Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a (CO2)-C-13 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of C-13-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded C-13 compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from C-12 and C-13 RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Accounting for the effects of lipids in stable isotope (δ13C and δ15N values) analysis of skin and blubber of balaenopterid whales

RATIONALE Stable isotope values (d¹³C and d¹⁵N) of darted skin and blubber biopsies can shed light on habitat use and diet of cetaceans, which are otherwise difficult to study. Non-dietary factors affect isotopic variability, chiefly the depletion of C due to the presence of C-rich lipids. The efficacy of post hoc lipid-correction models (normalization) must be tested. METHODS For tissues with high natural lipid content (e.g., whale skin and blubber), chemical lipid extraction or normalization is necessary. C:N ratios, d¹³C values and d¹⁵N values were determined for duplicate control and lipid-extracted skin and blubber of fin (Balaenoptera physalus), humpback (Megaptera novaeangliae) and minke whales (B. acutorostrata) by continuous-flow elemental analysis isotope ratio mass spectrometry (CF-EA-IRMS). Six different normalization models were tested to correct d¹³C values for the presence of lipids. RESULTS Following lipid extraction, significant increases in d¹³C values were observed for both tissues in the three species. Significant increases were also found for d¹⁵N values in minke whale skin and fin whale blubber. In fin whale skin, the d¹⁵N values decreased, with no change observed in humpback whale skin. Non-linear models generally out-performed linear models and the suitability of models varied by species and tissue, indicating the need for high model specificity, even among these closely related taxa. CONCLUSIONS Given the poor predictive power of the models to estimate lipid-free d13C values, and the unpredictable changes in d N values due to lipid-extraction, we recommend against arithmetical normalization in accounting for lipid effects on d13C values for balaenopterid skin or blubber samples. Rather, we recommend that duplicate analysis of lipid-extracted (d13C values) and non-treated tissues (d15N values) be used. Copyright © 2012 John Wiley & Sons, Ltd.

Stable Isotope Dietary Analysis of Prehistoric Populations from the Minusinsk Basin, Southern Siberia, Russia: A new chronological framework for the introduction of millet to the eastern Eurasian steppe

We report the results of stable carbon and nitrogen isotope analysis of 354 human and faunal samples from five archaeological cultures of the Minusinsk Basin, Southern Siberia – Afanasyevo, Okunevo, Andronovo, Karasuk and Tagar (ca. 2700–1 BC) – a key location in Eurasia due to its position on a northern corridor linking China and central Eurasia. The results indicate that the diet of Eneolithic to Middle Bronze Age (Afanasyevo to Andronovo) populations was primarily C3-based, with C4 plants only becoming an important component of the diet in the Late Bronze Age Karasuk and Early Iron Age Tagar cultures. Freshwater fish seems to have been an important constituent of the diets in all groups. The findings constitute the earliest concrete evidence for the substantial use of millet in the eastern Eurasian steppe. We propose that it was probably introduced from Northwestern China during the Karasuk culture at the start of the Late Bronze Age, ca. 1500 BC. We conclude with a discussion of the implications for the nature of pastoralist economies on the steppes.

A compositional approach to stable isotope data analysis

Isotopic data are currently becoming an important source of information regarding sources, evolution and mixing processes of water in hydrogeologic systems. However, it is not clear how to treat with statistics the geochemical data and the isotopic data together. We propose to introduce the isotopic information as new parts, and apply compositional data analysis with the resulting increased composition. Results are equivalent to downscale the classical isotopic delta variables, because they are already relative (as needed in the compositional framework) and isotopic variations are almost always very small. This methodology is illustrated and tested with the study of the Llobregat River Basin (Barcelona, NE Spain), where it is shown that, though very small, isotopic variations comp lement geochemical principal components, and help in the better identification of pollution sources

Carbon and nitrogen stable isotope ratio analysis of freshwater, brackish and marine fish from Belgian archaeological sites (1st and 2nd millennium AD)

Carbon and nitrogen stable isotope ratios were measured in 157 fish bone collagen samples from 15 different archaeological sites in Belgium which ranged in ages from the 3rd to the 18th c. AD. Due to diagenetic contamination of the burial environment, only 63 specimens produced results with suitable C:N ratios (2.9–3.6). The selected bones encompass a wide spectrum of freshwater, brackish, and marine taxa (N = 18), and this is reflected in the δ13C results (−28.2‰ to −12.9%). The freshwater fish have δ13C values that range from −28.2‰ to −20.2‰, while the marine fish cluster between −15.4‰ and −13.0‰. Eel, a catadromous species (mostly living in freshwater but migrating into the sea to spawn), plots between −24.1‰ and −17.7‰, and the anadromous fish (living in marine environments but migrating into freshwater to spawn) show a mix of freshwater and marine isotopic signatures. The δ15N results also have a large range (7.2‰ to 16.7‰) indicating that these fish were feeding at many different trophic levels in these diverse aquatic environments. The aim of this research is the isotopic characterization of archaeological fish species (ecology, trophic level, migration patterns) and to determine intra-species variation within and between fish populations differing in time and location. Due to the previous lack of archaeological fish isotope data from Northern Europe and Belgium in particular, these results serve as an important ecological backdrop for the future isotopic reconstruction of the diet of human populations dating from the historical period (1st and 2nd millennium AD), where there is zooarchaeological and historical evidence for an increased consumption of marine fish.

