Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability

Aims: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). Methods: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. Results: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. Conclusions: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture.

The Representative Soil Sampling Scheme of England and Wales: a statistical analysis of topsoil nutrient status and pH between 1971 and 2001

The Representative Soil Sampling Scheme of England and Wales has recorded information on the soil of agricultural land in England and Wales since 1969. It is a valuable source of information about the soil in the context of monitoring for sustainable agricultural development. Changes in soil nutrient status and pH were examined over the period 1971-2001. Several methods of statistical analysis were applied to data from the surveys during this period. The main focus here is on the data for 1971, 1981, 1991 and 2001. The results of examining change over time in general show that levels of potassium in the soil have increased, those of magnesium have remained fairly constant, those of phosphorus have declined and pH has changed little. Future sampling needs have been assessed in the context of monitoring, to determine the mean at a given level of confidence and tolerable error and to detect change in the mean over time at these same levels over periods of 5 and 10 years. The results of a non-hierarchical multivariate classification suggest that England and Wales could be stratified to optimize future sampling and analysis. To monitor soil quality and health more generally than for agriculture, more of the country should be sampled and a wider range of properties recorded.

The spatial prediction of soil mineral N and potentially available N using elevation

The precision farmer wants to manage the variation in soil nutrient status continuously, which requires reliable predictions at places between sampling sites. Ordinary kriging can be used for prediction if the data are spatially dependent and there is a suitable variogram model. However, even if data are spatially correlated, there are often few soil sampling sites in relation to the area to be managed. If intensive ancillary data are available and these are coregionalized with the sparse soil data, they could be used to increase the accuracy of predictions of the soil properties by methods such as cokriging, kriging with external drift and regression kriging. This paper compares the accuracy of predictions of the plant available N properties (mineral N and potentially available N) for two arable fields in Bedfordshire, United Kingdom, from ordinary kriging, cokriging, kriging with external drift and regression kriging. For the last three, intensive elevation data were used with the soil data. The mean squared errors of prediction from these methods of kriging were determined at validation sites where the values were known. Kriging with external drift resulted in the smallest mean squared error for two of the three properties examined, and cokriging for the other. The results suggest that the use of intensive ancillary data can increase the accuracy of predictions of soil properties in arable fields provided that the variables are related spatially. (c) 2005 Elsevier B.V. All rights reserved.

Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands

1 Plant species differ in their capacity to influence soil organic matter, soil nutrient availability and the composition of soil microbial communities. Their influences on soil properties result in net positive or negative feedback effects, which influence plant performance and plant community composition. 2 For two grassland systems, one on a sandy soil in the Netherlands and one on a chalk soil in the United Kingdom, we investigated how individual plant species grown in monocultures changed abiotic and biotic soil conditions. Then, we determined feedback effects of these soils to plants of the same or different species. Feedback effects were analysed at the level of plant species and plant taxonomic groups (grasses vs. forbs). 3 In the sandy soils, plant species differed in their effects on soil chemical properties, in particular potassium levels, but PLFA (phospholipid fatty acid) signatures of the soil microbial community did not differ between plant species. The effects of soil chemical properties were even greater when grasses and forbs were compared, especially because potassium levels were lower in grass monocultures. 4 In the chalk soil, there were no effects of plant species on soil chemical properties, but PLFA profiles differed significantly between soils from different monocultures. PLFA profiles differed between species, rather than between grasses and forbs. 5 In the feedback experiment, all plant species in sandy soils grew less vigorously in soils conditioned by grasses than in soils conditioned by forbs. These effects correlated significantly with soil chemical properties. None of the seven plant species showed significant differences between performance in soil conditioned by the same vs. other plant species. 6 In the chalk soil, Sanguisorba minor and in particular Briza media performed best in soil collected from conspecifics, while Bromus erectus performed best in soil from heterospecifics. There was no distinctive pattern between soils collected from forb and grass monocultures, and plant performance could not be related to soil chemical properties or PLFA signatures. 7 Our study shows that mechanisms of plant-soil feedback can depend on plant species, plant taxonomic (or functional) groups and site-specific differences in abiotic and biotic soil properties. Understanding how plant species can influence their rhizosphere, and how other plant species respond to these changes, will greatly enhance our understanding of the functioning and stability of ecosystems.

