TY - JOUR AB - Agricultural grassland management intensity strongly influences soil microbial community structure in Europe, though the influence of individual practices, such as fertilization and cutting frequency, requires further investigation. Using a 46 year old field experiment in the Swiss Jura region, we examined how both fertilizer input and cutting frequency influence both soil microbial community structure and functional potential. For community structures of soil bacteria and fungi (determined via genetic metabarcoding) and plants (determined via plant species relevés) the effect of fertilization had a stronger effect than that of cutting frequency. The fatty acid biomarker for arbuscular mycorrhizal fungi (AMF, 16:1ω5), however, responded more to cutting frequency (relative effect size = 87.71 %) than fertilization (relative effect size = −7.90 %). Among bacteria with genes linked to soil phosphorous (P) and nitrogen (N) mobilization, only the abundance of the gcd gene (inorganic P solubilisation) displayed a significant fertilization effect. These findings suggest that long-term mineral fertilizer application is a key driver of differences in microbial community structure in grasslands of contrasting management type, and may influence bacterial P solubilisation capacity. Some microbial groups, such as AMF, appear more sensitive to cutting frequency, possibly due to additional plant re-growth. This study highlights the importance of disentangling agricultural management practices to better predict grassland plant and soil microbial responses to intensification. AU - Fox, A. AU - Schulz, S. AU - Brennan, F.* AU - Gschwend, F.* AU - Barreiro, A.* AU - Widmer, F.* AU - Schloter, M. AU - Huguenin-Elie, O.* AU - Lüscher, A.* C1 - 75624 C2 - 58055 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Long-term mineral fertilization shaped aboveground plant and belowground bacterial and fungal communities more than cutting frequency in a temperate grassland. JO - Appl. Soil Ecol. VL - 215 PB - Elsevier PY - 2025 SN - 0929-1393 ER - TY - JOUR AB - The drilosphere is described as a microbial hotspot in soil, which is rich in labile nutrients. However, phosphorus (P) quality and availability change along the drilosphere from labile organically-bound P in upper layers to immobilized Ca-phosphate with increasing depth. In this study, we postulated (1) that microbial P turnover is generally accelerated in the drilosphere compared to bulk soil as a result of an increase in labile nutrients, and (2) that P mineralization is dominant in upper layers of the drilosphere and P solubilization in deeper layers of the drilosphere, respectively. Furthermore, we hypothesized (3) that the enhanced P mobilization in the drilosphere favors copiotrophic and earthworm gut derived bacteria like Pseudomonadaceae, which distinguishes the community composition from that of the bulk soil. We investigated the effect of earthworm activities on potential phosphatase activities, abundance and diversity of bacterial communities involved in P mobilization (gcd, phoD, appA, phnX, phoN) and uptake (pstS, pitA) along a soil depth gradient in a short rotation coppice in Northeast Germany. Potential phosphatase activities and gene abundances revealed increasing potentials for organic P mineralization and high-affinity P uptake via the Pst system in the drilosphere below 50 cm depth. Conversely, in the upper soil layers potential for bacterial P mobilization were similar between drilosphere and bulk soil. We also observed drilosphere-related changes in the composition of bacterial communities involved in P solubilization and low-affinity P uptake via the Pit system below 60 cm depth. In the drilosphere compared to bulk soil, Pseudomonadaceae were enriched and played a major role in solubilization and low-affinity uptake of P, while bacteria potentially involved in N turnover like Bradyrhizobiaceae and Phyllobacteriaceae were less abundant. Our study suggested that earthworms increased the potential enzyme activity and abundance of bacteria carrying the Pho-regulon genes in the drilosphere of the deeper soil layers. Furthermore, earthworm-derived bacteria were enriched in the drilosphere at the same soil depth, especially those involved in P solubilization and carrying the Pit system. AU - Chiba, A. AU - Vitow, N.* AU - Baum, C.* AU - Zacher, A.* AU - Kahle, P.* AU - Leinweber, P.