Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Abstract Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil.

Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Draft Genome of Rhodococcus rhodochrous TRN7, Isolated from the Coast of Trindade Island, Brazil.

Here, we present a draft genome and annotation of Rhodococcus rhodochrous TRN7, isolated from Trindade Island, Brazil, which will provide genetic data to benefit the understanding of its metabolism.

Responses of microbial community from tropical pristine coastal soil to crude oil contamination.

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

Bioremediation strategies of hydrocarbons and microbial diversity in the Trindade Island shoreline--Brazil.

This study analyzed the microbial diversity colonizing the surface of an oil sample during its contact with water, off the Trindade Island coast and simulated the efficiency of eight different bioremediation strategies for this environment. The diversity analysis was performed using acrylic coupons that served as the support for an oil inclusion at sea. The coupons were sampled over 30 days, and T-RFLP multiplex was employed to access the diversity of fungi, Bacteria and Archaea present on the oil surface. The bioremediation strategies were simulated in a respirometer. The results showed that the bacterial domain was the most dominant in oil colonization and that the richness of the species attached to the oil gradually increases with the exposure time of the coupons. The combination of biostimulation and bioaugmentation with a native population was proven to be an effective strategy for the remediation of oil off the Trindade Island shoreline.

Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil.

In the present study, acrylic coupons with a thin layer of oil on the surface were incubated in the coastal water of Trindade Island, Brazil, for 60 days. The microorganisms adhered to the coupons were isolated using enrichment medium with hexadecane and naphthalene as the sole carbon and energy source. A total of 15 bacterial isolates were obtained, and the ability of these isolates to use different hydrocarbons as the source of carbon and energy was investigated. None of the isolates produced biosurfactants under our experimental conditions. Subsequently, identification methods such as partial sequencing of the 16S rRNA gene and analysis of fatty acids (MIDI) profile were employed. Among the 15 isolates, representatives of Actinobacteria, Firmicutes, and Alphaproteobacteria were detected. The isolates Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 were able to use all the hydrocarbons added to the culture medium (toluene, octane, xylene, naphthalene, phenanthrene, pyrene, hexadecane, anthracene, eicosane, tetracosane, triacontane, and pentacontane). Polymerase chain reaction amplification of the DNA isolated by employing primers for catechol 2,3-dioxygenase, alkane dehydrogenase and the alpha subunit of hydroxylating dioxygenases polycyclic aromatic hydrocarbon rings genes demonstrated that various isolates capable of utilizing hydrocarbons do not exhibit genes of known routes of catabolism, suggesting the existence of unknown catabolic pathways in these microorganisms. Our findings suggest that the microbiota associated to the coast of tropical oceanic islands has the ability to assist in environmental regeneration in cases of accidents involving oil spills in its shore. Thus, it motivates studies to map bioremediation strategies using the autochthonous microbiota from these environments.

Data analysis for 16S microbial profiling from different benchtop sequencing platforms.

Progress in microbial ecology is confounded by problems when evaluating results from different sequencing methodologies. Contrary to existing expectations, here we demonstrate that the same biological conclusion is reached using different NGS technologies when stringent sequence quality filtering and accurate clustering algorithms are applied.

Spray drying as a strategy for biosurfactant recovery, concentration and storage.

The objective of this study was to analyze the use of Spray Drying for concentration and preservation of biosurfactants produced by Bacillus subtilis LBBMA RI4914 isolated from a heavy oil reservoir. Kaolinite and maltodextrin 10DE or 20DE were tested as drying adjuvants. Surface activity of the biosurfactant was analyzed by preparing dilution x surface activity curves of crude biosurfactant, crude biosurfactant plus adjuvants and of the dried products, after their reconstitution in water. The shelf life of the dried products was also evaluated. Spray drying was effective in the recovery and concentration of biosurfactant, while keeping its surface activity. Drying adjuvants were required to obtain a solid product with the desired characteristics. These compounds did not interfere with tensoactive properties of the biosurfactant molecules. The dehydrated product maintained its surfactant properties during storage at room temperature during the evaluation period (120 days), with no detectable loss of activity.

Endophytic microbial diversity in coffee cherries of Coffea arabica from southeastern Brazil.

