Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa

Design and regulation of engineered bacteria for environmental release

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

The impact of Beauveria species bioinocula on the soil microbial community structure in organic strawberry plantations

Introduction

The multifunctionality of microorganisms, including entomopathogenic fungi, represents a feature that could be exploited to support the development, marketing, and application of microbial-based products for plant protection. However, it is likely that this feature could affect the composition and dynamics of the resident soil microorganisms, possibly over a longer period. Therefore, the methodology utilized to evaluate such impact is critical for a reliable assessment. The present study was performed to evaluate the impact of strains of Beauveria brongniartii and Beauveria bassiana on soil bacterial and fungal communities using an approach based on the terminal restriction fragment polymorphism (T-RFLP) analysis.

Materials and methods

Soil samples in the vicinity of the root system were collected during a 3-year period, before and after the bioinocula application, in two organic strawberry plantations. Specific primers were used for the amplification of the bacterial 16S rRNA gene and the fungal ITS region of the ribosome.

Results and discussion

Data of the profile analysis from T-RFLP analysis were used to compare the operational taxonomic unit (OTU) occurrence and intensity in the inoculated soil with the uninoculated control. With regard to the impact on the bacterial community, both Beauveria species were not fully consistently affecting their composition across the seasons and fields tested. Nevertheless, some common patterns were pointed out in each field and, sometimes, also among them when considering the time elapsed from the bioinoculum application. The impact was even more inconsistent when analyzing the fungal community. It is thus concluded that the application of the bioinocula induced only a transient and limited effect on the soil microbial community, even though some changes in the structure dynamic and frequency of soil bacterial and fungal OTUs emerged.

Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives

The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.

Assessing effects of the entomopathogenic fungus Metarhizium brunneum on soil microbial communities in Agriotes spp. biological pest control

The release of large quantities of microorganisms to soil for purposes such as pest control or plant growth promotion may affect the indigenous soil microbial communities. In our study, we investigated potential effects of Metarhizium brunneum ART2825 on soil fungi and prokaryota in bulk soil using high-throughput sequencing of ribosomal markers. Different formulations of this strain, and combinations of the fungus with garlic as efficacy-enhancing agent, were tested over 4 months in a pot and a field experiment carried out for biological control of Agriotes spp. in potatoes. A biocontrol effect was observed only in the pot experiment, i.e. the application of FCBK resulted in 77% efficacy. Colony counts combined with genotyping and marker sequence abundance confirmed the successful establishment of the applied strain. Only the formulated applied strain caused small shifts in fungal communities in the pot experiment. Treatment effects were in the same range as the effects caused by barley kernels, the carrier of the FCBK formulation and temporal effects. Garlic treatments and time affected prokaryotic communities. In the field experiment, only spatial differences affected fungal and prokaryotic communities. Our findings suggest that M. brunneum may not adversely affect soil microbial communities.

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization

Rhizobia are α- and ß-proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature-tagged-Tn5 mutagenesis (STM) we performed a genome-wide screening for Ensifer meliloti genes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca. 80%) are chromosomally located, pointing to the relevance and ancestral origin of the bacterial ability to colonize plant roots. The identified genes were related to metabolic functions, transcription, signal transduction, and motility/chemotaxis among other categories; with several ORFs of yet-unknown function. Most remarkably, we identified a subset of genes that impacted more severely the colonization of the roots of alfalfa than of pea. Further analyses using other plant species revealed that such early differential phenotype could be extended to other members of the Trifoliae tribe (Trigonella, Trifolium), but not the Fabeae and Phaseoleae tribes. The results suggest that consolidation of E. meliloti into its current symbiotic state should have occurred in a rhizobacterium that had already been adapted to rhizospheres of the Trifoliae tribe.

Proline utilization system is required for infection by the pathogenic α-proteobacterium Brucella abortus

Proline utilization (Put) systems have been described in a number of bacteria; however, the importance and functionality of the Put system in the intracellular pathogen Brucellaabortus has not been explored. Generally, bacterial Put systems are composed of the bifunctional enzyme proline dehydrogenase PutA and its transcriptional activator PutR. Here, we demonstrate that the genes putA (bab2_0518) and putR (bab2_0517) are critical for the chronic infection of mice by B. abortus, but putA and putR are not required for the survival and replication of the bacteria in naive macrophages. Additionally, in vitro experiments revealed that putR is necessary for the ability of the bacteria to withstand oxidative stress, as a ΔputR deletion strain is hypersensitive to hydrogen peroxide exposure. Quantitative reverse transcription-PCR and putA-lacZ transcriptional reporter studies revealed that PutR acts as a transcriptional activator of putA in Brucella, and electrophoretic mobility shift assays confirmed that PutR binds directly to the putA promoter region. Biochemical analyses demonstrated that a purified recombinant B. abortus PutA protein possesses quintessential proline dehydrogenase activity, as PutA is capable of catalysing the conversion of proline to glutamate. Altogether, these data are the first to reveal that the Put system plays a significant role in the ability of B. abortus to replicate and survive within its host, as well as to describe the genetic regulation and biochemical activity of the Put system in Brucella.

