Bacterial Genomes: Habitat Specificity and Uncharted Organisms

The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.     

Bacteriosomes in axenic plants: endophytes as stable endosymbionts

Observations of cells of axenic peach palm (Bactris gasipaes) microplants by light microscopy revealed movements of small particles within the cells. The phenomenon was characterized initially as Brownian movement, but electron microscopy revealed the presence of an intracellular bacterial community in these plants. Microscopy observations revealed the particular shapes of bacterial cells colonizing inner tissues of analyzed plants. Applying a molecular characterization by polymerase chain reaction and denaturing gradient gel electrophoresis, it was revealed the existence of bacterial rRNA within the plants. Sequencing of the rRNA identified three different phylogenetic groups; two bands had a high degree of similarity to sequences from Moraxella sp. and Brevibacillus sp., and a third sequence was similar to a non-cultivated cyanobacterium. The presence of those endosymbionts, called bacteriosomes, in axenic peach palm microplants raises the question of whether these stable endosymbionts were acquired in the process of evolution and how could they benefit the process of plants micropropagation.     

Bacterial composition in brassica-cultivated soils with low and high severity of clubroot

The natural bacterial communities of the soil–plant system are relevant in the process of suppressing diseases caused by soilborne plant pathogens. However, little is known regarding the structure of these communities in soils cultivated with brassica vegetables and their relationship with clubroot severity, a disease caused by Plasmodiophora brassicae. In the present study, the composition of bacterial communities in soils cultivated with cauliflower with distinct levels of disease severity was compared. The bacterial composition in soils with lower and higher clubroot severity differs in phylum and genera levels. Soils associated with plants with lower disease severity showed predominance of Kaistobacter, Flavisolibacter, Sphingobacterium, Koribacter, Nitrospira, Bradyrhizobium and Bacillus. Our study reinforces the importance of management strategies that promote improving the physical–chemical characteristics of soil, which are essential to modulate bacterial populations correlated with plant disease suppression.     

Bacterial community in the rhizosphere and rhizoplane of wild type and transgenic eucalyptus

The rhizosphere is a niche exploited by a wide variety of bacteria. The expression of heterologous genes by plants might become a factor affecting the structure of bacterial communities in the rhizosphere. In a greenhouse experiment, the bacterial community associated to transgenic eucalyptus, carrying the Lhcb1-2 genes from pea (responsible for a higher photosynthetic capacity), was evaluated. The culturable bacterial community associated to transgenic and wild type plants were not different in density, and the Amplified Ribosomal DNA Restriction Analysis (ARDRA) typing of 124 strains revealed dominant ribotypes representing the bacterial orders Burkholderiales, Rhizobiales, and Actinomycetales, the families Xanthomonadaceae, and Bacillaceae, and the genus Mycobacterium. Principal Component Analysis based on the fingerprints obtained by culture-independent Denaturing Gradient Gel Electrophoresis analysis revealed that Alphaproteobacteria, Betaproteobacteria and Actinobacteria communities responded differently to plant genotypes. Similar effects for the cultivation of transgenic eucalyptus to those observed when two genotype-distinct wild type plants are compared.     

Genomic signatures and co‐occurrence patterns of the ultra‐small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle

The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co‐metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co‐occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.     

Use of antibiotics to control endophytic bacterial growth migration onto culture medium in Eucalyptus cloeziana F.Muell.: a micropropagation approach

