The dark side of orange: Multiorganismic continuum dynamics within a lichen of the Atacama Desert.

Over the decades our understanding of lichens has shifted to the fact that they are multiorganismic, symbiotic microecosystems, with their complex interactions coming to the fore due to recent advances in microbiomics. Here, we present a mutualistic-parasitic continuum dynamics scenario between an orange lichen and a lichenicolous fungus from the Atacama Desert leading to the decay of the lichen's photobiont and leaving behind a black lichen thallus. Based on isolation, sequencing, and ecophysiological approaches including metabolic screenings of the symbionts, we depict consequences upon infection with the lichenicolous fungus. This spans from a loss of the lichen's photosynthetic activity and an increased roughness of its surface to an inhibition of the parietin synthesis as a shared pathway between the photobiont and the mycobiont, including a shift of secondary metabolism products. This degree of relations has rarely been documented before, although lichenicolous fungi have been studied for over 200 years, adding an additional level to the view of interactions within lichens.

Early Ultrastructural Changes in Biopsies From Patients With Symptomatic CKD of Uncertain Etiology.

Introduction: Although the investigation of chronic kidney disease of uncertain etiology (CKDu) has identified many possible influencing factors in recent years, the exact pathomechanism of this disease remains unclear. Methods: In this study, we collected 13 renal biopsies from patients with symptomatic CKDu (Sym-CKDu) from Sri Lanka with well-documented clinical and socioeconomic factors. We performed light microscopy and electron microscopic evaluation for ultrastructural analysis, which was compared with 100 biopsies from German patients with 20 different kidney diseases. Results: Of the 13 Sri Lankan patients, 12 were men (92.3%), frequently employed in agriculture (50%), and experienced symptoms such as feeling feverish (83.3%), dysuria (83.3%), and arthralgia (66.6%). Light microscopic evaluation using activity and chronicity score revealed that cases represented early stages of CKDu except for 2 biopsies, which showed additional signs of diabetes. Most glomeruli showed only mild changes, such as podocyte foot process effacement on electron microscopy. We found a spectrum of early tubulointerstitial changes including partial loss of brush border in proximal tubules, detachment of tubular cells, enlarged vacuoles, and mitochondrial swelling associated with loss of cristae and dysmorphic lysosomes with electron-dense aggregates. None of these changes occurred exclusively in Sym-CKDu; however, they were significantly more frequent in these cases than in the control cohort. Conclusion: In conclusion, our findings confirm the predominant and early alterations of tubular structure in CKDu that can occur without significant glomerular changes. The ultrastructural changes do not provide concrete evidence of the cause of CKDu but were significantly more frequent in Sym-CKDu than in the controls.

Implications of Free and Occluded Fine Colloids for Organic Matter Preservation in Arable Soils.

Colloidal organo-mineral associations contribute to soil organic matter (OM) preservation and mainly occur in two forms: (i) as water-dispersible colloids that are potentially mobile (free colloids) and (ii) as building units of soil microaggregates that are occluded inside them (occluded colloids). However, the way in which these two colloidal forms differ in terms of textural characteristics and chemical composition, together with the nature of their associated OM, remains unknown. To fill these knowledge gaps, free and occluded fine colloids <220 nm were isolated from arable soils with comparable organic carbon (Corg) but different clay contents. Free colloids were dispersed in water suspensions during wet-sieving, while occluded colloids were released from water-stable aggregates by sonication. The asymmetric flow field-flow fractionation analysis on the free and occluded colloids suggested that most of the 0.6-220 nm fine colloidal Corg was present in size fractions that showed high abundances of Si, Al, and Fe. The pyrolysis-field ionization mass spectrometry revealed that the free colloids were relatively rich in less decomposed plant-derived OM (i.e., lipids, suberin, and free fatty acids), whereas the occluded colloids generally contained more decomposed and microbial-derived OM (i.e., carbohydrates and amides). In addition, a higher thermal stability of OM in occluded colloids pointed to a higher resistance to further degradation and mineralization of OM in occluded colloids than that in free colloids. This study provides new insights into the characteristics of subsized fractions of fine colloidal organo-mineral associations in soils and explores the impacts of free versus occluded colloidal forms on the composition and stability of colloid-associated OM.

Dissolved organic matter concentration, molecular composition, and functional groups in contrasting management practices of peatlands.

