A major checkpoint for protein expression in Rhodobacter sphaeroides during heat stress response occurs at the level of translation.

Temperature above the physiological optimum is a stress condition frequently faced by bacteria in their natural environments. Here, we were interested in the correlation between levels of RNA and protein under heat stress. Changes in RNA and protein levels were documented in cultures of Rhodobacter sphaeroides using RNA sequencing, quantitative mass spectrometry, western blot analysis, in vivo [35 S] methionine-labelling and plasmid-borne reporter fusions. Changes in the transcriptome were extensive. Strikingly, the proteome remained unchanged except for very few proteins. Examples include a heat shock protein, a DUF1127 protein of unknown function and sigma factor proteins from leaderless transcripts. Insight from this study indicates that R. sphaeroides responds to heat stress by producing a broad range of transcripts while simultaneously preventing translation from nearly all of them, and that this selective production of protein depends on the untranslated region of the transcript. We conclude that measurements of transcript abundance are insufficient to understand gene regulation. Rather, translation can be an important checkpoint for protein expression under certain environmental conditions. Furthermore, during heat shock, regulation at the level of transcription might represent preparation for survival in an unpredictable environment while regulation at translation ensures production of only a few proteins.

Impact of pollution on the microbial diversity of a tropical river in an urbanized region of northeastern Brazil.

Rivers are important ecosystems that are integrated into biogeochemical cycles and constitute an essential resource for numerous human uses. However, the assessment of the biological diversity and composition of microbial communities found in rivers remains incomplete, partly due to methodological constraints which are only recently being resolved with the advent of next generation sequencing (NGS) techniques. Using 454-pyrosequencing of the 16S gene, the present study analyzed the microbial diversity of the planktonic and sediment populations in a tropical river in northeastern Brazil that is exposed to severe pollution. Six water and six sediment samples were analysed. The dominant bacterial phyla in both sediment and water were the Proteobacteria, followed by Bacteroidetes and Actinobacteria in the water column and by Chloroflexi and Acidobacteria in the sediment. Biological diversity appeared to be greatly decreased by environmental pollution, whereas the microbial community structure was variable across the analyzed transect. Moreover, a narrow relationship between industrial and urban sources of contamination and the bacterial genera detected at these sites has been observed. A variety of potentially pathogenic bacteria was detected, including Klebsiella, Treponema, Faecalibacterium and Enterococcus, indicating that the river might pose a substantial risk to public health. [Int Microbiol 20(1): 11-24 (2017)].

Impact of pollution on the microbial diversity of a tropical river in an urbanized region of northeastern Brazil

Rivers are important ecosystems that are integrated into biogeochemical cycles and constitute an essential resource for numerous human uses. However, the assessment of the biological diversity and composition of microbial communities found in rivers remains incomplete, partly due to methodological constraints which are only recently being resolved with the advent of next generation sequencing (NGS) techniques. Using 454-pyrosequencing of the 16S gene, the present study analyzed the microbial diversity of the planktonic and sediment populations in a tropical river in northeastern Brazil that is exposed to severe pollution. Six water and six sediment samples were analysed. The dominant bacterial phyla in both sediment and water were the Proteobacteria, followed by Bacteroidetes and Actinobacteria in the water column and by Chloroflexi and Acidobacteria in the sediment. Biological diversity appeared to be greatly decreased by environmental pollution, whereas the microbial community structure was variable across the analyzed transect. Moreover, a narrow relationship between industrial and urban sources of contamination and the bacterial genera detected at these sites has been observed. A variety of potentially pathogenic bacteria was detected, including Klebsiella, Treponema, Faecalibacterium and Enterococcus, indicating that the river might pose a substantial risk to public health (AU)

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454-Pyrosequencing analysis of highly adapted azo dye-degrading microbial communities in a two-stage anaerobic-aerobic bioreactor treating textile effluent.

