Madhavi Z. Martin

Evaluation of different soil carbon determination methods.

Determining soil carbon (C) with high precision is an essential requisite for the success of the terrestrial C sequestration program. The informed choice of management practices for different terrestrial ecosystems rests upon accurately measuring the potential for C sequestration. Numerous methods are available for assessing soil C. Chemical analysis of field-collected samples using a dry combustion method is regarded as the standard method. However, conventional sampling of soil and their subsequent chemical analysis is expensive and time consuming. Furthermore, these methods are not sufficiently sensitive to identify small changes over time in response to alterations in management practices or changes in land use. Presently, several different in situ analytic methods are being developed purportedly offering increased accuracy, precision and cost-effectiveness over traditional ex situ methods. We consider that, at this stage, a comparative discussion of different soil C determination methods will improve the understanding needed to develop a standard protocol.

Laser-induced breakdown spectroscopy for the environmental determination of total carbon and nitrogen in soils

Soils from various sites have been analysed with the laser-induced breakdown spectroscopy (LIBS) technique for total elemental determination of carbon and nitrogen. Results from LIBS have been correlated to a standard laboratory-based technique (sample combustion), and strong linear correlations were obtained for determination of carbon concentrations. The LIBES technique was used on soils before and after acid washing, and the technique appears to be useful for the determination of both organic and inorganic soil carbon. The LIBS technique has the potential to be packaged into a field-deployable instrument.

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog

BackgroundDown-regulation of the caffeic acid 3-O-methyltransferase EC 2.1.1.68 (COMT) gene in the lignin biosynthetic pathway of switchgrass (Panicum virgatum) resulted in cell walls of transgenic plants releasing more constituent sugars after pretreatment by dilute acid and treatment with glycosyl hydrolases from an added enzyme preparation and from Clostridium thermocellum. Fermentation of both wild-type and transgenic switchgrass after milder hot water pretreatment with no water washing showed that only the transgenic switchgrass inhibited C. thermocellum. Gas chromatography–mass spectrometry (GCMS)-based metabolomics were undertaken on cell wall aqueous extracts to determine the nature of the microbial inhibitors.ResultsGCMS confirmed the increased concentration of a number of phenolic acids and aldehydes that are known inhibitors of microbial fermentation. Metabolomic analyses of the transgenic biomass additionally revealed the presence of a novel monolignol-like metabolite, identified as trans-3, 4-dimethoxy-5-hydroxycinnamyl alcohol (iso-sinapyl alcohol) in both non-pretreated, as well as hot water pretreated samples. iso-Sinapyl alcohol and its glucoside were subsequently generated by organic synthesis and the identity of natural and synthetic materials were confirmed by mass spectrometric and NMR analyses. The additional novel presence of iso-sinapic acid, iso-sinapyl aldehyde, and iso-syringin suggest the increased activity of a para-methyltransferase, concomitant with the reduced COMT activity, a strict meta-methyltransferase. Quantum chemical calculations were used to predict the most likely homodimeric lignans generated from dehydration reactions, but these products were not evident in plant samples.ConclusionsDown-regulation of COMT activity in switchgrass resulted in the accumulation of previously undetected metabolites resembling sinapyl alcohol and its related metabolites, but that are derived from para-methylation of 5-hydroxyconiferyl alcohol, and related precursors and products; the accumulation of which suggests altered metabolism of 5-hydroxyconiferyl alcohol in switchgrass. Given that there was no indication that iso-sinapyl alcohol was integrated in cell walls, it is considered a monolignol analog. Diversion of substrates from sinapyl alcohol to free iso-sinapyl alcohol, its glucoside, and associated upstream lignin pathway changes, including increased phenolic aldehydes and acids, are together associated with more facile cell wall deconstruction, and to the observed inhibitory effect on microbial growth. However, iso-sinapyl alcohol and iso-sinapic acid, added separately to media, were not inhibitory to C. thermocellum cultures.

