Search

One of the most prevalent symbioses on Earth is that formed between the majority of land plants and arbuscular mycorrhizal (AM) fungi. Through these intimate associations, AM fungi transfer soil nutrients to their plant hosts in exchange for photosynthetically fixed carbon resources. It has been hypothesised that this nutritional mutualism is evolutionarily stable because both partners are in control of the exchange of resources and can discriminate between partners according to whichever offers the highest returns. However, in nature, plant–AM symbioses are exposed to a wealth of additional biotic and abiotic interactions which can affect the regulation of carbon‐for‐nutrient exchange between symbionts. Moreover, the extraradical hyphae of AM fungi make up underground networks that may be interactive or physically connected, known as common mycorrhizal networks (CMNs). These can link neighbouring plants, potentially further influencing resource distribution across the network. How these layers of complexity interact to influence resource regulation and allocation between plants and AM fungi is not often considered by experimental designs. Here, we review resource allocation in AM symbioses, scaling up from evidence from reductionist experimental systems using axenic root organ cultures to complex systems incorporating multiple neighbouring plants dealing with other, co‐occurring symbionts. As experimental designs increase in scale and ecologically relevant complexity, the carbon‐for‐nutrient exchange between plants and their AM symbionts is increasingly subject to disruption associated with the wider ecological context, such as the intricacies of the plant‐fungal interactions in a CMN or the presence of co‐occurring organisms. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The microbiodata of aphids by two PCR based methods that are terminal restriction fragment length polymorphism (T- RELP) and denaturing gradient gel electrophoresis (DGGE) analysis of amplified 165 rRNA gene fragments that are used widely for the analysis of microbial communities are investigated. The results indicate that the accessory bacterial taxa are distributed across multiple aphid species, although with variable prevalence and the laboratory culture does not generally result in a shift in the bacterial community in aphids.

The yields of spring barley during a medium-term (7 years) compost and slurry addition experiment and the soil carbon (C) and nitrogen (N) contents, bacterial community structure, soil microbial biomass and soil respiration rates have been determined to assess the effects of repeated, and in some cases very large, organic amendments on soil and crop parameters. For compost, total additions were equivalent to up to 119 t C/ha and 1·7 t N/ha and for slurry they were 25 t C/ha and 0·35 t N/ha over 7 years, which represented very large additions compared to control soil C and N contents (69 t C/ha and 0·3 t N/ha in the 0–30 cm soil depth). There was an initial positive response to compost and slurry addition on barley yield, but over the experiment the yield differential between the amounts of compost addition declined, indicating that repeated addition of compost at a lower rate over several years had the same cumulative effect as a large single compost application. By the end of the experiment it was clear that the addition of compost and slurry increased soil C and N contents, especially towards the top of the soil profile, as well as soil respiration rates. However, the increases in soil C and N contents were not proportional to the amount of C and N added, suggesting either that: (i) a portion of the added C and N was more vulnerable to loss; (ii) that its addition rendered another C or N pool in the soil more susceptible to loss; or (iii) that the C inputs from additional crop productivity did not increase in line with the organic amendments. Soil microbial biomass was depressed at the highest rate of organic amendment, and whilst this may have been due to genuine toxic or inhibitory effects of large amounts of compost, it could also be due to the inaccuracy of the substrate-induced respiration approach used for determining soil biomass when there is a large supply of organic matter. At the highest compost addition, the bacterial community structure was significantly altered, suggesting that the amendments significantly altered soil community dynamics. [ABSTRACT FROM PUBLISHER]

Attention is being paid to the use of different tillage regimes as a means of retaining soil organic carbon ( SOC) and sequestering more SOC. Alongside earlier measurements of total SOC stocks under different tillage regimes, we have examined the distribution of nitrogen ( N), microbial activity and the structure of the soil bacterial community from differently tilled plots under continuous barley. The plots were established 5 yr before sampling and have been maintained annually under conventional tillage ( CT; moldboard ploughing to 20 cm and disking), deep ploughing ( DP; ploughing to 40 cm and disking), minimum tillage ( MT; disking to 7 cm) or zero tillage ( ZT). Our earlier work showed there was no difference in SOC contents down to 60-cm depth between the treatments, but now we report that there were significant differences in the total N and active microbial biomass (substrate-induced respiration) contents of the same soils. The N contents of the CT, DP and MT treatments were not significantly different, but the ZT contained significantly more N, indicating either greater N retention under the ZT treatment or preferential loss from the more intensively tilled treatments, or a combination of both. The microbial biomass content was greater for the CT and DP treatments than for the MT and ZT treatments, indicating greater sensitivity to treatment effects of the microbial biomass pool than the total C pool, consistent with its more dynamic nature. Terminal restriction fragment length polymorphism ( T- RFLP) analyses of the soil bacteria DNA (a method of assessing the bacterial community structure) enabled the samples to be distinguished both according to SOC content, which is to be expected, and to tillage regime with the greatest differences in community structure occurring in the ZT treatment and the least in DP and CT treatments, reflecting the degree of homogenization or disturbance resulting from tillage. [ABSTRACT FROM AUTHOR]

