RESUMEN

Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.

Asunto(s)

Metagenoma , Microbiota , Regiones Antárticas , Microbiota/genética , Bacterias/genética , Bacterias/clasificación , Bacterias/metabolismo , Familia de Multigenes , Biopelículas , Filogenia , Proteobacteria/genética , Proteobacteria/metabolismo , Proteobacteria/clasificación , Terpenos/metabolismo , Bacteroidetes/genética , Bacteroidetes/metabolismo , Bacteroidetes/clasificación

RESUMEN

BACKGROUND: Secondary symbionts of insects include a range of bacteria and fungi that perform various functional roles on their hosts, such as fitness, tolerance to heat stress, susceptibility to insecticides and effects on reproduction. These endosymbionts could have the potential to shape microbial communites and high potential to develop strategies for mosquito-borne disease control. METHODOLOGY/PRINCIPAL FINDINGS: The relative frequency and molecular phylogeny of Wolbachia, Microsporidia and Cardinium were determined of phlebotomine sand flies and mosquitoes in two regions from Colombia. Illumina Miseq using the 16S rRNA gene as a biomarker was conducted to examine the microbiota. Different percentages of natural infection by Wolbachia, Cardinium, and Microsporidia in phlebotomines and mosquitoes were detected. Phylogenetic analysis of Wolbachia shows putative new strains of Lutzomyia gomezi (wLgom), Brumptomyia hamata (wBrham), and a putative new group associated with Culex nigripalpus (Cnig) from the Andean region, located in Supergroup A and Supergroup B, respectively. The sequences of Microsporidia were obtained of Pi. pia and Cx. nigripalpus, which are located on phylogeny in the IV clade (terrestrial origin). The Cardinium of Tr. triramula and Ps. shannoni were located in group C next to Culicoides sequences while Cardinium of Mi. cayennensis formed two putative new subgroups of Cardinium in group A. In total were obtained 550 bacterial amplicon sequence variants (ASVs) and 189 taxa to the genus level. The microbiota profiles of Sand flies and mosquitoes showed mainly at the phylum level to Proteobacteria (67.6%), Firmicutes (17.9%) and Actinobacteria (7.4%). High percentages of relative abundance for Wolbachia (30%-83%) in Lu. gomezi, Ev. dubitans, Mi. micropyga, Br. hamata, and Cx. nigripalpus were found. ASVs assigned as Microsporidia were found in greater abundance in Pi. pia (23%) and Cx. nigripalpus (11%). An important finding is the detection of Rickettsia in Pi. pia (58,8%) and Bartonella sp. in Cx. nigripalpus. CONCLUSIONS/SIGNIFICANCE: We found that Wolbachia infection significantly decreased the alpha diversity and negatively impacts the number of taxa on sand flies and Culex nigripalpus. The Principal Coordinate Analysis (PCoA) is consistent, which showed statistically significant differences (PERMANOVA, F = 2.4744; R2 = 0.18363; p-value = 0.007) between the microbiota of sand flies and mosquitoes depending on its origin, host and possibly for the abundance of some endosymbionts (Wolbachia, Rickettsia).

Asunto(s)

Bacteroidetes/aislamiento & purificación , Culex/microbiología , Microbiota , Microsporidios/aislamiento & purificación , Filogenia , Psychodidae/microbiología , Wolbachia/aislamiento & purificación , Animales , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/fisiología , Biodiversidad , Colombia , Culex/fisiología , Microsporidios/clasificación , Microsporidios/genética , Microsporidios/fisiología , Psychodidae/fisiología , Simbiosis , Wolbachia/clasificación , Wolbachia/genética , Wolbachia/fisiología

RESUMEN

The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes.

