Biology subjects

Rojas-Jimenez, K.

Publications and source records attributed to Rojas-Jimenez, K..

16 recordsLinked to original sources

bioRxiv2026

Characterization of two Martinezella spp. species: M. legmii sp. nov. and M. ivanii sp. nov., from tropical legume trees in Costa Rica

Four rhizobial strains isolated from root nodules of tropical leguminous plants in Costa Rica were characterized. Strain LEGMi-135b was isolated from Lonchocarpus felipei root nodules, LEGMi-12c from Cojoba arborea, LEGMi-198b from Calliandra haematocephala and Rhizobium altiplani LEGMi-166a from Mimosa pigra. Phylogenetic analyses based on the 16S rRNA gene and four concatenated housekeeping genes (recA, atpD, GATase and gyrB) placed these strains within the genera Martinezella (LEGMi-12c, LEGMi-135b, and LEGMi-198b) and Rhizobium (LEGMi-166a). Genome-based analyses showed that strain LEGMi-135b exhibited an average nucleotide identity (ANI) value of 94% and a digital DNA-DNA hybridization (dDDH) value of 53.2% compared with its closest related species, Martinezella hainanensis CCBAU 57015T, supporting its classification as a distinct species. LEGMI-12c exhibited ANI and dDDH values of 98% and 87%, respectively, compared with Martinezella hainanensis CCBAU 57015T. LEGMi-198b showed the highest similarity to Rhizobium cerradonense CNPSo 3464, with ANI and dDDH values of 98% and 81.4%, respectively; however, this taxon has not been validly published. LEGMi-166a exhibited ANI and dDDH values of 100% and 99.3%, respectively, compared with Rhizobium altiplani BR 10423, confirming its assignment to this species. Additionally, differentiation of strains LEGMi-135b and LEGMi-198b from their closest phylogenetic relatives was supported by phenotypic, physiological, and biochemical analyses. Based on the combined genomic, phenotypic, and biochemical evidence, we propose the establishment of the novel rhizobial species Martinezella legmii sp. nov., with strain LEGMi-135b designated as the type strain (LEGMi-135b), and Martinezella ivanii sp. nov., with strain LEGMi-198b designated as the type strain (LEGMi-198b). This study expands our understanding of rhizobial diversity associated with nitrogen-fixing symbioses, particularly among tropical leguminous plants from Costa Rica

microbiology↗

bioRxiv2024

Exploring symbiotic legume-rhizobia relationships across tropical species

O_LIThe nitrogen-fixing symbiosis with rhizobia significantly contributes to the successful establishment of legumes in tropical environments. Here, we explored the symbiotic interactions between legumes and rhizobia across 109 tropical species. C_LIO_LIWe evaluated the presence of root nodules in 72 genera spanning four Fabaceae subfamilies, encompassing 53% of the genera in Costa Rica and approximately 9.4% globally. Our analysis revealed root nodules in 78% of the species belonging to Caesalpinioideae (67%) and Papilionoideae (84%). Also, we formulated a predictive model for nodulation in legumes, with fine-root color and flower symmetry as the main predictor criteria. C_LIO_LINodulating taxa consistently presented higher N levels in tissues, thinner roots, and a pronounced phylogenetic influence on nodulation. We also identified the bacterial genera associated with all nodulating legumes. Caesalpinioideae formed symbiotic relationships with ten rhizobial genera, whereas Papilionoideae were associated with only four. Bradyrhizobium emerged as the predominant symbiont in nodules, while Rhizobium, Mesorhizobium, Agrobacterium, Paraburkholderia, and Cupriavidus exhibited a more restricted host range. Furthermore, genomic analysis suggests that 15 out of the 22 sequenced rhizobial strains may represent novel species. C_LIO_LIOur study enhances the understanding of the different dimensions that comprise legume-rhizobia interactions, incorporating a diverse array of previously unexamined tropical forest legume taxa. C_LI

plant biology↗

bioRxiv2023

What happens with bacteria in the roots affects what happens with fungi in the leaves

The impact of plant-bacteria symbioses in roots on plant-fungus interactions in distant tissues, such as leaves, remains a significant knowledge gap, particularly for tropical ecosystems. We employed amplicon metabarcoding of ITS2 sequences to analyze the endophytic fungal communities of eight tropical Fabaceae tree species to determine variations according to the hosts root nodulation capacity and the hosts subfamily affiliation. Nitrogen-fixing bacteria in root nodules significantly impacted the diversity and composition of fungal endophytes, while subfamily affiliation had a less pronounced effect. In non-nodulating plants, leaves harbored a much larger diversity of fungi, with 25 fungal classes and 72 orders compared to 17 classes and 45 orders in nodulating plants. Notably, 40% of the orders were unique to non-nodulating plants, whereas only 5% were exclusive to nodulating species. This pattern was further reflected in the number of fungal ASVs, with non-nodulating plants averaging 130.5 compared to 42.7 in nodulating plants. Similarly, Shannon diversity was significantly higher in non-nodulating plants. This study demonstrates that interactions between Fabaceae plants and nitrogen-fixing root bacteria significantly influence the richness and diversity of the fungal community present in leaves. Our findings contribute valuable insights into the complex interplay between plants and microorganisms, particularly in the context of tropical Fabaceae tree species and their endophytic fungi.

