Atmospheric nitrate deposition and the microbial degradation of cellobiose and vanillin in a northern hardwood forest

Human activity has increased the amount of N entering terrestrial ecosystems from atmospheric NO₃⁻ deposition. High levels of inorganic N are known to suppress the expression of phenol oxidase, an important lignin-degrading enzyme produced by white-rot fungi. We hypothesized that chronic NO₃⁻ additions would decrease the flow of C through the heterotrophic soil food web by inhibiting phenol oxidase and the depolymerization of lignocellulose. This would likely reduce the availability of C from lignocellulose for metabolism by the microbial community. We tested this hypothesis in a mature northern hardwood forest in northern Michigan, which has received experimental atmospheric N deposition (30 kg NO₃⁻-N ha⁻¹ y⁻¹) for nine years. In a laboratory study, we amended soils with ¹³C-labeled vanillin, a monophenolic product of lignin depolymerization, and ¹³C-labeled cellobiose, a disaccharide product of cellulose degradation. We then traced the flow of ¹³C through the microbial community and into soil organic carbon (SOC), dissolved organic carbon (DOC), and microbial respiration. We simultaneously measured the activity of enzymes responsible for lignin (phenol oxidase and peroxidase) and cellobiose (β-glucosidase) degradation. Nitrogen deposition reduced phenol oxidase activity by 83% and peroxidase activity by 74% when compared to control soils. In addition, soil C increased by 76%, whereas microbial biomass decreased by 68% in NO₃⁻ amended soils. ¹³C cellobiose in bacterial or fungal PLFAs was unaffected by NO₃⁻ deposition; however, the incorporation of ¹³C vanillin in fungal PLFAs extracted from NO₃⁻ amended soil was 82% higher than in the control treatment. The recovery of ¹³C vanillin and ¹³C cellobiose in SOC, DOC, microbial biomass, and respiration was not different between control and NO₃⁻ amended treatments. Chronic NO₃⁻ deposition has stemmed the flow of C through the heterotrophic soil food web by inhibiting the activity of ligninolytic enzymes, but it increased the assimilation of vanillin into fungal PLFAs.     

Effects of modified Pb-, Zn-, and Cd- availability on the microbial communities and on the degradation of isoproturon in a heavy metal contaminated soil

The effects of modified heavy metal (HM) availability on the microbial community structure and on the microbe-mediated degradation of herbicide isoproturon (IPU) were evaluated in soil with a long-term HM contamination. The fate of ¹⁴C-ring labelled IPU was investigated for over 60 days under controlled microcosm conditions. Phosphate mineral apatite and a water solution of Pb, Zn, and Cd salts were previously homogeneously mixed into the soil material to reduce and to increase the proportion of bioavailable HM, respectively. The availability of Pb, Zn, and Cd was determined by HM fractionation and plant uptake 110 days after the addition of amendments, shortly before IPU addition. Apatite treatment reduced the availability of HM, but did not affect the microbial biomass and the microbial community structure on the genotype level (total soil DNA-RAPD). However, it changed the microbial community structure on the phenotype level, based on the composition of phospholipid fatty acids (PLFA) at the end of the degradation experiment. The degradation of IPU did not change. In contrast to apatite treatment, HM supplementation increased the bioavailability of Pb, Zn and Cd, which resulted in biomass reduction and changes of microbial community structure on the genotypic (total soil DNA-RAPD) and phenotypic (PLFA) level. Increased bioavailability of HM also significantly reduced the rate of IPU degradation and mineralisation. The total mineralisation over a period of 60 days decreased from 12 to 5% of initial ¹⁴C. Increased HM bioavailability did not influence the degradation pathways and kinetics of IPU.     