Asunto(s)

Alphaproteobacteria/metabolismo , Bacteroidetes/metabolismo , Burkholderiaceae/metabolismo , Genoma Bacteriano , Plantas/microbiología , Alphaproteobacteria/clasificación , Alphaproteobacteria/genética , Bacteroidetes/clasificación , Bacteroidetes/genética , Biodegradación Ambiental , Biomasa , Burkholderiaceae/clasificación , Burkholderiaceae/genética , Lignina/metabolismo , Metagenoma , Filogenia , Polisacáridos

RESUMEN

As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time, to establish a baseline for future studies of host-microbial-environment interactions and monitoring programs. During two consecutive reproductive seasons, 57 fecal samples were collected from seven different JFFS colonies within the Juan Fernandez Archipelago, Chile. Bacterial composition and abundance were characterized by sequencing the V4 region of the 16S rRNA gene. The overall microbiome composition was dominated by five phyla: Firmicutes (40% ±24), Fusobacteria (30% ±17), Bacteroidetes (22% ±10), Proteobacteria (6% ±4), and Actinobacteria (2% ±3). Alpha diversity was higher in Tierras Blancas. However, location was not found to be a dominant driver of microbial composition. Interestingly, the strongest signal in the data was a negative association between the genera Peptoclostridium and Fusobacterium, which explained 29.7% of the total microbial composition variability between samples. The genus Peptoclostridium has not been reported in other pinniped studies, and its role here is unclear, with interpretation challenging due to a lack of information regarding microbiome functionality in marine mammals. As a first insight into the JFFS fecal microbiome, these results contribute towards our understanding of the natural microbial diversity and composition in free-ranging pinnipeds.

Asunto(s)

Bacterias/clasificación , Heces/microbiología , Lobos Marinos/microbiología , Microbioma Gastrointestinal/genética , Microbiota/genética , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Animales , Bacterias/genética , Bacterias/aislamiento & purificación , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Biodiversidad , Chile , ADN Bacteriano/genética , Firmicutes/clasificación , Firmicutes/genética , Firmicutes/aislamiento & purificación , Fusobacterias/clasificación , Fusobacterias/genética , Fusobacterias/aislamiento & purificación , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN

RESUMEN

A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).

Asunto(s)

Microbiología del Aire , Bacteroidetes/aislamiento & purificación , Islas , Regiones Antárticas , Bacteroidetes/clasificación , Bacteroidetes/genética , Composición de Base , ADN Bacteriano/genética , Genoma Bacteriano , Funciones de Verosimilitud , Filogenia , ARN Ribosómico 16S/genética

RESUMEN

Seriola rivoliana intestinal microbiota (IM) was characterised under aquaculture conditions through 16S rRNA amplicon sequencing. Specimens of 30 days after hatching (DAH) were maintained in three tanks and fed under the same environmental conditions for characterisation 15 days prior to sampling. Three fish were randomly taken from each tank; total DNA extraction of the gut microbiota was performed to characterise microbial composition and its metabolic prediction. The V3 hypervariable region of the 16S rRNA was amplified and sequenced with Illumina pair-end technology. The prokaryotic components in the S. rivoliana intestine were dominated mainly by the phyla Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria and Actinobacteria. No significant differences in beta diversity were detected in the three samples (tanks). However in alpha diversity, they were detected in juveniles of the same cohort within the same group, as exemplified by enrichment of certain bacterial groups, mainly of the Clostridia class, which were specific in each fish within the same tank. The metabolic prediction analyses suggested that S. rivoliana IM contribute to the metabolism of amino acids, carbohydrates, lipids, and immune system. This study provides the first IM characterisation under rearing conditions of S. rivoliana-a species with broad economic potential-and contributes to novel information for potential use of probiotics in future trials.

Asunto(s)

Actinobacteria/metabolismo , Bacteroidetes/metabolismo , Cianobacterias/metabolismo , Firmicutes/metabolismo , Perciformes/microbiología , Proteobacteria/metabolismo , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Aminoácidos/inmunología , Aminoácidos/metabolismo , Animales , Acuicultura , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Metabolismo de los Hidratos de Carbono , Carbohidratos/inmunología , Cianobacterias/clasificación , Cianobacterias/genética , Cianobacterias/aislamiento & purificación , ADN Bacteriano/genética , Firmicutes/clasificación , Firmicutes/genética , Firmicutes/aislamiento & purificación , Microbioma Gastrointestinal/genética , Microbioma Gastrointestinal/inmunología , Inmunidad Innata , Metabolismo de los Lípidos , Lípidos/inmunología , Perciformes/inmunología , Perciformes/metabolismo , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Simbiosis/inmunología

