Methane fluxes, microbial activities and community structures in a wet tundra of the Lena Delta

Wet tundra environments of the Arctic are natural sources of the climate relevant trace gas methane. The underlying biogeochemical processes are not yet well understood. The field investigations were carried out on the island Samoylov (N 72°, E 126°) located in the Lena Delta, Siberia. The study site represented an area of typical polygonal patterned grounds with ice-wedges, which were considered for analyses of methane fluxes, organic matter quality and microbial communities.The mean flux rate of the depression was 53.2 ± 8.7 mg CH4 m-2 d-1, whereas the mean flux rate of the dryer rim part of the polygon was 4.7 ± 2.5 CH4 m-2 d-1. The quantity of dissolved organic matter (DOM), which represents an important C pool for microbial communities, correlated significant with the total concentrations of phospholipid fatty acids and ether lipids (PLFA and PLEL) a measure for microbial biomass. Although permafrost soils represent a large carbon pool, it was shown, that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. This is an important finding for modelling and calculating trace gas fluxes from permafrost environments, because the known models are consider only the total carbon amount.It can be concluded by the presented results firstly that microbial communities in permafrost environments are composed by members of all three domains of life at numbers comparable to temperate soil ecosystems and secondly that the permafrost microorganisms are well adapted to the extreme temperature gradient of their environment

Long-term impact of different fertilization management on microbial P mobilization and community structure in the bulk soil and rhizosphere of maize

The efficiency of the arable P use can be fundamentally increased by improving the management. We aim to disclose soil microbial fundamentals to optimize P storage, P mobilization and P turnover in agricultural systems for plant growth promotion. We investigated treatments from a long-term fertilization experiment in Rostock (Mecklenburg-Western Pomerania). Soil sampling was conducted in spring and autumn of 2015 and 2016. Microbial P storage, enzymatic P mobilization and the community structure of bacteria and arbuscular mycorrhizal fungi (AMF) as key players of the P mobilization and transfer were analysed at four fertilization treatments with no additional P (control), mineral P-fertilizer (TSP), organic P-fertilizer (compost) and a combination of mineral and organic P-fertilizers. Microbial P (Pmic) was significantly affected by the type of P-fertilization and increased by factor two to three in fertilized treatments compared to the control. The microbial P storage did not differ significantly between mineral and organic fertilization treatments. Organic P fertilization leads to a short term increase of the Pmic pool in the soil. Enzyme activities were significantly higher in treatments with organic fertilization compared to those with no or mineral fertilisation, independent on season. This pattern was found for enzymes of the P-cycle (acid and alkaline phosphomonoesterases, phosphodiesterase) and of the C-cycle (ß-glucosidases) indicating a strong correlation between C and P cycling. Further, enzymatic P mobilization is rather controlled by availability of substrates than by the current P demand of the vegetation. Community structure of AMF and bacteria show similar results. A pool of species was site-specific common in each treatment, whereas a small fraction was treatment-specific. The findings contribute to one of the overarching objective of the BonaRes-project (BMBF) InnoSoilPhos to improving the P use efficiency of arable crops by selection of suitable management strategies in the agricultural practice

On the Complexity of Conditional DAG Scheduling in Multiprocessor Systems

As parallel processing became ubiquitous in modern computing systems, parallel task models have been proposed to describe the structure of parallel applications. The workflow scheduling problem has been studied extensively over past years, focusing on multiprocessor systems and distributed environments (e.g. grids, clusters). In workflow scheduling, applications are modeled as directed acyclic graphs (DAGs). DAGs have also been introduced in the real-time scheduling community to model the execution of multi-threaded programs on a multi-core architecture. The DAG model assumes, in most cases, a fixed DAG structure capturing only straight-line code. Only recently, more general models have been proposed. In particular, the conditional DAG model allows the presence of control structures such as conditional (if-then-else) constructs. While first algorithmic results have been presented for the conditional DAG model, the complexity of schedulability analysis remains wide open. We perform a thorough analysis on the worst-case makespan (latest completion time) of a conditional DAG task under list scheduling (a.k.a. fixed-priority scheduling). We show several hardness results concerning the complexity of the optimization problem on multiple processors, even if the conditional DAG has a well-nested structure. For general conditional DAG tasks, the problem is intractable even on a single processor. Complementing these negative results, we show that certain practice-relevant DAG structures are very well tractable