* AU - Schloter, M. AU - Schulz, S. C1 - 68828 C2 - 53695 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Earthworm activities change phosphorus mobilization and uptake strategies in deep soil layers. JO - Appl. Soil Ecol. VL - 193 PB - Elsevier PY - 2024 SN - 0929-1393 ER - TY - JOUR AB - The distribution of enzymatic activity in soil aggregates is a key determinant in the turnover of organic matter. This study aimed to address how the application of a carbon-rich slurry influences extracellular enzymatic activity within aggregate-size fractions over a one-year period. Twenty-four pots of either a loam or sand soil, sown with Lolium perenne, were kept slurry-free (control), or were treated with a high dry matter slurry. Pots were sampled after 31, 137 and 361 days (n = 4). Soils were physically fractionated to obtain four aggregate-size fractions: ≥2 mm, ≥250 μm, ≤250 μm and ≤53 μm with enzyme assays of seven C-cycling enzymes conducted on each, and the potential extracellular enzymatic activity (pEEA) calculated. The strongest response in individual pEEA was seen after 137 days, where the pEEA of at least one C-cycling enzyme was significantly higher in the slurry treatment in each of the four aggregate-size fractions in both soil types (all at least P ≤ 0.05). Additionally, nearly all seven C-cycling enzymes were significantly higher in the slurry treatment compared to the control in the ≤53 μm fraction (all at least P ≤ 0.05) in both. No significant increase in pEEA was seen in the slurry treatment in any aggregate-size fraction after 361 days in the loam soil (all P > 0.05), and this was also largely the case for the sand soil. The results of this study clearly indicate that pEEA within aggregate-size fractions was strongly influenced by slurry application in the initial months, though this was not sustained. AU - Fox, A. AU - Lanigan, G.* AU - Schmalenberger, A.* C1 - 66729 C2 - 53282 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Response of C-cycling enzymes in soil aggregate-size fractions to slurry application over a one year period in two contrasting soil types. JO - Appl. Soil Ecol. VL - 182 PB - Elsevier PY - 2023 SN - 0929-1393 ER - TY - JOUR AB - It has been shown from diverse geographical locations that soils with repeated applications of pesticides display enhanced degradation of the pesticides which usually remain recalcitrant for a long time. In Kenya, agricultural activities have been using many different persistent pesticides for pest control. A study was undertaken to determine if the soils with repeated application history could show enhanced degradation of diuron. Laboratory degradation studies using non sterile sugarcane and pineapple-cultivated soils with over 5 years' application history showed enhanced degradation amounting to 80.2% and 86.2% of 5 mg/g initially applied diuron while sugarcane and pineapple-cultivated soils without application history degraded 34.4% and 48.4% of initially applied diuron after 146 days of incubation, respectively. Through liquid culture experiments with sugarcane and pineapple-cultivated soils and diuron as the carbon source, two bacterial strains capable of degrading diuron were isolated. By use of 16S rRNA comparative gene sequence technique, the strains were shown to be closely related to Bacillus muralis/Bacillus simplex and Bacillus pseudomycoides, respectively. These pure isolates were able to degrade diuron up to 51.0% and 54% of 50 mg/L after 46 days of incubation, respectively. The metabolites N-(3,4-dichlorophenyl)-N-methylurea and 3,4-dichloroaniline were reported as major by-products of diuron degradation in the two study sites with adapted microbes. The biodegradation capability of the strains isolated in this study indicates their microbial bioremediation potential for diuron mineralization in the contaminated soils. AU - Muendo, B.M.* AU - Shikuku, V.O.* AU - Lalah, J.O.* AU - Getenga, Z.M.* AU - Wandiga, S.O.* AU - Rothballer, M. C1 - 59960 C2 - 49146 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Enhanced degradation of diuron by two Bacillus species isolated from diuron contaminated sugarcane and pineapple-cultivated soils in Kenya. JO - Appl. Soil Ecol. VL - 157 PB - Elsevier PY - 2021 SN - 0929-1393 ER - TY - JOUR AB - In order to meet constantly increasing demands for land without damaging pristine environments like forests or grasslands, reclamation and re-purposing of historically contaminated areas should become a priority. Successful reclamation goes hand in hand with the soil functional recovery potential and with resilient microbial communities capable of