Does nature make provision for backups in the modification of bacterial community structures?

Self-balancing is an inherent character in nature in response to community structure modification pressure and modern biotechnology has revolutionized the way such detections are made. Presented here is an overview of the forces and process interactions between released bacteria and indigenous microflora which encompass soil bacterial diversity, community structure, indigenous endorhizosphere micro-organisms, molecular detection methodologies, and transgenic plants and microbes. Issues of soil bacterial diversity and community structure as well as the interpretation of results from various findings are highlighted and discussed as inferred from research articles. An understanding of the factors influencing bio-inoculant modification of bacterial community structure in the colonization of the rhizosphere is essential for improved establishment of biocontrol agents, and is critically reviewed.

Microbial inoculants and their impact on soil microbial communities: a review

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

Rhizobial extrachromosomal replicon variability, stability and expression in natural niches

In bacteria, niche adaptation may be determined by mobile extrachromosomal elements. A remarkable characteristic of Rhizobium and Ensifer (Sinorhizobium) but also of Agrobacterium species is that almost half of the genome is contained in several large extrachromosomal replicons (ERs). They encode a plethora of functions, some of them required for bacterial survival, niche adaptation, plasmid transfer or stability. In spite of this, plasmid loss is common in rhizobia upon subculturing. Rhizobial gene-expression studies in plant rhizospheres with novel results from transcriptomic analysis of Rhizobium phaseoli in maize and Phaseolus vulgaris roots highlight the role of ERs in natural niches and allowed the identification of common extrachromosomal genes expressed in association with plant rootlets and the replicons involved.

Impact of rhizobial inoculation on Acacia senegal (L.) Willd. growth in greenhouse and soil functioning in relation to seed provenance and soil origin

Rhizobial inoculation has a positive impact on plants growth; however, there is little information about its effect on soil microbial communities and their activity in the rhizosphere. It was therefore necessary to test the effect of inoculation of Acacia senegal (L.) Willd. seedlings with selected rhizobia on plant growth, structure and diversity of soil bacterial communities and soil functioning in relation to plant provenance and soil origin. In order to carry out this experiment, three A. senegal seeds provenance from Kenya, Niger, and Senegal were inoculated with selected rhizobial strains. They have been further grown during 4 months in greenhouse conditions in two non-disinfected soils, Dahra and Goudiry coming respectively from arid and semi-arid areas. The principal component analysis (ACP) showed an inoculation effect on plant growth, rhizospheric bacterial diversity and soil functioning. However, the performances of the rhizobial strains varied in relation to the seed provenance and the soil origin. The selected rhizobial strains, the A. senegal provenance and the soil origin have modified the structure and the diversity of soil bacterial communities as measured by principal component analysis/denaturing gradient gel electrophoresis analyses. It is interesting to note that bacterial communities of Dahra soil were highly structured according to A. senegal provenance, whereas they were structured in relation to rhizobial inoculation in Goudiry soil. Besides, the impact of inoculation on soil microbial activities measured by fluorescein diacetate analyses varied in relation to plant provenance and soil origin. Nevertheless, total microbial activity was about two times higher in Goudiry, arid soil than in Dahra, semi-arid soil. Our results suggest that the rhizobial inoculation is a suitable tool for improving plants growth and soil fertility. Yet, the impact is dependent on inoculants, plant provenance and soil origin. It will, therefore, be crucial to identify the appropriate rhizobial strains and plant provenance or species in relation to the soil type.

Effects of inoculation with plant growth-promoting rhizobacteria on resident rhizosphere microorganisms

Plant growth-promoting rhizobacteria (PGPR) are exogenous bacteria introduced into agricultural ecosystems that act positively upon plant development. However, amendment reproducibility as well as the potential effects of inoculation upon plant root-associated microbial communities can be sources of concern. To address these questions, an understanding of mutual interactions between inoculants and resident rhizosphere microorganisms is required. Mechanisms used by PGPR can be direct or indirect; the former entails the secretion of growth regulators and the latter occurs through the production of antimicrobial compounds that reduce the deleterious effects of phytopathogens. The different modes of action may lead to different relationships between an inoculant and root microbial communities. Rhizobacterial communities are also affected by the plant, engineered genes, environmental stresses and agricultural practices. These factors appear to determine community structure more than an exogenous, active PGPR introduced at high levels.

Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest

The rainforest of French Guiana is still largely unaffected by human activity. Various pristine sites like the Paracou Research Station are devoted to study this tropical ecosystem. We used culture-independent techniques, like polymerase chain reaction-temperature gradient gel electrophoresis, and construction of clone libraries of partial 16S rRNA and nifH genes, to analyze the composition of the bacterial community in the rhizosphere of mature trees of Eperua falcata and Dicorynia guianensis, both species within the Caesalpiniaceae family. E. falcata is one of the more abundant pioneer tree species in this ecosystem and so far, no root nodules have ever been found. However, its nitrogen-fixing status is regarded as "uncertain", whereas D. guianensis is clearly considered a non-nitrogen-fixing plant. The rhizospheres of these mature trees contain specific bacterial communities, including several currently found uncultured microorganisms. In these communities, there are putative nitrogen-fixing bacteria specifically associated to each tree: D. guianensis harbors several Rhizobium spp. and E. falcata members of the genera Burkholderia and Bradyrhizobium. In addition, nifH sequences in the rhizosphere of the latter tree were very diverse. Retrieved sequences were related to bacteria belonging to the alpha-, beta-, and gamma-Proteobacteria in the E. falcata rhizoplane, whereas only two sequences related to gamma-Proteobacteria were found in D. guianensis. Differences in the bacterial communities and the abundance and diversity of nifH sequences in E. falcata rhizosphere suggest that this tree could obtain nitrogen through a nonnodulating bacterial interaction.

Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.

Long-term field release of bioluminescent Sinorhizobium meliloti strains to assess the influence of a recA mutation on the strains' survival

A field release experiment was carried out to study the fate of the isogenic, firefly luciferase (luc) gene-tagged Sinorhizobium meliloti strains L1 (RecA-) and L33 (RecA+) in the environment. Both strains were released at concentrations of approximately 10(6) cfu g(-1) soil in replicate and randomized field plots, which had been sown with alfalfa (Medicago sativa). The survival of both strains during the following 7 years could be subdivided into three phases: a sharp decline for more than two orders of magnitude within the first 4 months (phase I), followed by fluctuations around an average number of 10(4) cfu g(-1) soil for nearly 4 years (phase II), and a further decline to approximately 60 cfu g(-1) (phase III). At most sampling dates, no significant differences in the survival of both strains were detected, indicating that the recA gene function was dispensable under these environmental conditions. During the field inoculation, both strains were dispersed accidentally by wind in small numbers to noninoculated field plots. Strain L33 established at a concentration of more than 10(3) cfu g(-1) soil with subsequent seasonal fluctuations. Although strain L1 must have been disseminated to a similar extent, it could never be recovered from noninoculated field plots, indicating that the recA mutation interfered with the strain's capability to establish there. At the beginning of the field experiment, an indigenous alfalfa-nodulating population was below the limit of detection. In the following years, however, an indigenous population arose, which finally outcompeted both strains for saprophytic growth and alfalfa nodulation. RecA- strain L1 was outcompeted for alfalfa nodulation slightly faster than its RecA+ counterpart L33. The diversity of the indigenous population was characterized by employing the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction fingerprint method. Typing of 2731 root nodule isolates revealed a total of 38 fingerprint groups. More than 80% of the isolates could be grouped into six dominant fingerprint groups, indicating that a few dominant bacterial strain types had outcompeted the released strains.

Symbiotic microorganisms, a key for ecological success and protection of plants

Plant-associated microbial diversity encompasses symbionts, protecting their host against various aggressions. Mycorrhizal and rhizospheric microorganisms buffer effects of soil toxic compounds and soil-borne pathogens. Endophytic bacteria and fungi, some of which are vertically inherited through seeds, take part in plant protection by acting directly on aggressive factors (mainly pathogens and herbivores) or by enhancing plant responses. Plant protective microbial symbionts determine the ecological success of plants; they drastically modify plant communities and related trophic webs. This review suggests approaches to improve the inventory of diversity and functions of in situ plant-associated microorganisms.

Genetically modified bacteria in agriculture

Certain bacteria isolated from soils possess properties that allow them to exert beneficial effects on plants either by enhancing crop nutrition or by reducing damages caused by pathogens or pests. Some of them, such as rhizobia, azospirilla, and agrobacteria, have been traditionally released in fields as seed inoculants and they often lead to increases in the yield of different crops while the application of others, such as pseudomonads, often fails to give the expected results. Bacteria genetically modified to be easily traceable and/or to be improved in their expression of beneficial traits have been constructed and released with plants in a number of experimental field plots. With these releases, it has been possible to monitor the modified inoculant bacteria after their introduction in field ecosystems and to assess their impact on the resident microflora. Local environmental factors appeared as playing a crucial role in the survival and persistence of bacteria once released in fields and in the expression of the beneficial traits whether improved or not. The spread of inoculant bacteria from their point of dissemination was limited. Transient shifts in favour of the released bacteria and in disfavour of some members of the bacterial and fungal populations present in the plant rhizosphere might occur with certain released bacteria. The changes observed were, however, less important than those observed under usual agricultural practices. Gene transfer from resident population to introduced bacteria was detected in one case. The transconjugants were found only transiently in the phytosphere of plants but not in soils. No differences between the survival, spread, persistence in field and ecological impacts of genetically modified bacteria and of the corresponding unmodified parent strain could be detected.