Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

In both managed and natural ecosystems, beneficial plant-associated bacteria play a key role in supporting and/or increasing plant health and growth. Plant growth-promoting bacteria (PGPB) can be applied in agricultural production or for the phytoremediation of pollutants. However, because of their capacity to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. The majority of plant-associated bacteria derives from the soil environment. They may migrate to the rhizosphere and subsequently the rhizoplane of their hosts before they are able to show beneficial effects. Some rhizoplane colonizing bacteria can also penetrate plant roots, and some strains may move to aerial plant parts, with a decreasing bacterial density in comparison to rhizosphere or root colonizing populations. A better understanding on colonization processes has been obtained mostly by microscopic visualisation as well as by analysing the characteristics of mutants carrying disfunctional genes potentially involved in colonization. In this review we describe the individual steps of plant colonization and survey the known mechanisms responsible for rhizosphere and endophytic competence. The understanding of colonization processes is important to better predict how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilisers or biocontrol agents.     

A new approach to trenching experiments for measuring root-rhizosphere respiration in a lowland tropical forest

Soil respiration in tropical forests is a major source of atmospheric CO₂. The ability to partition soil respiration into its individual components is becoming increasingly important to predict the effects of disturbance on CO₂ efflux from the soil as the responses of heterotrophic and autotrophic respiration to change are likely to differ. However, current field methods to partition respiration suffer from various methodological artefacts; root-rhizosphere respiration is particularly difficult to estimate. We used trenched subplots to estimate root-rhizosphere respiration in large-scale litter addition (L+), litter removal (L−) and control (CT) plots in a lowland tropical semi-evergreen forest in Panama. We took a new approach to trenching by making measurements immediately before-and-after trenching and comparing them to biweekly measurements made over one year. Root-rhizosphere respiration was estimated to be 38%, 17% and 27% in the CT, L+, and L− plots, respectively, from the measurements taken immediately before and one day after trenching in May-June 2007. Biweekly measurements over the following year provided no estimates of root-rhizosphere respiration for the first seven months due to decomposition of decaying roots. We were also unable to estimate root-rhizosphere respiration during the dry season due to differences in soil water content between trenched and untrenched soil. However, biweekly measurements taken during the early rainy season one year after trenching (May-June 2008) provided estimates of root-rhizosphere respiration of 39%, 24% and 36% in the CT, L+, and L− plots, respectively, which are very similar to those obtained during the first day after trenching. We suggest that measurements taken immediately before and one day after root excision are a viable method for a rapid estimation of root-rhizosphere respiration without the methodological artefacts usually associated with trenching experiments.     

Priming effects: Interactions between living and dead organic matter

In this re-evaluation of our 10-year old paper on priming effects, I have considered the latest studies and tried to identify the most important needs for future research. Recent publications have shown that the increase or decrease in soil organic matter mineralization (measured as changes of CO₂ efflux and N mineralization) actually results from interactions between living (microbial biomass) and dead organic matter. The priming effect (PE) is not an artifact of incubation studies, as sometimes supposed, but is a natural process sequence in the rhizosphere and detritusphere that is induced by pulses or continuous inputs of fresh organics. The intensity of turnover processes in such hotspots is at least one order of magnitude higher than in the bulk soil. Various prerequisites for high-quality, informative PE studies are outlined: calculating the budget of labeled and total C; investigating the dynamics of released CO₂ and its sources; linking C and N dynamics with microbial biomass changes and enzyme activities; evaluating apparent and real PEs; and assessing PE sources as related to soil organic matter stabilization mechanisms. Different approaches for identifying priming, based on the assessment of more than two C sources in CO₂ and microbial biomass, are proposed and methodological and statistical uncertainties in PE estimation and approaches to eliminating them are discussed. Future studies should evaluate directions and magnitude of PEs according to expected climate and land-use changes and the increased rhizodeposition under elevated CO₂ as well as clarifying the ecological significance of PEs in natural and agricultural ecosystems. The conclusion is that PEs - the interactions between living and dead organic matter - should be incorporated in models of C and N dynamics, and that microbial biomass should regarded not only as a C pool but also as an active driver of C and N turnover.     