The microbiota associated with coffee plants may play a critical role in the final expression of coffee quality. However, the microbial diversity in coffee cherries is still poorly characterized. Here, we investigated the endophytic diversity in cherries of Coffea arabica by using culture-independent approaches to identify the associated microbes, ultimately to better understand their ecology and potential role in determining coffee quality. Group-specific 16S rRNA and 26S rRNA genes polymerase chain reaction - denaturing gradient gel electrophoresis and clone library sequencing showed that the endophytic community is composed of members of the 3 domains of life. Bacterial sequences showing high similarity with cultured and uncultured bacteria belonged to the Betaproteobacteria, Gammaproteobacteria, and Firmicutes phyla. Phylogenetic analyses of cloned sequences from Firmicutes revealed that most sequences fell into 3 major genera: Bacillus, Staphylococcus, and Paenibacillus. Archaeal sequences revealed the presence of operational taxonomic units belonging to Euryarchaeota and Crenarchaeota phyla. Sequences from endophytic yeast were not recovered, but various distinct sequences showing high identity with filamentous fungi were found. There was no obvious correlation between the microbial composition and cultivar or geographic location of the coffee plant. To the best of our knowledge, this is the first report demonstrating internal tissue colonization of plant fruits by members of the Archaea domain. The finding of archaeal small-subunit rRNA in coffee cherries, although not sufficient to indicate their role as active endophytes, certainly expands our perspectives toward considering members of this domain as potential endophytic microbes.

Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer.

The gastrointestinal tracts (GIT) of herbivores harbor dense and diverse microbiota that has beneficial interactions with the host, particularly for agriculturally relevant animals like ruminants such as cattle. When assessing ruminant health, microbiological indicators are often derived from the rumen or feces. However, it is probable that ruminal and fecal microbiota do not reflect the microbial communities within the GIT of ruminants. To test this, we investigated the compartments of the GIT from a Brazilian Nelore steer and performed a 16S rRNA pyrosequencing analysis on the collected samples. Our results showed high intra-individual variation, with samples clustering according to their location in the GIT including the forestomach, small intestine, and large intestine. Although sequences related to the phyla Firmicutes and Bacteroidetes predominated all samples, there was a remarkable variation at the family level. Comparisons between the microbiota in the rumen, feces, and other GIT components showed distinct differences in microbial community. This work is the first intensive non-culture based GIT microbiota analysis for any ruminant and provides a framework for understanding how host microbiota impact the health of bovines.

Simultaneous phenanthrene and cadmium removal from contaminated soil by a ligand/biosurfactant solution.

Surfactants and inorganic ligands are pointed as efficient to simultaneous removal of heavy metals and hydrophobic organic pollutants from soil. However, the biosurfactants are potentially less toxic to soil organisms than other chemical agents. Thus, in this study the efficiency of combinations of iodide (I(-)) ligand and surfactants produced by different bacterial species in the simultaneous removal of cadmium (Cd(2+)) and phenanthrene in a Haplustox soil sample was investigated. Four microbial surfactants and the synthetic surfactant Triton X-100 were tested with different concentrations of ligand. Soil samples contaminated with Cd(2+) and phenanthrene underwent consecutive washings with a surfactant/ligand solution. The removal of Cd(2+) increased with increased ligand concentration, particularly in solutions containing biosurfactants produced by the bacterial strains Bacillus subtilis LBBMA155 (lipopeptide) and Flavobacterium sp. LBBMA168 (mixture of flavolipids) and Triton X-100. Maximum Cd(2+) removal efficiency was 99.2% for biosurfactant produced by Arthrobacter oxydans LBBMA 201 (lipopeptide) and 99.2% for biosurfactant produced by Bacillus sp. LBBMA111A (mixed lipopeptide) in the presence of 0.336 mol iodide l(-1), while the maximum efficiency of Triton X-100 removal was 65.0%. The biosurfactant solutions removed from 80 to 88.0% of phenanthrene in soil, and the removal was not influenced by the presence of the ligand. Triton X-100 removed from 73 to 88% of the phenanthrene and, differently from the biosurfactants, iodide influenced the removal efficiency. The results indicate that the use of a single washing agent, called surfactant-ligand, affords simultaneous removal of organic contaminants and heavy metals.

Biodegradability of bacterial surfactants.

This work aimed at evaluating the biodegradability of different bacterial surfactants in liquid medium and in soil microcosms. The biodegradability of biosurfactants by pure and mixed bacterial cultures was evaluated through CO(2) evolution. Three bacterial strains, Acinetobacter baumanni LBBMA ES11, Acinetobacter haemolyticus LBBMA 53 and Pseudomonas sp. LBBMA 101B, used the biosurfactants produced by Bacillus sp. LBBMA 111A (mixed lipopeptide), Bacillus subtilis LBBMA 155 (lipopeptide), Flavobacterium sp. LBBMA 168 (mixture of flavolipids), Dietzia Maris LBBMA 191(glycolipid) and Arthrobacter oxydans LBBMA 201(lipopeptide) as carbon sources in minimal medium. The synthetic surfactant sodium dodecyl sulfate (SDS) was also mineralized by these microorganisms, but at a lower rate. CO(2) emitted by a mixed bacterial culture in soil microcosms with biosurfactants was higher than in the microcosm containing SDS. Biosurfactant mineralization in soil was confirmed by the increase in surface tension of the soil aqueous extracts after incubation with the mixed bacterial culture. It can be concluded that, in terms of biodegradability and environmental security, these compounds are more suitable for applications in remediation technologies in comparison to synthetic surfactants. However, more information is needed on structure of biosurfactants, their interaction with soil and contaminants and scale up and cost for biosurfactant production.

