Field-Scale Pattern of Denitrifying Microorganisms and N2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil.

More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.

High emissions of greenhouse gases from grasslands on peat and other organic soils.

Drainage has turned peatlands from a carbon sink into one of the world's largest greenhouse gas (GHG) sources from cultivated soils. We analyzed a unique data set (12 peatlands, 48 sites and 122 annual budgets) of mainly unpublished GHG emissions from grasslands on bog and fen peat as well as other soils rich in soil organic carbon (SOC) in Germany. Emissions and environmental variables were measured with identical methods. Site-averaged GHG budgets were surprisingly variable (29.2 ± 17.4 t CO2 -eq. ha-1  yr-1 ) and partially higher than all published data and the IPCC default emission factors for GHG inventories. Generally, CO2 (27.7 ± 17.3 t CO2  ha-1  yr-1 ) dominated the GHG budget. Nitrous oxide (2.3 ± 2.4 kg N2 O-N ha-1  yr-1 ) and methane emissions (30.8 ± 69.8 kg CH4 -C ha-1  yr-1 ) were lower than expected except for CH4 emissions from nutrient-poor acidic sites. At single peatlands, CO2 emissions clearly increased with deeper mean water table depth (WTD), but there was no general dependency of CO2 on WTD for the complete data set. Thus, regionalization of CO2 emissions by WTD only will remain uncertain. WTD dynamics explained some of the differences between peatlands as sites which became very dry during summer showed lower emissions. We introduced the aerated nitrogen stock (Nair ) as a variable combining soil nitrogen stocks with WTD. CO2 increased with Nair across peatlands. Soils with comparatively low SOC concentrations showed as high CO2 emissions as true peat soils because Nair was similar. N2 O emissions were controlled by the WTD dynamics and the nitrogen content of the topsoil. CH4 emissions can be well described by WTD and ponding duration during summer. Our results can help both to improve GHG emission reporting and to prioritize and plan emission reduction measures for peat and similar soils at different scales.

Plasmodium falciparum antioxidant protein as a model enzyme for a special class of glutaredoxin/glutathione-dependent peroxiredoxins.

BACKGROUND: Peroxiredoxins are important heterogeneous thiol-dependent hydroperoxidases with a variety of isoforms and enzymatic mechanisms. A special subclass of glutaredoxin/glutathione-dependent peroxiredoxins has been discovered in bacteria and eukaryotes during the last decade, but the exact enzymatic mechanisms of these enzymes remain to be unraveled. METHODS: We performed a comprehensive analysis of the enzyme kinetics and redox states of one of these glutaredoxin/glutathione-dependent peroxiredoxins, the antioxidant protein from the malaria parasite Plasmodium falciparum, using steady-state kinetic measurements, site-directed mutagenesis, redox mobility shift assays, gel filtration, and mass spectrometry. RESULTS: P. falciparum antioxidant protein requires not only glutaredoxin but also glutathione as a true substrate for the reduction of hydroperoxides. One peroxiredoxin cysteine residue and one glutaredoxin cysteine residue are sufficient for catalysis, however, additional cysteine residues of both proteins result in alternative redox states and conformations in vitro with implications for redox regulation. Our data furthermore point to a glutathione-dependent peroxiredoxin activation and a negative subunit cooperativity. CONCLUSIONS: The investigated glutaredoxin/glutathione/peroxiredoxin system provides numerous new insights into the mechanism and redox regulation of peroxiredoxins. GENERAL SIGNIFICANCE: As a member of the special subclass of glutaredoxin/glutathione-dependent peroxiredoxins, the P. falciparum antioxidant protein could become a reference protein for peroxiredoxin catalysis and regulation.

Land-use induced soil carbon stabilization at the expense of rock derived nutrients: insights from pristine Andean soils.