About 91,300 ha of peatlands has been rewetted in western Europe since the mid-1990s. Still, it is unknown how long-term rewetting alters the dissolved organic matter (DOM) concentration, molecular composition, and functional groups. We examined these DOM characteristics in three peatland types subjected to 47- to 231-yr drainage and 18- to 24-yr rewetting to address this knowledge gap. Cold water-extractable DOM was characterized by pyrolysis field ionization mass spectrometry (Py-FIMS) and X-ray absorption near-edge structure (XANES) spectroscopy. The dissolved organic carbon (DOC) concentration in the rewetted forest peatland was 2.7 times higher than in the drained forest peatland. However, rewetting decreased the DOC concentrations by 1.5 and 4 times in the coastal peatland and percolation mire, respectively, compared with their respective drained peatlands at the topsoil horizons. The Py-FIMS analysis revealed that all nine DOM compound classes' relative abundances differed between the rewetted and drained forest peatland with the lower relative abundances of the labile DOM compound classes in the rewetted forest peatlands. However, most DOM compound classes' relative abundances were similar between the rewetted and drained coastal peatlands and percolation mires. The XANES also revealed nine carbon and seven nitrogen functional groups with no apparent differences between the two contrasting management practices. The influence of drainage and rewetting on DOC concentration and molecular composition depends on peatland type, drainage period, rewetting intensity, and peat degradation status that should be considered in future research for understanding DOM transformation and transportation from degraded and restored peatland ecosystems.

Desert breath-How fog promotes a novel type of soil biocenosis, forming the coastal Atacama Desert's living skin.

The Atacama Desert is the driest non-polar desert on Earth, presenting precarious conditions for biological activity. In the arid coastal belt, life is restricted to areas with fog events that cause almost daily wet-dry cycles. In such an area, we discovered a hitherto unknown and unique ground covering biocenosis dominated by lichens, fungi, and algae attached to grit-sized (~6 mm) quartz and granitoid stones. Comparable biocenosis forming a kind of a layer on top of soil and rock surfaces in general is summarized as cryptogamic ground covers (CGC) in literature. In contrast to known CGC from arid environments to which frequent cyclic wetting events are lethal, in the Atacama Desert every fog event is answered by photosynthetic activity of the soil community and thus considered as the desert's breath. Photosynthesis of the new CGC type is activated by the lowest amount of water known for such a community worldwide thus enabling the unique biocenosis to fulfill a variety of ecosystem services. In a considerable portion of the coastal Atacama Desert, it protects the soil from sporadically occurring splash erosion and contributes to the accumulation of soil carbon and nitrogen as well as soil formation through bio-weathering. The structure and function of the new CGC type are discussed, and we suggest the name grit-crust. We conclude that this type of CGC can be expected in all non-polar fog deserts of the world and may resemble the cryptogam communities that shaped ancient Earth. It may thus represent a relevant player in current and ancient biogeochemical cycling.

Origin and alteration of organic matter in termite mounds from different feeding guilds of the Amazon rainforests.

The impact of termites on nutrient cycling and tropical soil formation depends on their feeding habits and related material transformation. The identification of food sources, however, is difficult, because they are variable and changed by termite activity and nest construction. Here, we related the sources and alteration of organic matter in nests from seven different termite genera and feeding habits in the Terra Firme rainforests to the properties of potential food sources soil, wood, and microepiphytes. Chemical analyses comprised isotopic composition of C and N, cellulosic (CPS), non-cellulosic (NCPS), and N-containing saccharides, and molecular composition screening using pyrolysis-field ionization mass spectrometry (Py-FIMS). The isotopic analysis revealed higher soil δ13C (-27.4‰) and δ15N (6.6‰) values in nests of wood feeding Nasutitermes and Cornitermes than in wood samples (δ13C = -29.1‰, δ15N = 3.4‰), reflecting stable-isotope enrichment with organic matter alterations during or after nest construction. This result was confirmed by elevated NCPS:CPS ratios, indicating a preferential cellulose decomposition in the nests. High portions of muramic acid (MurAc) pointed to the participation of bacteria in the transformation processes. Non-metric multidimensional scaling (MDS) revealed increasing geophagy in the sequence Termes < Embiratermes < Anoplotermes and increasing xylophagy for Cornitermes < Nasutitermes., and that the nest material of Constrictotermes was similar to the microepiphytes sample, confirming the report that Constrictotermes belongs to the microepiphyte-feeders. We therewith document that nest chemistry of rainforest termites shows variations and evidence of modification by microbial processes, but nevertheless it primarily reflects the trophic niches of the constructors.

