Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations.

Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.

Study of zeolite anti-caking effects for fertilisers by 1H low-field NMR.

Caking is associated with the consolidation of dry powder and granules, leading to losses of function and/or quality. It has been object of studies in the pharmaceutical, food and fertiliser areas since 1920's because of its significant impact on product quality and value. Caking has been described as a three-step event consisting of sorption-dissolution-recrystallisation phases and constitutes a critical factor in fertilisers losses during storage while also hampering fertiliser application. Current methods for the evaluation of water sorption dynamics are expensive, time-consuming and/or inaccurate. This manuscript describes an unprecedented application of low-field 1H NMR relaxometry for the kinetic study of humidity uptake, in real-time, by urea mixed with different concentrations of an anti-caking agent (zeolite). The proposed method allows to follow the water uptake in different domains of the mixed fertiliser/zeolite samples. To our knowledge, this dynamic has not been observed and quantified so far in real-time. Furthermore, we presented the use of 2D-ILT for kinetic studies, being the first dimension the usual transverse relaxation and the second dimension the kinetic one. With this approach, the NMR relaxation times T2 correlated to time constants associated with the uptake kinetics of the water. This method could be extended to several kinetic studies and experiments with temperature variation. Depending on the kinetics of the studied process, the kernel of the Laplace transform must be suitably adapted.

Improved data efficiency for NMR diffusion-relaxation processing.

Two dimensional diffusion and transverse (T2) NMR relaxation measurements are effective for a variety of research and industrial processes. Conversion of the measurements into a D-T2 map is performed using an inverse integral transformation. A difficulty with D-T2 estimation from data acquired without pulsed field gradients (using, for example, the inherent static field gradient of a single-sided magnet) is that the diffusion and relaxation kernels are coupled. One commonly used solution is to introduce a time offset to enable the kernels to be decoupled, but this has the undesirable results of causing some of the data, and a large proportion of the signal energy, to become unusable. This paper presents two methods of processing the data that do not require this wastage. Both methods are based on insights that arise from considering the linear operator that describes the forwards integral transformation. One method involves data compression, while the other method is an application (that we call FLINT) of the fast iterative soft thresholding algorithm. Both methods are able to use all of the available data. The paper demonstrates the improved accuracy that results from these methods on simulated data, as well as the improved discovery of important features on measured data.

A two-year incubation study of transformations of crop residues into soil organic matter (SOM) and a procedure for the sequential isolation and the fractionation of components of SOM.

Maize (Zea mays) stover, with its natural 13C abundance, was incubated for two years in a gravelly brown earth sandy loam soil that had been under long term cultivation to wheat (Triticum aestivum) for more than 30 years. The relative abundances of 13C in the maize amendment allowed the contributions of the stover to be traced in the components of soil organic matter (SOM) isolated and fractionated using a sequential exhaustive extraction (SEE) process that gave 16 distinct fractions. These were caracterised using elemental, δ13C, FTIR, and 13C NMR analyses. Emphasis is placed on results for two years of incubation but to some extent data are compared with those for similar fractions taken after one year of incubation. Amounts of maize-derived organic carbon in the humic (HA) and fulvic (FA) isolates were more than twice those in the fractions after one year of incubation. The NMR results highlighted compositional differences between the fractions and showed increased contributions of lignin to the HAs and FAs (and especially in the cases of the HAs) as pH increased, and it was evident that humification was taking place after two years of incubation. The most recalcitrant humin fraction, isolated in the final solvent in the sequence, dimethylsulphoxide (DMSO) and sulfuric acid, is composed predominantly of methylene moieties, is compositionally and structurally very different from the humic and hydrophilic isolates, but identical to that which did not dissolve in the solvent. That suggests that exhaustively pre-extracting soil with the NaOH/urea solvent system used will allow a truly representative humin to be obtained using the DMSO/acid solvent system.

Biochar amendment improves degraded pasturelands in Brazil: environmental and cost-benefit analysis.