Azo dyes, which are widely used in the textile industry, exhibit significant toxic characteristics for the environment and the human population. Sequential anaerobic-aerobic reactor systems are efficient for the degradation of dyes and the mineralization of intermediate compounds; however, little is known about the composition of the microbial communities responsible for dye degradation in these systems. 454-Pyrosequencing of the 16S rRNA gene was employed to assess the bacterial biodiversity and composition of a two-stage (anaerobic-aerobic) pilot-scale reactor that treats effluent from a denim factory. The anaerobic reactor was inoculated with anaerobic sludge from a domestic sewage treatment plant. Due to the selective composition of the textile wastewater, after 210 days of operation, the anaerobic reactor was dominated by the single genus Clostridium, affiliated with the Firmicutes phylum. The aerobic biofilter harbored a diverse bacterial community. The most abundant phylum in the aerobic biofilter was Proteobacteria, which was primarily represented by the Gamma, Delta and Epsilon classes followed by Firmicutes and other phyla. Several bacterial genera were identified that most likely played an essential role in azo dye degradation in the investigated system.

Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing.

Microorganisms are responsible for degrading the raw leachate generated in sanitary landfills, extracting the soluble fraction of the landfill waste and biotransforming organic matter and toxic residues. To increase our understanding of these highly contaminated ecosystems, we analyzed the microbial communities in the leachate produced by three landfill cells of different ages. Using high-throughput 454 pyrosequencing of the 16S rRNA gene, we describe the structure of the leachate communities and present their compositional characteristics. All three communities exhibited a high level of abundance but were undersampled, as indicated by the results of the rarefaction analysis. The distribution of the taxonomic operational units (OTUs) was highly skewed, suggesting a community structure with a few dominant members that are key for the degradation process and numerous rare microorganisms, which could act as a resilient microorganism seeder pool. Members of the phylum Firmicutes were dominant in all of the samples, accounting for up to 62% of the bacterial sequences, and their proportion increased with increasing landfill age. Other abundant phyla included Bacteroidetes, Proteobacteria, and Spirochaetes, which together with Firmicutes comprised 90% of the sequences. The data illustrate a microbial community that degrades organic matter in raw leachate in the early stages, before the methanogenic phase takes place. The genera found fit well into the classical pathways of anaerobic digestion processes.

Water quality and microbial diversity in cisterns from semiarid areas in Brazil.

Harvesting rainwater is a common practice worldwide, particularly in areas with no access to a public water supply or insufficient groundwater reserves. More than two million people living in semiarid regions of Brazil consume rainwater stored in cisterns, and little information is available regarding the water quality. Despite the initial good quality of the rainwater, its harvest and storage can introduce contaminants that must be eliminated before consumption. To evaluate the influence of handling, cistern age and precipitation on the quality of harvested rainwater, we monitored seven cisterns in the semiarid Brazilian Northeast over 4 years. Microbial and physicochemical parameters were monitored once a month, and denaturant gradient gel electrophoresis (DGGE) was performed at the end of the monitoring period. Coliform bacteria were detected in 100% of samples, while Escherichia coli were observed in 73.8%. The alkalinity and conductivity were the highest for the recently built cisterns due to the dissolution of construction materials. The DGGE of the 16S r DNA did not reveal the presence of E. coli. Instead, DGGE bands sequencing indicated that species primarily affiliated with Alphaproteobacteria were present in all cisterns, indicating the presence of microbial ecosystems capable of purifying and stabilizing the stored rainwater.

Microbial community composition of anoxic marine sediments in the Bay of Cádiz (Spain).

The composition of the microbial community inhabiting the anoxic coastal sediments of the Bay of Cádiz (southern Spain) was investigated using a molecular approach consisting of PCR cloning and denaturing gradient gel electrophoresis (DGGE), based on 16S rRNA sequences. The total cell count was 1-5 × 108 cells/g sediment and, as determined by catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH), the proportion of Bacteria to Archaea was about 70:30. The analysis of 16S-rRNA gene sequences revealed a wide spectrum of microorganisms, which could be grouped into 111 operational taxonomic units (OTUs). Many of the OTUs showed high phylogenetic similarity to microorganisms living in marine sediments of diverse geographic origin. The phylogenetic groups that were predominantly detected were Firmicutes, Deltaproteobacteria, and Gammaproteobacteria, accounting for 23, 15, and 14% of the clones, respectively. Diversity in the domain Archaea was significantly lower than in the domain Bacteria. The majority of the archaeal OTUs belonged to the Crenarchaeota phylum. Since most of the sequences could not be identified precisely at the genus/species level, the functional roles of the microorganisms in the ecosystem could not be inferred. However, seven OTUs affiliated with the Delta- and Epsilonproteobacteria were identified down to the genus level, with all of the identified genera known to occur in sulfate-rich marine environments.