Decontamination activity of ryegrass exudates towards bisphenol A in the absence and presence of dissolved natural organic matter.

Bisphenol A (BPA) is an endocrine disruptor compound widespread in terrestrial and aquatic systems of urbanized and industrialized regions. This study evaluated the capacity of ryegrass (Lolium perenne) aqueous exudates to degrade BPA at a concentration of 10 mg L(-1) both in the absence and in the presence of an organic fraction often coexisting with plant exudates, i.e., natural organic matter (NOM), tested at a concentration of 20 mg L(-1). In exudates alone, BPA degradation ceased after one day from the product addition when residual BPA resulted 65% of the initial BPA, whereas in exudates with the addition of NOM the degradation process continued for 4 days when residual BPA resulted 49%. Measurements of peroxidase and laccase activities in exudates suggested a significant involvement of these enzymes in BPA degradation. This finding was further confirmed by the almost complete absence of BPA degradation in aqueous exudates strongly acidified. In some BPA-contaminated exudates, chromatographic analysis revealed the presence of a newly formed compound identified as a BPA oxidation product by Fourier transform - ion cyclotron resonance mass spectrometry analysis. In conclusion, ryegrass exudates possess a relevant decontamination capacity towards BPA which persists and appears to be enhanced by the addition of NOM.

Hydrothermal carbonization of biomass residues: mass spectrometric characterization for ecological effects in the soil-plant system.

Hydrochars, technically manufactured by hydrothermal carbonization (HTC) of biomass residues, are recently tested in high numbers for their suitability as feedstock for bioenergy production, the bioproduct industry, and as long-term carbon storage in soil, but ecological effects in the soil-plant system are not sufficiently known. Therefore, we investigated the influence of different biomass residues and process duration on the molecular composition of hydrochars, and how hydrochar addition to soils affected the germination of spring barley ( L.) seeds. Samples from biomass residues and the corresponding hydrochars were analyzed by pyrolysis-field ionization mass spectrometry (Py-FIMS) and gaseous emissions from the germination experiments with different soil-hydrochar mixtures by gas chromatography/mass spectrometry (GC/MS). The molecular-level characterization of various hydrochars by Py-FIMS clearly showed that the kind of biomass residue influenced the chemical composition of the corresponding hydrochars more strongly than the process duration. In addition to various detected possible toxic substances, two independent mass spectrometric methods (Py-FIMS and GC/MS) indicated long C-chain aliphatic compounds which are typically degraded to the C-unit ethylene that can evoke phytotoxic effects in high concentrations. This showed for the first time possible chemical compounds to explain toxic effects of hydrochars on plant growth. It is concluded that the HTC process did not result in a consistent product with defined chemical composition. Furthermore, possible toxic effects urgently need to be investigated for each individual hydrochar to assess effects on the soil organic matter composition and the soil biota before hydrochar applications as an amendment on agricultural soils.

Impact of ectomycorrhizal colonization and rust infection on the secondary metabolism of poplar (Populus trichocarpa x deltoides).

Fungal colonization can significantly affect the secondary metabolism of the host plants. We tested the impact of a common below-ground symbiosis, i.e., ectomycorrhiza formation, on poplar leaf chemical components that are involved in the defence against a common disease, i.e., rust fungi, in N-deficient soil. A rust-susceptible poplar clone (Populus trichocarpa × deltoides 'Beaupré') was (a) non-associated with ectomycorrhizal fungus (EM) Hebeloma mesophaeum (Pers.) Quélet MÜN and non-infected with rust fungus Melampsora larici-populina Kleb. (isolate 98AG31), (b) associated with EM, (c) inoculated with rust fungus and (d) associated with EM and inoculated with rust fungus. Poplar leaves were analysed by photometric and mass spectrometric techniques (liquid chromatography-tandem mass spectrometry (LC-MS/MS), pyrolysis-field ionization mass spectrometry (Py-FIMS)). Both rust infection and mycorrhiza formation led to increased proportions of condensed tannins in relation to total phenolics (13% in the control, 18-19% in the fungal treatments). In contrast, salicylic acid concentration (6.8 µg g(-1) in the control) was higher only in the rust treatments (17.9 and 25.4 µg g(-1) with rust infection). The Py-FIMS analysis revealed that the rust-infected treatments were significantly separated from the non-rust-infected treatments on the basis of six flavonoids and one lipid. The relative abundance of these components, which have known functions in plant defence, was decreased after rust infection of non-mycorrhizal plants, but not in mycorrhizal plants. The results indicate that the ectomycorrhizal formation compensated the rust infection by a decrease in the flavonoid syntheses. The study provides new evidence for an interactive response of mycorrhizal colonization and infection with rust fungi in the metabolism of poplar.