Most deforested lands in Brazil are occupied by low-productivity cattle ranching. Brazil is the second biggest meat producer worldwide and is projected to increase its agricultural output more than any other country. Biochar has been shown to improve soil properties and agricultural productivity when added to degraded soils, but these effects are context-dependent. The impact of biochar, fertilizer and inoculant on the productivity of forage grasses in Brazil (Brachiaria spp. and Panicum spp.) was investigated from environmental and socio-economic perspectives. We showed a 27% average increase in Brachiaria production over two years but no significant effects of amendment on Panicum yield. Biochar addition also increased the contents of macronutrients, soil pH and CEC. Each hectare amended with biochar saved 91 tonnes of CO2eq through land sparing effect, 13 tonnes of CO2eq sequestered in the soil, equating to U$455 in carbon payments. The costs of biochar production for smallholder farmers, mostly because of labour cost, outweighed the potential benefits of its use. Biochar is 617% more expensive than common fertilizers. Biochar could improve productivity of degraded pasturelands in Brazil if investments in efficient biochar production techniques are used and biochar is subsidized by low emission incentive schemes.

Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids.

Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The mevalonate pathway was also activated, thus increasing phytosterol synthesis. The improvement in cellular metabolism observed with PGPB+HA was compatible with high levels of vitamins. Glucuronate and amino sugars were stimulated in addition to the products and intermediary compounds of tricarboxylic acid metabolism. Lipids and amino acids were the main compounds induced by co-inoculation in addition to antioxidants, stress-related metabolites, and compounds involved in cellular redox. The primary compounds observed in each treatment were identified, and the effect of co-inoculation (HA+PGPB) on metabolite levels was discussed.

Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies.

BACKGROUND: Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. RESULTS: Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements. CONCLUSIONS: A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.

Characterization of transformations of maize residues into soil organic matter.

An awareness of the transformation of plant residues returned to cultivated soils is vital for a better understanding of carbon cycles, the maintenance of soil fertility and the practice of a sustainable agriculture. The transformation of maize (Zea mays L) straw residues into soil organic matter (SOM) in a one year incubation experiment was studied in a soil that had been under long term cultivation with wheat (Triticum aestivum L) for >30years. A novel sequential exhaustive extraction and fractionation procedure isolated a series of fractions of SOM. The samples were characterized by elemental and δ13C analyses, by amino acids and neutral sugars analyses, by Fourier transformed infrared (FTIR) spectrometry, and by solid state 13C nuclear magnetic resonance (NMR) spectroscopy and with chemical shift anisotropy (CSA) -filter and dipolar dephasing (DD) spectral editing NMR techniques. The δ13C data indicated that 59% and 38% of the newly transformed organic carbon was in the humic and fulvic acid fractions, respectively, and in general a greater proportion of the transformed carbon was in the fractions isolated at the higher pH values. Results for SOM fractions from the amended soil indicate dominant contributions from carbohydrate and lignin-like material, and that can be clearly identified by FTIR, CP/TOSS, and spectral editing of CSA-filter and DD. The compositions of the fractions from the amended and non-amended soils fractions can be clearly differentiated using principal component analysis (PCA) for the data collected. The sequential extraction procedure showed that the hydrophilicity of humic fractions increased as the result of the maize amendment, and the aromaticity of the fraction decreased. The data may give some indications of transformations that take place during humification processes.

Determination of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in Brazilian cow milk.

The determination of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in raw cow milks have never been reported in Brazil. Since the consumption of food of animal origin, including milk and dairy products, is the major source of human exposure to these compounds, this study aimed to establish the levels and profile of seven PCDDs and ten PCDFs in raw cow milk samples collected in eight Brazilian states which among the major milk producer states. Raw milk samples were collected in 34 different dairy cattle farms during the summer of 2013. All PCDD/Fs congeners were found at least in some of the 34 samples studied. The octa-chlorinated congeners (OCDD and OCDF) were ubiquitous and also present in high concentrations. The mean values of WHO-TEQ1998;2005 were respectively 1.66 and 1.36pgTEQg-1 fat and samples taken in São Paulo showed the highest WHO-TEQ values (2.46 TEQ1998g-1 fat and 2.10pgTEQ2005g-1 fat). Although all samples showed some contamination level, all values were below the limit established by European Union for total PCDD/Fs in cow milk (3pgWHO-TEQ1998g-1 fat). Principal Component Analysis (PCA) showed that OCDD and OCDF were responsible for 73% and 20% of the total data variance, respectively and they presented an independent behavior, probably as a result of distinct origins. The use of TEQ as weights in the PCA, revealed the importance of the penta-chloro congeners and it was possible to identify sample distribution patterns probably associated with the main PeCDD and PeCDF. The importance of local sources to PCDD/Fs concentrations is still to be evaluated and determined.

