Stephen J. Chapman

A Rapid Microtiter Plate Method To Measure Carbon Dioxide Evolved from Carbon Substrate Amendments so as To Determine the Physiological Profiles of Soil Microbial Communities by Using Whole Soil

ABSTRACT Sole-carbon-source tests (Biolog), designed to identify bacteria, have become very popular for metabolically fingerprinting soil microbial communities, despite disadvantages associated with the use of carbon source profiles that primarily select for fast-growing bacteria. In this paper we describe the use of an alternative method that combines the advantages of the Biolog community-level physiological profile (CLPP) method, in which microtiter-based detection plates are used, with the ability to measure carbon dioxide evolution from whole soil. This method facilitates measurement over short periods of time (4 to 6 h) and does not require the extraction and culturing of organisms. Deep-well microtiter plates are used as test wells into which soil is placed. The apparatus to fill the deep-well plates and interface it with a second removable detection plate is described. Two detection systems, a simple colorimetric reaction in absorbent alkali and scintillation counting with radioactive carbon sources, are described. The methods were compared to the Biolog-CLPP system by using soils under different vegetation types and soil treated with wastewater sludge. We aimed to test the hypothesis that using whole soil would have specific advantages over using extracts in that more immediate responses to substrates could be obtained that would reflect activity rather than growth. The whole-soil method was more rapid and gave earlier detection of C source use. Also, the metabolic fingerprints obtained could discriminate between sludge treatments.

Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey.

The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.

Explaining the variation in the soil microbial community: do vegetation composition and soil chemistry explain the same or different parts of the microbial variation?

AimTo assess whether vegetation composition and soil chemistry explain the same or different parts of the variation in the soil microbial community (SMC).MethodThe above and below-ground communities and soil chemical properties were studied along a successional gradient from moorland to deciduous woodland. The SMC was assessed using PLFAs and M-TRFLPs. Using variance partitioning, Co-Correspondence Analysis (CoCA) and Canonical Correspondence Analysis (CCA), the variation (total inertia) in the SMC was partitioned into variation which was uniquely explained by either plant composition or soil chemistry, variation explained by both soil chemistry and plant composition, and unexplained variation.ResultsPlant community composition uniquely explained 30, 13, 16 and 20% of the inertia and soil chemistry uniquely explained 5, 18, 9 and 9% of the inertia in the archaeal TRFLPs, bacterial TRFLPs, fungal TRFLPs and all PLFAs, respectively.ConclusionFor the first time, variance partitioning was used to include data from a CoCA; although the current limits of such an approach are shown, this study illustrates the potential of such analyses and shows that soil chemistry and plant composition are, in substantial amounts, explaining different parts of the variation within the SMC. This marks an important step in furthering our understanding of the relative importance of different drivers of change in the SMC.

13C PLFAs: a key to open the soil microbial black box?

BackgroundPhospholipid fatty acid (PLFA) analysis is an effective non-culture-based technique for providing information on the living soil microbial community. The coupling of 13C tracers with PLFA analysis can indicate the response of microbial populations to environmental change and has been widely used to trace C flux in soil-plant systems.ScopeBased on studies applying 13C PLFA analysis, the current technological status, current applications and future opportunities are discussed and evaluated. First we describe some aspects of the labelling and analytical methodology. The approaches to study the incorporation of 13C substrate and rhizodeposition C into soil microbial communities are compared. We continue with the application of 13C-labelling to study soil microbial communities, including the utilization of soil mineralisation products, the C flux from plants into the soil microbial pool, the biodegradation of pollutants and on the application to a specific microbial group, i.e. methanotrophs. Additionally, some perspectives on the limitations of the 13C PLFA method and future research avenues are noted.ConclusionsAlthough including some limitations and complications, the 13C PLFA method provides an excellent tool for understanding the relationship between microbial populations and soil biogeochemical cycling, thus providing a key to open the soil microbial black box.

Much beyond Mantel: Bringing Procrustes Association Metric to the Plant and Soil Ecologist’s Toolbox

The correlation of multivariate data is a common task in investigations of soil biology and in ecology in general. Procrustes analysis and the Mantel test are two approaches that often meet this objective and are considered analogous in many situations especially when used as a statistical test to assess the statistical significance between multivariate data tables. Here we call the attention of ecologists to the advantages of a less familiar application of the Procrustean framework, namely the Procrustean association metric (a vector of Procrustean residuals). These residuals represent differences in fit between multivariate data tables regarding homologous observations (e.g., sampling sites) that can be used to estimate local levels of association (e.g., some groups of sites are more similar in their association between biotic and environmental features than other groups of sites). Given that in the Mantel framework, multivariate information is translated into a pairwise distance matrix, we lose the ability to contrast homologous data points across dimensions and data matrices after their fit. In this paper, we attempt to familiarize ecologists with the benefits of using these Procrustean residual differences to further gain insights about the processes underlying the association among multivariate data tables using real and hypothetical examples.

