Showing papers by "Helmholtz Centre for Environmental Research - UFZ published in 2007"

Methods to account for spatial autocorrelation in the analysis of species distributional data : a review

Abstract: Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method’s implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing

The EPS Matrix: The “House of Biofilm Cells”

Abstract: In response to a suggestion by the Biofilms 2007 organizing committee to hold an evening session on biofilm extracellular polymeric substances (EPS), an exceptionally inspiring event followed contributions by Ken Bayles, Alan Decho, Martina Hausner, Jan Kreft, Thomas Neu, Per Nielsen, Ute Romling,

A new generation of climate-change experiments: events, not trends

Abstract: Intensification of weather extremes is currently emerging as one of the most important facets of climate change. Research on extreme events (“event-focused” in contrast to “trend-focused”) has increased in recent years and, in 2004, accounted for one-fifth of the experimental climate-change studies published. Numerous examples, ranging from microbiology and soil science to biogeography, demonstrate how extreme weather events can accelerate shifts in species composition and distribution, thereby facilitating changes in ecosystem functioning. However, assessing the importance of extreme events for ecological processes poses a major challenge because of the very nature of such events: their effects are out of proportion to their short duration. We propose that extreme events can be characterized by statistical extremity, timing, and abruptness relative to the life cycles of the organisms affected. To test system response to changing magnitude and frequency of weather events, controlled experiments are useful tools. These experiments provide essential insights for science and for societies that must develop coping strategies for such events. Here, we discuss future research needs for climate-change experiments in ecology. For illustration, we describe an experimental plan showing how to meet the challenge posed by changes in the frequency or magnitude of extreme events.

Epigenetics for ecologists

Abstract: There is now mounting evidence that heritable variation in ecologically relevant traits can be generated through a suite of epigenetic mechanisms, even in the absence of genetic variation. Moreover, recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations. These novel findings are potentially highly relevant to ecologists because they could significantly improve our understanding of the mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change. To understand the full significance of epigenetic processes, however, it is imperative to study them in an ecological context. Ecologists should therefore start using a combination of experimental approaches borrowed from ecological genetics, novel techniques to analyse and manipulate epigenetic variation, and genomic tools, to investigate the extent and structure of epigenetic variation within and among natural populations, as well as the interrelations between epigenetic variation, phenotypic variation and ecological interactions.

Spatial autocorrelation and the selection of simultaneous autoregressive models

Abstract: Aim Spatial autocorrelation is a frequent phenomenon in ecological data and can affect estimates of model coefficients and inference from statistical models. Here, we test the performance of three different simultaneous autoregressive (SAR) model types (spatial error = SAR err , lagged = SAR lag and mixed = SAR mix ) and common ordinary least squares (OLS) regression when accounting for spatial autocorrelation in species distribution data using four artificial data sets with known (but different) spatial autocorrelation structures. Methods We evaluate the performance of SAR models by examining spatial patterns in model residuals (with correlograms and residual maps), by comparing model parameter estimates with true values, and by assessing their type I error control with calibration curves. We calculate a total of 3240 SAR models and illustrate how the best models [in terms of minimum residual spatial autocorrelation (minRSA), maximum model fit ( R 2 ), or Akaike information criterion (AIC)] can be identified using model selection procedures. Results Our study shows that the performance of SAR models depends on model specification (i.e. model type, neighbourhood distance, coding styles of spatial weights matrices) and on the kind of spatial autocorrelation present. SAR model parameter estimates might not be more precise than those from OLS regressions in all cases. SAR err models were the most reliable SAR models and performed well in all cases (independent of the kind of spatial autocorrelation induced and whether models were selected by minRSA, R 2 or AIC), whereas OLS, SAR lag and SAR mix models showed weak type I error control and/or unpredictable biases in parameter estimates. Main conclusions SAR err models are recommended for use when dealing with spatially autocorrelated species distribution data. SAR lag and SAR mix might not always give better estimates of model coefficients than OLS, and can thus generate bias. Other spatial modelling techniques should be assessed comprehensively to test their predictive performance and accuracy for biogeographical and macroecological research.

