Specific response of fungal and bacterial residues to one-season tillage and repeated slurry application in a permanent grassland soil

The dynamics of fungal and bacterial residues to a one-season tillage event in combination with manure application in a grassland soil are unknown. The objectives of this study were (1) to assess the effects of one-season tillage event in two field trials on the stocks of microbial biomass, fungal biomass, microbial residues, soil organic C (SOC) and total N in comparison with permanent grassland; (2) to determine the effects of repeated manure application to restore negative tillage effects on soil microbial biomass and residues. One trial was started 2 years before sampling and the other 5 years before sampling. Mouldboard ploughing decreased the stocks of SOC, total N, microbial biomass C, and microbial residues (muramic acid and glucosamine), but increased those of the fungal biomarker ergosterol in both trials. Slurry application increased stocks of SOC and total N only in the short-term, whereas the stocks of microbial biomass C, ergosterol and microbial residues were generally increased in both trials, especially in combination with tillage. The ergosterol to microbial biomass C ratio was increased by tillage, and decreased by slurry application in both trials. The fungal C to bacterial C ratio was generally decreased by these two treatments. The metabolic quotient qCO₂ showed a significant negative linear relationship with the microbial biomass C to SOC ratio and a significant positive relationship with the soil C/N ratio. The ergosterol to microbial biomass C ratio revealed a significant positive linear relationship with the fungal C to bacterial C ratio, but a negative one with the SOC content. Our results suggest that slurry application in grassland soil may promote SOC storage without increasing the role of saprotrophic fungi in soil organic matter dynamics relative to that of bacteria.     

Short-term effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil

A field study was carried out to analyze the short-term (2 years) effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil. The experimental design was a split-plot arrangement of treatments, consisting of two tillage treatments—ridge tillage (RT) and no-tillage (NT)—in combination with two crop rotation treatments—corn (Zea mays L.) monoculture and a 2-year corn-soybean (Glycine max L.) rotation. Phospholipid fatty acid (PLFA) profiles were used to assess soil microbial community structure. No-tillage resulted in significantly higher total PLFAs compared to the RT treatment, which was accompanied by higher activities of protease, β-glucosaminidase, and β-glucosidase. This suggests a close link between soil microbial communities and enzyme activities in response to tillage. The increase of total microbial lipid biomass in the NT soils was due to the increase in both fungal and bacterial PLFAs. Crop rotation had little effect on soil bacterial communities and enzyme activities, but it significantly influenced soil fungal communities, particularly arbuscular mycorrhizal fungi. Soils under monoculture corn had higher fungal biomass than soils under corn-soybean rotation regardless of tillage treatment.     

Quantitative assessment of the fungal contribution to microbial tissue in soil

The fungi-to-bacteria ratio in soil ecological concepts and its application to explain the effects of land use changes have gained increasing attention over the past decade. Four different main approaches for quantifying the fungal and bacterial contribution to microbial tissue can be distinguished: (1) microscopic methods, (2) selective inhibition, (3) specific cell membrane components and (4) specific cell wall components. In this review, the different methods were compared and we hypothesized that all these approaches result in similar values for the fungal and bacterial contribution to total microbial biomass, activity, and residues (dead microbial tissue) if these methods are evenly reliable for the estimation of fungal biomass. The fungal contribution to the microbial biomass or respiration varied widely between 2 and 95% in different data sets published over the past three decades. However, the majority of the literature data indicated that fungi dominated microbial biomass, respiration or non-biomass microbial residues, with mean percentages obtained by the different methodological approaches varying between 35 and 76% in different soil groups, i.e. arable, grassland, and forest soils and litter layers. Microscopic methods generally gave the lowest average values, especially in arable and grasslands soils. Very low ratios in fungal biomass C-to-ergosterol obtained by microscopic methods suggest a severe underestimation of fungal biomass by certain stains. Relatively consistent ratios of ergosterol to linoleic acid (18:2ω6,9) indicate that both cell membrane components are useful indicators for saprotrophic and ectomycorrhizal fungi. More quantitative information on the PLFA content of soil bacteria and the 16:1ω5 content of arbuscular mycorrhizal fungi is urgently required to fully exploit the great potential of PLFA measurements. The most consistent results have been obtained from the analysis of fungal glucosamine and bacterial muramic acid in microbial residues. Component-specific δ¹³C analyses of PLFA and amino sugars are a promising prospect for the near future.     