ecology↗

bioRxiv2023

Comparison of the microbiome and mycobiome in tissues of the tropical carnivorous epiphytic herb Utricularia jamesoniana

Utricularia jamesoniana, a small epiphytic plant found in wet tropical forests, stands out for its carnivorous habit, intricate trap system, and small but beautiful and complex flowers. This species remains relatively understudied despite its wide geographical distribution and curious adaptations. In this study, we employed 16S rRNA and ITS sequencing to compare the prokaryotic and fungal communities within leaves and traps of U. jamesoniana. The analysis of amplicon sequence variants (ASVs) unveiled notable differences in community composition depending on the plant tissue and type of microorganism. Prokaryotic communities predominantly comprised Proteobacteria and Actinobacteriota, featuring genera such as Acidocella, Bradyrhizobium, Ferritrophicum, and Ferrovum. Fungal communities were dominated by Ascomycota and Basidiomycota, encompassing representatives of Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Agaricomycetes, as well as ASVs related to Mycosphaerellaceae, Colletotrichum, Aspergillus, and Thanatephorus. We determined that the prokaryotic diversity has higher in the bladders with respect to the leaves. Fungal communities, in turn, were more diverse in leaves than in bladders. This study sheds light on the microbial communities associated with this carnivorous epiphyte and provides valuable insights into the intricate relationships between the plant and its microbial inhabitants across different tissues.

plant biology↗

bioRxiv2023

Benchmarking AI-based plasmid annotation tools for antibiotic resistance genes mining from metagenome of the Virilla River, Costa Rica

Bioinformatics and Artificial Intelligence (AI) stand as rapidly evolving tools that have facilitated the annotation of mobile genetic elements (MGEs), enabling the prediction of health risk factors in polluted environments, such as antibiotic resistance genes (ARGs). This study aims to assess the performance of four AI-based plasmid annotation tools (Plasflow, Platon, RFPlasmid, and PlasForest) by employing defined performance parameters for the identification of ARGs in the metagenome of one sediment sample obtained from the Virilla River, Costa Rica. We extracted and sequenced complete DNA from the sample, assembled the metagenome, and then performed the plasmid prediction with each bioinformatic tool, and the ARGs annotation using the Resistance Gene Identifier web portal. Sensitivity, specificity, precision, negative predictive value, accuracy, and F1score were calculated for each ARGs prediction result of the evaluated plasmidomes. Notably, Platon emerged as the highest performer among the assessed tools, exhibiting exceptional scores. Conversely, Plasflow seems to face difficulties distinguishing between chromosomal and plasmid sequences, while PlasForest has encountered limitations when handling small contigs. RFPlasmid displayed diminished specificity and was outperformed by its taxon-dependent workflow. We recommend the adoption of Platon as the preferred bioinformatic tool for resistome investigations in the taxon-independent environmental metagenomic domain. Meanwhile, RFPlasmid presents a compelling choice for taxon-dependent prediction due to its exclusive incorporation of this approach. We expect that the results of this study serve as a guiding resource in selecting AI-based tools for accurately predicting the plasmidome and its associated genes.

bioinformatics↗

bioRxiv2023

Bacterial communities in residential wastewater treatment plants are physiologically adapted to high concentrations of quaternary ammonium compounds

Benzalkonium chloride (BAC) is a quaternary ammonium compound (QAC) widely used as the active ingredient of disinfectants. Its excessive discharge in wastewater is constant and in high concentrations, likely affecting the physiology of microbial communities. We compared the community physiological profile of activated sludge bacteria with and without in vitro previous exposure to a high concentration of BAC (10 mg/L). We measured the community functional diversity (FD), carbon substrate multifunctionality (MF), and the median effective concentration that inhibits carbon respiration (EC50) using Biolog(R) EcoPlatesTM supplemented with a gradient of 0 to 50 mg/L of BAC. Surprisingly, we did not find significant differences in the physiological parameters between treatments. Certain abundant bacteria, including Pseudomonas, could explain the communitys tolerance to high concentrations of BAC. We suggest that bacterial communities in wastewater treatment facilities activated sludge (AS) are "naturally" adapted to BAC due to frequent and high-dose exposure. We highlight the need to understand better the effects of QACs in wastewater, their impact on the selection of tolerant groups, and the alteration in community metabolic profiles.