Solid-phase cadmium speciation in soil using L3-edge XANES spectroscopy with partial least-squares regression.

Cadmium (Cd) has a high toxicity and resolving its speciation in soil is challenging but essential for estimating the environmental risk. In this study partial least-square (PLS) regression was tested for its capability to deconvolute Cd L(3)-edge X-ray absorption near-edge structure (XANES) spectra of multi-compound mixtures. For this, a library of Cd reference compound spectra and a spectrum of a soil sample were acquired. A good coefficient of determination (R(2)) of Cd compounds in mixtures was obtained for the PLS model using binary and ternary mixtures of various Cd reference compounds proving the validity of this approach. In order to describe complex systems like soil, multi-compound mixtures of a variety of Cd compounds must be included in the PLS model. The obtained PLS regression model was then applied to a highly Cd-contaminated soil revealing Cd(3)(PO(4))(2) (36.1%), Cd(NO(3))(2)·4H(2)O (24.5%), Cd(OH)(2) (21.7%), CdCO(3) (17.1%) and CdCl(2) (0.4%). These preliminary results proved that PLS regression is a promising approach for a direct determination of Cd speciation in the solid phase of a soil sample.

Composition of organic matter in particle size fractionated pig slurry.

Pig slurry is a heterogeneous mixture of different particle sizes that will have different mobility in soil. Therefore, a physically fractionated pig slurry sample was analysed, e.g. using pyrolysis-field ionisation mass spectrometry (Py-FIMS) in an effort to identify relationships between particle size and composition of organic matter. The presumably most mobile fractions in soils (<63 microm) accounted for approximately 50% of slurry dry matter and were dominated by lignins, and N-containing compounds. Sterols were especially abundant in the larger-sized fractions, which corresponds to their reported distribution in soils and surface waters. The averaged molecular masses indicated similarities of fractions <10 microm to aquatic humic substances and increasing content of plant material with increasing particle size. A statistical analysis of the compound class distribution revealed that the analysis of three particle size fractions is essential for the assessment of the composition and properties of slurry constituents.

Phosphorus L(2,3)-edge XANES: overview of reference compounds.

Synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy is becoming an increasingly used tool for the element speciation in complex samples. For phosphorus (P) almost all XANES measurements have been carried out at the K-edge. The small number of distinctive features at the P K-edge makes in some cases the identification of different P forms difficult or impossible. As indicated by a few previous studies, the P L(2,3)-edge spectra were richer in spectral features than those of the P K-edge. However, experimentally consistent spectra of a wide range of reference compounds have not been published so far. In this study a library of spectral features is presented for a number of mineral P, organic P and P-bearing minerals for fingerprinting identification. Furthermore, the effect of radiation damage is shown for three compounds and measures are proposed to reduce it. The spectra library provided lays a basis for the identification of individual P forms in samples of unknown composition for a variety of scientific areas.

A new rapid micro-method for the molecular-chemical characterization of rhizodeposits by field-ionization mass spectrometry.

Time-consuming investigation of rhizodeposit composition by leaching, freeze-drying of leachate, and pyrolysis-field ionization mass spectrometry (Py-FIMS) of solid samples was replaced by direct Py-FIMS of a 5 microL liquid rhizodeposit sample which was evaporated overnight in the quartz tube of a mass spectrometer inlet system. Application of this new rapid technique to a set of 14 liquid rhizodeposit samples from maize (Zea mays L.), leached twice with a time lag of 80 min, unequivocally showed the effect of soil texture on the chemical composition of the rhizodeposits. Irrespective of leaching time, a partial least-squares analysis separated the Py-FI mass spectra of the maize rhizodeposits leached from a soil from those leached from a soil + quartz sand-mixture (prepared by addition of 50% w/w quartz sand to the original soil). The signals which had the strongest discrimination power and were significantly enriched in leachates from the soil + quartz sand were assigned to sugars, peptides and polyamines. Mass signals of putrescine and cadaverine, a priori not expected in the rhizodeposits, were indicators of modified root environment and rhizosphere processes in the soil + quartz sand. In conclusion, the new rapid mass spectrometric profiling method is suitable for rhizosphere research because it requires very small sample volumes, is fast and highly sensitive to detect and quantify a wide range of a priori expected and unexpected organic substances.