Soils contain significantly more carbon than the atmosphere, hence we should understand how best to stabilize it. Unfortunately, the role of human interventions on soil organic carbon (SOC) persistence in the Anthropocene remains vague, lacking adequate sites that allow unbiased direct comparisons of pristine and human influenced soils. Here we present data from a unique study system in the High Andes that guarantees pristineness of the reference sites by physical inaccessibility through vertical cliffs. By comparing the isotopic signatures of SOC, mineral related carbon stabilization, and soil nutrient status across grazed versus pristine soils, we provide counterintuitive evidence that thousands of years of pastoralism increased soil C persistence. Mineral associated organic carbon (MAOC) was significantly higher in pastures. Land use increased poorly crystalline minerals (PCM's), of which aluminum correlated best with MAOC. On the other hand, human's acceleration of weathering led to acidification and higher losses of cations. This highlights a dilemma of lower soil quality but higher persistence of SOC due to millennia of pastoralism. The dynamics of soil genesis in the Anthropocene needs better understanding, but if human-induced weathering proves generally to promote soil carbon persistence it will need to be included in climate-soil feedback projections.

SLA/LP/tRNP((Ser)Sec) antigen in autoimmune hepatitis: identification of the native protein in human hepatic cell extract.

A diagnostic subgroup of AIH type 1 is characterized by specific serum antibodies against soluble liver protein. The respective autoantigen was named SLA/LP/tRNP((Ser)Sec), after three homologous recombinant polypeptides were isolated from expression gene libraries. We analyzed human cultured liver cells for the human homologue of recombinant SLA/LP/tRNP((Ser)Sec) by antigen purification. In addition, a monoclonal antibody was generated against recombinant SLA-p35, a truncated recombinant SLA-reactive polypeptide. With a positive patient serum, immune affinity chromatography was performed on the 52 kD-SLA main antigenic determinant pre-enriched by ion exchange chromatography. By mass spectrometry, the 52 kD-SLA/LP/tRNP ((Ser)Sec) autoantigen was unambiguously identified in the purification product. The identity of the recombinant SLA-p35 and its human homologue was further confirmed by a specific signal of the anti SLA-p35 monoclonal antibody with purified human SLA/LP/tRNP((Ser)Sec). The 48 kD-SLA species frequently comigrating in SLA-immunoblotting however was not identified by either approach. We conclude that the native counterpart of recombinant tRNP((Ser)(Sec)) indeed is detectable with a molecular weight of 52 kD in soluble liver extract of human cells as the major antigenic component of SLA/LP/tRNP((Ser)Sec).

First evidence of terrestrial ambrein formation in human adipocere.

To date, the only known occurrence of ambrein, an important perfumery organic molecule, is in coproliths found in about one in a hundred sperm whales. Jetsam ambergris coproliths from the whale are also found occasionally on beaches worldwide. Here we report on the surprising occurrence of ambrein in human adipocere. Adipocere is a waxy substance formed post-mortem during incomplete anaerobic decomposition of soft tissues. Adipocere samples obtained from grave exhumations were analysed using gas chromatography-mass spectrometry (GC-MS). In addition to the typical fatty acids of adipocere, lesser amounts of ambrein were identified in the samples, in abundances similar to those of the major accompanying faecal steroids. The distribution of these compounds suggests that ambrein was produced post-mortem during the microbial decomposition of faecal residues and tissues. It is assumed that the adipocere matrix of saturated fatty acidsaided the preservation of ambrein over extended periods of time, because adipocere is stable against degradation. The association of ambrein formation in ageing faecal material, under moist, oxygen-depleted conditions, now requires more attention in studies of other mammalian and geological samples. Indeed, ambrein and its transformation products may be useful novel chemical indicators of aged faecal matter and decomposed bodies.

Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman.

