Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere

Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts

Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.

Complete Genome Sequence of the Antibiotic-Resistant Pseudomonas fluorescens Strain Ant01, from the Rhizosphere of Antarctic Moss

Pseudomonas fluorescens Ant01 was isolated as an antibiotic-resistant strain from the rhizosphere of a moss from Barton Peninsula, King George Island, Antarctica. The assembled genome size is 6,249,144 bp, with 5,616 protein-coding genes, 69 tRNA genes, and 19 rRNA genes.

Bioinoculants-Natural Biological Resources for Sustainable Plant Production

Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.

Comparative Genomics and In Vitro Plant Growth Promotion and Biocontrol Traits of Lactic Acid Bacteria from the Wheat Rhizosphere

This study aimed to isolate lactic acid bacteria (LAB) from wheat rhizosphere, to characterize their in vitro plant growth promoting activities and to differentiate plant-associated LAB from those associated with foods or human disease through comparative genomic analysis. Lactococcus lactis subsp. lactis and Enterococcus faecium were isolated using de Man-Rogosa-Sharpe (MRS) and Glucose Yeast Peptone (GYP) as enrichment culture media. Comparative genomic analyses showed that plant-associated LAB strains were enriched in genes coding for bacteriocin production when compared to strains from other ecosystems. Isolates of L. lactis and E. faecium did not produce physiologically relevant concentrations of the phyto-hormone indolacetic acid. All isolates solubilized high amount of phosphate and 12 of 16 strains solubilized potassium. E. faecium LB5, L. lactis LB6, LB7, and LB9 inhibited the plant pathogenic Fusarium graminearum to the same extent as two strains of Bacillus sp. However, the antifungal activity of the abovementioned LAB strains depended on the medium of cultivation and a low pH while antifungal activity of Bacillus spp. was independent of the growth medium and likely relates to antifungal lipopeptides. This study showed the potential of rhizospheric LAB for future application as biofertilizers in agriculture.

A Flavor Lactone Mimicking AHL Quorum-Sensing Signals Exploits the Broad Affinity of the QsdR Regulator to Stimulate Transcription of the Rhodococcal qsd Operon Involved in Quorum-Quenching and Biocontrol Activities

In many Gram-negative bacteria, virulence, and social behavior are controlled by quorum-sensing (QS) systems based on the synthesis and perception of N-acyl homoserine lactones (AHLs). Quorum-quenching (QQ) is currently used to disrupt bacterial communication, as a biocontrol strategy for plant crop protection. In this context, the Gram-positive bacterium Rhodococcus erythropolis uses a catabolic pathway to control the virulence of soft-rot pathogens by degrading their AHL signals. This QS signal degradation pathway requires the expression of the qsd operon, encoding the key enzyme QsdA, an intracellular lactonase that can hydrolyze a wide range of substrates. QsdR, a TetR-like family regulator, represses the expression of the qsd operon. During AHL degradation, this repression is released by the binding of the γ-butyrolactone ring of the pathogen signaling molecules to QsdR. We show here that a lactone designed to mimic quorum signals, γ-caprolactone, can act as an effector ligand of QsdR, triggering the synthesis of qsd operon-encoded enzymes. Interaction between γ-caprolactone and QsdR was demonstrated indirectly, by quantitative RT-PCR, molecular docking and transcriptional fusion approaches, and directly, in an electrophoretic mobility shift assay. This broad-affinity regulatory system demonstrates that preventive or curative quenching therapies could be triggered artificially and/or managed in a sustainable way by the addition of γ-caprolactone, a compound better known as cheap food additive. The biostimulation of QQ activity could therefore be used to counteract the lack of consistency observed in some large-scale biocontrol assays.

Impacts of Microbial Inoculants on the Growth and Yield of Maize Plant

Background:

The use of microbial inoculants holds a great promise to improve crop yield without the negative environmental and health hazard associated with chemical fertilizer.