Dealing with the variability in biofumigation efficacy through an epidemiological framework

Biofumigation, as originally defined, is the use, in agriculture, of the toxicity of Brassica crop residues to control soilborne plant pathogens. This toxicity is specifically attributed to the release of toxic isothiocyanates, through the hydrolysis of glucosinolates present in the crop residues. This technique is considered a possible alternative to the use of pesticides, but field studies have generated conflicting data concerning the efficacy of biofumigation at field scale, limiting the use of this technique. Analytical studies based on a systematic approach involving evaluation of the potential effects of isothiocyanates can be used to address this problem in a rigorous manner. However, many recent studies have indicated that the mechanisms underlying biofumigation are much more complex than a simple toxic effect of residues. In this review, we dissect and discuss the problems encountered when trying to understand the variability in biofumigation efficacy and propose an integrative epidemiological approach to overcome these problems. This approach involves separating the effects of the different parameters of the system, such as the effects of different management phases of the biofumigant crop (i.e. the period of biofumigant crop growth and the phase during which crop residues are pulverised and incorporated into the soil) on the epidemiological mechanisms driving the development of an epidemic (density of primary inoculum and dynamics of disease progression). Finally, we propose new avenues of research into biofumigation in which the use of epidemiological tools and methods may improve our understanding of the factors underlying variation in the efficacy of biofumigant crops.     

三七根际链霉菌Streptomyces sp. YNUCC0233木聚糖酶性质研究

从三七根际分离到一株产木聚糖酶链霉菌Streptomycessp.YNUCC0233。该菌所产生的木聚糖酶的最适反应温度为67℃,最适pH为6.0,在pH5.0~9.0和60℃以下时相对稳定。Ba2+和K+对该木聚糖酶有较强的促进作用,Hg2+、Cu2+、Mn2+、Co2+、Ni2+和EDTA对该酶有较强的抑制作用。对Streptomycessp.YNUCC023316SrDNA的1105bp片段的序列分析结果表明,Streptomycessp.YNUCC0233的16SrDNA片段与GenBank中所有已注册的链霉菌分类单位均不同。     

Belowground interactions between intercropped wheat and Brassicas in acidic and alkaline soils

Our previous studies showed that, under P-limiting conditions, growth and P uptake were lower in the wheat genotype Janz than in three Brassica genotypes when grown in monoculture. The present study was conducted to answer the question if P mobilised by the Brassicas is available to wheat; leading to improved growth of wheat when intercropped with Brassicas compared to monocropped wheat. To assess if the interactions between the crops depend on soil type, the wheat genotype Janz and three Brassica genotypes (two canolas and one mustard) were grown for 6 weeks in monoculture or wheat intercropped with each Brassica genotype in an acidic and an alkaline soil with low P availability (with two plants per pot). Wheat grew equally well in the two soils, but the Brassicas grew better in the acidic than in the alkaline soil. In the acidic soil, monocropped Brassicas had a 3 to 4 fold greater plant dry weight (dw) and P uptake than wheat; plant dw and P uptake in wheat were decreased or not affected by intercropping and increased in the Brassicas. In the alkaline soil, dw and P uptake of the Brassicas was twice as high as in wheat, with intercropping having no effect on these parameters. The contribution of wheat to the total shoot dw and P uptake per pot was 4-21% and 32-40% in acidic and alkaline soil, respectively. Mycorrhizal colonisation was low in all genotypes in the acidic soil (1-6%). In the alkaline soil, mycorrhizal colonisation of monocropped wheat was 62%, but only 43-47% in intercropped wheat. Intercropping decreased P availability in the rhizosphere of wheat in the acidic soil but had no effect on rhizosphere P availability in the alkaline soil. Intercropping had a variable effect on rhizosphere microbial community composition (assessed by fatty acid methylester analysis (FAME) and ribosomal intergenic spacer amplification (RISA)), ranging from intercropping having no effect on the rhizosphere communities to intercropping resulting in a new and similar rhizosphere community composition in both genotypes. The results of this study show that intercropping with Brassicas does not improve growth and P uptake of wheat; thus there is no indication that P mobilised by the Brassicas is available to wheat.     

