Effects of genetically modified plants on microbial communities and processes in soil

The development and use of genetically modified plants (GMPs) has been a topic of considerable public debate in recent years. GMPs hold great promise for improving agricultural output, but the potential for unwanted effects of GMP use is still not fully understood. The majority of studies addressing potential risks of GMP cultivation have addressed only aboveground effects. However, recent methodological advances in soil microbial ecology have allowed research focus to move underground to try to gain knowledge of GMP-driven effects on the microbial communities and processes in soil that are essential to key terrestrial ecosystem functions. This review gives an overview of the research performed to date on this timely topic, highlighting a number of case studies. Although such research has advanced our understanding of this topic, a number of knowledge gaps still prevent full interpretation of results, as highlighted by the failure of most studies to assign a definitively negative, positive or neutral effect to GMP introduction. Based upon our accumulating, yet incomplete, understanding of soil microbes and processes, we propose a synthesis for the case-by-case study of GMP effects, incorporating assessment of the potential plant/ecosystem interactions, accessible and relevant indicators, and tests for unforeseen effects.     

Microbial community responses to disease management soil treatments used in flower bulb cultivation

Biology and Fertility of Soils - A number of management practices, such as soil fumigation and flooding, have been employed in efforts to control diseases and weeds in the cultivation of ornamental...     

Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis

Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to show that plants can detect, discriminate, and reward the best fungal partners with more carbohydrates. In turn, their fungal partners enforce cooperation by increasing nutrient transfer only to those roots providing more carbohydrates. On the basis of these observations we conclude that, unlike many other mutualisms, the symbiont cannot be "enslaved." Rather, the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.     

Rhizosphere fungal communities are influenced by Senecio jacobaea pyrrolizidine alkaloid content and composition

The contents and the compositions of the pyrrolizidine alkaloid (PA) complex of ragwort (Senecio jacobaea L.) were examined as potential drivers of fungal community structure in the rhizosphere. S. jacobaea plants within the coastal sand dune reserve of Meijendel (the Netherlands) were assayed for concentration and composition of PAs in roots. Rhizosphere soil was collected from pre-flowering plants, which differed up to 8-fold in PA production, and represented both jacobine and senecionine/seneciphylline chemotypes. Bulk soil samples from the same site were also collected for comparative examination. A culture-independent approach, involving direct DNA isolation, PCR of fungal 18S rRNA genes, and denaturing gradient gel electrophoresis (DGGE), was applied to compare the fungal communities of plants with different PA contents, as well as differences between bulk and rhizosphere samples. Cluster analysis of PCR-DGGE profiles revealed no clear evidence for PA-induced selection of specific fungal communities. However, canonical variance analysis showed that fungal communities associated with high-PA jacobine chemotypes could be discriminated from low PA samples and from the senecionine/seneciphylline chemotypes. The diversity of DGGE banding patterns, both in terms of band number and evenness, showed a trend toward lower diversity in the rhizosphere of high-PA plants as compared to low-PA plants and bulk soil. These results indicate that PA chemotypes of S. jacobaea differ in their influence on soil-borne fungal communities, with jacobine-containing plants exerting a greater selection in the rhizosphere than plants containing senecionine/seneciphylline.     

Climate change goes underground: effects of elevated atmospheric CO<Subscript>2</Subscript> on microbial community structure and activities in the rhizosphere

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO₂ in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO₂ may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO₂ on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO₂ concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO₂ on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO₂ on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions.     

Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition

The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.     

Links between pseudometallophytes and rhizosphere microbial communities in a metalliferous soil

Short-term improvements in soil health derived from pseudometallophytes growth and metal phytoremediation were quantified based upon specific microbial properties of potential value as bioindicators of soil functioning. To this aim, plant consortia, consisting of 1–3 pseudometallophytes with different metal-tolerance strategies (hyperaccumulator: Noccaea caerulescens; accumulator: Rumex acetosa; excluder: Festuca rubra), were grown in a mine soil. At the end of the experiment, soil microbial biomass, activity, structural and functional community profiling, and stability were determined. Growing together with N. caerulescens stimulated the growth of the other two pseudometallophytes. The combination of R. acetosa and N. caerulescens extracted the highest amounts of Zn. Except for β-glucosidase, a negative correlation was found between enzyme activities and number of pseudometallophytes present in the study pots. Microbial biomass C was highest in the presence of all three pseudometallophytes. The combination of different pseudometallophyte species, which may allow for a greater exploitation of potential niche space, appears promising for phytoremediation. When quantifying soil health, the importance of measuring various types of soil microbial properties has been highlighted, as the response observed was different in each of them.