The relevance of particulate organic carbon (POC) for carbon composition in the pore water of drained and rewetted fens of the "Donauried" (South-Germany)

International audienceNumerous studies have dealt with carbon (C) concentrations in Histosols, but there are no studies quantifying the relative importance of all individual C components in pore waters. For this study, measurements were made of all the carbon components (i.e., particulate organic carbon, POC; dissolved organic carbon, DOC; dissolved inorganic carbon, DIC; dissolved methane, CH4) in the soil pore water of a calcareous fen under three different water management regimes (re-wetted, deeply and moderately drained). Pore water was collected weekly or biweekly (April 2004 to April 2006) at depths between 10 and 150 cm. The main results obtained were: (1) DIC (94?280 mg C l?1) was the main C-component. (2) POC and DOC concentrations in the pore water (14?125 mg C l?1 vs. 41?95 mg C l?1) were pari passu. (3) Dissolved CH4 was the smallest C component (0.005?0.9 mg C l?1). Interestingly, about 30% of the POM particles were colonized by microbes indicating that they are active in the internal C transfer in the soil profile ("C-Shuttles"). Consequently, it was concluded that POC is at least as important as DOC for internal soil C turnover. There is no reason to assume significant biochemical differences between POC and DOC as they only differ in size. Therefore, both POC and DOC fractions are essential components of C budgets of peatlands. Furthermore dissolved CO2 in all forms of DIC apparently is an important part of peatland C-balances

Strukturelle und funktionelle Charakterisierung von mikrobiellen Gemeinschaften in ökologisch und konventionell bewirtschafteten Agrarböden

Soil samples from the DOK long-term field trial were investigated to study influences of different farming systems on structure and function of soil microbial communities. The DOK long-term field trial in Switzerland consists of plots managed bio-dynamically (D), bio-organically (O), conventionally (K) and of those which are managed conventionally but only receive mineral fertilizer (M). In spring 2003 soil samples from these differently managed plots were taken. All investigated fields were planted with winter wheat in 2003, but with different croppings in 2002: potato and maize cultivation, respectively. Analyses of phospholipid fatty acids (PLFA) and phospholipid etherlipids (PLEL) were carried out to determine bacterial, eukaryotic and archaeal phenotypic diversity. By combining this technique with isotope ratio mass spectrometry (GC/MS-C-IRMS) it was possible to analyse simultaneously 13C/12C ratios in PLFA and PLEL biomarkers for functional analyses of the soil microbiota. First results revealed differences in the total microbial biomass and community structure among the compared farming systems. Furthermore, the incorporation of the maize derived carbon could be detected in several PLFA at the natural abundance level. This may be an indication for the role of different microbial groups during organic matter degradation

Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of 13C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental “omics.” Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with 13C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio. reads per density-resolved RNA fraction), an average of 1.2% of reads per sample were identified as non-rRNA, including mRNA. Members of the Rhodocyclaceae (including those related to Quatrionicoccus spp.) were most abundant and enriched in 13C-rRNA, while well-known aerobic degraders such as Pseudomonas spp. remained unlabeled. Transcripts related to cell motility, secondary metabolite formation and xenobiotics degradation were highly labeled with 13C. mRNA of phenol hydroxylase genes were highly labeled and abundant, while other transcripts of toluene-activation were not detected. Clear labeling of catechol 2,3-dioxygenase transcripts supported previous findings that some of these extradiol dioxygenases were adapted to low oxygen concentrations. We introduce a novel combination of total RNA-SIP with calculation of transcript-specific enrichment factors (EFs) in 13C-RNA, enabling a targeted approach to process-relevant gene expression in complex microbiomes

Der Grenzbereich Torf-Mineralische Deckschicht ein Hotspot für Produktion und Umsetzung von CH4 und CO2

