Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France.

Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.

Isotopic Characterization (2H, 13C, 37Cl, 81Br) of Abiotic Degradation of Methyl Bromide and Methyl Chloride in Water and Implications for Future Studies.

Methyl bromide (CH3Br) and methyl chloride (CH3Cl) significantly contribute to stratospheric ozone depletion. The atmospheric budgets of both compounds are unbalanced with known degradation processes outweighing known emissions. Stable isotope analysis may be capable to identify and quantify emissions and to achieve a balanced budget. Degradation processes do, however, cause isotope fractionation in methyl halides after emission and hence knowledge about these processes is a crucial prerequisite for any isotopic mass balance approach. In the current study, triple-element isotope analysis (2H, 13C, 37Cl/81Br) was applied to investigate the two main abiotic degradation processes of methyl halides (CH3X) in fresh and seawater: hydrolysis and halide exchange. For CH3Br, nucleophilic attack by both H2O and Cl- caused significant primary carbon and bromine isotope effects accompanied by a secondary inverse hydrogen isotope effect. For CH3Cl only nucleophilic substitution by H2O was observed at significant rates causing large primary carbon and chlorine isotope effects and a secondary inverse hydrogen isotope effect. Observed dual-element isotope ratios differed slightly from literature values for microbial degradation in water and hugely from radical reactions in the troposphere. This bodes well for successfully distinguishing and quantifying degradation processes in atmospheric methyl halides using triple-element isotope analysis.

Higher temperature sensitivity for stable than for labile soil organic carbon--evidence from incubations of long-term bare fallow soils.

The impact of climate change on the stability of soil organic carbon (SOC) remains a major source of uncertainty in predicting future changes in atmospheric CO2 levels. One unsettled issue is whether the mineralization response to temperature depends on SOC mineralization rate. Long-term (>25 years) bare fallow experiments (LTBF) in which the soil is kept free of any vegetation and organic inputs, and their associated archives of soil samples represent a unique research platform to examine this issue as with increasing duration of fallow, the lability of remaining total SOC decreases. We retrieved soils from LTBF experiments situated at Askov (Denmark), Grignon (France), Ultuna (Sweden), and Versailles (France) and sampled at the start of the experiments and after 25, 50, 52, and 79 years of bare fallow, respectively. Soils were incubated at 4, 12, 20, and 35 °C and the evolved CO2 monitored. The apparent activation energy (Ea) of SOC was then calculated for similar loss of CO2 at the different temperatures. The Ea was always higher for samples taken at the end of the bare-fallow period, implying a higher temperature sensitivity of stable C than of labile C. Our results provide strong evidence for a general relationship between temperature sensitivity and SOC stability upon which significant improvements in predictive models could be based.

Effects of soil mineral matrix on the analysis of plant- and soil-derived polysaccharides after acid hydrolysis.

RATIONALE: The efficiency of extraction procedures for the determination of organic compounds in soil may be affected by the presence of the mineral phase. Our aim was to analyse the magnitude of such an effect on both total polysaccharide content and (13)C-isotopic signature of the polysaccharides. METHODS: After acid hydrolysis of (13)C-labelled wheat, soil and a mixture of these, sugars were quantified and analysed isotopically. Measured values were compared with theoretical contents. RESULTS: No matrix effect was apparent for total sugar-C content of the mixture. However, a matrix effect was observed for the contribution of (13)C-labelled wheat sugars. For the soil+plant mixture (13)C-labelled wheat sugar contribution was overestimated. Soil-derived sugar-C contribution to the mixture was underestimated. CONCLUSIONS: Studies using stable isotopes to follow the fate of added plant-derived compounds in soil need to take into account matrix effects. Further studies have to elaborate on correction procedures and/or the development of extraction procedures to overcome the influence of matrix effects and/or acid hydrolysis extraction on sugar-C contents.

Variability of 13C-labeling in plant leaves.

