Radiocarbon Isotopic Classification of Deep Tropical Forest Soils

Tropical forest soils have an important role in global carbon (C) stocks. Small changes in the cycling of C could drastically affect atmospheric carbon dioxide (CO2) concentrations and active cycling of carbon in a forest community. Currently, little is understood of how tropical forest soils will respond to the increasing global temperatures. To examine the effects of warming/ drought on losses of older versus younger soil C pools, we implemented radiocarbon (14C) isotopic characterization of various soil plot samples and depths from the Luquillo Experimental Forest, Puerto Rico. 14C was measured using Accelerated Mass Spectrometry (AMS) from catalytically condensed carbon in order to examine the initial carbon stocks of the test plots. This examination was done in order to determine the age of the carbon in the soil plots before implementation of a long term warming experiment. In addition to determining the age of the soil C, the samples were submitted to a Density Fractionation Process to obtain varying aggregate fractions. These were also submitted to AMS for mean residence time of the C stocks. The soil 14C was significantly different in the Heavy and Free Light density fractions. This implies that the soil C turnover increases as you near the top depth of the soil pit samples. The results will be used to establish the initial composition of the sample soils for a warming experiment that will model future changes in climate

Deep-C storage: Biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoils

Due to their substantial volume, subsoils contain more of the total soil carbon (C) pool than topsoils. Much of this C is thousands of years old, suggesting that subsoils offer considerable potential for long-term C sequestration. However, knowledge of subsoil C behaviour and manageability remains incomplete, and subsoil C storage potential has yet to be realised at a large scale, particularly in agricultural systems. A range of biological (e.g. deep-rooting), chemical (e.g. biochar burial) and physical (e.g. deep ploughing) C sequestration strategies have been proposed, but are yet to be assessed. In this review, we identify the main factors that regulate subsoil C cycling and critically evaluate the evidence and mechanistic basis of subsoil strategies designed to promote greater C storage, with particular emphasis on agroecosystems. We assess the barriers and opportunities for the implementation of strategies to enhance subsoil C sequestration and identify 5 key current gaps in scientific understanding. We conclude that subsoils, while highly heterogeneous, are in many cases more suited to long-term C sequestration than topsoils. The proposed strategies may also bring other tangible benefits to cropping systems (e.g. enhanced water holding capacity and nutrient use efficiency). Furthermore, while the subsoil C sequestration strategies we reviewed have large potential, more long-term studies are needed across a diverse range of soils and climates, in conjunction with chronosequence and space-for-time substitutions. Also, it is vital that subsoils are more consistently included in modelled estimations of soil C stocks and C sequestration potential, and that subsoil-explicit C models are developed to specifically reflect subsoil processes. Finally, further mapping of subsoil C is needed in specific regions (e.g. in the Middle East, Eastern Europe, South and Central America, South Asia and Africa). Conducting both immediate and long-term subsoil C studies will fill the knowledge gaps to devise appropriate soil C sequestration strategies and policies to help in the global fight against climate change and decline in soil quality. In conclusion, our evidence-based analysis reveals that subsoils offer an untapped potential to enhance global C storage in terrestrial ecosystems

Chemical imaging of biological materials by NanoSIMS using isotopic and elemental labels

The NanoSIMS 50 combines unprecedented spatial resolution (as good as 50 nm) with ultra-high sensitivity (minimum detection limit of {approx}200 atoms). The NanoSIMS 50 incorporates an array of detectors, enabling simultaneous collection of 5 species originating from the same sputtered volume of a sample. The primary ion beam (Cs{sup +} or O{sup -}) can be scanned across the sample to produce quantitative secondary ion images. This capability for multiple isotope imaging with high spatial resolution provides a novel new approach to the study of biological materials. Studies can be made of sub-regions of tissues, mammalian cells, and bacteria. Major, minor and trace element distributions can be mapped on a submicron scale, growth and metabolism can be tracked using stable isotope labels, and biogenic origin can be determined based on composition. We have applied this technique extensively to mammalian and prokaryotic cells and bacterial spores. The NanoSIMS technology enables the researcher to interrogate the fate of molecules of interest within cells and organs through elemental and isotopic labeling. Biological applications at LLNL will be discussed