Acidification of a sandy grassland favours bacteria and disfavours fungal saprotrophs as estimated by fatty acid profiling

We have investigated the structure of a microbial community in semi-natural sandy grassland in southeast Sweden. The sand is rich in lime, but in most places the soil is decalcified in the upper layers, and therefore this site shows a large variation in pH within short distances. We collected samples at three different soil depths (0-10 cm, 10-20 cm and 20-30 cm) and found the pH to range from 5 to 8 in the topsoil and from 4.5 to 9.5 in the deepest layer. The abundance of saprophytic fungi and bacteria was investigated using signature phospholipid fatty acids and arbuscular mycorrhizal fungi (AMF) using the neutral lipid fatty acid 16:1ω5. The PLFA pattern of the topsoil was different from that in the other two layers, as indicated by principal component analysis. The saprotrophic fungi were associated with high pH, and bacteria with low pH in these sandy soils. No relation was found between pH and AMF in the topsoil, while a positive relation was found in the deepest soil layer. The saprophytic fungi-to-bacteria ratio was constant with depth, while the AMF-to-bacteria ratio increased with soil depth. The results showed that high soil pH favoured fungal saprophytes in sandy grasslands and that AMF are relatively more abundant than the other two groups in deeper soil layers; particularly so when the pH is high.     

Influence of reduced tillage on earthworm and microbial communities under organic arable farming

Although reduced tillage is an agricultural practice reported to decrease soil erosion and external inputs while enhancing soil fertility, it has still rarely been adopted by European organic farmers. The objective of this study was to assess the long-term interactive effects of tillage (conventional (CT) vs. reduced (RT)) and fertilization (slurry (S) vs. composted manure/slurry (MCS)) on earthworms and microbial communities in a clay soil under spelt in an organic 6-year crop rotation. Earthworm populations (species, density and biomass, cocoons) were investigated by handsorting the soil nine years after initial implementation of the treatments. Soil microbial carbon (C_mic) and nitrogen (N_mic) were measured by chloroform-fumigation extraction and a simplified phospholipid fatty acid (PLFA) analysis was used to separate for populations of bacteria, fungi and protozoa. Significantly increased total earthworm density in RT plots was mainly attributed to increased numbers of juveniles. Moreover, we found five times more cocoons with RT. Species richness was not affected by the treatments, but tillage treatments had differentially affected populations at the species-level. In addition, cluster analysis at the community level revealed two distinct groups of plots in relation to tillage treatments. In RT plots C_mic increased in the 0–10 cm and 10–20 cm soil layers, while PLFA concentrations indicative of Gram-negative bacteria, fungi and protozoa only increased in the topsoil. Lower bacteria-to-fungi ratios in the upper soil layer of RT plots indicated a shift to fungal-based decomposition of organic matter whereas a higher C_mic-to-C_org ratio pointed towards enhanced substrate availability. Slurry application decreased microbial biomass and enhanced density of juvenile anecic earthworms but overall fertilization effect was weak and no interactions with tillage were found. In conclusion, tillage is a major driver in altering communities of earthworms and microorganisms in arable soils. The use of reduced tillage provides an approach for eco-intensification by enhancing inherent soil biota functions under organic arable farming.     

保护性耕作对黑土微生物群落的影响

耕作方式通过影响土壤微生物群落而影响土壤生态系统过程。本研究以传统耕作玉米连作处理为对照,通过测定土壤微生物量碳及磷脂脂肪酸含量,分析了保护性耕作(包括免耕玉米连作和免耕大豆-玉米轮作)对黑土微生物群落的影响。结果表明,保护性耕作可显著增加土壤表层(0～5cm)全碳、全氮、水溶性有机碳、碱解氮和微生物量碳(P0.05),为微生物代谢提供了丰富的资源。同时,保护性耕作显著提高了土壤表层(0～5cm)总脂肪酸量、真菌和细菌生物量(P0.05),提高了土壤的真菌/细菌值,有利于农田土壤生态系统的稳定性。研究结果对于探讨保护性耕作的内在机制具有重要意义。     

Microorganisms as driving factors for the community structure of testate amoebae along an altitudinal transect in tropical mountain rain forests

We investigated microbial biomass, fungal biomass and microbial community structure at three altitudes (1000, 2000 and 3000 m) and in two soil layers [L/F layer (Layer I) and underlying H/Ah layer (Layer II)] of tropical mountain rain forests in southern Ecuador. Basal respiration, microbial biomass and concentration of ergosterol generally declined from Layer I to Layer II and peaked at 2000 m. Compared to temperate forest ecosystems microbial biomass and ergosterol concentrations were generally low. Patterns in phospholipid fatty acids indicated that the composition of microbial communities markedly changed from Layer I to Layer II. These differences between layers decreased with increasing altitude. The concentration of the arbuscular mycorrhizal fungal marker PLFA 16:1ω5c decreased with altitude in Layer I but increased in Layer II. The fungal-to-bacterial ratio increased with altitude and was higher in Layer I than in Layer II. Presumably, low microbial biomass in soils of tropical forest ecosystems is due to high temperature associated with high respiration but also low litter quality, with the latter declining with altitude. These conclusions are supported by the fact that at higher altitude the microbial community changed from a bacterial-dominated to a fungal-dominated system. CCA showed that microbial biomass correlated closely with density of a number of putatively bacterial feeding testate amoeba species including Corythion dubium Taranek, 1871, Euglypha cristata Leidy, 1879, Trigonopyxis arcula Penard, 1912, Tracheleuglypha dentata Deflandre, 1928 and Trinema lineare Penard, 1890. Ergosterol concentrations, but not the PLFA 18:2ω6c, strongly correlated with the putatively fungal feeding species Phryganella acropodia (Hertwig, Lesser, 1874) Hopkinson, 1909. Generally, parallel to microbial biomass and ergosterol concentrations the density of testate amoebae peaked at 2000 m. However, compared to microbial parameters changes in testate amoebae communities between two layers were less pronounced. The data suggest that density and community structure of testate amoebae are driven by the availability of food resources (bacteria and fungi) which at high altitude decrease with increasing moisture and decreasing pH.     