Effects of incorporating spatial autocorrelation into the analysis of species distribution data

Abstract: Aim Spatial autocorrelation (SAC) in data, i.e. the higher similarity of closer samples, is a common phenomenon in ecology. SAC is starting to be considered in the analysis of species distribution data, and over the last 10 years several studies have incorporated SAC into statistical models (here termed ‘spatial models’). Here, I address the question of whether incorporating SAC affects estimates of model coefficients and inference from statistical models. Methods I review ecological studies that compare spatial and non-spatial models. Results In all cases coefficient estimates for environmental correlates of species distributions were affected by SAC, leading to a mis-estimation of on average c. 25%. Model fit was also improved by incorporating SAC. Main conclusions These biased estimates and incorrect model specifications have implications for predicting species occurrences under changing environmental conditions. Spatial models are therefore required to estimate correctly the effects of environmental drivers on species present distributions, for a statistically unbiased identification of the drivers of distribution, and hence for more accurate forecasts of future distributions.

How landscape structure, land-use intensity and habitat diversity affect components of total arthropod diversity in agricultural landscapes

Abstract: 1. Agricultural intensification poses a serious threat to biodiversity as a consequence of increased land-use intensity, decreased landscape heterogeneity and reduced habitat diversity. Although there is interest in the preservation of total species richness of an agricultural landscape (γ diversity), the effects of intensification have been assessed primarily by species richness at a local scale (α diversity). This ignores species richness between local communities (β diversity), which is an important component of total species richness. 2. In this study, measures of land-use intensity, landscape structure and habitat diversity were related to γ, α and β diversity of wild bees (Apoidea), carabid beetles (Carabidae), hoverflies (Syrphidae), true bugs (Heteroptera) and spiders (Araneae) within 16 local communities in 24 temperate European agricultural landscapes. 3. The total landscape species richness of all groups was most strongly affected by increased proximity of semi-natural habitat patches. Bees also decreased in landscapes with a high intensity of farmland management, demonstrating additive effects of both factors. 4. Separating total species diversity into components, the decrease in total species richness could be attributed primarily to a decrease in species diversity between local communities. Species richness of the local communities of all investigated groups decreased with increasing land-use intensity and, in the case of spiders, decreasing proximity of the semi-natural habitat patches. 5. The effect of increased habitat diversity appeared to be of secondary importance to total species richness but caused a shift in the relative contribution of α and β diversity towards the latter.

Monitoring the effect of chemicals on biological communities. The biofilm as an interface

Abstract: Biofilms can be regarded as early warning systems for detection of the effects of toxicants on aquatic systems, because they have been successfully used for detection of other environmental stressors (e.g. pH, salinity, organic pollution). A variety of methods is used for detection of the effects of toxicants by use of biofilms. The methods range from structurally-based to functionally-based, and from in vitro-based to systemic approaches. Physiological approaches may be appropriate for detection of acute effects. Among these methods, photosynthesis is more related to the effect of toxicants affecting algal communities, directly or indirectly, and extracellular enzyme activity is less specific. Selecting one or the other may depend on the suspected direct effect of the toxicant. Integrated studies have revealed the relevance of toxicants to top-down or bottom-up regulation of the biofilm community. Persistent or chronic effects should affect other biofilm indicators, for example growth or biomass-related factors (e.g. chlorophyll), or community composition. Among these, community composition might better reflect the effects of the toxicant(s), because this may cause a shift from a sensitive to a progressively tolerant community. Community composition-based approaches do not usually adequately reflect cause-effect relationships and require complementary analysis of properties affected in the short-term, for example physiological properties. The current array of methods available must be wisely combined to disentangle the effects of chemicals on biofilms, and whether these effects are transient or persistent, to successfully translate the chemical action of toxicants into the effect they might have on the river ecosystem.

Comparison of empirical methods for building agent-based models in land use science

Abstract: The use of agent-based models (ABMs) for investigating land-use science questions has been increasing dramatically over the last decade. Modelers have moved from ‘proofs of existence’ toy models to case-specific, multi-scaled, multi-actor, and data-intensive models of land-use and land-cover change. An international workshop, titled ‘Multi-Agent Modeling and Collaborative Planning—Method2Method Workshop’, was held in Bonn in 2005 in order to bring together researchers using different data collection approaches to informing agent-based models. Participants identified a typology of five approaches to empirically inform ABMs for land use science: sample surveys, participant observation, field and laboratory experiments, companion modeling, and GIS and remotely sensed data. This paper reviews these five approaches to informing ABMs, provides a corresponding case study describing the model usage of these approaches, the types of data each approach produces, the types of questions those data can answer, and an ...