Microbial community composition of anoxic marine sediments in the Bay of Cádiz (Spain)

The composition of the microbial community inhabiting the anoxic coastal sediments of the Bay of Cádiz (southern Spain) was investigated using a molecular approach consisting of PCR cloning and denaturing gradient gel electrophoresis (DGGE), based on 16S rRNA sequences. The total cell count was 1-5 × 10⁸ cells/g sediment and, as determined by catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH), the proportion of Bacteria to Archaea was about 70:30. The analysis of 16S-rRNA gene sequences revealed a wide spectrum of microorganisms, which could be grouped into 111 operational taxonomic units (OTUs). Many of the OTUs showed high phylogenetic similarity to microorganisms living in marine sediments of diverse geographic origin. The phylogenetic groups that were predominantly detected were Firmicutes, Deltaproteobacteria, and Gammaproteobacteria, accounting for 23, 15, and 14% of the clones, respectively. Diversity in the domain Archaea was significantly lower than in the domain Bacteria. The majority of the archaeal OTUs belonged to the Crenarchaeota phylum. Since most of the sequences could not be identified precisely at the genus/species level, the functional roles of the microorganisms in the ecosystem could not be inferred. However, seven OTUs affiliated with the Delta- and Epsilonproteobacteria were identified down to the genus level, with all of the identified genera known to occur in sulfate-rich marine environments (AU)

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Monitoring the primary biodegradation of linear alkylbenzene sulfonates and their coproducts in anoxic sediments using liquid chromatography-mass spectrometry.

An accompanying article has demonstrated the anaerobic degradation of the surfactant linear alkylbenzene sulfonate (LAS) in microcosms filled with marine sediments through the generation of sulfophenylcarboxylic acids (SPCs). A detailed study shows that this process was uniform in the blanks (non-spiked natural sediments) for every LAS homologue during the complete course of the experiment. However, when sediments were spiked with commercial LAS and, therefore, enriched with short-chain homologues, degradation was enhanced for these homologues until their percentages were close to those for non-spiked sediments. The reason is that short-chain homologues are more bioavailable due to their higher solubility and lower sorption capacity. Thus, sorption on sediments was found to be increased with the length of the alkyl chain for LAS homologues, following a linear Freundlich isotherm, whereas the metabolites generated were predominant in solution due to their much higher polarity. Intermediate-chain SPC homologues (C7-C9 SPCs) were the most abundant during the experiment, but a significant increase in the concentration of shorter-chain SPC homologues (C4-C6 SPCs) was detected toward the end. In the case of isomers, the steric effect of the aromatic group implies that LAS primary degradation took place preferentially over external isomers. Therefore, the generation of external isomers of SPCs was predominant during the complete experiment although internal isomers of SPCs became more evident when the degradation process had advanced and external isomers of LAS became scarce. The identity of both types of SPC isomer was confirmed by tandem mass spectrometry. With respect to LAS coproducts, the relative percentage of iso-LAS increased during the complete experiment and removal percentages for dialkyl tetralinsulfonates (<30%) were typically lower that those for LAS (66-79%), although a similar behavior was observed for their homologues in both cases.

Anaerobic degradation of linear alkylbenzene sulfonates in coastal marine sediments.

This research shows for the first time the degradation of linear alkylbenzene sulfonates (LAS) under anaerobic conditions, together with the presence of metabolites and the identification of microorganisms involved in this process. This compound is the most widely used surfactant and its main environmental concern is related to its persistence in the absence of oxygen as LAS accumulates in anaerobic sediments and sewage sludges. Laboratory experiments performed with anoxic marine sediments spiked with 10-50 ppm of LAS demonstrated, however, that its degradation reached 79% in 165 days via the generation of sulfophenyl carboxylic acids (SPCs). Almost all of the added LAS (>99%) was found to be attached to the sediment while the less hydrophobic SPCs were predominant in solution, as their concentration increased progressively up to 3 ppm during the full course of the experiment. Average half-life for LAS has been estimated to be 90 days, although higher values should be expected when the LAS concentration exceeds 20 ppm, due to inhibition of the microbial community. Sulfate-reducing and methanogenic activities proved to be intense during the experiment. Several sulfate-reducing bacteria and firmicutes/clostridia have been identified as possible candidates for effecting this degradation. Our results imply that the persistence of LAS in anoxic compartments, such as marine sediments, should be reconsidered when evaluating its environmental risk.