities from the Yucat... more A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products § The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other fresh-water environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.
Frontiers in Microbiology, 2016
PLoS Computational Biology, 2009
Metagenomic studies characterize both the composition and diversity of uncultured viral and micro... more Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.
FEMS Microbiology Ecology, 2013
Sediment samples collected off the coast of San Diego were analyzed for actinomycete diversity us... more Sediment samples collected off the coast of San Diego were analyzed for actinomycete diversity using culture-independent techniques. Eight new operational taxonomic units (OTUs) in the Streptomycetaceae were identified as well as new diversity within previously cultured marine OTUs. Sequences belonging to the marine actinomycete genus Salinispora were also detected, despite the fact that this genus has only been reported from more tropical environments. Independent analyses of marine sediments from the Canary Basin (3814 m) and the South Pacific Gyre (5126 and 5699 m) also revealed Salinispora sequences providing further support for the occurrence of this genus in deepsea sediments. Efforts to culture Salinispora spp. from these samples have yet to be successful. This is the first report of Salinispora spp. from marine sediments > 1100 m and suggests that the distribution of this genus is broader than previously believed.
Environmental Microbiology, 2012
Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodive... more Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral to microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95 % of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8 % were novel. Of the average 3.2 % of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict, however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.
Aquaculture, 2014
The advantages of FLOC over clear water (CW) in rearing juvenile L. vannamei and its effects on V... more The advantages of FLOC over clear water (CW) in rearing juvenile L. vannamei and its effects on Vibrio communities were evaluated. Survival rate in FLOC and clear water were recorded and a probiotic was tested under both conditions. Daily growth rate (DGR) was higher in FLOC (p < 0.05) than in CW. Survival in each system increased significantly when a probiotic was included in the diet (p < 0.05). The Vibrionaceae community from the hepatopancreas (HP) and the culture medium did not differ between the two culture media. Nevertheless, a novel group of Vibrio strains was found to be unique to FLOC. No high level of lesions was observed in shrimp tissues from the FLOC + probiotic treatment; it suggests that the probiotic contributed to homeostasis and prevented outbreak of opportunistic pathogenic species. ► It is described a vibriosis situation in a rearing system for shrimp ► Molecular analysis of Vibrios in "floc" for shrimp was conducted ► Phylogenetic tree for Vibrios in shrimp and seawater is displayed ► The addition of probiotic in clear water and "floc" conditions are examined ► Hepatopancreas histopathology showed that shrimp in floc had a better immune status than in clear water
In the past 150 years, marine microbial ecology has followed and exciting journey. Beginning with... more In the past 150 years, marine microbial ecology has followed and exciting journey. Beginning with the isolation of a few marine bacteria, it went on to establish the omnipresence of these microorganisms in the marine environment as well as their crucial roles in global nutrient and carbon cycles. Advances in molecular techniques have allowed the study of the microbial realm including the exploration of the whole ocean's microbial genes. It is underneath the ocean and covering over 70% of our planet that lays an incredible reservoir of 1x109 bacteria per gram of marine sediment. This environment represents a new frontier for microbial diversity, including that of marine actinomycetes. These Gram- positive, high G+C content, filamentous bacteria have been extensively studied due to their widely known ability to produce bioactive secondary metabolites. The diversity of cultured actinomycete bacteria was compared between near- shore and offshore marine sediments. Results revealed th...
Journal of microbiology (Seoul, Korea), 2017
Applied and Environmental Microbiology, 2017
Wetlands constitute the main natural source of methane on Earth due to their high content of natu... more Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting c...
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Papers by Alejandra Prieto-Davo