RESUMEN

BACKGROUND: The gut microbiome has been increasingly acknowledged as playing a pivotal role in human health. Therefore, a number of studies have focused on variables that impact its microbial structure and consequent functionality. A wide range of factors, such as diet, age, sex, life stage, behavior, ethnicity, and diseases have been considered, and strong links were set out. However, some aspects regarding the microbiome determinants are still under-explored. DISCUSSION: Recently, Bosman et al. presented evidence that skin exposure to narrowband UVB light modulated the gut microbiome of a specific human cohort. This cohort presented an increase of biodiversity, Firmicutes and Proteobacteria, and a decrease of Bacteroidetes. Based on these findings, we revisited our data on a hunter-gatherer gut microbiome (Yanomami) and identified similarities in the gut microbiome of these two cohorts. Both presented a high abundance of Proteobacteria, which had been observed as a unique feature in the Yanomami gut microbiome, and based on Bosman et al study, could be associated with their natural sunlight exposure. CONCLUSION: In this commentary, we would like to point out that the human lifestyle concerning sunlight exposure should be considered as one force modulating the gut microbiome, highlighting, as proposed by Bosman et al, a novel skin-gut axis which is associated with health and disease.

Asunto(s)

Bacterias/clasificación , Bacterias/crecimiento & desarrollo , Microbioma Gastrointestinal , Piel/efectos de la radiación , Luz Solar , Rayos Ultravioleta , Bacterias/aislamiento & purificación , Bacteroidetes/clasificación , Bacteroidetes/crecimiento & desarrollo , Bacteroidetes/aislamiento & purificación , Biodiversidad , Firmicutes/clasificación , Firmicutes/aislamiento & purificación , Humanos , Indígenas Sudamericanos , Estilo de Vida , Proteobacteria/clasificación , Proteobacteria/crecimiento & desarrollo , Proteobacteria/aislamiento & purificación

RESUMEN

The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.

Asunto(s)

Bacterias , Plancton , Poliaminas/metabolismo , Agua de Mar/microbiología , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Cianobacterias/clasificación , Cianobacterias/genética , Cianobacterias/aislamiento & purificación , Golfo de México , Metagenómica , Microbiota , Nitrógeno/metabolismo , Filogenia , Planctomycetales/clasificación , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Plancton/metabolismo , Plancton/microbiología , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Agua de Mar/química , Transcriptoma

RESUMEN

Two Gram-stain-negative, strictly aerobic, marine bacteria, designated as strains RKSG066T and RKSG123T, were isolated from a sponge Aplysina fistularis collected at a depth of 15 m off the west coast of San Salvador, The Bahamas. Investigation of nearly full-length 16S rRNA gene and whole genome-based phylogenies revealed that both strains belong to the order Cytophagales within the class Cytophagia and phylum Bacteroidetes. Strain RKSG066T formed a monophyletic clade with described members of the genus Fulvivirga, while strain RKSG123T formed a well-supported paraphyletic branch apart from this and other related genera within the family Flammeovirgaceae. For both RKSG066T and RKSG123T, optimal growth parameters were 30-37 °C, pH 7-8 and 2-3 % (w/v) NaCl; cells were catalase- and oxidase-positive, and flexirubin-type pigments were absent. The predominant fatty acids were iso-C15 : 0, C16 : 0, C18 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C18 : 1 ω9c and iso-C15 : 1 G for RKSG066T, and iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0, C16 : 0 3-OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) for RKSG123T. Menaquinone-7 was the major respiratory quinone for both strains. The DNA G+C contents of RKSG066T and RKSG123T were 39.5 and 36.7 mol%, respectively. On the basis of phylogenetic distinctiveness and polyphasic analysis, the type strain RKSG066T (=TSD-73T=LMG 29870T) is proposed to represent a novel species of the genus Fulvivirga, for which the name Fulvivirga aurantia sp. nov. is proposed. The type strain RKSG123T (=TSD-75T=LMG 30075T) is proposed to represent the type species of a novel genus and species with the proposed name Xanthovirga aplysinae gen. nov., sp. nov. Additionally, the genus Fulvivirga is emended to include strains of orange-pigmented colonies that contain the predominant cellular fatty acids C16 : 0, C18 : 0, C16  :  1 ω5c and C18  :  1 ω9c.