RATIONALE: Plant tissues artificially labeled with (13)C are increasingly used in environmental studies to unravel biogeochemical and ecophysiological processes. However, the variability of (13)C-content in labeled tissues has never been carefully investigated. Hence, this study aimed at documenting the variability of (13)C-content in artificially labeled leaves. METHODS: European beech and Italian ryegrass were subjected to long-term (13)C-labeling in a controlled-environment growth chamber. The (13)C-content of the leaves obtained after several months labeling was determined by isotope ratio mass spectrometry. RESULTS: The (13)C-content of the labeled leaves exhibited inter- and intra-leaf variability much higher than those naturally occurring in unlabeled plants, which do not exceed a few per mil. This variability was correlated with labeling intensity: the isotope composition of leaves varied in ranges of ca 60‰ and 90‰ for experiments that led to average leaf (13)C-content of ca +15‰ and +450‰, respectively. CONCLUSIONS: The reported variability of isotope composition in (13)C-enriched leaves is critical, and should be taken into account in subsequent experimental investigations of environmental processes using (13)C-labeled plant tissues.

Effect of 13C enrichment and sugar type on analysis of sugars by gas chromatography/combustion/isotope ratio mass spectrometry.

RATIONALE: The objective of this investigation was to test gas-chromatographic compound-specific analysis for studies on the isotopic composition of (13)C-enriched sugar molecules. The effects of (13)C enrichment and type of sugar (C5, C6) will provide valuable information on isotopic correction for future studies employing (13)C-enriched sugars. METHODS: Five sugar solutions of xylose, mannose and glucose with (13)C enrichments ranging between 1.1 and 1.5 atom-% were prepared. The (13)C enrichments of the initial sugars were measured by elemental analyser/isotope ratio mass spectrometry (EA/IRMS); (13)C enrichments for derivatised sugars were obtained by gas chromatography/combustion/IRMS (GC/C/IRMS). RESULTS: The linear relationships between the (13)C enrichments of the initial sugars and the values for the derivatised sugars were sugar-type dependent. Corrections for GC/C/IRMS values took into account the kinetic isotope effect (KIE) of the derivatising agent associated with the coefficient (K(d)) and a newly introduced second coefficient (K(c)) associated with the KIE of the sugar. While K(d) was constant, K(c) varied with sugar type. During derivatisation acetate groups with (12)C and sugars with more (13)C reacted faster. CONCLUSIONS: Coefficients for the specific ranges of (13)C enrichments under study have to be assessed and the reactions of different sugar types have to be taken into account to avoid underestimation of (13)C enrichment of up to 9% (C5) or overestimation of up to 4% (C6).

Elemental and molecular evidence of soot- and char-derived black carbon inputs to New York City's atmosphere during the 20th century.

Soot black carbon (here expressed as GBC) is present in sediments of Central Park and Prospect Park Lakes, New York City (NYC), and peaks in the middle of the 20th Century at the highest values (1-3% dry weight) ever reported in urban lakes. During that period (approximately 1940-1970), the GBC represents up to 28% of the total organic carbon (OC). Radionuclide-normalized whole core inventories of accumulated GBC are similar in the two lakes which are separated by approximately 15 km, suggesting that emissions of fine soot particles may have accumulated homogeneously over at least the urban center of NYC. The distribution of polycyclic aromatic hydrocarbons (PAHs) in the sediments is decoupled from that of GBC. The highest levels of total PAHs correspond to peak coal use for space heating in NYC in the early 1900s. In contrast, GBC concentrations were highest in the mid 1900s, a period when oil combustion dominated local fossil fuel use and incineration of municipal solid waste (MSW) was common practice in NYC. Decreases in GBC levels observed in more recently deposited sediments are consistent with improvements in particle emissions control systems. Non-soot BC (char) was identified by a high carbon to nitrogen (C/N) ratio that persisted after correction for GBC. This likely tracer of MSW incineration was estimated to contribute an additional '35% of total organic carbon found in the sediments deposited during the peak period of combustion. The temporal trends of soot-BC observed in our lake cores do not agree with published historical reconstructions based on fuel consumption and estimated emission factors.