Bacterial root endophytes reside in a vast number of plant species as part of their root microbiome, with some being shown to positively influence plant growth. Endophyte community structure (species diversity: richness and relative abundances) within the plant is dynamic and is influenced by abiotic and biotic factors such as soil conditions, biogeography, plant species, microbe-microbe interactions and plant-microbe interactions, both at local and larger scales. Plant-growth-promoting bacterial endophytes (PGPBEs) have been identified, but the predictive success at positively influencing plant growth in field conditions has been limited. Concurrent to the development of modern molecular techniques, the goal of predicting an organism's ability to promote plant growth can perhaps be realized by more thorough examination of endophyte community dynamics. This paper reviews the drivers of endophyte community structure relating to plant growth promotion, the mechanisms of plant growth promotion, and the current and future use of molecular techniques to study these communities.

A lysimeter-based field study was done to monitor the transfer of culturable Escherichia coli, general (ALLBAC), human (Hf183) and swine (PIG-BAC-1) specific 16S rRNA Bacteroides spp. markers, nutrients and metals through soils and leachate over time following land application of a CP1/Class A as well as two CP2/Class B municipal biosolids (MBs). Hf183 markers were detected up to six days following application in soils receiving dewatered and liquid MBs, but not in leachate, suggesting their use in source tracking is better suited for recent pollution events. The CP2/Class B biosolids and swine manure contributed the highest microbial load with E. coli loads (between 2.5 and 3.7 log CFU (100 mL)(-1)) being greater than North American concentration recommendations for safe recreational water. ALLBAC persisted in soils and leachate receiving all treatments and was detected prior to amendment application demonstrating its unsuitability for identifying the presence of fecal pollution. A significant increase in NO₃-N (for Lystek and dewatered MBs) and total-P (for dewatered and liquid MBs) in leachate was observed in plots receiving the CP1/Class A and CP2/Class B type MBs which exceeded North American guidelines, suggesting impact to surface water. Metal (As, Cd, Cr, Co, Cu, Pb, Mo, Ni, Se, Zn and Hg) transfer was negligible in soil and leachate samples receiving all treatments. This study is one of the first to examine the fate of E. coli and Bacteroides spp. markers in situ following the land application of MBs where surface runoff does not apply.

Municipal biosolids (MBs) that are land-applied in North America are known to possess an active microbial population that can include human pathogens. Activated sludge is a hotspot for the accumulation of antibiotics and has been shown to be a selective environment for microorganisms that contain antibiotic resistance genes (ARGs); however, the prevalence of ARGs in MBs is not well characterized. In this study, we enriched the plasmid metagenome from raw sewage sludge and two CP2 MBs, a mesophilic anaerobic digestate and a dewatered digestate, to evaluate the presence of ARGs in mobile genetic elements. The CP2-class biosolids are similar to Class B biosolids in the United States. The CP2 biosolids must meet a microbiological cut off of 2 × 10 colony-forming units (CFU) per dry gram or 100 mL of biosolids. The enriched plasmid DNA was sequenced (Illumina MiSeq). Sequence matching against databases, including the Comprehensive Antibiotic Resistance Database (CARD), MG-RAST, and INTEGRALL, identified potential genes of interest related to ARGs and their ability to transfer. The presence and abundance of different ARGs varied between treatments with heterogeneity observed among the same sample types. The MBs plasmid-enriched metagenomes contained ARGs associated with resistance to a variety of antibiotics, including β-lactams, rifampicin, quinolone, and tetracycline as well as the detection of extended spectrum β-lactamase genes. Cultured bacteria from CP2 MBs possessed antibiotic resistances consistent with the MBs metagenome data including multiantibiotic-resistant isolates. The results from this study provide a better understanding of the ARG and MGE profile of the plasmid-enriched metagenome of CP2 MBs.