Petra Marschner

Soil and plant specific effects on bacterial community composition in the rhizosphere

Eubacterial community structures in the plant rhizosphere were examined with respect to plant species, soil type, and root zone location. Three plant species (chickpea, rape and Sudan grass) were grown in intact cores of three California soils (a sandy soil, a sandy loam, and a clay) and were provided with a complete fertilizer solution with or without nitrogen supplied as ammonium nitrate. After 7.5 weeks, the plants were harvested and DNA was extracted from soil adhering to the root tips and from mature root zones at the sites of lateral root emergence. Eubacterial community structures were examined by PCR-DGGE of 16S rDNA to determine the relative abundance and species diversity. While both soil type and nitrogen fertilization affected plant growth, canonical correspondence analyses showed that nitrogen had no significant effect on eubacterial community structures. Eubacterial species diversity was higher in the mature root zones than at the root tips in the sandy soil and the clay but not in the loamy sand. Monte Carlo permutation tests indicated that plant species, root zone and soil type as well as the interactions between these variables had significant effects on community structure. The bacterial rhizosphere community of chickpea was influenced primarily by soil type, whereas root zone was less important. In contrast to chickpea, the community in the rhizosphere of rape and Sudan grass was more affected by the root zone than the soil type. In the sandy soil and the loamy sand, the eubacterial rhizosphere community structure was more affected by the root zone than the plant species and the three plant species had distinct communities. In the clay however, the root zone was less important than the plant species and the rhizosphere communities of chickpea differed from those of rape and Sudan grass. It is concluded that the bacterial community composition in the rhizosphere is affected by a complex interaction between soil type, plant species and root zone location.

Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type

Rhizosphere microbial communities are important for plant nutrition and plant health. Using the culture-independent method of PCR-DGGE of 16S rDNA for community analyses, we conducted several experiments to investigate the importance of pH, soil type, soil amendment, nutritional status of the plant, plant species and plant age on the structure of the bacterial community in the rhizosphere. At the same time, we assessed the spatial variability of bacterial communities in different root zone locations. Our results showed that the bacterial community structure is influenced by soil pH and type of P fertilization. In a short-term experiment (15–22 days) with cucumber and barley growing in a N deficient or a P deficient soil, the bacterial community structure in the rhizosphere was affected by soil type and fertilization but not by plant species. In a 7.5-week experiment with three plant species (chickpea, canola, Sudan grass) growing in three different soils (a sand, a loam and a clay), the complex interactions between soil and plant effects on the rhizosphere community were apparent. In the sand and the loam, the three plant species had distinct rhizosphere communities while in the clay soil the rhizosphere community structures of canola and Sudan grass were similar and differed from those of chickpea. In all soils, the rhizosphere community structures of the root tip were different from those in the mature root zone. In white lupin, the bacterial community structure of the non-cluster roots differed from those of the cluster roots. As plants matured, different cluster root age classes (young, mature, old) had distinct rhizosphere communities. We conclude that many different factors will contribute to shaping the species composition in the rhizosphere, but that the plant itself exerts a highly selective effect that is at least as great as that of the soil. Root exudate amount and composition are the key drivers for the differences in community structure observed in this study.

Changes in bacterial community structure induced by mycorrhizal colonisation in split-root maize

Maize plants were grown in an autoclaved quartz sand–soil mix to which the bacterial communities of the soil and the mycorrhizal inocula were reintroduced. The root systems of the plants were divided with the two halves growing in separate pots. There were five different treatments: plants with both root halves non-mycorrhizal either at high or low P availability (nm-nm HP and nm-nm LP) or mycorrhizal plants grown at low P availability with one side of the root system non-mycorrhizal while the other side was inoculated with Glomus intraradices (GI-nm) or G. mosseae (GM-nm) or plants with both sides mycorrhizal but each side inoculated with a different fungus (GI–GM). The plants were harvested after 3 or 6 weeks. Shoot dry weight and shoot P concentration of the nm-nm HP plants were always higher than the plants grown at low P supply. Acid phosphatase activity in the rhizosphere was similar in all treatments and did not change over time. However, after 6 weeks alkaline phosphatase activity was higher in the rhizosphere of both root halves in the mycorrhizal plants as compared to the non-mycorrhizal plants. Mycorrhizal colonisation increased from 15–34% after 3 weeks to 78–87% after 6 weeks with no significant difference between GI and GM. The bacterial community structure, assessed by denaturing gradient gel electrophoresis (DGGE), changed over time and was specific for each of the three compartments, non-rhizosphere soil, rhizosphere soil and root surface. While the two P levels in the non-mycorrhizal treatments had no significant effect on the bacterial communities, mycorrhizal colonisation changed the bacterial community structure on the root surface and in the non-rhizosphere soil. The bacterial communities of the GI–GM plants differed more from the non-mycorrhizal plants than those of the plants with only one half of the root system mycorrhizal. The bacterial communities of both root halves of the GI-nm plants did not differ from each other and were very similar to those of the non-mycorrhizal plants. After 3 weeks, the bacterial communities of the two sides of the GM-nm plants differed: the mycorrhizal side of the resembled that of the GI–GM plants, while the non-mycorrhizal side of the root system was similar to that of the nm-nm plants. However after 6 weeks, the bacterial community structures of the two sides of the root system of the GM-nm plants were similar and differed from those of the nm-nm plants. It is concluded that the effect of mycorrhizal colonisation on the bacterial community structure in the rhizosphere may, at least in part, be plant-mediated.

Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.)

White lupin was grown in a quartz sand–soil mix with poorly available Ca phosphate. The plants were harvested on days 21, 35 and 51 and DNA was extracted from the non-cluster roots, the young, mature and senescent cluster roots with adhering soil. Bacterial community structure was examined by PCR-DGGE of 16S rDNA, digitisation of the band patterns and multivariate analyses. In all root zones the bacterial community structure changed with plant age. The communities in the rhizosphere of the non-cluster roots were always different from those of the cluster roots. The bacterial communities of the cluster roots were cluster age and plant age dependent. The differences in bacterial community structure between the cluster root age classes were significant on days 35 and day 51 but not on d 21. A separate experiment, in which root exudates and samples for PCR-DGGE were collected simultaneously, showed that both bacterial and eukaryotic (18S rDNA) community structures change with organic acid exudation. While eukaryotic community structure of the cluster roots was correlated with citric acid exudation, bacterial community structure was correlated with cis-acconitic, citric and malic acid exudation.

Isolation of culturable phosphobacteria with both phytate-mineralization and phosphate-solubilization activity from the rhizosphere of plants grown in a volcanic soil

Chilean volcanic soils contain large amounts of total and organic phosphorus, but P availability is low. Phosphobacteria [phytate-mineralizing bacteria (PMB) and phosphate-solubilizing bacteria (PSB)] were isolated from the rhizosphere of perennial ryegrass (Lolium perenne), white clover (Trifolium repens), wheat (Triticum aestivum), oat (Avena sativa), and yellow lupin (Lupinus luteus) growing in volcanic soil. Six phosphobacteria were selected, based on their capacity to utilize both Na-phytate and Ca-phosphate on agar media (denoted as PMPSB), and characterized. The capacity of selected PMPSB to release inorganic P (Pi) from Na-phytate in broth was also assayed. The results showed that from 300 colonies randomly chosen on Luria–Bertani agar, phosphobacteria represented from 44% to 54% in perennial ryegrass, white clover, oat, and wheat rhizospheres. In contrast, phosphobacteria represented only 17% of colonies chosen from yellow lupin rhizosphere. This study also revealed that pasture plants (perennial ryegrass and white clover) have predominantly PMB in their rhizosphere, whereas PSB dominated in the rhizosphere of crops (oat and wheat). Selected PMPSB were genetically characterized as Pseudomonas, Enterobacter, and Pantoea; all showed the production of phosphoric hydrolases (alkaline phosphatase, acid phosphatase, and naphthol phosphohydrolase). Assays with PMPSB resulted in a higher Pi liberation compared with uninoculated controls and revealed also that the addition of glucose influenced the Pi-liberation capacity of some of the PMPSB assayed.

Nutrient Cycling in Terrestrial Ecosystems

Principles of Nutrient Cycling.- Composition and Cycling of Organic Carbon in Soil.- The Nitrogen Cycle in Terrestrial Ecosystems.- Phosphorus and Sulphur Cycling in Terrestrial Ecosystems.- Cycling of Micronutrients in Terrestrial Ecosystems.- Root Exudates and Nutrient Cycling.- Plant-Microbe Interactions in the Rhizosphere and Nutrient Cycling.- Nutrient Cycling Budgets in Terrestrial Ecosystems.- The Role of Crop Residues in Improving Soil Fertility.- Nutrient Cycling Budgets in Managed Pastures.- Natural Grasslands - a Case Study in Greece.- Dryland Ecosystems.- Nutrient Cycling in the Tundra.- Nutrient Cycling in Forests and Heathlands: an Ecosystem Perspective from the Water-Limited South.- Modelling Nitrogen and Phosphorus Cycling in Agricultural Systems at Field and Regional Scales.

Microbial community composition and functional diversity in the rhizosphere of maize

This study investigates the small-scale stratification of bacterial community composition and functional diversity in the rhizosphere of maize. Maize seedlings were grown in a microcosm with a horizontal mesh (53 μM) creating a planar root mat and rhizosphere soil. An unplanted microcosm served as control. Thin slices of soil were cut at different distances from the mesh surface (0.2–5.0 mm) and analysed for bacterial community composition by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rDNA and tested for activities of different enzymes involved in C, N, P and S cycling. Bacterial community composition and microbial functional diversity were affected by the presence of the maize roots. The bacterial composition showed a clear gradient up to 2.2 mm from the root surface, while no such gradient was observed in the unplanted pot. Invertase and phosphatase activities were higher in the close vicinity of maize roots (0.2–0.8 mm), whereas xylanase activity was unaffected. This study shows that the changes in bacterial community composition and functional diversity induced by roots may extend several millimetres into the soil.