performing the necessary ecosystem services. In this context, we designed a greenhouse pot experiment as a mock reclamation situation, where traces of lindane at hazard threshold and twice the concentration accepted for waste deposits are left in the soil after conventional clean-up by excavation and land filling. We assessed the effects of lindane at 50 and 100 mg kg(-1) regarding crop growth and nutrient turnover (with focus on the nitrogen cycle) as two key parameters for soil functions. The bulk and rhizosphere soil bacterial community composition were chosen as parameters for soil resilience in lindane contamination conditions. Lindane severely affected plant growth and development. The potential nitrogen fixation, quantified as nifH gene copy number, suffered direct negative effects of lindane contamination in bulk soil, which could represent an additional obstacle for phytoremediation. Changes in rhizosphere bacterial community composition were related to lindane toxic effects towards the plants, which might have supported the growth of opportunists and saprophytes. In bulk soil, the bacterial community shifted towards lindane tolerant taxa like Sphingomonas and Porphyrobacter that are interesting with regard to their applications in bioremediation. We concluded that lindane at hazard threshold concentration left in soil after clean-up has negative effects both soil functionality, and the recovery of the bacterial communities to their original composition when lindane resistant plant crops are not involved. AU - Balazs, H.-E. AU - Schmid, C. AU - Podar, D.* AU - Hufnagel, G. AU - Radl, V. AU - Schröder, P. C1 - 57731 C2 - 47891 CY - Radarweg 29, 1043 Nx Amsterdam, Netherlands TI - Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective. JO - Appl. Soil Ecol. VL - 150 PB - Elsevier PY - 2020 SN - 0929-1393 ER - TY - JOUR AB - Soil microbes play an important role in terrestrial carbon (C) cycling, but their functional response to global warming remains yet unclear. Soil metaproteomics has the potential to contribute to a better understanding of warming effects on soil microbes as proteins specifically represent active microbes and their physiological functioning. To quantify warming effects on microbial proteins and their distribution among different functional and phylogenetic groups, we sampled forest soil that had been artificially warmed (+4 °C) during seven consecutive growing seasons and analyzed its metaproteomic fingerprint and linked to soil respiration as a fundamental ecosystem service. Bacterial protein abundances largely exceeded fungal abundances at the study site but protein abundances showed only subtle differences among control and warmed soil at the phylum and class level, i.e. a temperature-induced decrease in Firmicutes, an increase in Agaricomycetes and Actinobacteria, and a decrease in the Asco/Basidiomycota ratio. Community function in warmed soil showed a clear trend towards increased proteins involved in microbial energy production and conversion, related to the increased CO2 efflux from warmed soil as a result of stress environmental conditions. The differences in community function could be related to specific phyla using metaproteomics, indicating that microbial adaptation to long-term soil warming mainly changed microbial functions, which is related to enhanced soil respiration. The response of soil respiration to warming (+35% soil CO2 efflux during sampling) has not changed over time. Accordingly, potential long-term microbial adaptations to soil warming were too subtle to affect soil respiration rates or, were overlaid by other co-varying factors (e.g. substrate availability). AU - Liu, D.* AU - Keiblinger, K.M.* AU - Schindlbacher, A.* AU - Wegner, U.* AU - Sun, H. AU - Fuchs, S.* AU - Lassek, C.* AU - Riedel, K.* AU - Zechmeister-Boltenstern, S.* C1 - 51244 C2 - 43084 CY - Amsterdam SP - 196-202 TI - Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey. JO - Appl. Soil Ecol. VL - 117-118 PB - Elsevier Science Bv PY - 2017 SN - 0929-1393 ER - TY - JOUR AB - In a field trial comprising organic farming and minimum tillage management strategies in Scheyern, Germany, we evaluated the long-term (21-year) effects of organic farming (use of a diverse crop rotation with legume cover crop and without application of synthetic fertilizer or pesticides) and minimum tillage (6–8 cm depth) on the microbial community structure and microbial residues in Cambisols. Organic farming had a positive effect on microbial biomass, total