The Representative Soil Sampling Scheme of England and Wales: the spatial variation of topsoil nutrient status and pH between 1971 and 2001

The Representative Soil Sampling Scheme (RSSS) has monitored the soil of agricultural land in England and Wales since 1969. Here we describe the first spatial analysis of the data from these surveys using geostatistics. Four years of data (1971, 1981, 1991 and 2001) were chosen to examine the nutrient (available K, Mg and P) and pH status of the soil. At each farm, four fields were sampled; however, for the earlier years, coordinates were available for the farm only and not for each field. The averaged data for each farm were used for spatial analysis and the variograms showed spatial structure even with the smaller sample size. These variograms provide a reasonable summary of the larger scale of variation identified from the data of the more intensively sampled National Soil Inventory. Maps of kriged predictions of K generally show larger values in the central and southeastern areas (above 200 mg L-1) and an increase in values in the west over time, whereas Mg is fairly stable over time. The kriged predictions of P show a decline over time, particularly in the east, and those of pH show an increase in the east over time. Disjunctive kriging was used to examine temporal changes in available P using probabilities less than given thresholds of this element. The RSSS was not designed for spatial analysis, but the results show that the data from these surveys are suitable for this purpose. The results of the spatial analysis, together with those of the statistical analyses, provide a comprehensive view of the RSSS database as a basis for monitoring the soil. These data should be taken into account when future national soil monitoring schemes are designed.

Morphology, biomass and nutrient status of fine roots of Scots pine (Pinus sylvestris) as influenced by seasonal fluctuations in soil moisture and soil solution chemistry

A field monitoring study was carried out to follow the changes of fine root morphology, biomass and nutrient status in relation to seasonal changes in soil solution chemistry and moisture regime in a mature Scots pine stand on acid soil. Seasonal and yearly fluctuations in soil moisture and soil solution chemistry have been observed. Changes in soil moisture accounted for some of the changes in the soil solution chemistry. The results showed that when natural acidification in the soil occurs with low pH (3.5-4.2) and high aluminium concentration in the soil solution (> 3-10 mg l(-1)), fine root longevity and distribution could be affected. However, fine root growth of Scots pine may not be negatively influenced by adverse soil chemical conditions if soil moisture is not a limiting factor for root growth. In contrast, dry soil conditions increase Scots pine susceptibility to soil acidification and this could significantly reduce fine root growth and increase root mortality. It is therefore important to study seasonal fluctuations of the environmental variables when investigating and modelling cause-effect relationships.

Over-parameterised, uncertain 'mathematical marionettes' - How can we best use catchment water quality models? An example of an 80-year catchment-scale nutrient balance

The Integrated Catchment Model of Nitrogen (INCA-N) was applied to the River Lambourn, a Chalk river-system in southern England. The model's abilities to simulate the long-term trend and seasonal patterns in observed stream water nitrate concentrations from 1920 to 2003 were tested. This is the first time a semi-distributed, daily time-step model has been applied to simulate such a long time period and then used to calculate detailed catchment nutrient budgets which span the conversion of pasture to arable during the late 1930s and 1940s. Thus, this work goes beyond source apportionment and looks to demonstrate how such simulations can be used to assess the state of the catchment and develop an understanding of system behaviour. The mass-balance results from 1921, 1922, 1991, 2001 and 2002 are presented and those for 1991 are compared to other modelled and literature values of loads associated with nitrogen soil processes and export. The variations highlighted the problem of comparing modelled fluxes with point measurements but proved useful for identifying the most poorly understood inputs and processes thereby providing an assessment of input data and model structural uncertainty. The modelled terrestrial and instream mass-balances also highlight the importance of the hydrological conditions in pollutant transport. Between 1922 and 2002, increased inputs of nitrogen from fertiliser, livestock and deposition have altered the nitrogen balance with a shift from possible reduction in soil fertility but little environmental impact in 1922, to a situation of nitrogen accumulation in the soil, groundwater and instream biota in 2002. In 1922 and 2002 it was estimated that approximately 2 and 18 kg N ha(-1) yr(-1) respectively were exported from the land to the stream. The utility of the approach and further considerations for the best use of models are discussed. (C) 2008 Elsevier B.V. All rights reserved.

