Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances.

Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.

The Effects of Conservation Tillage on Chemical and Microbial Soil Parameters at Four Sites across Europe.

Conservation tillage is often discussed as an effective tool to improve the soil quality in agriculture. Four sites across Europe (in Germany, Romania, Spain, and Sweden) were investigated as case studies for country-specific reductions in tillage intensity. Conventional tillage (CT) by mouldboard ploughing was compared with shallow and deep non-inversion minimum tillage (MT) and/or no-tillage (NT). In Sweden, NT and MT had positive effects on the concentrations of soil organic carbon (SOC), total nitrogen (N), and microbial biomass carbon (MBC) in the upper 20 cm compared with CT. At the German site, MT increased SOC, N, and MBC concentrations in the top 10 cm. In contrast, CT increased MBC contents and bulk density between 20 and 30 cm soil depth. At the Romanian site, soil parameters showed no differences between inverse tillage (CT) and non-inverse tillage (MT), both with a working depth of 25 to 30 cm. At the Spanish site, the use of NT significantly increased the concentrations as well as the stocks of C, N, and MBC compared to CT. In conclusion, reduced tillage improved soil microbial properties in most cases. However, the effectiveness of reduced tillage appears to be highly dependent on site conditions such as pH, soil texture, and climatic conditions.

Functions of elements in soil microorganisms.

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Evidence of considerable C and N transfer from peas to cereals via direct root contact but not via mycorrhiza.

Intercropping of legumes and cereals is an important management method for improving yield stability, especially in organic farming systems. However, knowledge is restricted on the relevance of different nutrient transfer pathways. The objective of the study was to quantify nitrogen (N) and carbon (C) transfer from peas to triticale by (1) direct root contact (= R), (2) arbuscular mycorrhizal fungi (AMF; = A), and (3) diffusion (= D). Pea (Pisum sativum cv. Frisson and P2) and triticale (Triticum × Secale cv. Benetto) plants as intercrop were grown for 105 days. Treatment ADR enabled all transfer paths between the two crops. Treatment AD with root exclusion enabled AMF and diffusion transfer between peas and triticale. Treatment A with a diffusion gap barrier only allowed AMF transfer. Pea plants were labelled every 14 days with a 13C glucose and 15N urea solution, using the cotton wick technique. Direct root contact resulted in the highest pea rhizodeposition and thus the largest absolute amounts of N and C transfer to triticale. Root exclusion generally changed composition of rhizodeposits from fine root residues towards root exudates. Pea plant-N consisted of 17% N derived from rhizodeposition (NdfR) in treatment ADR but only 8% in the treatments AD and A, independently of pea variety, whereas pea plant-C consisted of 13% C derived from rhizodeposition (CdfR), without pea variety and transfer path treatment effects. Averaging all transfer path treatments, 6.7% of NdfR and 2.7% of CdfR was transferred from Frisson and P2 to triticale plants. Approximately 90% of this NdfR was transferred by direct root contact from Frisson to triticale and only 10% by AMF, whereas only 55% of CdfR was transferred to triticale by direct root contact, 40% by AMF and 5% by diffusion. Similar percentages were transferred from mutant P2 to triticale. Root exclusion generally changed RD composition from fine root residues towards root exudates.

Feed Quality and Feeding Level Effects on Faecal Composition in East African Cattle Farming Systems.

Effects of feeding levels below maintenance requirements of metabolizable energy (MER) and of feed supplementation on fecal nutrient and microbial C concentrations were evaluated. In experiment 1, Rhodes grass hay only was offered to Boran steers at 80%, 60%, and 40% of individual MER, while steers at 100% MER additionally received a concentrated mixture. This reduction in MER decreased N, increased fungal C but did not affect bacterial C concentrations in feces. In experiment 2, Holstein × Boran heifers were offered a poor-quality roughage diet without supplement, with sweet potato vine silage or with a urea-molasses block. These two supplements did not affect the fecal chemical composition or fungal C but increased bacterial C concentrations in feces. Across all data, the fungal C/bacterial C ratio was positively related to N and negatively to neutral detergent fiber concentrations in feces, indicating diet-induced shifts in the fecal microbial community.

Soil microbial properties of subalpine steppe soils at different grazing intensities in the Chinese Altai Mountains.

