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Rhizobial symbiotic interactions are known for nitrogen fixation, providing commercial crops and other plants with self-sufficiency in nitrogen requirements. An enormous contribution from nitrogen fixation is vital to the global nitrogen cycle. The symbiotic nitrogen reduces the carbon footprint of crop cultivation, which underlines its importance in agricultural sustainability. Extensive research efforts have been made to understand the symbiotic relationship at molecular, physiological, and ecological levels. This led to the isolation and modification of symbiotic strains for enhanced nitrogen efficiency. During the evaluation of strains for nitrogen fixation in exchange for supporting the bacterium in terms of space and resources, it has been observed that the accrued benefits to the host plants extend well beyond the nitrogen fixation. The symbiotic interaction has been advantageous to the host for better growth and development, tolerating a stressful environment, and even keeping the pathogenic microbial enemies at bay. Additionally, it enabled the availability of the mineral nutrients, which otherwise were inaccessible to the host. In this chapter, we bring together the information with a focus on the role of rhizobial symbiotic interactions that promote plant growth and productivity through phytohormone synthesis, by facilitating the availability of mineral nutrients, and by improving the plant tolerance to sub-optimal growth conditions.

Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.

Stored liquid dairy manure provides a conducive environment to microbial communities for methane (CH4) production. Significant reductions of emissions from these systems have been observed by using different management strategies and treatment technologies. However, knowledge on how microbial communities respond to the mitigation actions is lacking, and is important for developing and refining mitigation strategies. Using lab and meso-scale studies, the responses of microbial communities to varying levels of total solids content, residual slurry, pH, and chemical agents were assessed. Gas chromatography and laser-based trace gas analysis were used to monitor CH4 flux whereas molecular techniques including denaturing gradient gel electrophoresis, quantitative real-time PCR, and next generation sequencing of marker genes were used to study the microbes. With reduction of total solids content (9.5% to 0.3%), we found up to ~23% increases in the mean abundance and activity of methanogens. Cumulative CH4 emissions, however, decreased by ~70% as total solid levels decreased. These results indicated that available carbon substrate, and not methanogen abundance, may be limiting cumulative CH4 emissions at reduced total solids of dairy slurries. In a follow-up study, abundant bacterial and methanogenic communities were detected, and related to significant increases in cumulative CH4 emissions from stored dairy slurries with 10% and 20% residual slurry. The presence of residual slurry, did not alter the core methanogenic phylotypes, although, Methanocorpusculum predominated the methanogen population, RNA data indicated that methanogens related to Methanosarcina were the major players in CH4 production. Microbial communities in residual slurries may be reduced by chemical treatments. In a lab-scale study, significant reductions in the abundance of methanogens (up to ~28%) were observed when sodium persulfate, potassium permanganate, or their combination with sodium hypochlorite. In slurries treated with H2SO4, the abundance of methanogen populations was not impacted. In a subsequent pilot-scale study, the transcriptional activities of methanogen populations and CH4 production were significantly affected by acidification of manure. Taken together, the findings of these studies suggest that the activity responses of slurry microorganisms can help in the refinement and/or development of effective mitigation strategies.