phospho-lipid fatty acids (PLFA), Gram (+) bacteria, Gram (−) bacteria and the arbuscular mycorrhizal fungi (AMF) indicator PLFA 16:1ω5 and amino sugars. The increase in presence of Gram (+) bacteria when compared to integrated farming was also reflected by increased content of bacterial muramic acid (MurN), i.e. an increased formation of bacterial residues. Minimum tillage significantly increased microbial biomass N and the fungal PLFA 18:2ω6,9, averaging the values of upper (0–8 cm) and deeper (12–25 cm) soil, but had no effects on PLFA 16:1ω5. Minimum tillage generally resulted in a negative depth gradient of almost all microbial properties analyzed. The only important exception was fungal galactosamine (GlcN), which led to increases in the fungal C/bacterial C ratio and in the contribution of microbial residue C to SOC in the deeper soil. Significant second order tillage × management interactions indicated that minimum tillage effects on microbial biomass and PLFA indices (Gram (+) and (i15:0 + i17:0)/(a15:0 + a17:0)) were much stronger in the organic farming system than in the integrated farming system. Redundancy analysis (RDA) showed SOC and H2O content predominantly affected the microbial community structure in the present study. Minimum tillage in combination with organic farming appears to be an effective agricultural strategy that enhances soil microbial biomass, microbial residues and bacterial and fungal abundances. The results indicate that the positive effects of minimum tillage on microbial community can be enhanced by organic farming. Microbial residues as a fraction of SOC respond faster to farming management than to tillage. AU - Sun, H. AU - Koal, P. AU - Liu, D.* AU - Gerl, G. AU - Schroll, R. AU - Gattinger, A.* AU - Joergensen, R.G.* AU - Munch, J.-C.* C1 - 49242 C2 - 33546 CY - Amsterdam SP - 16-24 TI - Soil microbial community and microbial residues respond positively to minimum tillage under organic farming in Southern Germany. JO - Appl. Soil Ecol. VL - 108 PB - Elsevier Science Bv PY - 2016 SN - 0929-1393 ER - TY - JOUR AB - Application of manure for soil fertilization is a common practice in arable and pasture soils. As antibiotics are regularly used in animal husbandry, these compounds often enter the soil via manure application. The effects of antibiotics on microbial communities, however, might depend on soil moisture, as water availability may influence both the fate of the compound and the activity of the microbes. To test this hypothesis, we investigated the effects of the application of manure containing the antibiotic sulfadiazine (SDZ) on the abundance and activity of nitrifies and denitrifies in soil, based on the copy number of marker genes and their related potential activities, as affected by different moisture regimes. We observed significant effects of SDZ on potential denitrification activity, but those were not influenced by the soil moisture regime. Nevertheless, neither SDZ nor changes on moisture significantly affected the abundance of denitrifies. In contrast, both potential nitrification activity and abundance of ammonia oxidizing bacteria were significantly affected by the application of manure containing SDZ and moisture regime. Interestingly, no effects were observed for ammonia oxidizing archaea. Overall, our data show that soil moisture modulates the effects of antibiotics in soil microbial communities, and we recommend to include this parameter in the risk assessment of new chemicals. AU - Radl, V. AU - Kindler, R.* AU - Welzl, G. AU - Albert, A. AU - Wilke, B.M.* AU - Amelung, W.* AU - Schloter, M. C1 - 46397 C2 - 37633 CY - Amsterdam SP - 99-106 TI - Drying and rewetting events change the response pattern of nitrifiers but not of denitrifiers to the application of manure containing antibiotic in soil. JO - Appl. Soil Ecol. VL - 95 PB - Elsevier Science Bv PY - 2015 SN - 0929-1393 ER - TY - JOUR AB - In areas used for cattle overwintering detrimental effects normally associated with grazing are intensified. Among the alterations observed, increases on the N availability and soil pH may highly influence structure of ammonia oxidizing microbes and thus influence nitrification pattern in soil. To evaluate this assumption, we assessed the abundance and diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in three sites with different degrees of animal impact (severe, moderate or no impact) of an overwintering pasture by means of qPCR and T-RFLP of amoA genes. In areas where no animal impact could be identified AOA was dominating over AOB. However, AOB abundance increased as the degree of animal impact enhances, becoming most dominant in the severely impacted site. Interestingly, the diversity of AOB was the highest in the severely impacted area, where AOA diversity was the lowest. Obviously the pressure imposed by altered environmental conditions created by cattle husbandry lead to the selection of AOB and AOA populations, adapted to alkaline pH and higher ammonia concentration. AU - Radl, V. AU - Chronakova, A.