Aerosol Measurement by Laser-Induced Plasma Technique: A Review

Literature on laser-induced plasma spectroscopy (LIPS) published since the 1960s is reviewed and presented in this report, although LIPS of solid samples has been emphasized in the past. The LIPS is found to be the most convenient technique for in-situ and real-time measurement of metal species in the gaseous and aerosol phases. This technique is a strong candidate for the develop ment of a next-generation field portable instrument for characterizing metal species from the emission sources as well as ambient environments. The instru ment can provide a highly resolved spatial and temporal data of significance to environmental and health research on metal and particle toxicity. An instrument based on LIPS can be a viable tool for continuously monitoring toxic metal emissions at an industrial source, for example. The wide range of lasers used and other experimental and theoretical factors to be considered in the design of a LIPS instrument for aerosol measurements was discussed in this report. Experimental r...

Detection of Chromium Aerosol Using Time-Resolved Laser-Induced Plasma Spectroscopy

Time-resolved laser-induced plasma spectroscopy (LIPS) has been used as a tool for the detection of chromium in aerosol. In this article, LIPS has been used to achieve the lowest limits of detection for chromium (400 ng/dscm) in droplets. A comparison with other LIPS instruments and inductively coupled plasma atomic emission spectroscopy (ICP-AES) shows that the limits of detection for chromium metal in aerosol range from 12 to 60 μg/dscm and 200 ng/dscm for LIPS and ICP-AES, respectively. We have studied the effects of laser wavelength, excitation energy, and optimum spectrometer delay time to optimize these low limits of detection. A Nd:YAG laser with output wavelengths of 1064, 532, and 266 nm has been used to study the effects of wavelength on laser energy and aerosol interactions—specifically, plasma initiation and efficiency of ionization in the detection of elemental species. Measured time-resolved spectra are used to establish the most appropriate time delay producing an optimum signal-to-background ratio.

Pseudomonas fluorescens Induces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness

Colonization of plants by nonpathogenic Pseudomonas fluorescens strains can confer enhanced defense capacity against a broad spectrum of pathogens. Few studies, however, have linked defense pathway regulation to primary metabolism and physiology. In this study, physiological data, metabolites, and transcript profiles are integrated to elucidate how molecular networks initiated at the root-microbe interface influence shoot metabolism and whole-plant performance. Experiments with Arabidopsis thaliana were performed using the newly identified P. fluorescens GM30 or P. fluorescens Pf-5 strains. Co-expression networks indicated that Pf-5 and GM30 induced a subnetwork specific to roots enriched for genes participating in RNA regulation, protein degradation, and hormonal metabolism. In contrast, only GM30 induced a subnetwork enriched for calcium signaling, sugar and nutrient signaling, and auxin metabolism, suggesting strain dependence in network architecture. In addition, one subnetwork present in shoots was enriched for genes in secondary metabolism, photosynthetic light reactions, and hormone metabolism. Metabolite analysis indicated that this network initiated changes in carbohydrate and amino acid metabolism. Consistent with this, we observed strain-specific responses in tryptophan and phenylalanine abundance. Both strains reduced host plant carbon gain and fitness, yet provided a clear fitness benefit when plants were challenged with the pathogen P. syringae DC3000.

Cellular Response of Shewanella oneidensis to Strontium Stress

ABSTRACT The physiology and transcriptome dynamics of the metal ion-reducing bacterium Shewanella oneidensis strain MR-1 in response to nonradioactive strontium (Sr) exposure were investigated. Studies indicated that MR-1 was able to grow aerobically in complex medium in the presence of 180 mM SrCl2 but showed severe growth inhibition at levels above that concentration. Temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase MR-1 cells shocked with 180 mM SrCl2 and analyzed for significant differences in mRNA abundance with reference to data for nonstressed MR-1 cells. Genes with annotated functions in siderophore biosynthesis and iron transport were among the most highly induced (>100-fold [P < 0.05]) open reading frames in response to acute Sr stress, and a mutant (SO3032::pKNOCK) defective in siderophore production was found to be hypersensitive to SrCl2 exposure, compared to parental and wild-type strains. Transcripts encoding multidrug and heavy metal efflux pumps, proteins involved in osmotic adaptation, sulfate ABC transporters, and assimilative sulfur metabolism enzymes also were differentially expressed following Sr exposure but at levels that were several orders of magnitude lower than those for iron transport genes. Precipitate formation was observed during aerobic growth of MR-1 in broth cultures amended with 50, 100, or 150 mM SrCl2 but not in cultures of the SO3032::pKNOCK mutant or in the abiotic control. Chemical analysis of this precipitate using laser-induced breakdown spectroscopy and static secondary ion mass spectrometry indicated extracellular solid-phase sequestration of Sr, with at least a portion of the heavy metal associated with carbonate phases.