Solvent-tolerant bacteria for biotransformations in two-phase fermentation systems.

Abstract: Product removal from aqueous media poses a challenge in biotechnological whole-cell biotransformation processes in which substrates and/or products may have toxic effects. The assignment of an additional liquid solvent phase provides a solution, as it facilitates in situ product recovery from aqueous media. In such two-phase systems, toxic substrates and products are present in the aqueous phase in tolerable but still bioavailable amounts. As a matter of course, adequate organic solvents have to possess hydrophobicity properties akin to substrates and products of interest, which in turn involves intrinsic toxicity of the solvents used. The employment of bacteria being able to adapt to otherwise toxic solvents helps to overcome the problem. Adaptive mechanisms enabling such solvent tolerant bacteria to survive and grow in the presence of toxic solvents generally involve either modification of the membrane and cell surface properties, changes in the overall energy status, or the activation and/or induction of active transport systems for extruding solvents from membranes into the environment. It is anticipated that the biotechnological production of a number of important fine chemicals in amounts sufficient to compete economically with chemical syntheses will soon be possible by making use of solvent-tolerant microorganisms.

Functional metaproteome analysis of protein extracts from contaminated soil and groundwater

Abstract: Using proteins from soil or groundwater as functional biomarkers requires efficient extraction. We developed an extraction method in which the separation of proteins from the inorganic and organic constituents of the soil matrix was achieved by a combination of 0.1 M NaOH treatment and phenol extraction. Incubation with NaOH released humic acids and proteins from soil minerals, and simultaneously, disrupted microorganisms. The subsequent phenol extraction separated the proteins from the humic organic matter. Protein extracts were applied to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 2D-electrophoresis (2-DE). Spots and bands were excised and individual proteins identified by liquid chromatography online linked to mass spectrometry (MS) via electrospray ionization source (LC-ESI-MS). To assess the suitability of the method for the functional analysis of environmental metaproteomes, it was applied to soil that had been enriched in chlorophenoxy acid-degrading bacteria by incubation with 2,4-dichlorophenoxy acetic acid (2,4-D) for 22 days. The method was also used to analyze groundwater from the aquifer of a chlorobenzene-contaminated site. The identification of enzymes such as chlorocatechol dioxygenases was consistent with bacterial metabolic pathways expected to be expressed in these samples. The protocol enabled thus the analysis of the metaproteome of soil and groundwater samples. It thereby provides a means to study the diversity of environmental microbial communities while addressing functional aspects more directly than metagenome or even metatranscriptome analysis.

Species Associations in a Heterogeneous Sri Lankan Dipterocarp Forest

Abstract: We used point pattern analysis to examine the spatial distribution of 46 common tree species (diameter at breast height 110 cm) in a fully mapped -m tropical forest plot in Sin- 500 # 500 haraja, Sri Lanka. We aimed to disentangle the effect of species in- teractions (second-order effects) and environment (first-order ef- fects) on the species' spatial distributions. To characterize first-order associations (segregation, overlap), we developed a classification scheme based on Ripley's K and nearest-neighbor statistics. We sub- sequently used heterogeneous Poisson null models, accounting for possible environmental heterogeneity, to reveal significant uni- and bivariate second-order interactions (regularity, aggregation and re- pulsion, attraction). First-order effects were strong; overall, 53% of all species pairs occupied largely disjoint areas (segregation), 40% showed partial overlap, and 6% overlapped. Only 5% of all species pairs showed significant second-order effects, but about half of the species showed significant intraspecific effects. Significant plant-plant interactions occurred mostly within 2-4 m and disappeared within 15-20 m of the focal plant. While lack of significant species inter- actions suggests support for the unified neutral theory, species' ob- served spatial segregation does not support the assumptions of the neutral theory. The strong observed tendency of species to segregate may have supplementary effects on other processes promoting species coexistence.

