Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.

Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline

This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (− 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between − 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between − 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between − 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between − 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.

Genomic Insights into the Diversity of Non-Coding RNAs in Bacillus Cereus Sensu Lato.

Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes.

Comparative Analysis of Three Trypanosomatid Catalases of Different Origin

Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene transfer from Gammaproteobacteria, extending the list of known bacterial sources of this gene. Comparative biochemical analyses revealed that the enzymes of V. ingenoplastis, Leptomonas pyrrhocoris, and Blastocrithidia sp., representing the three independent catalase-bearing trypanosomatid lineages, have similar properties, except for the unique cyanide resistance in the catalase of the latter species.

A Comprehensive Evaluation of Enterobacteriaceae Primer Sets for Analysis of Host-Associated Microbiota

Enterobacteriaceae is one of the most important bacterial groups within the Proteobacteria phylum. This bacterial group includes pathogens, commensal and beneficial populations. Numerous 16S rRNA gene PCR-based assays have been designed to analyze Enterobacteriaceae diversity and relative abundance, and, to the best of our knowledge, 16 primer pairs have been validated, published and used since 2003. Nonetheless, a comprehensive performance analysis of these primer sets has not yet been carried out. This information is of particular importance due to the recent taxonomic restructuration of Enterobacteriaceae into seven bacterial families. To overcome this lack of information, the identified collection of primer pairs (n = 16) was subjected to primer performance analysis using multiple bioinformatics tools. Herein it was revealed that, based on specificity and coverage of the 16S rRNA gene, these 16 primer sets could be divided into different categories: Enterobacterales-, multi-family-, multi-genus- and Enterobacteriaceae-specific primers. These results highlight the impact of taxonomy changes on performance of molecular assays and data interpretation. Moreover, they underline the urgent need to revise and update the molecular tools used for molecular microbial analyses.

Molecular Responses of Lactobacilli to Plant Phenolic Compounds: A Comparative Review of the Mechanisms Involved

Lactobacilli are well-studied bacteria that can undergo oxidative selective pressures by plant phenolic compounds (PPCs) in plants, during some food fermentations or in the gastrointestinal tract of animals via dietary inputs. Lactobacilli are known to be more tolerant to PPCs than other bacterial groups and, therefore, must have mechanisms to cope with the effects of these metabolites. In this review, we intend to present what is currently known about the basics beyond the responses of Lactobacillus spp. to individual PPCs. We review the molecular mechanisms that are engaged in the PPC-modulated responses studied to date in these bacteria that have been mainly characterized by system-based strategies, and we discuss their differences and similarities. A wide variety of mechanisms are induced to increase the oxidative stress response highlighting the antimicrobial nature of PPCs. However other uncovered mechanisms that are involved in the response to these compounds are reviewed, including the capacity of PPCs to modulate the expression of molecular functions used by lactobacilli to adapt to host environments. This shows that these phytochemicals can act as more than just antimicrobial agents in the dual interaction with lactobacilli.

Study of biodegradation of Poly(butylene adipate co-terephthalate) (PBAT) by maritime microorganisms from the Atlhantic Coast of Recife-PE (Brazil)

Biodegradable polymers undergo a degradation process resulting from the action of microorganisms such as bacteria, fungi and algae. Poly(butylene adipate co-terephthalate) (PBAT) is considered a biodegradable synthetic polymer, even if its degradation has been confirmed under industrial composting conditions, the investigation of its degradation in the marine environment is still limited. Therefore, this work aims to study the biodegradation in the marine environment, of the biodegradable polymer (PBAT), and for that, it was submerged in a static system, using seawater from the coastal region of Pernambuco/Brazil as a fluid. The samples were studied by chemical, thermal and microbiological analyses, after 7, 14, 30, 90, 120 and 180 days of immersion. Microbiological analyzes indicated that aerobic heterotrophic bacteria (AHB), anaerobic heterotrophic bacteria (AnHB) and iron precipitating bacteria (IPB) were quantified in the system at all times at high concentrations, with the exception of Sulfate reducing bacteria (SRB), fungi and Pseudomonas that showed lower concentrations compared to other bacterial groups. Biodegradation was observed by the percentage of mass loss of approximately 2.25%. In the DSC, the expansion of melting peaks after exposure to the marine environment was noted, while the TGA did not show changes in the curve trends. The FTIR showed that no new band appeared, nor displacement, since the vibrations of the covalent bonds of the groups are present regardless of the biodegradation. Indicating that no significant microbiological degradation of PBAT was observed.

Co-Treatment with Single and Ternary Mixture Gas of Dimethyl Sulfide, Propanethiol, and Toluene by a Macrokinetic Analysis in a Biotrickling Filter Seeded with Alcaligenes sp. SY1 and Pseudomonas Putida S1

The biotrickling filter (BTF) treatment is an effective way of dealing with air pollution caused by volatile organic compounds (VOCs). However, this approach is typically used for single VOCs treatment but not for the mixtures of VOC and volatile organic sulfur compounds (VOSCs), even if they are often encountered in industrial applications. Therefore, we investigated the performance of BTF for single and ternary mixture gas of dimethyl sulfide (DMS), propanethiol, and toluene, respectively. Results showed that the co-treatment enhanced the removal efficiency of toluene, but not of dimethyl sulfide or propanethiol. Maximum removal rates (rmax) of DMS, propanethiol and toluene were calculated to be 256.41 g·m−3·h−1, 204.08 g·m−3·h−1 and 90.91 g·m−3·h−1, respectively. For a gas mixture of these three constituents, rmax was measured to be 114.94 g·m−3·h−1, 104.17 g·m−3·h−1 and 99.01 g·m−3·h−1, separately. Illumina MiSeq sequencing analysis further indicated that Proteobacteria and Bacteroidetes were the major bacterial groups in BTF packing materials. A shift of bacterial community structure was observed during the biodegradation process.