Plasmids associated with heavy metal resistance and herbicide degradation potential in bacterial isolates obtained from two Brazilian regions

Coinoculation of arbuscular mycorrhizal fungi and rhizobia stimulates atrazine dissipation by changing the atrazine-degrading bacterial community at the soil aggregate scale

As a potential low-cost and environmentally friendly strategy, bioremediation of herbicide polluted soil has attracted increasing attention. However, there is a lack of knowledge regarding the response of the atrazine-degrading bacterial community to coinoculation of arbuscular mycorrhizal (AM) fungi and rhizobia for atrazine dissipation. In this study, a pot experiment was conducted with AM fungi Glomus mosseae (AM), rhizobia Rhizobium trifolii TA-1 (R) and their coinoculation (AMR) with atrazine. In each treatment, the atrazine-degrading bacterial community of four soil size aggregates, namely large macroaggregates (LMa), small macroaggregates (SMa), microaggregates (Mia) and primary particles (P) were investigated. The results showed that the atrazine residue concentration was lowest in AMR, and that in LMa was also significantly lower than that in the other smaller aggregate sizes. Overall, inoculation, the aggregate fraction and their interaction had significant effects on soil TN, SOC, AP and pH. For the atrazine-degrading bacterial community, the Chao1 index increased with decreasing particle size, but the Shannon index decreased. Moreover, the abundances of the dominant atrazine-degrading bacterial genera Arthrobacter, Bacillus, Marmoricola and Nocardioides in the Mia and P particle size groups were greater than those in the LMa and SMa groups in each treatment. The bacterial communities in the Mia and P particle sizes in each treatment group were more complex. Therefore, coinoculation of AM fungi and rhizobia stimulated atrazine dissipation by changing the atrazine-degrading bacterial community, and the response of the atrazine-degrading bacterial community to each aggregate size varied depending on its distinct soil physicochemical properties.

Plasmid-Encoded Traits Vary across Environments

Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.