Evaluation of bacterial surfactant toxicity towards petroleum degrading microorganisms.

The acute toxicity of bacterial surfactants LBBMA111A, LBBMA155, LBBMA168, LBBMA191 and LBBMA201 and the synthetic surfactant sodium dodecyl sulfate (SDS) on the bioluminescent bacterium Vibrio fischeri was evaluated by measuring the reduction of light emission (EC(20)) by this microorganism when exposed to different surfactant concentrations. Moreover, the toxic effects of different concentrations of biological and synthetic surfactants on the growth of pure cultures of isolates Acinetobacter baumannii LBBMA04, Acinetobacter junni LBBMA36, Pseudomonas sp. LBBMA101B and Acinetobacter baumanni LBBMAES11 were evaluated in mineral medium supplemented with glucose. The EC(20) values obtained confirmed that the biosurfactants have a significantly lower toxicity to V. fischeri than the SDS. After 30 min of exposure, bacterial luminescence was almost completely inhibited by SDS at a concentration of 4710 mg L(-1). Growth reduction of pure bacterial cultures caused by the addition of biosurfactants to the growth medium was lower than that caused by SDS.

Competition between insecticide-susceptible and -resistant populations of the maize weevil, Sitophilus zeamais.

Insecticide resistance is an evolutionary response to insecticides and, as such, important for environmental biomonitoring and for pest management. Fitness disadvantage in the absence of insecticide is a frequent assumption in models of insecticide resistance evolution, which was observed in different insect species. Fitness studies are based in demographic performance of isolated populations without direct interaction between insecticide-resistant and -susceptible populations. Here we reported a study of direct competition following a factorial bivariate design between an insecticide-susceptible population of the maize weevil, Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae), and one of two insecticide-resistant populations - one exhibiting fitness disadvantage based on demographic studies (Juiz de Fora) and other not exhibiting it (Jacarezinho). Total number of insects, mortality by insecticide, insect body mass and respiration rate were recorded after three generations of competition. Indeed, fitness disadvantage was observed in the resistant population from Juiz de Fora, but not in the population from Jacarezinho, as expected. The higher body mass and respiration rate of the insecticide-resistant insects from Jacarezinho are probably mitigating the physiological costs associated with the insecticide resistance minimizing their fitness disadvantage, what does not take place with the insecticide-resistant insects from Juiz de Fora. These distinct responses between the insecticide-resistant populations are probably related to the length and intensity of field-selection with insecticides.

Phosphine resistance, respiration rate and fitness consequences in stored-product insects.

Resistance to fumigants has been frequently reported in insect pests of stored products and is one of the obstacles in controlling these pests. The authors studied phosphine resistance and its physiological basis in adult insects of 12 populations of Tribolium castaneum (Herbst) (Tenebrionidae), ten populations of Rhyzopertha dominica (F.) (Bostrichidae) and eight populations of Oryzaephilus surinamensis L. (Silvanidae) from Brazil, and the possible existence of fitness costs associated with phosphine resistance in the absence of this fumigant. The bioassays for the detection of phosphine resistance followed the FAO standard method. The production of carbon dioxide and the instantaneous rate of population increase (r(i)) of each population of each species were correlated with their resistance ratios at the LC(50). The resistance ratio at LC(50) in T. castaneum ranged from 1.0- to 186.2-fold, in R. dominica from 2.0- to 71.0-fold and in O. surinamensis from 1.9- to 32.2-fold. Ten populations of T. castaneum, nine populations of R. dominica and seven populations of O. surinamensis were resistant to phosphine. In all three species there was significant association (P < 0.05) between respiration rate and phosphine resistance. The populations with lower carbon dioxide production showed a higher resistance ratio, suggesting that the lower respiration rate is the physiological basis of phosphine resistance by reducing the fumigant uptake in the resistant insects. Conversely, populations with higher r(i) showed lower resistance ratios, which could indicate a lower rate of reproduction of the resistant populations compared with susceptible populations. Thus, management strategies based on the interruption of phosphine fumigation may result in reestablishment of susceptibility, and shows good potential for more effective management of phosphine-resistant populations.