Splintering Urban Populations: Emergent Landscapes of Reurbanisation in Four European Cities

Abstract: During the last three decades, the countries of the developed world have been engulfed by the 'second demographic transition', which involves new family relations, less and later marriage, declining fertility rates, population ageing, postponement of child-bearing and smaller households, among other trends. It is being increasingly argued that such population dynamics are having a powerful transformative effect on the inner city, by diversifying and redensifying its social landscapes, and creating a 'splintered' urban form. Based on the findings of a recent EU Framework 5 research project, this paper investigates the demographic contingencies of this process-also known as reurbanisation-in four European cities: Leipzig (Germany), Ljubljana (Slovenia), Bologna (Italy) and Leon (Spain). Analyses of census and municipal registry data, as well as on-site questionnaire surveys and interviews, have revealed that the reviewed cities are being populated with, and fragmented by, multiple migration trends and new h...

A century of the ornamental plant trade and its impact on invasion success.

Abstract: We identify a significant relationship between domestic market-based propagule pressure, as measured both in presence in the British horticultural market and in seed prices of ornamental plant species, with success in invasion. We employ a multispecies temporal approach and use a Generalized Estimation Equation model comparing ornamental non-native species introduced into Britain which started to invade with species introduced but not known outside cultivation. Historical nursery catalogues gave information on the availability and prices of seeds of 506 ornamental species in the British horticultural market every 20 years from 1885 to 1985. Higher market frequency and cheap prices of seeds were more significant and had a greater impact on the invading probability 20 years later than at the date of listing in a nursery catalogue. Our results suggest that national economic factors are an important part of the explanation for the invasiveness of ornamental plant species, and hence for the development of potential solutions.

Humic acid modified Fenton reagent for enhancement of the working pH range

Abstract: The suitability of the Fenton process for the remediation of soil and groundwater is limited by the necessity to acidify the reaction medium. This study examines the applicability of humic acid (HA) as an iron chelator in a modified Fenton system with the aim of extending the optimum pH range for this process towards neutral conditions. Addition of HA at a concentration of 50–100 mg L−1 greatly enhances the rate of oxidation of organic compounds in a catalytic Fenton system in the range of pH 5–7. Similar rates at pH 5 in the presence of HA can be achieved as at pH 3 for a typical Fenton process in the absence of HA (k′ = 9 × 10−3 min−1 for benzene degradation at c H 2 O 2 = 0.13 M ). A comparison of the relative reactivities of various model compounds supported the hypothesis that OH radicals are the main reactive species in the HA-modified Fenton system. In contrast, however, another type of chelated Fe-catalyst (Fe-TAML) proved to be more selective than expected for OH radicals. A long-term study revealed that the HA itself is oxidized and thereby loses its ability to enhance the degradation of the pollutant molecules. Therefore, the HA-modified Fenton system is effective for degrading pollutants which are at least as reactive towards OH radicals as the HA itself, such as BTEX, phenols or PAHs. The results obtained indicate that the HA-modified Fenton system is also applicable for compounds with a high sorption tendency towards HA.

Limits of propidium iodide as a cell viability indicator for environmental bacteria

Abstract: Background: Viability measurements of individual bacteria are applied in various scopes of research and industry using approaches where propidium iodide (PI) serves as dead cell indicator. The reliability of PI uptake as a cell viability indicator for dead (PI permeable) and viable (PI impermeable) bacteria was tested using two soil bacteria, the gram−Sphingomonas sp. LB126 and the gram+Mycobacterium frederiksbergense LB501T. Methods: Bacterial proliferation activities observed viaDAPI and Hoechst 33342 staining were linked to the energy charge and the proportion of dead cells as obtained by diOC6 (3)-staining and PI-uptake, respectively. Calibration and verification experiments were performed using batch cultures grown on different substrates. Results: PI uptake depended on the physiological state of the bacterial cells. Unexpectedly, up to 40% of both strains were stained by PI during early exponential growth on glucose when compared to 2–5% of cells in the early stationary phase of growth. Conclusions: The results question the utility of PI as a universal indicator for the viability of (environmental) bacteria. It rather appears that in addition to nonviable cells, PI also stains growing cells of Sphingomonas sp. and M. frederiksbergense during a short period of their life cycle. © 2007 International Society for Analytical Cytology

Differences in the species composition of arbuscular mycorrhizal fungi in spore, root and soil communities in a grassland ecosystem