Aim:

To investigate ifPseudomonasspp. (Pseudomonas kilonensisF113 andPseudomonas protegensCHA0 strains) have promoting effects on vegetative growth and yield of different maize genotypes (viz. AFLATOXIN SYN 4W, TZB-SR, AFLATOXIN R SYN 2Y, AFLATOXIN SYN 3W and AFLATOXIN SYN-2Y) under different soil types.

Methods:

Both pot and field experiments were employed. Bacterialized seeds were sown (2 seeds/pot/stand).

Results:

Pot experiment showed that both the bacterial species significantly stimulated the growth of maize shoot length, stem girth, leaf length, root length and root weight. The effect of genotypes AFLATOXIN SYN 4W, TZB-SR, AFLATOXIN R SYN 2Y and AFLATOXIN SYN 3W are not significantly different from one another but AFLATOXIN SYN-2Y showed a significantly lower increase in the measured parameters. No significant difference was observed according to soil types. AFLATOXIN SYN 4W showed a significantly higher root weight while AFLATOXIN R SYN 2Y showed a significantly higher root length compared to the other maize genotypes. Moreover,Pseudomonassignificantly increased maize growth and yield under field experiment. AFLATOXIN R SYN 2Y and AFLATOXIN SYN 4W showed a significantly higher yield than the other maize genotypes studied.

Conclusion:

We concluded thatPseudomonas kilogenensisF113 andPseudomonas protegensCHA0 are potential biofertilizers.

Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions. However, many stones in this area are left unturned. For example, the role and diversity of uncultivable microbes in PCB degradation are still not fully understood. Improved knowledge and understanding on this front will open up new avenues for improved bioremediation technologies which will bring economic, environmental and societal benefits. This article highlights on recent advances in bioremediation of PCBs in soil. It is demonstrated that bioremediation is the most effective and innovative technology which includes biostimulation, bioaugmentation, phytoremediation and rhizoremediation and acts as a model solution for pollution abatement. More recently, transgenic plants and genetically modified microorganisms have proved to be revolutionary in the bioremediation of PCBs. Additionally, other important aspects such as pretreatment using chemical/physical agents for enhanced biodegradation are also addressed. Efforts have been made to identify challenges, research gaps and necessary approaches which in future, can be harnessed for successful use of bioremediation under field conditions. Emphases have been given on the quality/efficiency of bioremediation technology and its related cost which determines its ultimate acceptability.

Intensify production, transform biomass to energy and novel goods and protect soils in Europe-A vision how to mobilize marginal lands

The rapid increase of the world population constantly demands more food production from agricultural soils. This causes conflicts, since at the same time strong interest arises on novel bio-based products from agriculture, and new perspectives for rural landscapes with their valuable ecosystem services. Agriculture is in transition to fulfill these demands. In many countries, conventional farming, influenced by post-war food requirements, has largely been transformed into integrated and sustainable farming. However, since it is estimated that agricultural production systems will have to produce food for a global population that might amount to 9.1 billion by 2050 and over 10 billion by the end of the century, we will require an even smarter use of the available land, including fallow and derelict sites. One of the biggest challenges is to reverse non-sustainable management and land degradation. Innovative technologies and principles have to be applied to characterize marginal lands, explore options for remediation and re-establish productivity. With view to the heterogeneity of agricultural lands, it is more than logical to apply specific crop management and production practices according to soil conditions. Cross-fertilizing with conservation agriculture, such a novel approach will provide (1) increased resource use efficiency by producing more with less (ensuring food security), (2) improved product quality, (3) ameliorated nutritional status in food and feed products, (4) increased sustainability, (5) product traceability and (6) minimized negative environmental impacts notably on biodiversity and ecological functions. A sustainable strategy for future agriculture should concentrate on production of food and fodder, before utilizing bulk fractions for emerging bio-based products and convert residual stage products to compost, biochar and bioenergy. The present position paper discusses recent developments to indicate how to unlock the potentials of marginal land.