Asunto(s)

Bacteroidetes/clasificación , Filogenia , Poríferos/microbiología , Animales , Técnicas de Tipificación Bacteriana , Bacteroidetes/aislamiento & purificación , Bahamas , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Pigmentación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química

RESUMEN

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.

Asunto(s)

Bacteroidetes/clasificación , Biodiversidad , Cianobacterias/clasificación , Agua Dulce/microbiología , Sedimentos Geológicos/microbiología , Microbiota , Proteobacteria/clasificación , Bacteroidetes/genética , Bacteroidetes/crecimiento & desarrollo , Cianobacterias/genética , Cianobacterias/crecimiento & desarrollo , Sedimentos Geológicos/análisis , Secuenciación de Nucleótidos de Alto Rendimiento , México , Nutrientes , Filogenia , Proteobacteria/genética , Proteobacteria/crecimiento & desarrollo , ARN Ribosómico 16S/genética

RESUMEN

BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.

Asunto(s)

Bacterias/clasificación , Enfermedad de Chagas/transmisión , Insectos Vectores/microbiología , Microbiota , Rhodnius/microbiología , Actinobacteria/clasificación , Actinobacteria/genética , Análisis de Varianza , Animales , Bacterias/genética , Bacteroidetes/clasificación , Bacteroidetes/genética , Biodiversidad , Código de Barras del ADN Taxonómico , Ecosistema , Firmicutes/clasificación , Firmicutes/genética , Biblioteca de Genes , Humanos , Insectos Vectores/fisiología , Panamá , Filogeografía , Reacción en Cadena de la Polimerasa , Proteobacteria/clasificación , Proteobacteria/genética , ARN Ribosómico 16S/química , Rhodnius/fisiología

RESUMEN

White clover widely cultivated in China is one of the most important perennial leguminous forages in temperate and subtropical regions. There is a large quantity of white clover seeds imported into China each year for demands of high-quality grass seeds. Seedborne diseases may cause significant economic losses. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. Therefore, we used 16S rRNA gene sequencing to investigate the bacterial communities in white clover seeds collected from four different countries. The results showed that a total of 484,715 clean reads were obtained for further subsequent analysis. In total, 341, 340, 382, and 297 operational taxonomic units were obtained at 3% distance cutoff in DB, MB, TB, and XB samples, respectively. The richness indexes revealed that TB sample from Argentina had the highest bacterial richness in four samples. Our results demonstrated that Proteobacteria was the dominant phyla in MB, TB, and XB; however, Bacteroidetes was the dominant phyla in DB. The dominant genus of DB was Prevotella (11.9%), while Sphingomonas was the major genus of MB (46.9%), TB (55.08%), and XB (47.2%) samples. These results provide useful information for seedborne diseases and transmission of bacteria from seed to seedling.

Asunto(s)

Bacterias/clasificación , Medicago/microbiología , Microbiota , Semillas/microbiología , Argentina , Bacterias/aislamiento & purificación , Técnicas de Tipificación Bacteriana , Bacteroidetes/clasificación , Bacteroidetes/aislamiento & purificación , ADN Bacteriano/genética , Dinamarca , Secuenciación de Nucleótidos de Alto Rendimiento , Nueva Zelanda , Filogenia , Proteobacteria/clasificación , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Estados Unidos

RESUMEN

The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability. Altogether, the results indicated an open pan-genome for the family Salinibacteraceae, as well as the codification of relevant traits such as diverse rhodopsin genes, CRISPR-Cas systems and spacers, and one T6SS secretion system that could give ecological advantages to an EHB-2 isolate. For the new Salinibacter species, we propose the name Salinibacter altiplanensis sp. nov. (the designated type strain is AN15T=CECT 9105T=IBRC-M 11031T).