Biological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. The results were interpreted based on the environmental parameters of the different sites. Whereas at lowland sites, mainly cyanobacteria-dominated biocrusts were observed, both cyanobacteria- and lichen-dominated biocrusts occurred at mountain sites. The majority of bacterial sequences (32-83% of total sequences) belonged to Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes, whereas fungal sequences belonged to Ascomycota, Basidiomycota, and Chytridiomycota (>95%). With biocrust development, a notable increase in cyanobacterial and decrease in actinobacterial proportions was observed for cyanobacteria-dominated crusts. In coastal areas, where salinity is high, biocrusts were replaced by a unique marine mat-like microbial community, dominated by halotolerant taxa. Redundancy analysis revealed a significant contribution of soil texture, cover type, carbon content, and elevation to the variations in bacterial and fungal communities. Multivariate analysis placed microbial communities in significantly separated clusters based on their carbon content, elevation and electrical conductivity. We conclude that Oman hosts a variety of cyanobacteria- and lichen-dominated crusts with their bacterial and fungal communities being largely dictated by soil properties and environmental parameters.

[Macroscopical estimation of the post mortem interval (PMI) and exclusion of the forensically relevant resting period--a comparison of data presented in the literature with recent osteological findings]. / Makroskopische Abschätzung des postmortalen Intervalls (PMI) und Ausschluss einer forensisch relevanten Liegezeit--ein Vergleich von Literaturangaben mit rezenten osteologischen Funden.

The aim of the present study was to determine to what extent macroscopical parameters mentioned in the literature are suitable for the estimation of the post mortem interval (PMI) and particularly for the exclusion of the forensically relevant resting period for recent bone material. The macroscopical examination of recent bone material with a known PMI showed that only one published parameter (relics of adipocere in the cross section of the compacta) was consistent with our findings for this particular resting period (27-28 years). Other macroscopical parameters presented in the literature were contradictory to the results observed in this study. Among those are the rigidity of bones, the adhesion of soft tissue, the filling of the marrow cavity, and the permeation of the epiphyses with adipocere. Concerning the exclusion of the forensically relevant resting period, a similar result was observed. This study identified some diagnostic findings in bones with a resting period of less than 50 years which according to the literature should only be present after a resting period of more than 50 years. These features included the lack of macroscopical traces of adipocere, degradation of the compacta surface, detachment of the cortical substance, the ability of bone to be broken with bare hands, and superficial usures. Moreover, in one-third of our cases we identified some intra-individual differences not previously described in the literature. In addition to the other results, those intra-individual differences make an estimation of the PMI more difficult. However it should be noted that those published parameters were collected from bone material which was stored in a "relatively arid sand-grit-clay soil of the broken stone layer of Munich". The bones in the present study were stored in acidic and clayey-loamy soil, partly with lateral water flow. In conclusion, the present study demonstrates that one should use caution estimating the post mortem interval and excluding the forensically relevant resting period, even when all available results are considered.

Do cemeteries emit drugs? A case study from southern Germany.

The risk of earth burials for the environment and public health is a matter of controversial debate. The aim of the present study is to characterise the drainage of cemeteries with regard to the concentration of a number of pharmaceuticals and to the soil's hydrochemical properties, and to discuss these data in comparison with data obtained for surface waters located upstream of the cemeteries. Of the 12 drainage samples analysed using LC-ESI-MS/MS, seven contained carbamazepine (< 225 ng l-1), five contained hydrochlorothiazide, one contained metoprolol (23 ng l-1) and one contained traces of ibuprofen. The surface water samples contained a larger number of different drugs (8 of the 12 drugs under investigation) and higher concentrations (e.g. metropolol 2230 ng l-1). The NO3, NH4, PO4 and DOC concentrations and the electrical conductivity of the cemetery drainages were in several samples higher than those of the surface water samples. The NO3 and NH4 concentrations exceeded the legal contaminant limits of drinking water in only one case. The present study found that the release of drugs and nutrients from cemeteries, measured in surface water drug loads, presents a low environmental risk. However, the study is only a snapshot and long-term monitoring of cemetery drainages, including a broad range of pharmaceuticals and detailed hydrological investigations, will have to be carried out before more substantiated statements can be made.

Discovering the importance of lateral CO(2) transport from a temperate spruce forest.