Capacity of fatty acid profiles and substrate utilization patterns to describe differences in soil microbial communities associated with increased salinity or alkalinity at three locations in South Australia

 Fatty acid methyl ester (FAME) profiles, together with Biolog substrate utilization patterns, were used in conjunction with measurements of other soil chemical and microbiological properties to describe differences in soil microbial communities induced by increased salinity and alkalinity in grass/legume pastures at three sites in SE South Australia. Total ester-linked FAMEs (EL-FAMEs) and phospholipid-linked FAMEs (PL-FAMEs), were also compared for their ability to detect differences between the soil microbial communities. The level of salinity and alkalinity in affected areas of the pastures showed seasonal variation, being greater in summer than in winter. At the time of sampling for the chemical and microbiological measurements (winter) only the affected soil at site 1 was significantly saline. The affected soils at all three sites had lower organic C and total N concentrations than the corresponding non-affected soils. At site 1 microbial biomass, CO₂-C respiration and the rate of cellulose decomposition was also lower in the affected soil compared to the non-affected soil. Biomarker fatty acids present in both the EL- and PL-FAME profiles indicated a lower ratio of fungal to bacterial fatty acids in the saline affected soil at site 1. Analysis of Biolog substrate utilization patterns indicated that the bacterial community in the affected soil at site 1 utilized fewer carbon substrates and had lower functional diversity than the corresponding community in the non-affected soil. In contrast, increased alkalinity, of major importance at sites 2 and 3, had no effect on microbial biomass, the rate of cellulose decomposition or functional diversity but was associated with significant differences in the relative amounts of several fatty acids in the PL-FAME profiles indicative of a shift towards a bacterial dominated community. Despite differences in the number and relative amounts of fatty acids detected, principal component analysis of the EL- and PL-FAME profiles were equally capable of separating the affected and non-affected soils at all three sites. Redundancy analysis of the FAME data showed that organic C, microbial biomass, electrical conductivity and bicarbonate-extractable P were significantly correlated with variation in the EL-FAME profiles, whereas pH, electrical conductivity, NH₄-N, CO₂-C respiration and the microbial quotient were significantly correlated with variation in the PL-FAME profiles. Redundancy analysis of the Biolog data indicated that cation exchange capacity and bicarbonate-extractable K were significantly correlated with the variation in Biolog substrate utilization patterns. Received: 8 March 2000     

Microbial immobilisation of C rhizodeposits in rhizosphere and root-free soil under continuous C labelling of oats

A greenhouse experiment was conducted by growing oats (Avenasativa L.) in a continuously ¹³CO₂ labeled atmosphere. The allocation of ¹³C-labeled photosynthates in plants, microbial biomass in rhizosphere and root-free soil, pools of soil organic C, and CO₂ emissions were examined over the plant's life cycle. To isolate rhizosphere from root-free soil, plant seedlings were placed into bags made of nylon monofilament screen tissue (16 μm mesh) filled with soil. Two peaks of ¹³C in rhizosphere pools of microbial biomass and dissolved organic carbon (DOC), as well as in CO₂ emissions at the earing and ripeness stages were revealed. These ¹³C maxima corresponded to: (i) the end of rapid root growth and (ii) beginning of root decomposition, respectively. The δ¹³C values of microbial biomass were higher than those of DOC and of soil organic matter (SOM). The microbial biomass C accounted for up to 56 and 39% of ¹³C recovered in the rhizosphere and root-free soil, respectively. Between 4 and 28% of ¹³C assimilated was recovered in the root-free soil. Depending on the phenological stage, the contribution of root-derived C to total CO₂ emission from soil varied from 61 to 92% of total CO₂ evolved, including 4-23% attributed to rhizomicrobial respiration. While 81-91% of C substrates used for microbial growth in the root-free soil and rhizosphere came from SOM, the remaining 9-19% of C substrates utilized by the microbial biomass was attributable to rhizodeposition. The use of continuous isotopic labelling and physical separation of root-free and rhizosphere soil, combined with natural ¹³C abundance were effective in gaining new insight on soil and rhizosphere C-cycling.     

Sensitivity analysis of critical parameters in microbial maintenance-energy models

Summary Overestimates of microbial biomass and high maintenance rates have caused calculations of annual maintenance requirements to exceed annual C inputs to soil ecosystems. An integrated approach is needed to resolve this inconsistency in the literature. In the present study a mechanistic model for soil microbial systems was used to calculate the maintenance-energy requirements of the soil microbial biomass. This model is base on product formation rather than substrate use and describes an active and sustaining population, with cryptic growth and necromass recycling. Several assumptions, such as death rates, the percentage of active population, and the yield, are required to calculate the maintenance energies, and the sensitivity of these estimated parameters on the maintenance-rate calculation was tested. The total biomass and the yield factor had the greatest effect on the calculated maintenance value. The fraction of active organisms, the death rates, and the different maintenance values for each population had little effect on the maintenance value.     