* AU - Cuhel, J.* AU - Simek, M.* AU - Elhottova, D.* AU - Welzl, G. AU - Schloter, M. C1 - 31555 C2 - 34558 CY - Amsterdam SP - 68-71 TI - Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering. JO - Appl. Soil Ecol. VL - 77 PB - Elsevier Science Bv PY - 2014 SN - 0929-1393 ER - TY - JOUR AB - The present field study documents substantial changes in the soil microbial community (SMC) and organic matter (SOM) in an upland pasture soil resulting from 10 years of “cattle outdoor over-wintering practice”. Soils from a long-term investigated pasture area were compared under three different levels of cattle impact (SI – severe, MI – moderate, NI – no impact). Extended polar lipids analysis (PLA) confirmed a qualitatively new microbial community profile and a several-fold increase of the microbial biomass in the impacted soils (SI) compared to the control NI soil. The new SMC was derived from cattle intestine microorganisms, typical by increased content of archaeal phospholipid ether lipids and by new fatty acids indicative for bacterial and fungal fecal anaerobes. A quality of the SI-SOM, evaluated by the relative content of the pyrolytic fragments profile was more similar to the cattle excrements than to the MI and NI soils, and an organic carbon content of the SI soil was not more than three times higher in comparison to the control NI soil. The quality and quantity of the SOM as well as the SMC in both, the most impacted SI and the control NI soils, were stable in contrast to the moderately impacted MI soil. During the growing season, the MI soil lost 75% of the Corg and 65% of the soil microbial biomass that had accumulated during winter; its aromatic-rich-SOM showed transformation into SOM, enriched by N, P-organic derivates. This transformation was positively correlated to a significant recovery of the actinobacteria and reduction of anaerobic microorganisms during the vegetation season. Results in this study showed that the stability of the soil microbial changes due to the cattle outdoor over-wintering husbandry depended on the stability of the quantitative and qualitative changes of the SOM. AU - Elhottova, D.* AU - Koubová, A.* AU - Simek, M.* AU - Cajthaml, T.* AU - Jirout, J.* AU - Esperschütz, J.A. AU - Schloter, M. AU - Gattinger, A. C1 - 7308 C2 - 29669 SP - 56-65 TI - Changes in soil microbial communities as affected by intensive cattle husbandry. JO - Appl. Soil Ecol. VL - 58 PB - Elsevier PY - 2012 SN - 0929-1393 ER - TY - JOUR AB - The impact of tillage practices on microbial N transformations in Vertisols is poorly understood and data from long-term field experiments are scarce, particularly in semiarid regions. We evaluated the effects of traditional tillage (TT) vs no-tillage (NT) on denitrification in a long-term field experiment under a rainfed crop rotation system (cereal-sunflower-legumes) on a Vertisol (SW Spain). In general, the abundance of denitrifiers and the respective potential denitrification rates was higher under NT compared to TT during the vegetation period, but not after harvesting. However differences in denitrifier numbers were within the same order of magnitude (0.5-3 x 10(7) copies g soil dw). The abundance of nitrite reducers and N2O reducers was relatively similar. In addition, N2O/N-2 ratios between 1 and 2 were found for both treatments. These results emphasize that NT has a limited impact on denitrification in Vertisols under fertilizer regime and legume-crop rotation and thus losses of N2O are expected to be comparable to those of traditional tillage systems. AU - Melero, S.* AU - Pérez-de-Mora, A. AU - Murillo, M.* AU - Buegger, F. AU - Kleineidam, K. AU - Kublik, S. AU - Vanderlinden, K.* AU - Moreno, F.