Long-term provision of ecosystem services by grasslands is threatened by increasing stocking densities. The functions of grassland ecosystems depend on a mutual relationship between aboveground and belowground biota. While the effects of increasing stocking density on plant biomass are well studied, little is known about its impact on soil microbial properties. To fill this knowledge gap a grazing experiment was conducted on a summer pasture in the Chinese Altai Mountains during the summers of 2014 and 2015 using a randomized block design with stocking densities of 0, 8, 16, and 24 sheep ha-1 replicated four times. After two summer grazing periods (each 56 days), topsoil samples (1-7 cm) were taken in September 2015 and analyzed for major physical, chemical, and microbial soil properties. Except for the metabolic quotient (qCO2; p < 0.05), the examined soil properties remained unaffected by the increasing stocking densities, likely due to high spatial variability. The qCO2 declined from 13.5 mg CO2-C g-1 microbial biomass C d-1 at zero grazing to 12.2 mg CO2-C g-1 microbial biomass C d-1 at a stocking density of 24 sheep ha-1. Low values of qCO2 indicate an aged and dormant microbial community that diverts less soil organic carbon (SOC) to catabolic processes within their cells, characteristic for C limiting conditions. The aboveground biomass affected by grazing intensity correlated positively with SOC (rs = 0.60, p = 0.015) and ergosterol (rs = 0.76, p = 0.001) pointing indirectly to the effect of stocking density. Additionally to the relatively high values of qCO2, highest values of SOC (39.2 mg g-1 soil), ergosterol (6.01 µg g-1 soil), and basal respiration (10.7 µg g-1 soil d-1) were observed at a stocking density of 8 sheep ha-1 indicating that a low grazing intensity is recommendable to avoid soil degradation.

Relationships between feeding and microbial faeces indices in dairy cows at different milk yield levels.

A study was carried out to gain quantitative information on the diet-dependent faecal microbial biomass of dairy cows, especially on the biomass fractions of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. Groups of high-yield, low-yield and non-lactating cows were investigated at four different farms. A mean faecal microbial biomass C (MBC) concentration of 33.5 mg g-1 DM was obtained by the chloroform fumigation extraction method. This is similar to a mean microbial C concentration of 31.8 mg g-1 DM, which is the sum of bacterial C and fungal C, estimated by cell-wall derived muramic acid (MurN) and fungal glucosamine (GlcN), respectively. However, the response of these two approaches to the feeding regime was contradictory, due to feeding effects on the conversion values. The higher neutral detergent fibre (NDF) and acid detergent fibre (ADF) concentrations in the non-lactating group led to higher (P < 0.05) concentrations of cellulose and lignin in their faeces in comparison with the lactating cows. This change in faecal chemical composition in the non-lactating group was accompanied by usually higher ratios of G+/G- phospholipid fatty acids (PLFA), ergosterol/MBC and fungal C/bacterial C. Although bacteria dominate the faecal microbial biomass, fungi contribute a considerable mean percentage of roughly 20% to the faecal microbiome, according to PLFA and amino sugar data, which requires more attention in the future. Near-infra red spectroscopic estimates of organic N and C fractions of cow faeces were able to model microbial biomarkers successfully, which might be useful in the future to predict its N2O emission potential and fertilizer value.

Changes in soil microbial biomass and residual indices as ecological indicators of land use change in temperate permanent grassland.

The relationship between microbial biomass, residues and their contribution to microbial turnover is important to understand ecosystem C storage. The effects of permanent grassland (100 % ryegrass--PG), conversion to modified grassland (mixture of grass and clover--MG) or maize monoculture (MM) on the dynamics of soil organic C (SOC), microbial biomass, fungal ergosterol and microbial residues (bacterial muramic acid and fungal glucosamine) were investigated. Cattle slurry was applied to quantify the effects of fertilisation on microbial residues and functional diversity of microbial community across land use types. Slurry application significantly increased the stocks of microbial biomass C and S and especially led to a shift in microbial residues towards bacterial tissue. The MM treatment decreased the stocks of SOC, microbial biomass C, N and S and microbial residues compared with the PG and MG treatments at 0-40 cm depth. The MM treatment led to a greater accumulation of saprotrophic fungi, as indicated by the higher ergosterol-to-microbial biomass C ratio and lower microbial biomass C/S ratio compared with the grassland treatments. The absence of a white clover population in the PG treatment caused a greater accumulation of fungal residues (presumably arbuscular mycorrhizal fungi (AMF), which do not contain ergosterol but glucosamine), as indicated by the significantly higher fungal C-to-bacterial C ratio and lower ergosterol-to-microbial biomass C ratio compared with the MG treatment. In addition to these microbial biomass and residual indices, the community level physiological profiles (CLPP) demonstrated distinct differences between the PG and MG treatments, suggesting the potential of these measurements to act as an integrative indicator of soil functioning.

Dose-dependent reactions of Aporrectodea caliginosa to perfluorooctanoic acid and perfluorooctanesulfonic acid in soil.

As a consequence of their widespread use, e.g. as protective coatings for fabrics, and their resistance to thermal and biological breakdown, perfluorinated compounds are increasingly found in the environment, but little is known about their ecotoxicological properties. A 40-day microcosm experiment was carried out to examine the effects of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) on the endogeic geophagus earthworm Aporrectodea caliginosa, its survival and feeding on soil organic C and microbial biomass C. Three levels of concentration (1, 100, and 500 mg kg(-1)) were chosen. The lowest represented the maximum found in sediments and soils and the other two are extreme concentrations that might occur in pollution hotspots and that have been shown to poison organisms. Earthworms promoted the production of CO2 and decreased microbial biomass C in soil, regardless of the presence of PFOA or PFOS. Both compounds significantly decreased the surviving numbers and dry weight of earthworms at concentrations of 100 mg kg(-1). No earthworms survived at PFOA and PFOS concentrations of 500 mg kg(-1). At concentrations of 1 mg kg(-1), no negative effects were observed. The δ(13)C values of A. caliginosa did not differ between treatments. In contrast, the δ(15)N values were significantly increased after adding 1 mg kg(-1) of PFOA, reflecting elevated portions of soil-derived N in the earthworm tissue. In contrast, these portions of soil-derived N were lower in the earthworms after addition of 100 mg kg(-1) of PFOA and PFOS. In conclusion, extreme concentrations of PFOA and PFOS negatively affected endogeic A. caliginosa, whereas a concentration of 1 mg kg(-1) of PFOA and PFOS was related to an increased uptake of soil N by the earthworms.