Isolation and fractionation of soil humin using alkaline urea and dimethylsulphoxide plus sulphuric acid.

Humin, the most recalcitrant and abundant organic fraction of soils and of sediments, is a significant contributor to the stable carbon pool in soils and is important for the global carbon budget. It has significant resistance to transformations by microorganisms. Based on the classical operational definition, humin can include any humic-type substance that is not soluble in water at any pH. We demonstrate in this study how sequential exhaustive extractions with 0.1 M sodium hydroxide (NaOH) + 6 M urea, followed by dimethylsulphoxide (DMSO) + 6% (v/v) sulphuric acid (H(2)SO(4)) solvent systems, can extract 70-80% of the residual materials remaining after prior exhaustive extractions in neutral and aqueous basic media. Solid-state (13)C NMR spectra have shown that the components isolated in the base + urea system were compositionally similar to the humic and fulvic acid fractions isolated at pH 12.6 in the aqueous media. The NMR spectra indicated that the major components isolated in the DMSO + H(2)SO(4) medium had aliphatic hydrocarbon associated with carboxyl functionalities and with lesser amounts of carbohydrate and peptide and minor amounts of lignin-derived components. The major components will have significant contributions from long-chain fatty acids, waxes, to cuticular materials. The isolates in the DMSO + H(2)SO(4) medium were compositionally similar to the organic components that resisted solvation and remained associated with the soil clays. It is concluded that the base + urea system released humic and fulvic acids held by hydrogen bonding or by entrapment within the humin matrix. The recalcitrant humin materials extracted in DMSO + H(2)SO(4) are largely biological molecules (from plants and the soil microbial population) that are likely to be protected from degradation by their hydrophobic moieties and by sorption on the soil clays. Thus, the major components of humin do not satisfy the classical definitions for humic substances which emphasise that these arise from microbial or chemical transformations in soils of the components of organic debris.

Compositional changes in the hydrophobic acids fraction of drainage water from different land management practices.

Dissolved organic matter (DOM) can play a key role in many environmental processes, including carbon cycling, nutrient transport and the fates of contaminants and of agrochemicals. Hydrophobic acids (Ho), the major components of the DOM, were recovered from the drainage waters from well-drained (WDS) and poorly-drained (PDS) Irish grassland soils in lysimeters, amended with N fertiliser (F) and with bovine urine (U) and were studied using 1D and 2D solution-state Nuclear Magnetic Resonance (NMR) spectroscopy. The Diffusion Edited (DE) (1)H NMR spectra indicated that the Ho consisted largely of larger molecules, or of molecules that formed rigid aggregates, and the 1D and the 2D (Heteronuclear Multiple Quantum Coherence - HMQC, the Total Correlation Spectroscopy - TOCSY, and the Nuclear Overhauser Effect - NOESY) spectra indicated that the samples were composed of lignin residues, carbohydrates, protein/peptides, and aliphatic components derived from plant waxes/cuticular materials and from microbial lipids. The F amendments increased the concentrations of Ho in the waters by 1.5 and 2.5 times those in the controls in the cases of WDS and PDS, respectively. The lignin-derived components were increased by 50% and 300% in the cases of the Ho from the WDS and PDS, respectively. Applications of F + U decreased the losses of Ho, (compared to the F amendments alone) and very significantly decreased those of the lignin-derived materials, indicating that enhanced microbial activity from U gave rise to enhanced metabolism of the Ho components, and especially of lignin. In contrast the less biodegradable aliphatic components containing cuticular materials increased as the result of applications of F + U. This study helps our understanding of how management practices influence the movement of C between terrestrial and aquatic environments.

