Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Endophytes promote plant growth and yield, suppress pathogens, may help to remove contaminants, solubilize phosphate, or contribute assimilable nitrogen to plants. Some endophytes are seed-borne, but others have mechanisms to colonize the plants that are being studied. Bacterial mutants unable to produce secreted proteins are impaired in the colonization process. Plant genes expressed in the presence of endophytes provide clues as to the effects of endophytes in plants. Molecular analysis showed that plant defense responses limit bacterial populations inside plants. Some human pathogens, such as Salmonella spp., have been found as endophytes, and these bacteria are not removed by disinfection procedures that eliminate superficially occurring bacteria. Delivery of endo-phytes to the environment or agricultural fields should be carefully evaluated to avoid introducing pathogens.

https://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-19-0827

Bacterial Endophytes and Their Interactions with Hosts

Phytoremediation: plant–endophyte partnerships take the challenge

It is well known that hundreds of thousands of bacterial species remain to be discovered and cultured, representing a substantial reservoir of genetic diversity and great potential for biotechnological applications. Although most of the bacteria inhabiting common environments (e.g., agricultural soils and plants) have not yet been grown in culture, many of them could be cultivated using standard methods. However, for many environments, research on microbial taxonomy and ecology is lacking. Unfortunately, novel bacterial species are often described based on the analysis of a very limited set of isolates (59), commonly one to three. This is true for many bacterial species, including several belonging to the genus Burkholderia. For example, the species B. kururiensis (80), B. sacchari (9), B. phenoliruptrix (16), B. terrae (79), B. tuberum, and B. phymatum (73) were recently described on the basis of a single isolate analyzed, and consequently, their environmental distribution and ecological role are unknown. B. kururiensis and B. sacchari were described as species with abilities to degrade trichloroethylene and to biotechnologically produce polyhydroxyalkanoic acids, respectively, but new studies related to their ecologies or applications are largely lacking. The nitrogen-fixing species B. xenovorans was described on the basis of three isolates (32); strain LB400T was isolated from polychlorinated biphenyl (PCB)-contaminated soil in Moreau, NY, strain CAC-124 was isolated from the rhizosphere of a coffee plant cultivated in Veracruz, Mexico, and strain CCUG 28445 was recovered from a blood culture in Sweden. Although strain LB400T is the best-studied PCB degrader, and its pathways for degradation of these compounds have been extensively characterized at the genetic and molecular levels (25, 35), strains CAC-124 and CCUG 28445 have been only partially analyzed and do not share the biphenyl-biodegrading capacities of strain LB400T (32). Recently, one B. xenovorans isolate was recovered from the rhizosphere of maize cultivated in The Netherlands (62). Although the complete genome of B. xenovorans LB400T was recently sequenced (12), it is noteworthy that the four extant B. xenovorans strains described in diverse studies have been randomly recovered from different environments and widely distant geographical regions, and there are no studies on the distribution of this PCB-degrading, nitrogen-fixing species or its association with plants. Emphasis has been given to studies of the isolation, taxonomy, and distribution of Burkholderia species related to human opportunistic pathogens, especially the B. cepacia complex species found in cystic fibrosis patients (33, 45, 52; for reviews, see references 15 and 42). In contrast, few studies have been performed on the overall diversity of the genus Burkholderia (61, 63), even though nonpathogenic Burkholderia species are frequently recovered from different environments (6, 40, 70), and despite their biotechnological potential in bioremediation and other applications (34, 70; for a review, see reference 48). Knowledge of novel diazotrophic Burkholderia species (11, 32, 50, 54), including legume nodule symbionts (14, 73), phylogenetically greatly distant from the B. cepacia complex species, has come very recently, but their environmental distribution and relevant features for agronomic and environmental applications are little known (13, 27, 32, 49).

Bacteria are involved in degradation processes of many aromatic compounds released into the environment by the decay of plant material or by anthropogenic activity. Phenolic compounds and polymers containing benzene rings (e.g., lignins) are natural aromatic compounds (21, 29). However, phenol is a man-made aromatic compound and along with its derivatives is considered a major hazardous compound in industrial wastewater. Similarly, aromatic hydrocarbons like benzene and toluene are common pollutants of soil and groundwater (78). Soil microorganisms are capable of using aromatic compounds as sole carbon sources, owing to aerobic biodegradation catalyzed by mono- or dioxygenases (3, 78). In the last few years, rhizoremediation (microbial degradation of hazardous compounds in the rhizosphere) and phytoremediation (the use of plants to extract and degrade harmful substances) have been considered alternatives for decontamination of soils. In addition, bacteria are able to exert positive effects on plants through various mechanisms. For instance, nitrogen fixation (the natural transformation of atmospheric N2 to ammonia) contributes organic nitrogen for plant growth (28), while the bacterial enzyme 1-amino-cyclopropane-1-carboxylate (ACC) deaminase hydrolyzes ACC (the immediate precursor of ethylene) and lowers the levels of ethylene produced in developing or stressed plants, promoting root elongation (30). Some bacteria solubilize insoluble minerals through the production of acids, increasing the availability of phosphorus and other nutrients to plants in deficient soils (55). Several bacteria improve plant growth through suppression of pathogens by competing for nutrients, by antibiosis, or by synthesizing siderophores, which can solubilize and chelate iron from the soil and inhibit the growth of phytopathogenic microorganisms (23).

This work was aimed at revealing the occurrence of nitrogen-fixing Burkholderia species associated with tomato (Lycopersicon esculentum) plants cultivated in different locations in Mexico. We found that the rhizosphere of tomato is a reservoir of different known and unknown diazotrophic Burkholderia species that are able to exhibit in vitro some activities involved in bioremediation, plant growth promotion, and biological control.

The Tomato Rhizosphere, an Environment Rich in Nitrogen-Fixing Burkholderia Species with Capabilities of Interest for Agriculture and Bioremediation

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

/pdf/the-interaction-between-plants-and-bacteria-in-the-2lq1v88m25.pdf

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Plant roots are associated with diverse communities of endophytic bacteria which do not exert adverse effects. The diversity of bacterial endophytes associated with ginseng roots cultivated in three different areas in Korea was investigated. Sixty-three colonies were isolated from the interior of ginseng roots. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to three major phylogenetic groups: the high G+C Gram-positive bacteria (HGCGPB), low G+C Gram-positive bacteria (LGCGPB), and the Proteobacteria. The dominant species at the three different ginseng growing areas were: HGCGPB at Ganghwa (55.0%), LGCGPB at Geumsan (45.5%), and Proteobacteria at Jinan (61.9%). Most cellulase-, xylanase-, and pectinase-producing colonies among the isolates belong to the LGCGPB group, except for Pectobacterium carotovora which belonged to the Proteobacteria. The 13 isolates belonging to LGCGPB and Proteobacteria were assessed for their antifungal activity against phytopathogenic fungi such as Rhizoctonia solani. Among them, Paenibacillus polymyxa GS01, Bacillus sp. GS07, and Pseudomonas poae JA01 show potential activity as biocontrol agents against phytopathogenic fungi. Finally, most of the low G+C Gram-positive bacteria with antifungal activity against phytopathogenic microorganisms showed cellulolytic enzyme activity while some Proteobacteria with the antifungal activity and the high G+C Gram-positive bacteria did not show any cellulolytic activity.

Endophytic Bacterial Communities in Ginseng and their Antifungal Activity Against Pathogens

Endophytic nitrogen fixation in dune grasses (Ammophila arenaria and Elymus mollis) from Oregon

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Endophytic nitrogen fixation in dune grasses (Ammophila arenaria and Elymus mollis) from Oregon