Influence of long-term fertilisation and crop rotation on changes in fungal and bacterial residues in a tropical rice-field soil

Amino sugars, as a microbial residue biomarker, are highly involved in microbial-mediated soil organic matter formation. However, accumulation of microbial biomass and responses of bacterial and fungal residues to the management practices are different and poorly characterized in rice soils. The objectives of this study were to evaluate the effects of mineral fertiliser (MIN), farmyard manure (FYM) and groundnut oil cake (GOC) on crop yield and co-accumulation of microbial residues and microbial biomass under rice-monoculture (RRR) and rice–legume–rice (RLR) systems. In the organic fertiliser treatments and RLR, rice grain yield and stocks of soil and microbial nutrients were significantly higher than those of the MIN treatment and RRR, respectively. The increased presence of saprotrophic fungi in the organic fertiliser treatments and RRR was indicated by significantly increased ergosterol/C_mic ratio and extractable sulphur. In both crop rotation systems, the long-term application of FYM and GOC led to increased bacterial residues as indicated by greater accumulation of muramic acid. In contrast, the higher fungal C/bacterial C ratio and lower ergosterol/C_mic ratio in the MIN treatment, is likely caused by a shift within the fungal community structure towards ergosterol-free arbuscular mycorrhizal fungi (AMF). The organic fertiliser treatments contributed 22 % more microbial residual C to soil organic C compared to the MIN treatment. Our results suggest that the negative relationship between the ratios ergosterol/C_mic and fungal C/bacterial C encourages studying responses of both saprotrophic fungi and AMF when assessing management effects on the soil microbial community.     

Long-term no-till management affects microbial biomass but not community composition in Canadian prairie agroecosytems

No-till (NT) management greatly reduces soil physical disturbance and can result in a stratification of nutrients and organic matter in the soil profile due to the retention of crop residues on the soil surface potentially affecting the dynamics of microbial interactions in the soil. Microbial abundance and diversity can be used to assess the relative impact of management on the long-term sustainability of cropping systems. The objective of this study was to assess the impact of long-term NT vs. conventional tillage (CT) management on soil microbial community structure at four different sites on the Canadian prairies using phospholipid fatty acid analysis (PLFA) and DNA fingerprinting. Analysis of 16S and 18S rDNA using denaturing gradient gel electrophoresis revealed high inherent variability within bacterial and fungal community fingerprints among replicate field plots. Differences in bacterial and fungal phylogeny were related to depth in the soil profile but not to tillage management. Abundance of individual PLFA biomarkers were 7 to 86% greater in NT surface soils (0- to 5-cm depth), except at the Ellerslie site in 2005 where biomass was greater in CT. Responses at the 5- to 10-cm and 10- to 15-cm depths were more varied, in some cases with greater biomass in CT than NT soils. Ordination analysis of PLFA profiles showed clear community separation with depth but not tillage. Physiological stress biomarkers were correlated with simple measures of nutrient concentration and indicated that resource availability was likely the main factor determining community structure. It was concluded that tillage disturbance was not an overriding factor in determining microbial community composition in the long-term NT and CT soils studied. Further study of the interaction of cropping frequency with tillage management is needed to understand the effects of tillage disturbance on microbial turnover of plant derived residues.     

Relationships between microbial indices in roots and silt loam soils forming a gradient in soil organic matter

Perennial rye grass (Lolium perenne) was grown in a greenhouse pot experiment on seven soils to answer the question whether the microbial colonisation of roots is related to existing differences in soil microbial indices. The soils were similar in texture, but differed considerably in soil organic matter, microbial biomass, and microbial community structure. Ergosterol and fungal glucosamine were significantly interrelated in the root material. This ergosterol was also significantly correlated with the average ergosterol content of bulk and rhizosphere soil. In addition, the sum of fungal C and bacterial C in the root material revealed a significant linear relationship with microbial biomass C in soil. The colonisation of roots with microorganisms increased apparently with an increase in soil microbial biomass. In the root material, microbial tissue consisted of 77% fungi and 23% bacteria. In soil, the fungal dominance was slightly, but significantly lower, with 70% fungi and 30% bacteria. Fungal glucosamine in the root material was significantly correlated with that in soil (r=0.65). This indicates a close relationship between the composition of dead microbial remains in soil and the living fraction in soil and root material for unknown reasons.