Decomposition in soil and chemical characteristics of pollen

The input to soils made by pollen and its subsequent mineralization has rarely been investigated from a soil microbiological point of view even though the small but significant quantities of C and N in pollen may make an important contribution to nutrient cycling. The relative resistance to decomposition of pollen exines (outer layers) has led to much of the focus of pollen in soil being on its preservation for archaeological and palaeo-ecological purposes. We have examined aspects of the chemical composition and decomposition of pollen from birch (Betula alba) and maize (Zea mays) in soil. The relatively large N contents, small C-to-N ratios and large water-soluble contents of pollen from both species indicated that they would be readily mineralized in soil. When added to soil and incubated at 16 degrees C an amount of C equivalent to 22-26% of the added pollen C was lost as CO2 within 22 days, with the Z. mays pollen decomposing faster. For B. alba pollen, the water-soluble fraction decomposed faster than the whole pollen and the insoluble fraction decomposed more slowly over 22 days. By contrast, there were no significant differences in the decomposition rates of the different fractions from Z. mays pollen. Solid-state C-13 nuclear magnetic resonance (NMR) revealed no gross chemical differences between the pollen of these two species, with strong resonances in the alkyl- and methyl-C region (0-45 p.p.m.) indicative of aliphatic compounds, the O-alkyl-C (60-90 p.p.m.) and the acetal- and ketal-C region (90-110 p.p.m.) indicative of polysaccharides, and the carbonyl-C region indicative of peptides and carboxylic acids. In addition, both pollens gave a small but distinct resonance at 55 p.p.m. attributed to N-alkyl-C. The resonances attributed to polysaccharides were lost completely or substantially reduced after decomposition.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable -cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality. (C) 2004 Elsevier Ltd. All rights reserved.

Temporal patterns of nutrient availability around nests of leaf-cutting ants (Atta colombica) in secondary moist tropical forest

Leaf-cutting ants consume up to 10% of canopy leaves in the foraging area of their colony and therefore represent a key perturbation in the nutrient cycle of tropical forests. We used a chronosequence of nest sites on Barro, Colorado Island, Panama, to assess the influence of leaf-cutting ants (Atta colombica) on nutrient availability in a neotropical rainforest. Twelve nest sites were sampled, including active nests, recently abandoned nests (<1 year) and long-abandoned nests (>1 year). Waste material discarded by the ants down-slope from the nests contained large concentrations of nitrogen and phosphorus in both total and soluble forms, but decomposed within one year after the nests were abandoned. Despite this, soil under the waste material contained high concentrations of nitrate and ammonium that persisted after the disappearance of the waste, although soluble phosphate returned to background concentrations within one year of nest abandonment. Fine roots were more abundant in soil under waste than control soils up to one year after nest abandonment, but were not significantly different for older sites. In contrast to the waste dumps, soil above the underground nest chambers consistently contained lower nutrient concentrations than control soils, although this was not statistically significant. We conclude that the 'islands of fertility' created by leaf-cutting ants provide a nutritional benefit to nearby plants for less than one year after nest abandonment in the moist tropical environment of Barro Colorado Island. Published by Elsevier Ltd.

The analysis of ranked observations of soil structure using indicator geostatistics

Structure is an important physical feature of the soil that is associated with water movement, the soil atmosphere, microorganism activity and nutrient uptake. A soil without any obvious organisation of its components is known as apedal and this state can have marked effects on several soil processes. Accurate maps of topsoil and subsoil structure are desirable for a wide range of models that aim to predict erosion, solute transport, or flow of water through the soil. Also such maps would be useful to precision farmers when deciding how to apply nutrients and pesticides in a site-specific way, and to target subsoiling and soil structure stabilization procedures. Typically, soil structure is inferred from bulk density or penetrometer resistance measurements and more recently from soil resistivity and conductivity surveys. To measure the former is both time-consuming and costly, whereas observations made by the latter methods can be made automatically and swiftly using a vehicle-mounted penetrometer or resistivity and conductivity sensors. The results of each of these methods, however, are affected by other soil properties, in particular moisture content at the time of sampling, texture, and the presence of stones. Traditional methods of observing soil structure identify the type of ped and its degree of development. Methods of ranking such observations from good to poor for different soil textures have been developed. Indicator variograms can be computed for each category or rank of structure and these can be summed to give the sum of indicator variograms (SIV). Observations of the topsoil and subsoil structure were made at four field sites where the soil had developed on different parent materials. The observations were ranked by four methods and indicator and the sum of indicator variograms were computed and modelled for each method of ranking. The individual indicators were then kriged with the parameters of the appropriate indicator variogram model to map the probability of encountering soil with the structure represented by that indicator. The model parameters of the SIVs for each ranking system were used with the data to krige the soil structure classes, and the results are compared with those for the individual indicators. The relations between maps of soil structure and selected wavebands from aerial photographs are examined as basis for planning surveys of soil structure. (C) 2007 Elsevier B.V. All rights reserved.