Multivariate analysis of stable isotope data in the traceability process for birds

A análise isotópica tem se mostrado uma ferramenta de suma importância ao processo de rastreabilidade, no entanto, existem divergências nas análises estatísticas dos resultados, uma vez que os dados são dependentes e advindos de vários elementos químicos tais como Carbono, Hidrogênio, Oxigênio, Nitrogênio e Enxofre (CHON'S). Com o intuito de estabelecer a análise propícia para os dados de rastreabilidade em aves pela técnica de isótopos estáveis e avaliar a necessidade da análise conjunta das variáveis, foram usados dados de carbono-13 e de nitrogênio-15 de ovos (albúmen + gema) de poedeiras e músculo peitoral de frangos de corte, os quais foram submetidos à análise estatística univariada (Anova e complementada pelo teste de Tukey) e multivariada (Manova e Discriminante). Os dados foram analisados no software Minitab 16, e os resultados, consolidados na teoria, confirmam a necessidade de análise multivariada, mostrando também que a análise discriminante esclarece as dúvidas apresentadas nos resultados de outros métodos de análise comparados nesta pesquisa.

Applications of Stable Isotope Ratio Analysis for Social Science Research

Stable Isotope Ratio Analysis (SIRA) is the measurement of variation in different isotopes of same elements in a material. This technique is well-established in the natural sciences and has been long part of the methodological arsenal in fields such as geology and biology. More recently this technique has begun to be utilized in the social sciences, moving from initial applications in anthropology to potential uses in geography, public health, forensic science, and others. This presentation will discuss the techniques behind SIRA, examples of current applications in the natural and social sciences, and potential avenues of future research.

Whole Proteome Analysis of the Protozoan Parasite Trypanosoma brucei using Stable Isotope Labeling by Amino Acids in Cell Culture and Mass Spectrometry

The single-celled protozoan Trypanosoma brucei spp. is the causative agent of human African trypanosomiasis and nagana in cattle. Quantitative proteomics for the first time allowed for the characterization of the proteome from several different life stages of the parasite (1-3). To achieve this, stable isotope labeling by amino acids in cell culture (SILAC; (4)) was adapted to T. brucei spp. cultures. T. brucei cells grown in standard media with dialyzed fetal calf serum containing heavy isotope-labeled amino acids (arginine and lysine) show efficient incorporation of the labeled amino acids into the whole cell proteome (8-12 divisions) and no detectable amino acid conversions. The method can be applied to both of the major life stages of the parasite and in combination with RNAi or gene knock-out approaches.

Social stratigraphy in Late Iron Age Switzerland: Stable carbon, nitrogen and sulphur isotope analysis of human remains from Münsingen

The Iron Age cemetery of Münsingen in Switzerland with 220 abundantly equipped burials marked a milestone for Iron Age research. The horizontal spread throughout the time of its occupancy laid the foundation for the chronology system of the Late Iron Age. Today, skulls of 77 individuals and some postcranial bones are still preserved. The aim of the study was to obtain information about diet, mobility and social stratification of the individuals. Stable isotope ratios of carbon, nitrogen and sulphur were analysed for 63 individuals. For all of them C3 plants were found to be the staple food. There are significant differences between males and females in δ13C and δ15N values. This points to a gender restriction in the access to animal protein with males probably having more access to meat and dairy products. Differences in δ15N values were also observed for different age classes. δ34S values indicate a terrestrial-based diet with no significant intake of marine or freshwater fish. Seven adults with enriched δ34S values might have immigrated to Münsingen, four of which were found in the oldest part of the cemetery. Furthermore, possible changes of the vegetation are indicated by the more positive stable carbon ratios in the later phases. The results lead to the suggestion that especially males buried with weapons might have played a special role in the Iron Age society.

Diet and mobility of an Iron Age population in Switzerland; Stable carbon, nitrogen and sulphur isotope analysis of the human remains from Münsingen

The 220 abundantly equipped burials from the Late Iron Age cemetery of Münsingen (420 – 240 BC) marked a milestone for Iron Age research. The evident horizontal spread throughout the time of occupancy laid the foundation for the chronology system of the Late Iron Age. Today the skulls of 77 individuals and some postcranial bones are still preserved. The aim was to obtain information about nutrition, social stratification and migration of the individuals from Münsingen. Stable isotope ratios of carbon, nitrogen and sulphur were analysed. The results of 63 individuals show that all consumed C3 plants as staple food with significant differences between males and females in δ13C and δ15N values. The results indicate a gender restriction in access to animal protein. Stable isotope values of one male buried with weapons and meat as grave goods suggest a diet with more animal proteins than the other individuals. It is possible that he was privileged due to high status. Furthermore, the δ34S values indicate minor mobility. Assuming that the subadults represent the local signal of δ34S it is very likely that adults with enriched δ34S could have migrated to Münsingen at some point during their lives. This study presents stable isotope values of one of the most important Late Iron Age burial sites in Central Europe. The presented data provide new insight into diet, migration and social stratification of the population from Münsingen.