The natural endophytic bacterial growth migration onto a culture medium is commonly associated with unnecessary microplant discards. In micropropagation procedures, some bacteria can exude from the internal tissues of plants to colonize the culture medium and compete with the plants for nutrients, which may lead to a reduction in plant development. To find an efficient antibiotic protocol to control this bacterial growth migration onto the culture medium without affecting plant development, Eucalyptus cloeziana F.Muell. microstumps were subjected to four antibiotic treatments for 30 d. They were treated with gentamicin, ciprofloxacin, rifampicin, or Timentin^®, in addition to the control treatment (antibiotic free). The effects of the antibiotics were monitored weekly, and the endophytic bacterial community structures were evaluated in two periods of plant development (15 d and 30 d).The denaturing gradient gel electrophoresis (DGGE) technique was used to compare the control and post-antibiotic treatment plant microbiological composition, to determine if the antibiotic treatment played a specific role on the endophytic bacterial community structure. The gentamicin treatment was composed of a distinct community from the control treatment. Nonetheless, the plants treated with ciprofloxacin and rifampicin manifested similar endophytic community structures compared to the control. In contrast, plants treated with Timentin^® showed a specific bacterial community composition and a higher plant dry mass, number of shoots, and nutritional content. These results suggested that Timentin^® treatment could be applied for 30 days to control endophytic bacterial growth migration onto the culture medium, without affecting the homeostatic balance between the bacteria and plants.

     

Changes of bacterial communities in the rhizosphere of sugarcane under elevated concentration of atmospheric CO2

It is believed that climate change will influence most of interactions that sustain life on Earth. Among these, the recruitment exerted by plants in their roots vicinity can change, leading to differential assemblages of microbiomes in the rhizosphere. We approached this issue analyzing the variations in the composition of bacterial communities in the rhizosphere of sugarcane cultivated under two concentrations of atmospheric CO₂ (350 or 700 ppm). In addition to the analysis of bacterial community, the use of DNA‐SIP allowed the comparison of bacterial groups assimilating roots exudates (based on ¹³C‐labeled DNA) in both conditions, in a period of 8 days after the CO₂ pulse. The separation of ¹³C‐DNA indicated the low but increasing frequency of labeling in the rhizosphere, as averages of 0.6, 2.4 and 5.0% of total DNA were labeled after 2, 4, and 8 days after the ¹³CO₂ pulse, respectively. Based on large‐scale sequencing of the V6 region in the gene 16S rRNA, we found an increase in the bacterial diversity in the ¹³C‐DNA along the sampling period. We also describe the occurrence of distinct bacterial groups assimilating roots exudates from sugarcane cultivated under each CO₂ concentration. Bacilli, Gammaproteobacteria, and Clostridia showed high affinity for the C‐sources released by sugarcane under 350 ppm of CO₂, while under elevated concentration of CO₂, the assimilation of roots exudates was prevalently made by members of Bacilli and Betaproteobacteria. The communities became more similar along time (4 and 8 days after CO₂ pulse), in both concentrations of CO₂, electing Actinobacteria, Sphingobacteriia, and Alphaproteobacteria as the major cross‐feeders on sugarcane exudates. In summary, we described the bacterial groups with higher affinity to assimilate roots exudates in the rhizosphere of sugarcane, and also demonstrated that the rhizosphere community can be differentially assembled in a future scenario with increased contents of CO₂.     

Bacterial communities involved in sulfur transformations in wastewater treatment plants

The main sulfate-reducing (SRB) and sulfur-oxidizing bacteria (SOB) in six wastewater treatment plants (WWTPs) located at southern Brazil were described based on high-throughput sequencing of the 16S rDNA. Specific taxa of SRB and SOB were correlated with some abiotic factors, such as the source of the wastewater, oxygen content, sample type, and physical chemical attributes of these WWTPs. When the 22 families of SRB and SOB were clustered together, the samples presented a striking distribution, demonstrating grouping patterns according to the sample type. For SOB, the most abundant families were Spirochaetaceae, Chromatiaceae, Helicobacteriaceae, Rhodospirillaceae, and Neisseriaceae, whereas, for SRB, were Syntrophaceae, Desulfobacteraceae, Nitrospiraceae, and Desulfovibriaceae. The structure and composition of the major families related to the sulfur cycle were also influenced by six chemical attributes (sulfur, potassium, zinc, manganese, phosphorus, and nitrogen). Sulfur was the chemical attribute that most influenced the variation of bacterial communities in the WWTPs (λ = 0.14, p = 0.008). The OTUs affiliated to Syntrophus showed the highest response to the increase of total sulfur. All these findings can contribute to improve the understanding in relation to the sulfur-oxidizing and sulfate-reducing communities in WWTPs aiming to reduce H₂S emissions.