Abstract: Summary Most studies on the species composition of arbuscu- lar mycorrhizal fungi (AMF) have solely analysed mycorrhizal roots or AM spores collected from soil samples. However, the spore production rate and pro- portions of AMF mycelium in roots and soils have all been shown to vary substantially in a taxon-specific manner. Therefore, in the study presented here we used a molecular approach to analyse the species composition of AMF in spores, intra-radical and extra- radical mycelium in an intensively farmed meadow in central Germany. By polymerase chain reaction and sequencing of the ITS region members of seven dif- ferent families and species groups within Glomero- mycota were identified. The data revealed remarkable differences in the composition of AMF taxa both between the spores and the mycelia, and between the two types of mycelia. Glomus group Ab was dominant in roots and spores, in accordance with previous research. However, members of this group were rarely detected as extra-radical mycelium, in which Paraglomeraceae were dominant, although we found no evidence for the presence of Paraglomeraceae in roots or spores, even when a specific primer set was used. These results may be interpreted as a further indication that AMF are not necessarily obligate sym- bionts of plants.

Deleterious Mutations Can Surf to High Densities on the Wave Front of an Expanding Population

Abstract: There is an increasing recognition that evolutionary processes play a key role in determining the dynamics of range expansion. Recent work demonstrates that neutral mutations arising near the edge of a range expansion sometimes surf on the expanding front leading them rather than that leads to reach much greater spatial distribution and frequency than expected in stationary populations. Here, we extend this work and examine the surfing behavior of nonneutral mutations. Using an individual-based coupled-map lattice model, we confirm that, regardless of its fitness effects, the probability of survival of a new mutation depends strongly upon where it arises in relation to the expanding wave front. We demonstrate that the surfing effect can lead to deleterious mutations reaching high densities at an expanding front, even when they have substantial negative effects on fitness. Additionally, we highlight that this surfing phenomenon can occur for mutations that impact reproductive rate (i.e., number of offspring produced) as well as mutations that modify juvenile competitive ability. We suggest that these effects are likely to have important consequences for rates of spread and the evolution of spatially expanding populations.

In Situ Soil Water Extraction: A Review

Abstract: The knowledge of the composition and fluxes of vadose zone water is essential for a wide range of scientific and practical fields, including water-use management, pesticide registration, fate of xenobiotics, monitoring of disposal from mining and industries, nutrient management of agricultural and forest ecosystems, ecology, and environmental protection. Nowadays, water and solute flow can be monitored using either in situ methods or minimally invasive geophysical measurements. In situ information, however, is necessary to interpret most geophysical data sets and to determine the chemical composition of seepage water. Therefore, we present a comprehensive review of in situ soil water extraction methods to monitor solute concentration, solute transport, and to calculate mass balances in natural soils. We distinguished six different sampling devices: porous cups, porous plates, capillary wicks, pan lysimeters, resin boxes, and lysimeters. For each of the six sampling devices we discuss the basic principles, the advantages and disadvantages, and limits of data acquisition. We also give decision guidance for the selection of the appropriate sampling system. The choice of material is addressed in terms of potential contamination, filtering, and sorption of the target substances. The information provided in this review will support scientists and professionals in optimizing their experimental set-up for meeting their specific goals.

Analyzing the spatial structure of a Sri Lankan tree species with multiple scales of clustering.

Abstract: Clustering at multiple critical scales may be common for plants since many different factors and processes may cause clustering. This is especially true for tropical rain forests for which theories explaining species coexistence and community structure rest heavily on spatial patterns. We used point pattern analysis to analyze the spatial structure of Shorea congestiflora, a dominant species in a 25-ha forest dynamics plot in a rain forest at Sinharaja World Heritage Site (Sri Lanka), which apparently shows clustering at several scales. We developed cluster processes incorporating two critical scales of clustering for exploring the spatial structure of S. congestiflora and interpret it in relation to factors such as competition, dispersal limitation, recruitment limitation, and Janzen-Connell effects. All size classes showed consistent large-scale clustering with a cluster radius of approximately 25 m. Inside the larger clusters, small-scale clusters with a radius of 8 m were evident for recruits and saplings, weak for intermediates, and disappeared for adults. The pattern of all trees could be divided into two independent patterns: a random pattern (nearest neighbor distance > 8 m) comprising approximately 12% of the trees and a nested double-cluster pattern. This finding suggests two independent recruitment and/or seed dispersal mechanisms. Saplings were several times as abundant as recruits and may accumulate several recruit generations. Recruits were only weakly associated with adults and occupied about half of the large-scale clusters, but saplings almost all. This is consistent with recruitment limitation. For approximately 70% (95%) of all juveniles the nearest adult was less than 26 m away (53 m), suggesting a dispersal limitation that may also be related to the critical large-scale clustering. Our example illustrates the manner in which the use of a specific and complex null hypothesis of spatial structure in point pattern analysis can help us better understand the biology of a species and generate specific hypotheses to be further investigated in the field.