Microbial biomass in faeces of dairy cows affected by a nitrogen deficient diet.

Since more than half of the faecal nitrogen (N) originates from microbial N, the objective of the study was to develop a method for quantitatively detecting microbial biomass and portion of living microorganisms in dairy cattle faeces, including bacteria, fungi and archaea. Three techniques were tested: (1) the chloroform fumigation extraction (CFE) method, (2) detection of the fungal cell-membrane component ergosterol and (3) analysis of the cell wall components fungal glucosamine and bacterial muramic acid. In a second step, an N deficient (ND) and an N balanced (NB) diets were compared with respect to the impacts on faecal C and N fractions, microbial indices and digestibility. The mean values of microbial biomass C and N concentrations averaged around 37 and 4.9 mg g(-1) DM, respectively. Ergosterol, together with fungal glucosamine and bacterial muramic acid, revealed a 25% fungal C in relation to the total microbial C content in dairy cattle faeces. Changes in ruminal N supply showed significant effects on faecal composition. Faecal concentrations of NDF, hemicelluloses and undigested dietary N and the total C/N ratio were significantly higher in ND treatment compared to the NB treatment. N deficiency was reflected also by a higher microbial biomass C/N ratio. It was concluded that the assessment of microbial indices provides valuable information with respect to diet effects on faecal composition and the successive decomposition. Further studies should be conducted to explore the potentials for minimising nutrient losses from faeces.

Changes in microbial biomass and P fractions in biogenic household waste compost amended with inorganic P fertilizers.

The present study was conducted to evaluate the changes in microbial biomass indices (C, N, and especially P) and in P fractions in compost amended with inorganic P fertilizers. In the non-amended control, the average contents of microbial biomass C, N, and P were 1744, 193, and 63 microg g(-1) compost, respectively. On average, 1.3% of total P was stored as microbial biomass P. The addition of KH(2)PO(4) and TSP (triple super phosphate) led to immediate significant increases in microbial biomass C, N, and P. Approximately, 4.6% of the added TSP and 5.8% of the added KH(2)PO(4) were incorporated on average into the microbial biomass throughout the incubation. Approximately, 4.7% of the 1mg and 5.8% of the 2mg addition rate were incorporated on average into the microbial biomass. In the amendment treatments, the average contents of microbial biomass C, N, and P declined by 44%, 64%, and 49%, respectively. Initially, the average size of the P fractions in the non-amended compost increased in the order (% of total P in brackets) resin P (0.7%)

Decomposition of heavy metal contaminated nettles (Urtica dioica L.) in soils subjected to heavy metal pollution by river sediments.

Two incubation experiments were conducted to evaluate differences in the microbial use of non-contaminated and heavy metal contaminated nettle (Urtica dioica L.) shoot residues in three soils subjected to heavy metal pollution (Zn, Pb, Cu, and Cd) by river sediments. The microbial use of shoot residues was monitored by changes in microbial biomass C, biomass N, biomass P, ergosterol, N mineralisation, CO(2) production and O(2) consumption rates. Microbial biomass C, N, and P were estimated by fumigation extraction. In the non-amended soils, the mean microbial biomass C to soil organic C ratio decreased from 2.3% in the low metal soil to 1.1% in the high metal soils. In the 42-d incubation experiment, the addition of 2% nettle residues resulted in markedly increased contents of microbial biomass P (+240%), biomass C (+270%), biomass N (+310%), and ergosterol (+360%). The relative increase in the four microbial properties was similar for the three soils and did not show any clear heavy metal effect. The contents of microbial biomass C, N and P and ergosterol contents declined approximately by 30% during the incubation as in the non-amended soils. The ratios microbial biomass C to N, microbial biomass C to P, and ergosterol to microbial biomass C remained constant at 5.2, 26, and 0.5%, respectively. In the 6-d incubation experiment, the respiratory quotient CO(2)/O(2) increased from 0.74 in the low metal soil to 1.58 in the high metal soil in the non-amended soils. In the treatments amended with 4% nettle residues, the respiratory quotient was constant at 1.13, without any effects of the three soils or the two nettle treatments. Contaminated nettle residues led generally to significantly lower N mineralisation, CO(2) production and O(2) consumption rates than non-contaminated nettle residues. However, the absolute differences were small.