High resolution trace element and isotopic imaging of microbial systems by NanoSIMS

The NanoSIMS 50 is the state of the art in high spatial resolution secondary ion mass spectrometry (SIMS), combining unprecedented spatial resolution (as good as 50 nm) with ultra-high sensitivity (minimum detection limit of {approx}200 atoms). The NanoSIMS has an array of detectors, enabling simultaneous collection of 5 species originating from the same sputtered volume of a sample. The primary ion beam (Cs{sup +} or O{sup -}) can be scanned across the sample to produce quantitative secondary ion images. This capability provides a novel new approach to the study of microbial systems. We have applied our NanoSIMS to various microbial systems. We have analyzed sub-regions of bacterial cells, biofilms, and other associated materials to map trace element and isotopic ratios on a submicron scale. Growth and metabolism have been tracked using stable isotope labels. High resolution SIMS is particularly powerful when used in combination with other high resolution techniques, such as FIB and TEM. Examples will be presented to demonstrate the range of capabilities of this technique for microbial systems

Mineral protection of soil carbon counteracted by root exudates

Multiple lines of existing evidence suggest that climate change enhances root exudation of organic compounds into soils. Recent experimental studies show that increased exudate inputs may cause a net loss of soil carbon. This stimulation of microbial carbon mineralization ('priming') is commonly rationalized by the assumption that exudates provide a readily bioavailable supply of energy for the decomposition of native soil carbon (co-metabolism). Here we show that an alternate mechanism can cause carbon loss of equal or greater magnitude. We find that a common root exudate, oxalic acid, promotes carbon loss by liberating organic compounds from protective associations with minerals. By enhancing microbial access to previously mineral-protected compounds, this indirect mechanism accelerated carbon loss more than simply increasing the supply of energetically more favourable substrates. Our results provide insights into the coupled biotic-abiotic mechanisms underlying the 'priming' phenomenon and challenge the assumption that mineral-associated carbon is protected from microbial cycling over millennial timescales

Estimating taxon-specific population dynamics in diverse microbial communities

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon- specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortal- ity, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of ¹³C- and ¹⁵N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of ¹⁵N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/geochimica-et-cosmochimica-acta

Nano-Scale Secondary Ion Mass Spectrometry - A new analytical tool in biogeochemistry and soil ecology

Soils are structurally heterogeneous across a wide range of spatio-temporal scales. Consequently, external environmental conditions do not have a uniform effect throughout the soil, resulting in a large diversity of micro-habitats. It has been suggested that soil function can be studied without explicit consideration of such fine detail, but recent research has indicated that the micro-scale distribution of organisms may be of importance for a mechanistic understanding of many soil functions. Due to a lack of techniques with adequate sensitivity for data collection at appropriate scales, the question 'How important are various soil processes acting at different scales for ecological function?' is challenging to answer. The nano-scale secondary ion mass spectrometer (NanoSIMS) represents the latest generation of ion microprobes which link high-resolution microscopy with isotopic analysis. The main advantage of NanoSIMS over other secondary ion mass spectrometers is the ability to operate at high mass resolution, whilst maintaining both excellent signal transmission and spatial resolution ({approx}50 nm). NanoSIMS has been used previously in studies focusing on presolar materials from meteorites, in material science, biology, geology and mineralogy. Recently, the potential of NanoSIMS as a new tool in the study of biophysical interfaces in soils has been demonstrated. This paper describes the principles of NanoSIMS and discusses the potential of this tool to contribute to the field of biogeochemistry and soil ecology. Practical considerations (sample size and preparation, simultaneous collection of isotopes, mass resolution, isobaric interference and quantification of the isotopes of interest) are discussed. Adequate sample preparation avoiding biases in the interpretation of NanoSIMS data due to artifacts and identification of regions-of interest are of most concerns in using NanoSIMS as a new tool in biogeochemistry and soil ecology. Finally, we review the areas of research most likely to benefit from the high resolving power attainable with this new approach