Asunto(s)

Bacteroidetes/clasificación , Genoma Bacteriano , Lagos/microbiología , Filogenia , Salinidad , Altitud , Argentina , Técnicas de Tipificación Bacteriana , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Sistemas CRISPR-Cas , ADN Bacteriano/genética , ARN Ribosómico 16S/genética , Rodopsina/genética , Análisis de Secuencia de ADN , Sistemas de Secreción Tipo VI/genética , Microbiología del Agua

RESUMEN

The effect of pressure and temperature on microbial communities of marine environments contaminated with petroleum hydrocarbons is understudied. This study aims to reveal the responses of marine bacterial communities to low temperature, high pressure, and contamination with petroleum hydrocarbons using seawater samples collected near an offshore Brazilian platform. Microcosms containing only seawater and those containing seawater contaminated with 1% crude oil were subjected to three different treatments of temperature and pressure as follows: (1) 22°C/0.1 MPa; (2) 4°C/0.1 MPa; and (3) 4°C/22 MPa. The effect of depressurization followed by repressurization on bacterial communities was also evaluated (4°C/22 MPaD). The structure and composition of the bacterial communities in the different microcosms were analyzed by PCR-DGGE and DNA sequencing, respectively. Contamination with oil influenced the structure of the bacterial communities in microcosms incubated either at 4°C or 22°C and at low pressure. Incubation at low temperature and high pressure greatly influenced the structure of bacterial communities even in the absence of oil contamination. The 4°C/22 MPa and 4°C/22 MPaD treatments resulted in similar DGGE profiles. DNA sequencing (after 40 days of incubation) revealed that the diversity and relative abundance of bacterial genera were related to the presence or absence of oil contamination in the nonpressurized treatments. In contrast, the variation in the relative abundances of bacterial genera in the 4°C/22 MPa-microcosms either contaminated or not with crude oil was less evident. The highest relative abundance of the phylum Bacteroidetes was observed in the 4°C/22 MPa treatment.

Asunto(s)

Bacteroidetes/metabolismo , Hidrocarburos/efectos adversos , Microbiota/efectos de los fármacos , Contaminación por Petróleo/efectos adversos , Petróleo/efectos adversos , Proteobacteria/metabolismo , Organismos Acuáticos/genética , Organismos Acuáticos/metabolismo , Bacteroidetes/clasificación , Bacteroidetes/genética , Frío , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota/fisiología , Proteobacteria/clasificación , Proteobacteria/genética , ARN Ribosómico 16S/genética , Agua de Mar/microbiología

RESUMEN

Acid mine drainage (AMD) is characterized by an acid and metal-rich run-off that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea and are closely related to Hydrotalea flava. The phylogeny and average nucleotide identity analysis suggest that all single amplified genomes (SAGs) form two clades that may represent different strains. These cells have the genomic potential for denitrification, copper and other metal resistance. Two coexisting CRISPR-Cas loci were recovered across SAGs, and we observed heterogeneity in the population with regard to the spacer sequences, together with the loss of trailer-end spacers. Our results suggest that the genomes of Hydrotalea sp. strains studied here are adjusting to a quickly changing selective pressure at the microhabitat scale, and an important form of this selective pressure is infection by foreign DNA.

Asunto(s)

Bacteroidetes/clasificación , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Genoma Bacteriano , Minería , Ácidos , Bacteroidetes/genética , ADN Bacteriano/genética , Ecosistema , Evolución Molecular , Filogenia , Análisis de Secuencia de ADN , Análisis de la Célula Individual

RESUMEN

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Asunto(s)

Arsénico/metabolismo , Bacterias/clasificación , Sedimentos Geológicos/microbiología , Metagenómica/métodos , Altitud , Bacterias/genética , Bacteroidetes/clasificación , Bacteroidetes/genética , Firmicutes/clasificación , Firmicutes/genética , Redes Reguladoras de Genes , Filogenia , Proteobacteria/clasificación , Proteobacteria/genética , Análisis de Secuencia de ADN