Emerging microbial biocontrol strategies for plant pathogens

To address food security, agricultural yields must increase to match the growing human population in the near future. There is now a strong push to develop low-input and more sustainable agricultural practices that include alternatives to chemicals for controlling pests and diseases, a major factor of heavy losses in agricultural production. Based on the adverse effects of some chemicals on human health, the environment and living organisms, researchers are focusing on potential biological control microbes as viable alternatives for the management of pests and plant pathogens. There is a growing body of evidence that demonstrates the potential of leaf and root-associated microbiomes to increase plant efficiency and yield in cropping systems. It is important to understand the role of these microbes in promoting growth and controlling diseases, and their application as biofertilizers and biopesticides whose success in the field is still inconsistent. This review focusses on how biocontrol microbes modulate plant defense mechanisms, deploy biocontrol actions in plants and offer new strategies to control plant pathogens. Apart from simply applying individual biocontrol microbes, there are now efforts to improve, facilitate and maintain long-term plant colonization. In particular, great hopes are associated with the new approaches of using "plant-optimized microbiomes" (microbiome engineering) and establishing the genetic basis of beneficial plant-microbe interactions to enable breeding of "microbe-optimized crops".

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions

Sixty-four native bacterial colonies were isolated from mycorrhizal roots of Helianthemum almeriense colonized by Terfezia claveryi, mycorrhizosphere soil, and peridium of T. claveryi to evaluate their effect on mycorrhizal plant production. Based on the phylogenetic analysis of the 16S rDNA partial sequence, 45 different strains from 17 genera were gathered. The largest genera were Pseudomonas (40.8 % of the isolated strains), Bacillus (12.2 % of isolated strains), and Varivorax (8.2 % of isolated strains). All the bacteria were characterized phenotypically and by their plant growth-promoting rhizobacteria (PGPR) traits (auxin and siderophore production, phosphate solubilization, and ACC deaminase activity). Only bacterial combinations with several PGPR traits or Pseudomonas sp. strain 5, which presents three different PGPR traits, had a positive effect on plant survival and growth. Particularly relevant were the bacterial treatments involving auxin release, which significantly increased the root-shoot ratio and mycorrhizal colonization. Moreover, Pseudomonas mandelii strain 29 was able to considerably increase mycorrhizal colonization but not plant growth, and could be considered as mycorrhiza-helper bacteria. Therefore, the mycorrhizal roots, mycorrhizosphere soil, and peridium of desert truffles are environments enriched in bacteria which may be used to increase the survival and mycorrhization in the desert truffle plant production system at a semi-industrial scale.

Glycerophospholipid synthesis and functions in Pseudomonas

The genus Pseudomonas is one of the most heterogeneous groups of eubacteria, presents in all major natural environments and in wide range of associations with plants and animals. The wide distribution of these bacteria is due to the use of specific mechanisms to adapt to environmental modifications. Generally, bacterial adaptation is only considered under the aspect of genes and protein expression, but lipids also play a pivotal role in bacterial functioning and homeostasis. This review resumes the mechanisms and regulations of pseudomonal glycerophospholipid synthesis, and the roles of glycerophospholipids in bacterial metabolism and homeostasis. Recently discovered specific pathways of P. aeruginosa lipid synthesis indicate the lineage dependent mechanisms of fatty acids homeostasis. Pseudomonas glycerophospholipids ensure structure functions and play important roles in bacterial adaptation to environmental modifications. The lipidome of Pseudomonas contains a typical eukaryotic glycerophospholipid--phosphatidylcholine -, which is involved in bacteria-host interactions. The ability of Pseudomonas to exploit eukaryotic lipids shows specific and original strategies developed by these microorganisms to succeed in their infectious process. All compiled data provide the demonstration of the importance of studying the Pseudomonas lipidome to inhibit the infectious potential of these highly versatile germs.

Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective.