Unraveling the structural components of soil humin by use of solution-state nuclear magnetic resonance spectroscopy.

Humin is the most recalcitrant and least understood fraction of soil organic matter. By definition, humin is that fraction not extracted by traditional aqueous alkaline soil extractants. Here we show that > or = 70% of the traditional humin fraction is solubilized when 0.1 M NaOH + 6 M urea and dimethyl sulfoxide (DMSO) + 6% H2SO4 are used in series after conventional extraction. Multidimensional solution-state NMR is applied in this study to gain an understanding of the major constituents present in these "solubilized humin fractions". The spectra indicated strong contributions from five main categories of components, namely, peptides, aliphatic species, carbohydrates, peptidoglycan, and lignin. Diffusion edited spectroscopy indicated that all species are present as macromolecules (or stable aggregate species). Although the distribution of the components is generally similar, peptidoglycan is present at significant levels supporting a higher microbial contribution to humin than to humic and fulvic fractions. The abundance of plant- and microbial-derived materials found does not exclude "humic" materials (e.g., oxidized lignin) or the presence of novel compounds at lower concentrations but suggests that a large proportion of humin is formed from classes of known compounds and parent biopolymers.

Studies of the compositions of humic acids from Amazonian Dark Earth soils.

The compositions of humic acids (HAs) isolated from cultivated and forested "Terra Preta de Indio" or Amazonian Dark Earth soils (anthropogenic soils) were compared with those from adjacent non-anthropogenic soils (control soils) using elemental and thermogravimetric analyses, and a variety of solid-state nuclear magnetic resonance techniques. The thermogravimetric index, which indicates the molecular thermal resistance, was greater for the anthropogenic soils than for the control soils suggesting polycyclic aromatic components in the former. The cultivated anthropogenic soils were more enriched in C and depleted in H than the anthropogenic soils under forest, as the result of the selective degradation of aliphatic structures and the possible enrichment of H-deficient condensed aromatic structures. The combination of variable amplitude cross-polarization (VACP) and chemical shift anisotropy with total suppression of spinning sidebands experiments with composite pi pulses could be used to quantify the aromaticity of the HAs from the anthropogenic soils. From principal component analysis, using the VACP spectra, it was possible to separate the different constituents of the HAs, such as the carboxylated aromatic structures, from the anthropogenic soils and plant derived compounds. The data show that the HAs from anthropogenic soils have high contents of aryl and ionisable oxygenated functional groups, and the major functionalities from adjacent control soils are oxygenated functional groups from labile structures (carbohydrates, peptides, and with evidence for lignin structures). The anthropogenic soils HAs can be considered to be more recalcitrant, and with more stable reactive functional groups which may, in part, explain their more sustainable fertility due to the organic matter contribution to the soil cation exchange capacity.

Characterisation of black carbon-rich samples by (13)C solid-state nuclear magnetic resonance.

There are difficulties in quantifying and characterising the organic matter (OM) in soils that contain significant amounts of partially oxidised char or charcoal materials. The anthropogenic black carbon (BC), such as that found in the Terra Preta de Indio soils of the Amazon region, is a good example of the OM that is difficult to analyse in such soils. (13)C direct polarisation/magic angle spinning (DP/MAS) at high MAS frequency, (1)H-(13)C cross polarisation (CP)/MAS with total suppression of spinning sidebands (TOSS), and chemical shift anisotropy (CSA) filter nuclear magnetic resonance techniques have been applied successfully for quantifying the different components of OM. However, because pyrogenic materials present strong local magnetic susceptibility heterogeneities, the use of CSA-filter and TOSS make the pulse sequences very sensitive to imperfections in the pi pulses. In this study, the DP/MAS pulse sequence was replaced by a CP with a radio frequency ramp--variable amplitude CP (VACP)--VACP/MAS pulse sequence, and composite pi pulses were used in the CSA-filter and TOSS pulse sequences. In that way, the component functionalities in a humic acid from a BC soil were successfully determined. The spectrometer time needed was greatly decreased by employing this VACP/MAS technique. This development provides an accurate method for characterising BC-rich samples from different origins.