Eine gängige Annahme ist, dass eine mineralische Deckschicht den Torfkörper vor Abbau schützt, Eigene CO2 Messungen auf einem ackerbaulich genutzten, mineralisch überdeckten Niedermoor (Oberrheingraben) zeigen das Gegenteil. Wir stellten die These auf, dass die hohen CO2-Flüsse aus der aeroben Methanoxidation in der mineralischen Deckschicht resultieren. Der belüftete Profilbereich im Grenzbereich Torf-mineralische Deckschicht entscheidet über die Höhe der CO2-Flüsse. Zur Überprüfung wählten wir 6 Plots entlang eines Gradienten der Deckschichtmächtigkeit (31-90 cm) aus, um sie mit Bodenluftsammlern zu bestücken. Die Bodenluft wurden in den Tiefenstufen 0-25, 26-50 und 51-75 cm (April 2016) beprobt. Parallel wurde der Gasaustausch zwischen Pedo- und Atmosphäre ermittelt, δ13C von CO2 und CH4 in der Gasphase und δ13C im Boden bestimmt. Die Erfassung des Grundwasserstandes und der Redoxpotentiale dienten zur Identifikation des durchlüfteten Profilbereiches. Um das mikrobielle Potential für die Bildung und Oxidation von Methan in den unterschiedlichen Bodenschichten zu quantifizieren, wurde eine Quantitative Real-Time PCR (qPCR) durchgeführt. Es wurden sowohl Markergene für die Methanogenese durch Archaeen (mcrA) als auch für die aerobe Methanoxidation durch Bakterien erfasst (pmoA). Da die partikuläre Methanmonooxygenase mit der Ammoniakmonooxygenase eng verwandt ist und diese unter Ammoniak-Limitation auch CH4 oxidieren kann, wurden zusätzlich Ammoniak-oxidierende Bakterien und Archaeen quantifiziert (amoA). Unabhängig von der Mächtigkeit der Deckschicht nahm mit der Tiefe die CO2-Konzentrationen zu. Die CO2-Konzentrationen zeigten einen positiven Zusammenhang mit der Höhe des Grundwasserspiegels und der Höhe des organischen Kohlenstoffes im Boden. Mit abnehmender Mächtigkeit der Deckschicht wurde eine Zunahme der CO2-Konzenztration beobachtet. Die höchsten CO2-Konzentrationen wurden dann beobachtet, wenn ein Teil des Torfköpers belüftet war. Hier wurde ein Shift von Methanogenese zu Methanoxidation beobachtet. Der Effekt wurde geringer, wenn oberhalb des Grundwasserspiegels nur mineralischen Horizonte ware

Impact of high carbon amendments and pre-crops on soil bacterial communities

A 2-year outdoor mesocosm experiment was carried out to determine the effects of high C amendments (HCAs; wheat straw and sawdust) compared to a control with no addition of HCAs (no-HCA) and 2 different crop rotation systems (spring barley/winter barley and faba bean/winter barley) on soil bacterial communities using a molecular barcoding approach. Samples were analyzed after pre-crop harvest (T1) and harvest of winter barley (T2). Our data demonstrate a clear drop in bacterial diversity after winter barley harvest in the no-HCA and wheat straw treatment compared to the pre-crops. Sawdust application had a stabilizing effect on bacterial diversity compared to the pre-crops and induced an increase in carbon (C) stocks in soil which were however negatively correlated with yields. Main responders in the no-HCA and wheat straw treatment compared to the pre-crops were bacteria of the phyla Actinobacteria and Bacteroidetes which were enriched and bacteria belonging to Firmicutes, Gemmatimonadetes, Proteobacteria, and Gemmatimonadaceae which were depleted. Overall differences between wheat straw-amended and no-HCA control samples were small and included single ASVs from various phyla. In sawdust-amended samples, only a shift of some Proteobacteria families was observed compared to the no-HCA control. Overall, pre-crop plant species had small influence on the observed response pattern of the soil microbiome towards the amendments and was only visible for wheat straw

Denitrifying pathways dominate nitrous oxide emissions from managed grassland during drought and rewetting

Nitrous oxide is a powerful greenhouse gas whose atmospheric growth rate has accelerated over the past decade. Most anthropogenic N2O emissions result from soil N fertilization, which is converted to N2O via oxic nitrification and anoxic denitrification pathways. Drought-affected soils are expected to be well oxygenated; however, using high-resolution isotopic measurements, we found that denitrifying pathways dominated N2O emissions during a severe drought applied to managed grassland. This was due to a reversible, drought-induced enrichment in nitrogen-bearing organic matter on soil microaggregates and suggested a strong role for chemo- or codenitrification. Throughout rewetting, denitrification dominated emissions, despite high variability in fluxes. Total N2O flux and denitrification contribution were significantly higher during rewetting than for control plots at the same soil moisture range. The observed feedbacks between precipitation changes induced by climate change and N2O emission pathways are sufficient to account for the accelerating N2O growth rate observed over the past decade