Extraction of information from laser-induced breakdown spectroscopy spectral data by multivariate analysis

Laser-induced breakdown spectroscopy (LIBS) is being proposed more and more as a high-throughput technology to assess the elemental composition of materials. When a specific element is of interest, semiquantification is possible by building a calibration model using the emission line intensity of this element for known samples. However, a unique element has usually more than one emission line, and there are many examples where several emission lines used in combination give dramatically better results than any of the individual variables used alone. With a multivariate approach, models can be constructed that take into account all the emission lines related to a specific element; therefore more robust models can be developed. In this work, chemometric methods such as principal component analysis and partial least squares are proposed to resolve and extract useful information from the LIBS spectral data collected on biological materials.

Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach

BackgroundThe inherent recalcitrance of lignocellulosic biomass is one of the major economic hurdles for the production of fuels and chemicals from biomass. Additionally, lignin is recognized as having a negative impact on enzymatic hydrolysis of biomass, and as a result much interest has been placed on modifying the lignin pathway to improve bioconversion of lignocellulosic feedstocks.ResultsDown-regulation of the caffeic acid 3-O-methyltransferase (COMT) gene in the lignin pathway yielded switchgrass (Panicum virgatum) that was more susceptible to bioconversion after dilute acid pretreatment. Here we examined the response of these plant lines to milder pretreatment conditions with yeast-based simultaneous saccharification and fermentation and a consolidated bioprocessing approach using Clostridium thermocellum, Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Unlike the S. cerevisiae SSF conversions, fermentations of pretreated transgenic switchgrass with C. thermocellum showed an apparent inhibition of fermentation not observed in the wild-type switchgrass. This inhibition can be eliminated by hot water extraction of the pretreated biomass, which resulted in superior conversion yield with transgenic versus wild-type switchgrass for C. thermocellum, exceeding the yeast-based SSF yield. Further fermentation evaluation of the transgenic switchgrass indicated differential inhibition for the Caldicellulosiruptor sp. strains, which could not be rectified by additional processing conditions. Gas chromatography–mass spectrometry (GC-MS) metabolite profiling was used to examine the fermentation broth to elucidate the relative abundance of lignin derived aromatic compounds. The types and abundance of fermentation-derived-lignin constituents varied between C. thermocellum and each of the Caldicellulosiruptor sp. strains.ConclusionsThe down-regulation of the COMT gene improves the bioconversion of switchgrass relative to the wild-type regardless of the pretreatment condition or fermentation microorganism. However, bacterial fermentations demonstrated strain-dependent sensitivity to the COMT transgenic biomass, likely due to additional soluble lignin pathway-derived constituents resulting from the COMT gene disruption. Removal of these inhibitory constituents permitted completion of fermentation by C. thermocellum, but not by the Caldicellulosiruptor sp. strains. The reason for this difference in performance is currently unknown.

Elemental Analysis of Environmental and Biological Samples Using Laser‐Induced Breakdown Spectroscopy and Pulsed Raman Spectroscopy

Abstract Laser‐induced breakdown spectroscopy (LIBS) and a relatively new technique, pulsed Raman spectroscopy (P‐RAMS) are used in this investigation to measure the elemental composition of soils and heterogeneous biological matrices. The LIBS method was used effectively to determine the elemental concentration of carbon and nitrogen in soils, and the presence of metal contaminants in invertebrates. The P‐RAMS method was used in exploratory studies to assess prominent molecular vibration peaks from the same soils analyzed using LIBS. The P‐RAMS spectra for the different soils show a close relationship to the fraction of organic carbon in soils. Our results demonstrate that these techniques greatly facilitate elemental analysis of heterogeneous environmental and biological matrices by reducing sample preparation and analysis times. These techniques can also provide semi‐quantitative results on a regular basis and quantitative results in particular cases.