* AU - Schloter, M. C1 - 6288 C2 - 28465 CY - Amsterdam, Netherlands SP - 221-225 TI - Denitrification in a vertisol under long-term tillage and no-tillage management in dryland agricultural systems: Key genes and potential rates. JO - Appl. Soil Ecol. VL - 47 IS - 3 PB - Elsevier PY - 2011 SN - 0929-1393 ER - TY - JOUR AB - Soils found in semiarid areas of the Mediterranean Basin are particularly prone to degradation due to adverse climatic conditions with annual rainfall <300 mm and high temperatures being responsible for the scant vegetal growth and the consequent lack of organic matter. A three-year field experiment was conducted to test the potential of two organic amendments (sludge and compost) to improve soil quality and plant growth in a semiarid degraded Mediterranean ecosystem. Since little is known about N dynamics in such assisted ecosystems, we investigated the effects of this practice on key processes of the global N cycle. Besides soil chemical and biological parameters and vegetation cover, we measured absolute and specific potential nitrification and denitrification rates and quantified the size of the ammonia oxidising and denitrifying bacterial populations via quantitative PCR (amoA and nirS genes). At the end of the experiment soil fertility, microbial activity and plant growth had improved in treated plots. Amendments increased the amount of ammonia oxidisers and denitrifiers in soil, but the relative proportion of these groups varied in relation to the total microbial community, being higher in the case of ammonia oxidisers but not in the case of denitrifiers. As a consequence, significantly higher potential nitrification and denitrification rates were measured on a global basis in amended soils. Yet specific activities (potential rate/gene copy numbers) were lower for ammonia oxidisers in amended soils and for denitrifiers in sludge treated soils than those observed in control plots. Organic amendments influenced resource availability, the size and the activity patterns of microbial populations involved in long-term N dynamics. Therefore N cycling processes may play a key role to assist sustainable restoration practices in semiarid degraded areas. AU - Bastida, F.* AU - Pérez-de-Mora, A. AU - Babic, K. AU - Hai, B. AU - Hernandez, T.* AU - Garcia, C.* AU - Schloter, M. C1 - 1488 C2 - 26072 SP - 195-205 TI - Role of amendments on N cycling in Mediterranean abandoned semiarid soils. JO - Appl. Soil Ecol. VL - 41 IS - 2 PB - Elsevier Science PY - 2009 SN - 0929-1393 ER - TY - JOUR AB - This study describes an integrated approach (1) to monitor the quantity and quality of water extractable organic matter (WEOM) and size, structure and function of microbial communities in space (depth) and time, and (2) to explore the relationships among the measured properties. The study site was an arable field in Southern Germany under integrated farming management including reduced tillage. Samples of this Eutric Cambisol soil were taken in July 2001, October 2001, April 2002 and July 2002 and separated into three depths according to the soil profile (0–10 cm, 10–28 cm and 28–40 cm). For each sample, the quantity and quality (humification index, HIX) of water extractable organic matter (WEOM) were measured concomitantly with soil enzyme activities (alkaline phosphatase, ß-glucosidase, protease) and microbial community size (Cmic). Furthermore, microbial community structure was characterised based on the fingerprints of nucleic acids (DNA) as well as phospholipid fatty acids (PLFA). We observed strong influences of sampling date and depth on the measured parameters, with depth accounting for more of the observed variability than date. Increasing depth resulted in decreases in all parameters, while seasonal effects differed among variants. Principal component (PC) analysis revealed that both DNA and PLFA fingerprints differentiated among microbial communities from different depths, and to a smaller extent, sampling dates. The majority of the 10 PLFAs contributing most to PC 1 were specific for anaerobes. Enzyme activities were strongly related to Cmic, which was depending on water extractable organic carbon and nitrogen (WEOC and WEON) but not to HIX. HIX and WEOM interact with the microbial community, illustrated by (1) the correlation with the number of PLFA peaks (community richness), and (2) the correlations with community PC analysis scores. AU - Bausenwein, U. AU - Gattinger, A. AU - Langer, U.* AU - Embacher, A. AU - Hartmann, H.-P. AU - Sommer, M.* AU - Munch, J.-C. AU - Schloter, M. C1 - 1559 C2 - 25391 SP - 67-77 TI - Exploring soil microbial communities and soil organic matter: Variability and interactions in arable soils under minimum tillage practice. JO - Appl. Soil Ecol. VL - 40 IS - 1 PB - Elsevier PY - 2008 SN - 0929-1393 ER -