The role of root exuded low molecular weight organic anions in facilitating petroleum hydrocarbon degradation: current knowledge and future directions

Rhizoremediation is a bioremediation technique whereby enhanced microbial degradation of organic contaminants occurs within the plant root zone (rhizosphere). It is considered an effective and affordable 'green technology' for remediating soils contaminated with petroleum hydrocarbons (PHCs). This paper critically reviews the potential role of root exuded compounds in rhizoremediation, with emphasis on commonly exuded low molecular weight aliphatic organic acid anions (carboxylates). The extent to which remediation is achieved shows wide disparity among plant species. Therefore, plant selection is crucial for the advancement and widespread adoption of this technology. Root exudation is speculated to be one of the predominant factors leading to microbial changes in the rhizosphere and thus the potential driver behind enhanced petroleum biodegradation. Carboxylates can form a significant component of the root exudate mixture and are hypothesised to enhance petroleum biodegradation by: i) providing an easily degradable energy source; ii) increasing phosphorus supply; and/or iii) enhancing the contaminant bioavailability. These differing hypotheses, which are not mutually exclusive, require further investigation to progress our understanding of plant-microbe interactions with the aim to improve plant species selection and the efficacy of rhizoremediation.

Burkholderia ambifaria and B. caribensis promote growth and increase yield in grain amaranth (Amaranthus cruentus and A. hypochondriacus) by improving plant nitrogen uptake

Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism and transport.

Diversity and antimicrobial properties of lactic acid bacteria isolated from rhizosphere of olive trees and desert truffles of Tunisia

A total of 119 lactic acid bacteria (LAB) were isolated, by culture-dependant method, from rhizosphere samples of olive trees and desert truffles and evaluated for different biotechnological properties. Using the variability of the intergenic spacer 16S-23S and 16S rRNA gene sequences, the isolates were identified as the genera Lactococcus, Pediococcus, Lactobacillus, Weissella, and Enterococcus. All the strains showed proteolytic activity with variable rates 42% were EPS producers, while only 10% showed the ability to grow in 9% NaCl. In addition, a low rate of antibiotic resistance was detected among rhizospheric enterococci. Furthermore, a strong antibacterial activity against plant and/or pathogenic bacteria of Stenotrophomonas maltophilia, Pantoea agglomerans, Pseudomonas savastanoi, the food-borne Staphylococcus aureus, and Listeria monocytogenes was recorded. Antifungal activity evaluation showed that Botrytis cinerea was the most inhibited fungus followed by Penicillium expansum, Verticillium dahliae, and Aspergillus niger. Most of the active strains belonged to the genera Enterococcus and Weissella. This study led to suggest that environmental-derived LAB strains could be selected for technological application to control pathogenic bacteria and to protect food safety from postharvest deleterious microbiota.

Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas

Background

Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity.

Results

The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained the cus operon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability.

Conclusions

Comparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.

Genotypic diversity, antibiotic resistance and bacteriocin production of enterococci isolated from rhizospheres

This study aimed to identify and to characterize rhizospheric-derived enterococci. The results showed the prevalence of Enterococcus faecium species (97%) vs. Enterococcus durans (3%). Susceptibility testing for antibiotics showed a low percentage of resistance to erythromycin (3.2%) and tetracycline (11.2%), and intermediate resistance to vancomycin (6.5%). Nevertheless, a high proportion of bacteriocin production was recorded. Furthermore, PCR detection of antibiotic resistance and bacteriocin production-encoding genes was investigated. Pulsed-field gel electrophoresis typing (PFGE) showed a great variability of enterococci in the rhizosphere. Moreover, mutilocus-sequence-typing analysis (MLST) revealed the identification of three new sequence types (STs), which were registered as ST613, ST614 and ST615.