Our study investigated the concentration of dissolved carbon at the point when water leaves the pedosphere and whether this amount represents a significant proportion of terrestrial carbon cycling. The investigations were carried out in a temperate forest catchment (Black Forest, Germany) over a period of 1 year. The annual export of dissolved C compounds (14.4 g C m(-2) year(-1)) was dominated by CO(2) (9.7 vs. 4.7 g C m(-2) year(-1) DOC). Even though the direct CO(2) degassing at the spring was inferior (0.4 kg C year(-1)), considerably lower CO(2) concentrations were measured 17 m downstream of the spring. This shows that a large proportion of dissolved CO(2) (93%) originating from the pedosphere is not captured anymore within a short distance from the spring. The measured lateral C-transport was in the same order of magnitude as reported for the net ecosystem exchange (NEE) observed for German spruce forests (-4 to -55 g C m(-2) year(-1)). Therefore, the results clearly demonstrated that the lateral transport of dissolved carbon can be a significant part of terrestrial carbon budgets and for this study site CO(2) was dominating this 'indirect' pathway. However, for generalisation, it is important to extend this investigation to other landscapes and climatic zones.

Phenotypic subunit composition of the tobacco (Nicotiana tabacum L.) vacuolar-type H(+)-translocating ATPase.

The model plant tobacco (Nicotiana tabacum L.) was chosen for a survey of the subunit composition of the V-ATPase at the protein level. V-ATPase was purified from tobacco leaf cell tonoplasts by solubilization with the nonionic detergent Triton X-100 and immunoprecipitation. In the purified fraction 12 proteins were present. By matrix-assisted laser-desorption ionization mass spectrometry (MALDI-MS) and amino acid sequencing 11 of these polypeptides could be identified as subunits A, B, C, D, F, G, c, d and three different isoforms of subunit E. The polypeptide which could not be identified by MALDI analysis might represent subunit H. The data presented here, for the first time, enable an unequivocal identification of V-ATPase subunits after gel electrophoresis and open the possibility to assign changes in polypeptide composition to variations in respective V-ATPase subunits occurring as a response to environmental conditions or during plant development.

Isolation and identification of heterogeneous nuclear ribonucleoproteins (hnRNP) from purified plasma membranes of human tumour cell lines as albumin-binding proteins.

Since albumin is being developed as a drug carrier to target tumours the search for albumin-binding proteins (ABPs), which play a role in cell surface binding and endocytosis of native and conjugated albumins becomes more and more interesting. We isolated five different proteins from purified plasma membranes from three different human tumour cell lines (CCRF-CEM, MV3 and MCF7) by albumin affinity chromatography and identified them as four members of the heterogeneous nuclear ribonucleoproteins (hnRNP) family and calreticulin by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. Contamination of the plasma membrane preparation by nuclear membranes was excluded with anti-nucleopore antibodies. Western blot analyses of plasma membranes showed ABPs with the same molecular weights as the albumin-affinity isolates. Tryptic digestion of intact cells was used to determine the sidedness of the albumin-binding property, which is oriented to the exterior of the cell. Localisation to the plasma membrane and albumin binding is a novel property of hnRNP.

Human chimera-type galectin-3: defining the critical tail length for high-affinity glycoprotein/cell surface binding and functional competition with galectin-1 in neuroblastoma cell growth regulation.

Many human proteins have a modular design with receptor and structural domains. Using adhesion/growth-regulatory galectin-3 as model, we describe an interdisciplinary strategy to define the functional significance of its tail established by nine non-triple helical collagen-like repeats (I-IX) and the N-terminal peptide. Genetic engineering with sophisticated mass spectrometric product analysis provided the tools for biotesting, i.e. eight protein variants with different degrees of tail truncation. Evidently,various aspects of galectin-3 activity (cis binding and cell bridging) are affected by tail shortening in a different manner. Thus, this combined approach reveals an unsuspected complexity of structure-function relationship, encouraging further application beyond this chimera-type galectin.

Investigation of sterols as potential biomarkers for the detection of pig (S. s. domesticus) decomposition fluid in soils.