Pyruvate dehydrogenase activity is important for colonization of seeds and roots by Enterobacter cloacae

Enterobacter cloacae is a plant-beneficial bacterium that shows promise for suppression of damping-off of cucumber and other crops caused by Pythium ultimum. We have been using a mutational approach to determine the E. cloacae genes important in bacterial-plant and bacterial-pathogen interactions in the spermosphere and rhizosphere. E. cloacae M43 is a transposon mutant of E. cloacae 501R3 that was significantly impaired in colonization of seeds and roots of diverse crop plants. Strain M43 did not increase in population on cucumber, sunflower, and wheat seeds and was significantly reduced in growth on pea seeds relative to strain 501R3. Populations of M43 were also dramatically lower than those of strain 501R3 in cucumber, pea, sunflower, and wheat rhizosphere in 42 d experiments. Molecular characterization of M43 demonstrated that there was a single transposon insertion in the genome of this strain and that this insertion was in a region of the E. cloacae genome with a high degree of DNA sequence identity with aceF. aceF encodes the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex (PDHC). Cell lysates from strain 501R3 grown on minimal medium plus 50 mM glycerol and 2 mM acetate contained 0.011±0.0036 U pyruvate dehydrogenase activity while cell lysates from M43 grown under identical conditions contained no detectable pyruvate dehydrogenase activity. Additionally, the nutritional use profile of M43 under aerobic and anaerobic conditions was as expected for an ace mutant. Experiments reported here strongly suggest a role for aceF and the PDHC in colonization of seeds and roots of diverse crop plants by E. cloacae.     

Nitrogen fixation by Azospirillium brasilense in soil and the rhizosphere under controlled environmental conditions

Summary Acetylene reduction activity by Azospirillum brasilense, either free-living in soils or associated with wheat roots, was determined in a sterilised root environment at controlled levels of O₂ tension and with different concentrations of mineral N. In an unplanted, inoculated soil nitrogenase activity remained low, at approximately 40 nmol C₂H₄ h^-1 per 2kg fresh soil, increasing to 300 nmol C₂H₄ h^-1 when malic acid was added as a C source via a dialyse tubing system. The N₂ fixation by A. brasilense in the rhizosphere of an actively growing plant was much less sensitive to the repressing influence of free O₂ than the free-living bacteria were. An optimum nitrogenase activity was observed at 10 kPa O₂, with a relatively high level of activity remaining even at an O₂ concentration of 20 kPa. Both NO _inf3 ^sup- and NH _inf4 ^sup+ repressed nitrogenase activity, which was less pronounced in the presence than in the absence of plants. The highest survival rates of inoculated A. brasilense and the highest rates of acetylene reduction were found in plants treated with azospirilli immediately after seedling emergence. Plants inoculated at a later stage of growth showed a lower bacterial density in the rhizosphere and, as a consequence, a lower N₂-fixing potential. Subsequent inoculations with A. brasilense during plant development did not increase root colonisation and did not stimulate the associated acetylene reduction. By using the ¹⁵N dilution method, the affect of inoculation with A. brasilense in terms of plant N was calculated as 0.067 mg N₂ fixed per plant, i.e., 3.3% of the N in the root and 1.6% in the plant shoot were of atmospheric origin. This ¹⁵N dilution was comparable to that seen in plants inoculated with non-N₂-fixing Psudomonas fluorescens.     

Growth,P uptake and rhizosphere properties of wheat and canola genotypes in an alkaline soil with low P availability

The aim of the present study was to assess the role of soil type on growth, P uptake and rhizosphere properties of wheat and canola genotypes in an alkaline soil with low P availability. Two wheat (Goldmark and Janz) and two canola genotypes (Drum and Outback) were grown in a calcareous soil (pH 8.5) at two P levels [no P addition (0P) or addition of 200 mg kg⁻¹ P as Ca₃(PO₄)₂ (200P)] and harvested at flowering or maturity. Shoot and root dry weight, root length and shoot P content were greater in the two canola genotypes than in wheat. There were no consistent differences in available P, microbial P and phosphatase activity in the rhizosphere of the different genotypes. Shoot P content was significantly positively correlated with root length, pH and phosphatase activity in the rhizosphere. The microbial community composition, assessed by fatty acid methylester analysis, of the canola genotypes differed strongly from that of the wheat genotypes. The weight percentage bacterial fatty acids, the bacteria/fungi (b/f) ratio and the diversity of fatty acids were greater in the rhizosphere of the canolas than in the rhizosphere of the wheat genotypes. In contrast to the earlier studies in an acidic soil, only small differences in growth and P uptake between the genotypes of one crop were detected in the alkaline soil used here. The results confirmed the importance of root length for P uptake in soils with low P availability and suggest that the rhizosphere microbial community composition may play a role in the better growth of the canola compared to the wheat genotypes.