Microbial utilization of rice straw and its derived biochar in a paddy soil.

The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using (13)C-labeled rice straw and its derived biochar ((13)C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96mgCkg(-1)soilh(-1)) at 1d and 3d after incubation, respectively. Straw amendment significantly (p<0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and (13)C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p<0.05) higher in (13)C-labeled straw amended soil than the (13)C-labeled biochar amended soil. According to the (13)C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of (13)C-PLFAs derived from straw amendment was significantly (p<0.01) different from biochar amendment. The PLFAs18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest that the function, size and structure of the microbial community were strongly influenced by the substrate composition and availability.

Land use and a low-carbon society

Land use and the management of our natural resources such as soils and water offer great opportunities to sequester carbon and mitigate the effects of climate change. Actions on forestry, soil carbon and damaged peatlands each have the potential to reduce Scottish emissions in 2020 by hundreds of thousands of tonnes. Most actions to reduce emissions from land use have beneficial effects on other ecosystem services, so if we can cut emissions we can in many circum- stances improve the environment. The cost of reducing emissions through land use change can be low in relation to other means of cutting emissions. The Scottish Land Use Strategy and the Eco- system Approach it calls for, employing the concept of ecosystem services, offers a way of balancing environmental, social and economic demands on the land. Scotlands land, soils, forests and waters are all likely to be significantly altered by future climate change. Each of these components of the land-based environment offers opportunities for mitigation and adaptation to climate change. The emerging new imperatives for securing food, water and energy at a global level are equally impor- tant for Scotland, and interact with the need for environmental security and for dealing with climate change.

Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil

Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000xa0mgxa0kg−1 of NO3−-N) addition. Results showed the highest N2O emission (10.1xa0mgxa0kg−1 over 21xa0days) from the soil at pH 3.71 with 1000xa0mgxa0kg−1 NO3− addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH <7.0) were significantly higher than that of soils at pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil.

Effects of temperature, rainfall and conifer felling practices on the surface water chemistry of northern peatlands

Afforested peatlands account for about 25xa0% of human-affected peatlands worldwide. In some regions, particularly the British Isles, forest-to-bog conversions are now underway in the hope of increasing carbon storage and restoring original ecosystem functions. In this study, the effects on surface water quality of forest-to-bog restoration in the Flow Country peatlands of northern Scotland were monitored during 15xa0months. The hydrochemistry of rainwater, resurgence ground water, forestry drainage ditch water, open bog surface water, forestry-influenced loch water and stream water was examined before, during and after felling. The seasonal cycles of biologically active (C, Si, P) and organically complexed (Fe, Al) elements were characterised by major changes in concentration. The felling operations amplified these effects due to (i) the decomposition of felling residues (leaching K and C) and (ii) the disturbance and partial mineralisation of shallow peat soils (releasing P, Fe and Al). Shorter term changes (1–10xa0days) produced by rainfall events and associated changes in hydrological flow paths controlled the concentrations of Na, Ca, Mg, Mn, and to a lesser extent K and Al. There were significant negative correlations with flow of [K], [Ca] and [Mg] but a positive correlation between stream flow and [Al]. Concentration-flow relationships were not significantly altered by the felling operations because of the relatively low volume of water released from the felled area. Fluctuations in the water table represented another important control of surface water composition. Resurgence waters produced high [Fe] and [Si] values when water table levels were low. These contributions were diluted with runoff and surface soil waters enriched in dissolved organic carbon (DOC) when levels rose. Sequential ultrafiltration revealed that Fe, C and P co-occurred in the >30xa0kDa molecular weight fraction in constant relative concentrations. Since forest-to-bog restoration raises the water table, it can be anticipated to result initially in more intense flushing of DOC, including the >30xa0kDa molecular weight fraction where Fe and P co-occur.

Effect of rice straw application on microbial community and activity in paddy soil under different water status.

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10xa0gxa0kg−1 soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp™ method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7xa0%, while soil water status explained 7.5 and 29.1xa0%, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.