Soil viruses are potentially of great importance as they may influence the ecology and evolution of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Despite this importance, the area of soil virology is understudied. Here, we report the isolation and preliminary characterisation of viruses from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod shaped, filamentous and bacilliform particles were detected in the soil samples. An apparent predominance of small spherical and filamentous bacteriophages was observed, whereas tailed bacteriophages were significantly less abundant. In this report, we also present observations and characterisation of viruses from different soil functional domains surrounding wheat roots: rhizosheath, rhizosphere and bulk soil. In spite of the differences in abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically, there were approximately 1.1–1.2 × 109 virions g−1 dry weight, implicating remarkable differences in virus-to-bacteria ratios in domains close to roots, rhizosphere and rhizosheath (approximately 0.27) and in bulk soil (approximately 4.68). [ABSTRACT FROM AUTHOR]

Application of polymerase chain reaction (PCR) techniques has developed significantly from a qualitative technology to include powerful quantitative technologies, including real-time PCR, which are regularly used for detection and quantification of nucleic acids in many settings, including community analysis where culture-based techniques are not suitable. Many applications of real-time PCR involve absolute quantification which is susceptible to inaccuracies caused by losses during DNA extraction or inhibition caused by co-extracted compounds. We present here an improvement to this approach involving the addition of an artificial internal standard, prior to nucleic acid extraction. The standard was generated by in-situ mutagenesis from an E. coli template to ensure it both did not amplify with bacterial primers used for quantification and was short enough to minimise possible interference with other analyses. By estimating gene target copies by relative abundance, this approach accounts for both loss during extraction and inhibition effects. We present a novel application of relative real time PCR, using the internal standard as a reference, allowing accurate estimation of total bacterial populations both within and across a wide range of soils and demonstrate its improvement over absolute quantification by comparison of both approaches to ester linked fatty acid analysis of the same soils., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Aims: To isolate, select, identify and assess the potential for the biodegradation of synthetic pyrethroids (SPs) in sheep dips., Methods and Results: SP-degrading bacteria were isolated from a mixed soil sample consisting of garden soil and soils from farms where SPs had been used. The two largest in size were then identified using microscopy, biochemical and genetic techniques to be members of the genera Pseudomonas and Serratia. By comparing the 16S rRNA gene sequences, the Pseudomonas sp. discovered was shown to group within the Pseudomonas fluorescens intrageneric cluster. The Serratia isolated was closely related to Serratia plymuthica. Cell growth and degradation was greatest in the Pseudomonas sp. culture where there was breakdown of 60 mg l(-1) to 6 mg l(-1) technical cypermethrin in 20 days. Tolerance to the SPs was greater in the Pseudomonas sp. but was found to depend on the availability of other carbon sources and nutrients., Conclusions: The bacteria characterized show the potential to be used in a bioremediation application for the treatment of SP residues., Significance and Impact of the Study: The SP-degrading bacteria may have use in the disposal of used SP residues and with further research could lead to an alternative route of disposal for use in agriculture or industry.

In order to determine why the activated methyl cycle is up-regulated in plants undergoing defence responses to fungal pathogens we have monitored the utilisation of methyl groups derived from methionine in cell-suspension cultures of alfalfa (Medicago sativa L.) treated for various times with fungal elicitor, by carrying out a parallel labelling study with [(35)S]methionine and [methyl-(3)H]methionine. The distribution of the two radiolabels among the medium, soluble cellular components and cell wall was then determined. In the absence of elicitor the utilisation of the two radiolabels was similar. However, in the presence of the elicitor the total incorporation of radioactivity from [methyl-(3)H]methionine into metabolites was far greater than from [(35)S]methionine, indicating that the methyl label had been utilised in methylation reactions. Elicitor treatment resulted in up to a sixfold increase in the use of (3)H-methyl groups in the methylation of hydrophobic metabolites. In the period 0-24 h after elicitor treatment, increased methylation was directed largely into the synthesis of the isoflavonoid phytoalexin medicarpin and related metabolites. Newly synthesized phytoalexins were exported into the medium, while a significant proportion of the medicarpin accumulating in the cell in the early stages of elicitation was derived from the hydrolysis of its respective conjugate. Elicitor treatment also modified the incorporation of (3)H-methyl groups into the cell wall. Between 0 and 24 h after elicitor treatment the methylation of pectin in the cell wall declined. After 24 h, pectin methylation recovered and was associated with an increase in the methylation of other wall-bound polysaccharide components. Since no other major metabolic sink for the increased methylation was determined we conclude that the increased activity of the activated methyl cycle during defence interactions in alfalfa is required to support phytoalexin synthesis and cell wall modifications.