RESUMEN

Biodegradation of phenolic compounds in bioreactors is well documented, but the changes in the bacterial populations dynamics during degradation were not that often. A glass bubble column used as reactor was inoculated with activated sludge, spiked with 2-chlorophenol, phenol and m-cresol after 28 days and maintained for an additional 56 days, while the 16S rRNA gene from metagenomic DNA was monitored. Proteobacteria (68.1%) dominated the inoculum, but the bacterial composition changed rapidly. The relative abundance of Bacteroidetes and Firmicutes decreased from 4.8 and 9.4 to <0.1 and 0.2% respectively, while that of Actinobacteria and TM7 increased from 4.8 and 2.0 to 19.2 and 16.1% respectively. Phenol application increased the relative abundance of Proteobacteria to 94.2% (mostly Brevundimonas 17.6%), while that of Bacteroidetes remained low (1.2%) until day 42. It then increased to 47.3% (mostly Leadbetterella 46.9%) at day 84. It was found that addition of phenolic compounds did not affect the relative abundance of the Alphaproteobacteria initially, but it decreased slowly while that of the Bacteroidetes increased towards the end.

Asunto(s)

Bacterias/efectos de los fármacos , Bacterias/metabolismo , Biodegradación Ambiental , Reactores Biológicos , Consorcios Microbianos/efectos de los fármacos , Fenoles/metabolismo , Fenoles/farmacología , Aguas del Alcantarillado/microbiología , Actinobacteria/clasificación , Actinobacteria/efectos de los fármacos , Actinobacteria/genética , Actinobacteria/fisiología , Bacterias/clasificación , Bacterias/genética , Bacteroidetes/clasificación , Bacteroidetes/efectos de los fármacos , Bacteroidetes/genética , Bacteroidetes/fisiología , Clorofenoles/metabolismo , Clorofenoles/farmacología , Cresoles/metabolismo , Cresoles/farmacología , Secuenciación de Nucleótidos de Alto Rendimiento , Metagenómica , Consorcios Microbianos/genética , Consorcios Microbianos/fisiología , Fenol/metabolismo , Fenol/farmacología , Proteobacteria/clasificación , Proteobacteria/efectos de los fármacos , Proteobacteria/genética , Proteobacteria/fisiología , ARN Ribosómico 16S , Aguas del Alcantarillado/análisis

RESUMEN

The environmental impact of major oil spills on marine microorganisms has yet to be thoroughly investigated using molecular biology techniques. The Deepwater Horizon (DWH) drilling rig explosion of 2010 affected an approximately 176,000 km2 surface area of the Gulf of Mexico (GOM) when an estimated 210 million gallons of oil from the Macondo Prospect spilled into the environment. Pelagic Sargassum, a complex of two surface drifting species (Sargassum natans and Sargassum fluitans) of marine brown macroalgae and a critically important habitat in the GOM ecosystem, was suffused by Macondo Prospect 252 oil released during the DWH event. Using 16S rRNA PCR and Roche 454 pyrosequencing, the effect of the oil on the bacterial population associated with pelagic Sargassum and contiguous waters was examined by comparing sequence data generated from samples collected from oiled and non-oiled locations in the northern GOM. Sequence data showed similar microbial composition in Sargassum regardless of exposure to oil primarily dominated by five phyla; Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and unclassified bacteria. The microbial composition in water samples was significantly less diverse than for Sargassum and consisted primarily of Proteobacteria, Firmicutes, and Bacteroidetes. Due to the evenly distributed abundance of microbial species on oiled and non-oiled pelagic Sargassum, study findings indicate that DWH spilled oil had minimal effect on the composition and diversity of the microbial community associated with Sargassum and contiguous waters. However, higher abundances of Sulfitobacter and one species of Psychrobacter were found in oiled water samples when compared to non-oiled water samples indicating some effect of DHW oil in the microbial composition of seawater. Though there are a number of marine studies using molecular biology approaches, this is the first molecular examination of the impact of the DWH oil spill on bacterial communities associated with pelagic Sargassum and contiguous waters from the GOM.