microbiology↗

bioRxiv2023

Mechanisms of low susceptibility to the disinfectant benzalkonium chloride in a multidrug-resistant environmental isolate of Aeromonas hydrophila

Excessive discharge of quaternary ammonium disinfectants such as benzalkonium chloride (BAC) into aquatic systems can trigger several physiological responses in environmental microorganisms. In this study, we isolated a low susceptible strain of Aeromonas hydrophila, namely INISA09, to from a wastewater treatment plant in Costa Rica. We characterized its phenotypic response upon exposure to three different concentrations of BAC and determined the primary mechanisms related to its resistance using genomic and proteomic tools. The genome of the strain is 4.6-Mb with 4,273 genes, and we found a propound genome rearrangement and thousands of missense mutations when compared to the reference strain A. hydrophila ATCC 7966. We identified 15,762 missense mutations mainly associated with transport, antimicrobial resistance, and outer membrane proteins. In addition, quantitative proteomic analysis revealed the significant upregulation of several efflux pumps and the downregulation of porins when the strain was exposed to three BAC concentrations. Other genes related to membrane fatty acid metabolism and redox metabolic reactions also showed an altered expression. Our findings suggest that the response of A. hydrophila INISA09 to BAC primarily occurs at the membrane level, which is BACs primary target. This study sheds light on the mechanisms of antimicrobial susceptibility in tropical aquatic environments against a widely-used disinfectant, using an environmental strain that could serve as a new study model.

microbiology↗

bioRxiv2022

Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths

Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. In addition, we isolated nine strains of Brevibacterium and Rothia able to produce substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales inhabiting sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem.

microbiology↗

bioRxiv2020

Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica

In this work, we characterize the geochemistry and microbial community of Bajo las Penas, a neutral (pH 6.5-7.4), hot spring (T = 62.0-68.0{degrees}C) located near Turrialba Volcano, Costa Rica. The microbiota at its two sources belongs mainly to the family Aquificae, comprising OTUs closely related to the genera Sulfurihydrogenibium, Thermosulfidibacter, Thermodesulfovibrio and Thermocrinis which is consistent with the presence of moderate levels of sulfate (243-284 mg/L) along the stream. We determined a dramatic shift in the microbial community just a few meters downstream of the sources of the hot spring (15-20 meters), with a change from sulfur related chemoautotrophic (e.g. Sulfurihydrogenibium and an OTU closely related to Thermodesulfovibrio) to chemoheterotrophic prokaryotes (e.g. Meiothermus, Nitrososphaera, Thermoflexus, Thermus). Thus, in this neutral hot spring, the first level of the trophic chain is associated with photosynthesis as well other anaerobic CO2 fixing bacteria. Then, thermotolerant chemoheterotrophic bacteria colonize the environment to degrade organic matter and use fermentative products from the first level of the trophic chain. Our data demonstrate how quickly the microbial community of an ecosystem can change in response to environmental variables and sheds light on the microbial ecology of less common circumneutral pH hot springs.

microbiology↗

bioRxiv2020

Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments

Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microbial communities to early planet life conditions such as high temperatures, high metal concentrations, and low pH. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in the Central Volcanic mountain range of Costa Rica. Both locations hold a very low pH (pH 1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO42- = 1170-2460 mg/L measured as S), but significant differences in their temperature (90.0-95.0{degrees}C in the seepages at Poas Volcano versus 19.1-26.6 {degrees}C in Agrio River) and in the abundance of elemental sulfur. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp., sulfur-oxidizing bacteria, represented more than half (58.4-78.4%) of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by the iron- and sulfur-oxidizing Leptospirillum (7.4-55.5%) and members of the archeal order Thermoplasmatales (16.0-58.2%). Both environments share some chemical characteristics and part of their microbiota, however the temperature and the presence of reduced sulfur are likely the main distinguishing feature ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.

microbiology↗

bioRxiv2020

C1 compounds shape the microbial community of an abandoned century-old oil exploration well.