Nitrogen K-edge XANES - an overview of reference compounds used to identify unknown organic nitrogen in environmental samples.

The chemical nature of soil organic nitrogen (N) is still poorly understood and one-third to one-half of it is typically classified as ;unknown N'. Nitrogen K-edge XANES spectroscopy has been used to develop a systematic overview on spectral features of all major N functions in soil and environmental samples. The absolute calibration of the photon energy was completed using the 1s --> pi* transitions of pure gas-phase N(2). On this basis a library of spectral features is provided for mineral N, nitro N, amino acids, peptides, and substituted pyrroles, pyridines, imidazoles, pyrazoles, pyrazines, pyrimidines and purine bases. Although N XANES was previously considered ;non-destructive', effects of radiation damage were shown for two compound classes and an approach was proposed to minimize it. This new evidence is integrated into a proposal for the evaluation spectra from environmental samples with unknown composition. Thus a basis is laid to develop N K-edge XANES as a complementary standard research method to study the molecular composition and ecological functions of ;unknown N' in soil and the environment.

Pyrolysis-field ionization mass spectrometry of rhizodeposits - a new approach to identify potential effects of genetically modified plants on soil organisms.

The objectives of the present study were (1) to investigate the qualitative composition of rhizodeposits leached from soils cropped with non-transgenic and genetically modified (GM) potatoes, and disclose if there were GM-specific modifications in potato rhizodeposition, and (2) to compare these results with conventional bulk parameters of microbial activity in soil. We have raised potatoes from a non-transgenic line (Solanum tuberosum L. cv. Désirée) and three GM lines, which expressed a gene for the resistance to kanamycin (DLH 9000) and a gene for T4 lysozyme (DL10 and DL12). A sandy soil placed in 340 cm3-"CombiSart" containers was used, from which the rhizodeposit was leached after a six-week growth period. The freeze-dried leachates were analyzed by pyrolysis-field ionization mass spectrometry (Py-FIMS). The Py-FI mass spectra gave detailed molecular-chemical information about the composition of leachates, indicating that the potato growth generally altered the composition of the soil solution. Moreover, a principal component analysis of the mass spectra showed differences between the leachates from the non-transgenic parent line and the GM potatoes as well as among the latter group. However, these differences in molecular composition could not be assigned to the release of T4-lysozyme into soil. Dehydrogenase activity and substrate-induced soil respiration as more common bulk parameters of soil microbial activity failed to disclose any significant effects of the various potatoes grown. The limitations of the described rhizodeposit leaching and analysis for risk assessment of GM potato cropping under field conditions are discussed critically. However, it could be concluded that the Py-FI mass spectrometric "fingerprint" can be developed as a fast, comprehensive, highly sensitive and reproducible analytical approach to discern any effects GM-crops may exert on soil ecological parameters.

Characterization of different decomposition stages of biowaste using FT-IR spectroscopy and pyrolysis-field ionization mass spectrometry.

The decomposition stage and stabilization of organic matter in biowaste (mixture of yard waste and kitchen waste), originating from an open windrow process, were investigated using Fourier transform infrared (FT-IR) spectroscopy and pyrolysis-field ionization mass spectrometry (Py-FIMS). These investigations provided detailed information about chemical constituents and their behavior during the composting process. The chemical compounds were classified by their molecular signals in Py-FIMS. Multivariate statistical analysis revealed, that during the composting process, the group containing lipids, fatty acids and other chemical compounds with aliphatic skeletons changed the most. Corresponding with Py-FIMS findings changes were observed in absorbance bands of infrared spectra that reflect this group of organic compounds: the aliphatic methylene bands at 2925 and 2850 cm(-1), the band of C=O vibrations of carboxylates at 1640 cm(-1) , the O-H in-plane bend of carboxylic acids, the CO2 stretch of carboxylates and the CH2 group of alkanes at around 1430 cm(-1). During decomposition these bands decreased up to a steady level that indicated stabilization. The band at 1260-1240 cm(-1) that can be assigned to the C--O stretch of carboxylic acids or to the C-N stretch of amides and the band of aromatic amines at 1320 cm(-1) disappeared completely. The nitrate band at 1384 cm(-1) appeared at a later stage of the composting process. The relative increase of chemical compounds like moieties of lignin, humic acids and tannins in the composted material contributed to the aromatic C=C band at around 1640 cm(-1).