Endophytic bacterial diversity in roots of Typha angustifolia L. in the constructed Beijing Cuihu Wetland (China)

We investigated the community structure of endophytic bacteria in narrowleaf cattail (Typha angustifolia L.) roots growing in the Beijing Cuihu Wetland, China, using the 16S rDNA library technique. In total, 184 individual sequences were used to assess the diversity of endophytic bacteria. Phylogenetic analysis revealed that 161 clones (87.5%) were affiliated with Proteobacteria, other clones grouped into Cytophaga/Flexibacter/Bacteroids (3.3%), Fusobacteria (3.8%), and nearly 5% were uncultured bacteria. In Proteobacteria, the beta and gamma subgroups were the most abundant, accounting for approximately 46% and 36.6% of all Proteobacteria, respectively. The dominant genera included Rhodoferax, Pelomonas, Uliginosibacterium, Pseudomonas, Aeromonas, Rhizobium, Sulfurospirillum, Ilyobacter and Bacteroides. While some of these endophytic bacteria are capable of fixing nitrogen and can therefore improve plant growth, other endophytes may play important biological roles by removing nitrogen, phosphorus and/or organic matter from the water body and thus have the potential to enhance the phytoremediation of eutrophic water bodies. These bacteria have the potential to degrade xenobiota such as methane, methanol, methylated amines, catechol, oxochlorate, urea, cyanide, and 2,4-dichlorophenol. Hence, the use of certain endophytic bacteria in the process of phytoremediation could be a powerful approach for the restoration of eutrophic systems.

Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil

AIMS

To assess the degradation potential and plant colonization capacity of four alkane-degrading strains (ITSI10, ITRI15, ITRH76 and BTRH79) in combination with birdsfoot trefoil and Italian ryegrass and to evaluate the diversity of indigenous alkane-degrading soil bacteria in the rhizo- and endosphere.

METHODS AND RESULTS

Contaminated soil was prepared by spiking agricultural soil with 10 g diesel fuel per kg soil. Italian ryegrass (Lolium multiflorum var. Taurus) and birdsfoot trefoil (Lotus corniculatus var. Leo) were inoculated with four alkane-degrading strains. Hydrocarbon degradation (up to 57%) was observed in all inoculated treatments of vegetated and unvegetated samples. Italian ryegrass in combination with compost and BTRH79 showed highest degradation, while birdsfoot trefoil performed best with compost and strain ITSI10. Cultivation-based as well as cultivation-independent analysis showed that both strains were competitive colonizers.

CONCLUSIONS

The combination between vegetation, inoculation with well-performing degrading bacteria and compost amendment was an efficient approach to reduce hydrocarbon contamination. Two Pantoea sp. strains, ITSI10 and BTRH79, established well in the plant environment despite the presence of a variety of other, indigenous alkane-degrading bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study suggests that the application of degrading bacterial strains, which are able to compete with the native microflora and to tightly associate with plants, are promising candidates to be used for phytoremediation applications.

Bacterial responses and interactions with plants during rhizoremediation

With the increase in quality of life standards and the awareness of environmental issues, the remediation of polluted sites has become a priority for society. Because of the high economic cost of physico-chemical strategies for remediation, the use of biological tools for cleaning-up contaminated sites is a very attractive option. Rhizoremediation, the use of rhizospheric microorganisms in the bioremediation of contaminants, is the biotechnological approach that we explore in this minireview. We focus our attention on bacterial interactions with the plant surface, responses towards root exudates, and how plants and microbes communicate. We analyse certain strategies that may improve rhizoremediation, including the utilization of endophytes, and finally we discuss several rhizoremediation strategies that have opened ways to improve biodegradation.

Bacillus lipopeptides: versatile weapons for plant disease biocontrol

In the context of biocontrol of plant diseases, the three families of Bacillus lipopeptides - surfactins, iturins and fengycins were at first mostly studied for their antagonistic activity for a wide range of potential phytopathogens, including bacteria, fungi and oomycetes. Recent investigations have shed light on the fact that these lipopeptides can also influence the ecological fitness of the producing strain in terms of root colonization (and thereby persistence in the rhizosphere) and also have a key role in the beneficial interaction of Bacillus species with plants by stimulating host defence mechanisms. The different structural traits and physico-chemical properties of these effective surface- and membrane-active amphiphilic biomolecules explain their involvement in most of the mechanisms developed by bacteria for the biocontrol of different plant pathogens.