This study was carried out to evaluate the potential of using cholesterol and coprostanol, as indicators for the detection of decomposition fluid of buried pigs (S. s. domesticus) in soils. In May 2007, four pig carcasses (∼35kg) were buried in shallow graves (∼40 cm depth) at the University of Ontario Institute of Technology in Canada. Two pigs were exhumed after three months (Pig 1, Pig 2) and six months (Pig 3, Pig 4) post burial. Soil samples were collected beneath the pig carcasses (∼40cm depth) and from grave walls (∼15-20 cm depth) as well as from a parallel control site. Coprostanol and cholesterol were extracted from soils, purified with solid phase extraction (SPE) and analysed with gas chromatography/mass spectrometry (GC/MS). A significant increase in cholesterol concentrations (p<0.05) and amounts of coprostanol were detected in soil located beneath the pig carcasses after three months of burial. It is assumed that during the putrefaction and liquefaction stages of decomposition pig fluid which contains cholesterol and coprostanol is released into the underlying soil. Therefore, cholesterol and coprostanol could be used as potential biomarkers to detect the presence of decomposition fluid three months after burial under comparable soil and environmental conditions. Further research is suggested for additional soil sampling before and after three months to investigate the abundance of these and other sterols.

The carbon count of 2000 years of rice cultivation.

More than 50% of the world's population feeds on rice. Soils used for rice production are mostly managed under submerged conditions (paddy soils). This management, which favors carbon sequestration, potentially decouples surface from subsurface carbon cycling. The objective of this study was to elucidate the long-term rates of carbon accrual in surface and subsurface soil horizons relative to those of soils under nonpaddy management. We assessed changes in total soil organic as well as of inorganic carbon stocks along a 2000-year chronosequence of soils under paddy and adjacent nonpaddy management in the Yangtze delta, China. The initial organic carbon accumulation phase lasts much longer and is more intensive than previously assumed, e.g., by the Intergovernmental Panel on Climate Change (IPCC). Paddy topsoils accumulated 170-178 kg organic carbon ha(-1) a(-1) in the first 300 years; subsoils lost 29-84 kg organic carbon ha(-1) a(-1) during this period of time. Subsoil carbon losses were largest during the first 50 years after land embankment and again large beyond 700 years of cultivation, due to inorganic carbonate weathering and the lack of organic carbon replenishment. Carbon losses in subsoils may therefore offset soil carbon gains or losses in the surface soils. We strongly recommend including subsoils into global carbon accounting schemes, particularly for paddy fields.

Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil.

In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.

Characteristics of dissolved organic matter following 20years of peatland restoration.

The changes in the amounts and composition of dissolved organic matter (DOM) following long-term peat restoration are unknown, although this fraction of soil organic matter affects many processes in such ecosystems. We addressed this lack of knowledge by investigating a peatland in south-west Germany that was partly rewetted 20 years ago. A successfully restored site and a moderately drained site were compared, where the mean groundwater levels were close to the soil surface and around 30 cm below surface, respectively. The concentrations of dissolved organic carbon (DOC) at 4 depths were measured over one year. The specific absorbance was measured at 280 nm and the fluorescence spectra were used to describe the aromaticity and complexity of DOM. The investigations showed that 20 years of peatland restoration was able to create typical peatland conditions. The rewetted site had significantly lower DOC concentrations at different depths compared to the drained site. The specific UV absorbance showed that the rewetted site had a lower level of aromatic DOM structures. The decreasing specific UV absorbance might indicate an increasing contribution of small organic molecules to DOM. It was hypothesized that the decreasing DOC concentrations and the relative enrichment of small, readily degradable organic molecules, reflect the slower decomposition of organic matter after the re-establishment of the water table. Seasonal trends provided substantial evidence for our hypothesis that reduced DOC concentrations were caused by reduced peat decomposition. During summer, the elevated DOC values were accompanied by an increase in DOM aromaticity and complexity. Our results demonstrated a close link between C mineralization and DOC production. We concluded that long-term peatland restoration in the form of the successful re-establishment of the water table might result in reduced peat decomposition and lower DOC concentrations. The restoration of peatlands seems to have a positive impact on C sequestration.