The search for microorganisms that degrade hydrocarbons is highly relevant because it enables the bioremediation of these substances cheaply and without dangerous by-products. In this work, we studied the microbial communities of an exploratory oil well, abandoned a century ago, located in the Cahuita National Park of Costa Rica. Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including C2-dibenzothiophene, phenanthrene or anthracene, fluoranthene pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria (Methylobacillus (6.3-26.0 % of total reads) and Methylococcus (4.1-30.6 %)) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6 %), Hydrogenophaga (1.5-3.3 %) Rhodobacter (1.0-4.9 %) and Flavobacterium (1.1-6.5 %). We evidenced the presence of methane monooxygenase (MMO) activities, responsible for the first step in methane metabolism, by amplifying the pmo gene from environmental DNA. We also isolated a strain of Methylorubrum rhodesianum, which was capable of using methanol as its sole carbon source. This work represents a contribution to the understanding of the ecology of communities of microorganisms in environments with permanently high concentrations of methane and hydrocarbons, which also has biotechnological implications for the bioremediation of highly polluting petroleum components.

microbiology↗

bioRxiv2020

Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific

Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3474 m) in two transects of about 1500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). Although we distinguished a cluster dominated by yeasts and a second cluster dominated by filamentous fungi, we were unable to detect a strong effect of depth, temperature, salinity, dissolved oxygen, and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.

microbiology↗

bioRxiv2019

Variation of bacterial communities along the vertical gradient in Lake Issyk Kul, Kyrgyzstan

In this study, we explored the diversity and community composition of bacteria along a vertical gradient in Lake Issyk Kul, Kyrgyzstan, one of the largest and deepest brackish lakes in in the world. We identified 4904 bacterial ASVs based on analysis of 16S rRNA gene sequences and determined significant changes in the composition responding mainly to the variables depth and salinity. A higher abundance of Proteobacteria and Bacteroidetes was observed in the surface waters and the lake tributaries. Cyanobacteria were more abundant in the deep chlorophyll maximum (28.5 to 128 m), while Planctomycetes and Chloroflexi were dominant at depths between 128 to 600 m. According to our machine learning analysis used for identifying the most critical environmental factors, depth and temperature revealed the strongest effect on members of Proteobacteria, Planctomycetes, and Chloroflexi, while oxygen is associated with the variations in Cyanobacteria. Also, a notable increase in alpha diversity estimations was observed with increasing water depth. This work evidences significant differences in the structure of bacterial communities along the depth gradient in deep, transparent lake ecosystems. Notably, there is a dominance of Planctomycetes and Chloroflexi in the deepest layers, which can only be seen in a few other lakes with similar characteristics as Lake Issyk Kul and raises questions about their ecological role.

ecology↗

bioRxiv2019

Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran

Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran. Evaluation of the ligno-, cellulo- and chitinolytic activities were also measured using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar but functional different aquatic fungi in freshwater ecosystems.

ecology↗

bioRxiv2019

Microplastic ingestion by a herring Opisthonema sp., in the Pacific coast of Costa Rica

Despite there is a growing interest in studying the presence and effects of microplastics (MP) in fishes and other aquatic species, knowledge is still limited in tropical areas. In this study, we examined the presence of MP in the gastrointestinal content of 30 filter feeders of thread herring, Opisthonema complex (Clupeiformes: Clupeidae) from the Central Pacific coast of Costa Rica. We detected the presence of MP in 100% of the individuals with an average of 36.7 pieces per fish, of which 79.5% were fibers and 20.5% particles. To our knowledge, this is the first study in Costa Rica that demonstrates the presence of MP in planktivorous fishes. The effects of microplastics ingestion by O. libertate and its transit through aquatic food webs should be studied in greater detail, with greater number of sampling points at different times of the year. However, our work confirms that contamination by microplastics is having direct effects on the marine life of Costa Rica.\n\nCapsuleThis is the first multidisciplinary study in Costa Rica demonstrating the presence and nature of microplastics in the digestive tract of planktivorous fish.

zoology↗

bioRxiv2019

Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany

Fungi are an important component of microbial communities and are well known for their ability to degrade refractory, highly polymeric organic matter. In soils and aquatic systems, fungi play an important role in carbon processing, however, their diversity, community structure and function as well as ecological role, particularly in groundwater, are poorly studied. The aim of this study was to examine the fungal community composition, diversity and function of 16 groundwater boreholes located in the vicinity of two lakes in NE Germany that are characterized by contrasting trophic status. The analysis of 28S rRNA gene sequences amplified from the groundwater revealed high fungal diversity and clear differences in community structure between both aquifers. Most sequences were assigned to Ascomycota and Basidiomycota, but members of Chytridiomycota, Cryptomycota, Zygomycota, Blastocladiomycota, Glomeromycota and Neocallmastigomycota were also detected. In addition, 27 species of fungi were successfully isolated from the groundwater wells and tested for their ability to degrade complex organic polymers - the predominant carbon source in the wells. Most isolates showed positive activities for at least one of the tested polymer types, with three strains, belonging to the genera Gibberella, Isaria and Cadophora, being able to degrade all tested substrates. Our results highlight the high diversity of fungi in groundwater, and point to their important ecological role in breaking down highly polymeric organic matter in these isolated microbial habitats.

microbiology↗