Effect of manure application on crop yield and soil chemical properties in a long-term field trial of semi-arid Kenya

The sustainability of cereal/legume intercropping was assessed by monitoring trends in grain yield, soil organic C (SOC) and soil extractable P (Olsen method) measured over 13 years at a long-term field trial on a P-deficient soil in semi-arid Kenya. Goat manure was applied annually for 13 years at 0, 5 and 10 t ha(-1) and trends in grain yield were not identifiable because of season-to-season variations. SOC and Olsen P increased for the first seven years of manure application and then remained constant. The residual effect of manure applied for four years only lasted another seven to eight years when assessed by yield, SOC and Olsen P. Mineral fertilizers provided the same annual rates of N and P as in 5 t ha(-1) manure and initially ,gave the same yield as manure, declining after nine years to about 80%. Therefore, manure applications could be made intermittently and nutrient requirements topped-up with fertilizers. Grain yields for sorghum with continuous manure were described well by correlations with rainfall and manure input only, if data were excluded for seasons with over 500 mm rainfall. A comprehensive simulation model should correctly describe crop losses caused by excess water.

Hydrological controls on soil redox dynamics in a peat-based, restored wetland

Increasing areas of altered wetland are being restored by re-flooding the soil. Evidence in the literature indicates that this practice can induce the redox-mediated release of soil nutrients, thereby increasing the risk of diffuse water pollution. However, for the sake of improving wedand management decisions, there is a need for more detailed studies of the underlying relationship between the hydrological and redox dynamics that explain this risk; this is particularly the case in agricultural peatlands that are commonly targeted for the creation of lowland wet grassland. A 12-month field study was conducted to evaluate the relationship between hydrological fluctuations and soil redox potential (Eh) in a nutrient-rich peat field (32 g N kg(-1) and 1100 mg P kg(-1) in the surface 0-30 cm soil) that had been restored as lowland wet grassland from intensive arable production. Field tensiometers were installed at the 30-, 60- and 90-cm soil depths, and Pt electrodes at the 10-, 30-, 60- and 90-cm depths, for daily logging of soil water tension and Eh, respectively. The values for soil water tension displayed a strong negative relationship (P < 0.001) with monthly dip well observations of water table height. Calculations of soil water potential from the logged tension values were used, therefore, to provide a detailed profile of field water level and, together with precipitation data, explained some of the variation in Eh. For example, during the summer, alternating periods of aerobism (Eh > 330 mV) in the surface, 0-10 cm layer of peat coincided with intense precipitation events. Redox potential throughout the 30-100 cm profile also fluctuated seasonally; indeed, at all depths Eh displayed a strong, negative relationship (P < 0.001) with water table height over the 12-month study period. However, Eh throughout the 30-100 cm profile remained relatively low (< 230 mV), indicating permanently reduced conditions that are associated with denitrification and reductive dissolution of Fe-bound P. The implications of these processes in the N- and P-rich peat for wetland plant diversity and water quality are discussed. (c) 2006 Elsevier B.V. All rights reserved.

A simple model for predicting soil temperature in snow-covered and seasonally frozen soil: model description and testing

Microbial processes in soil are moisture, nutrient and temperature dependent and, consequently, accurate calculation of soil temperature is important for modelling nitrogen processes. Microbial activity in soil occurs even at sub-zero temperatures so that, in northern latitudes, a method to calculate soil temperature under snow cover and in frozen soils is required. This paper describes a new and simple model to calculate daily values for soil temperature at various depths in both frozen and unfrozen soils. The model requires four parameters average soil thermal conductivity, specific beat capacity of soil, specific heat capacity due to freezing and thawing and an empirical snow parameter. Precipitation, air temperature and snow depth (measured or calculated) are needed as input variables. The proposed model was applied to five sites in different parts of Finland representing different climates and soil types. Observed soil temperatures at depths of 20 and 50 cm (September 1981-August 1990) were used for model calibration. The calibrated model was then tested using observed soil temperatures from September 1990 to August 2001. R-2-values of the calibration period varied between 0.87 and 0.96 at a depth of 20 cm and between 0.78 and 0.97 at 50 cm. R-2 -values of the testing period were between 0.87 and 0.94 at a depth of 20cm. and between 0.80 and 0.98 at 50cm. Thus, despite the simplifications made, the model was able to simulate soil temperature at these study sites. This simple model simulates soil temperature well in the uppermost soil layers where most of the nitrogen processes occur. The small number of parameters required means, that the model is suitable for addition to catchment scale models.