Root exudation and physiological status of a root-colonizing fluorescent pseudomonad in mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L.)

The effect of mycorrhizal infection on root exudation and the survival and physiological status of a bioluminescent fluorescent pseudomonad on the roots of pepper was examined. Pepper plants were grown for 27 days in split-root microcosms with one side mycorrhizal with Glomus deserticola (GD) or Glomus intraradices (GI) while the other side was non-mycorrhizal. Plants with both sides non-mycorrhizal served as controls. The soil was inoculated with a bioluminescent fluorescent pseudomonad (P. fluorescens 2-79RL). This strain emits light in its exponential growth phase, such that the length of the lag phase prior to bioluminescence can be used to assess the physiological status of the bacterium. Mycorrhizal infection had no significant effect on plant growth. The percent root length infected was 8% for GD and 34% for GI. After pulse-labeling of the shoots with 14CO2, quartz filter strips were used to collect 14C labeled root exudates at specific locations on the roots. Compared with the non-mycorrhizal roots, GI decreased 14C labeled root exudation by 78% at the root tip and by 50% at the older root parts. GD had no effect on 14C labeled root exudation. Rhizosphere soil solutions collected with quartz filter strips were analyzed for amino acids and organic acids by GC-MS. The overall pattern of the chromatograms of the rhizosphere soil solution was similar in the non-mycorrhizal and the mycorrhizal roots. The number of peaks detected was higher in the non-mycorrhizal roots than in the mycorrhizal roots. Compared with the non-mycorrhizal plants, GI decreased the population density of P. fluorescens 2-79RL on the roots by one order of magnitude, both on the mycorrhizal and the non-mycorrhizal side. GD decreased the population density by one order of magnitude only on the side where the fungus was present. The physiological status of P. fluorescens 2-79RL on the roots, as measured by the length of the lag phase prior to bioluminescence, decreased significantly from day 3 to day 6 and remained at a similar level thereafter. Mycorrhizal infection had little effect on the physiological status. Compared to the non-mycorrhizal plants, GI increased the physiological status of P. fluorescens 2-79RL only during the first 6 days, while GD had no effect at all. It is concluded that mycorrhizal infection may decrease root exudation and alter the composition of the rhizosphere soil solution, thereby reducing the population density of certain bacterial groups in the rhizosphere.

Effect of intercropping on crop yield and chemical and microbiological properties in rhizosphere of wheat (Triticum aestivum L.), maize (Zea mays L.), and faba bean (Vicia faba L.)

In this study, we investigated crop yield and various chemical and microbiological properties in rhizosphere of wheat, maize, and faba bean grown in the field solely and intercropped (wheat/faba bean, wheat/maize, and maize/faba bean) in the second and third year after establishment of the cropping systems. In both years, intercropping increased crop yield, changed N and P availability, and affected the microbiological properties in rhizosphere of the three species compared to sole cropping. Generally, intercropping increased microbial biomass C, N, and P availability, whereas it reduced microbial biomass N in rhizosphere of wheat. The rhizosphere bacterial community composition was studied by denaturing gradient gel electrophoresis of 16S rRNA. In the third year of different cropping systems, intercropping significantly changed bacterial community composition in rhizosphere compared with sole cropping, and the effects were most pronounced in the wheat/faba bean intercropping system. The effects were less pronounced in the second year. The results show that intercropping has significant effects on microbiological and chemical properties in the rhizosphere, which may contribute to the yield enhancement by intercropping.

Growth response of Atriplex nummularia to inoculation with arbuscular mycorrhizal fungi at different salinity levels

Chenopods are generally regarded as non-host plants for mycorrhizal fungi and are believed not to benefit from colonization by mycorrhizal fungi. Perennial Atriplex nummularia Lindl., growing under field conditions, showed a relatively high level of colonization by mycorrhizal fungi (10–30% of root length colonized) in spring and summer. Accordingly, two glasshouse experiments were designed to assess the effects of inoculation with mycorrhizal fungi (with a single species or a mixture of different species) on growth, nutrient uptake, and rhizosphere bacterial community composition of A. nummularia at high and low salinity levels (2.2 and 12 dSm−1). Only low and patchy colonization by mycorrhizal fungi (1–2 of root length colonized) was detected in inoculated plants under glasshouse conditions which was unaffected by salinity. Despite the low colonization, inoculation increased plant growth and affected nutrient uptake at both salinity levels. The effects were higher at an early stage of plant development (6 weeks) than at a later stage (9–10 weeks). Salinity affected the bacterial community composition in the rhizosphere as examined by ribosomal intergenic spacer amplification (RISA) of 16S rDNA, digitization of the band patterns and multivariate analysis. The effects of inoculation with mycorrhizal fungi on growth of A. nummularia may be attributed to (i) direct effects of mycorrhizal fungi on plant nutrient uptake and/or (ii) indirect effects via mycorrhizal-induced changes in the bacterial community composition.