Asunto(s)

Actinobacteria/clasificación , Bacteroidetes/clasificación , Monitoreo del Ambiente/métodos , Firmicutes/clasificación , Contaminación por Petróleo , Proteobacteria/clasificación , Sargassum/microbiología , Verrucomicrobia/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , ADN Bacteriano/genética , Ambiente , Firmicutes/genética , Firmicutes/aislamiento & purificación , Golfo de México , Microbiota/genética , Industria del Petróleo y Gas , Petróleo/toxicidad , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Sargassum/crecimiento & desarrollo , Agua de Mar/química , Agua de Mar/microbiología , Verrucomicrobia/genética , Verrucomicrobia/aislamiento & purificación

RESUMEN

In this study, we surveyed the bacteriome-associated microbiota of the corn leafhopper Dalbulus maidis by means of histological, ultrastructural, and molecular analyses. Amplification and sequencing of 16S rDNA genes revealed that the endosymbiont "Candidatus Sulcia muelleri" (Phylum Bacteroidetes) resides in bacteriomes of D. maidis. Phylogenetic analysis showed that the sequence was closely allied to others found in representatives of the subfamily Deltocephalinae. We failed to amplify other sequences as "Candidatus Nasuia deltocephalinicola," a co-primary symbiont frequently associated to deltocephaline leafhoppers. In addition, a metagenetic analysis carried out in order to investigate the presence of other bacteriome-associated bacteria of D. maidis showed that the sequence of Sulcia accounted for 98.56 % of all the sequences. Histological and ultrastructural observations showed that microorganisms harbored in bacteriomes (central syncytium and cytoplasm of uninucleate bacteriocytes) look like others Sulcia described in hemipteran species and they were transovarially transmitted from mother to offspring which is typical of obligate endosymbionts. The only presence of Sulcia in the bacteriomes of D. maidis was discussed.

Asunto(s)

Bacteroidetes , Hemípteros/microbiología , Microbiota/genética , Simbiosis/genética , Animales , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Secuencia de Bases , ADN Bacteriano/genética , Femenino , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN

RESUMEN

AIM: To determine the composition and diversity of the microbiota associated to Crassostrea sikamea treated during 30 days with Streptomyces strains N7 and RL8. METHODS AND RESULTS: DNA was extracted from oysters followed by 16S rRNA gene amplification and pyrosequencing. The highest and lowest species diversity richness was observed in the initial and final control group, whereas Streptomyces-treated oysters exhibited intermediate values. Proteobacteria was the most abundant phylum (81·4-95·1%), followed by Bacteroidetes, Actinobacteria and Firmicutes. The genera Anderseniella, Oceanicola, Roseovarius, Ruegeria, Sulfitobacter, Granulosicoccus and Marinicella encompassed the core microbiota of all experimental groups. The genus Bacteriovorax was detected in all groups except in the final control and the depurated N7, whereas Vibrio remained undetected in all Streptomyces-treated groups. RL8 was the only group that harboured the genus Streptomyces in its microbiota. Principal component analysis showed that Streptomyces strains significantly changed oyster microbiota with respect to the initial and final control. CONCLUSIONS: Crassostrea sikamea treated with Streptomyces showed high species diversity and a microbiota composition shift, characterized by keeping the predator genus Bacteriovorax and decreasing the pathogenic Vibrio. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first culture-independent study showing the effect of Streptomyces over the oyster microbiota. It also sheds light about the potential use of Streptomyces to improve mollusc health and safety for consumers after the depuration process.

Asunto(s)

Crassostrea/microbiología , Microbiota , Streptomyces/fisiología , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Animales , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Biodiversidad , Gammaproteobacteria/clasificación , Gammaproteobacteria/genética , Gammaproteobacteria/aislamiento & purificación , Análisis de Componente Principal , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Rhodobacteraceae/clasificación , Rhodobacteraceae/genética , Rhodobacteraceae/aislamiento & purificación , Streptomyces/genética , Vibrio/clasificación , Vibrio/genética , Vibrio/aislamiento & purificación