Signal strength and climate calibration of a European tree-ring isotope network

Abstract: [1] We present the first European network of tree ring δ13C and δ18O, containing 23 sites from Finland to Morocco. Common climate signals are found over broad climatic-ecological ranges. In temperate regions we find positive correlations with summer maximum temperatures and negative correlations with summer precipitation and Palmer Drought Severity Indices (PDSI) with no obvious species-specific differences. Regional δ13C and δ18O chronologies share high common variance in year-to-year variations. Long-term variations, however, exhibit differences that may reflect spatial variability in environmental forcings, age trends and/or plant physiological responses to increasing atmospheric CO2 concentration. Rotated principal component analysis (RPCA) and climate field correlations enable the identification of four sub-regions in the δ18O network - northern and eastern Central Europe, Scandinavia and the western Mediterranean. Regional patterns in the δ13C network are less clear and are timescale dependent. Our results indicate that future reconstruction efforts should concentrate on δ18O data in the identified European regions.

Long-term impacts of anthropogenic perturbations on dynamics and speciation of organic carbon in tropical forest and subtropical grassland ecosystems

Abstract: Anthropogenic perturbations have profoundly modified the Earth’s biogeochemical cycles, the most prominent of these changes being manifested by global carbon (C) cycling. We investigated long-term effects of human-induced land-use and land-cover changes from native tropical forest (Kenya) and subtropical grassland (South Africa) ecosystems to agriculture on the dynamics and structural composition of soil organic C (SOC) using elemental analysis and integrated 13 C nuclear magnetic resonance (NMR), near-edge X-ray absorption fine structure (NEXAFS) and synchrotron-based Fourier transform infrared-attenuated total reflectance (Sr-FTIR-ATR) spectroscopy. Anthropogenic interventions led to the depletion of 76%, 86% and 67% of the total SOC; and 77%, 85% and 66% of the N concentrations from the surface soils of Nandi, Kakamega and the South African sites, respectively, over a period of up to 100 years. Significant proportions of the total SOC (46‐73%) and N (37‐73%) losses occurred during the first 4 years of conversion indicating that these forest- and grassland-derived soils contain large amounts of labile soil organic matter (SOM), potentially vulnerable to degradation upon human-induced land-use and land-cover changes. Anthropogenic perturbations altered not only the C sink capacity of these soils, but also the functional group composition and dynamics of SOC with time, rendering structural composition of the resultant organic matter in the agricultural soils to be considerably different from the SOM under natural forest and grassland ecosystems. These molecular level compositional changes were manifested: (i) by the continued degradation of O-alkyl and acetal-C structures found in carbohydrate and holocellulose biomolecules, some labile aliphatic-C functionalities, (ii) by side-chain oxidation of phenylpropane units of lignin and (iii) by the continued aromatization and aliphatization of the humic fractions possibly through selective accumulation of recalcitrant H and C substituted aryl-C and aliphatic-C components such as (poly)-methylene units, respectively. These changes appeared as early as the fourth year after transition, and their intensity increased with duration of cultivation until a new quasi-equilibrium of SOC was approached at about 20 years after conversion. However, subtle but persistent changes in molecular structures of the resultant SOM continued long after (up to 100 years) a steady state for SOC was approached. These molecular level changes in the inherent structural composition of SOC may exert considerable influence on biogeochemical cycling of C and bioavailability of essential nutrients present in association with SOM, and may significantly affect the sustainability of agriculture as well as potentials of the soils to sequester C in these tropical and subtropical highland agroecosystems.