Long-term tillage and rotation effects on soil microbial biomass,carbon and nitrogen

Summary Three mollisols, typical of the Palouse winter wheat region of eastern Washington and northern Idaho, were analyzed for microbial biomass, total C and total N after 10 years of combined tillage and rotation treatments. Treatments included till, no-till and three different cereal-legume rotations. All crop phases in each rotation were sampled in the same year. Microbial biomass was monitored from April to October, using a respiratory-response method. Microbial biomass, total C and total N were highest under no-till surface soils (0–5 cm), with minimal differences for tillage or depth below 5 cm. Microbial biomass differences among rotations were not large, owing to the relative homogeneity of the treatments. A rotation with two legume crops had the highest total C and N. Microbial biomass was significantly higher in no-till surface soils where the current crop had been preceded by a high-residue crop. The opposite was true for the tilled plots. There was little change in microbial biomass over the seasons until October, when fresh crop residues and rains had a strong stimulatory effect. The seasonal pattern of biomass in no-till surface soils reflected the dry summer/winter rainfall climate of the region. The results of this study show that numerous factors affect soil microbial biomass and that cropping history and seasonal changes must be taken into account when microbial biomass data are compared.Scientific paper no. 7634     

羟基磷灰石–植物联合修复对Cu/Cd污染植物根际 土壤微生物群落的影响

针对江西贵溪Cu、Cd重金属污染土壤,通过田间试验,比较无机生物材料羟基磷灰石及3种植物(海州香薷、巨菌草、伴矿景天)与羟基磷灰石联合修复对土壤总Cu、Cd的吸收及对活性Cu、Cd的钝化吸收能力差异。采用磷脂脂肪酸(PLFA)分析法,比较不同修复模式对土壤微生物群落结构的影响,以评估土壤微生态环境对不同修复措施的响应。研究结果表明:羟基磷灰石的施加可显著提高土壤pH,并有效钝化土壤活性Cu、Cd含量,但对土壤总Cu、Cd的含量影响较小。植物与羟基磷灰石的联合修复在显著降低土壤活性Cu、Cd(P0.05)的同时,减少了植物根际土壤总Cu、Cd的含量(P0.05)。不同修复措施对土壤微生物群落组成影响差异明显。单独施加羟基磷灰石与土壤真菌群落呈显著正相关,使土壤真菌生物量提高,从而引起真菌/细菌(F/B)的升高。植物与羟基磷灰石的联合修复可有效缓解土壤真菌化的趋势,其中巨菌草与羟基磷灰石的联合修复可有效提高土壤革兰氏阳性、革兰氏阴性细菌生物量及多样性,降低F/B值,从而降低土壤真菌病害的风险。不同植物根系活性代谢引起有机质的积累促进植物与羟基磷灰石处理中根际有机碳含量显著提高。聚类增强树(Aggregated boosted tree,ABT)分析结果表明:不同修复模式是影响土壤微生物群落的重要因素,其次土壤pH和Cu的含量及活性也是改变重金属污染区域微生物群落的因子。该研究从微生物群落结构角度解释了植物与羟基磷灰石联合修复对土壤微生态体系的作用,为开展Cu、Cd等重金属污染地植物与无机生物材料的联合修复方式的筛选及实施提供可靠的理论依据。     

Determination of phospholipid- and lipopolysaccharide-derived fatty acids as an estimate of microbial biomass and community structures in soils

Several soils subject to different cultivation and management practices were examined by analysis of fatty acid profiles derived from phospholipids and lipopolysaccharides, using an improved sequential method which is capable of measuring ester-linked and non-ester-linked phospholipid fatty acids (EL-PLFA, NEL-PLFA, respectively) and the hydroxy fatty acids in lipopolysaccharides. A good correlation was obtained (r>0.90) between the soil biomass and total EL-PLFA in the soils investigated, which ranged from forest soils to a variety of agricultural soils. Elucidation of the composition of the community structure was an additional task. Eukaryotes can be differentiated from bacteria by the presence of polyunsaturated and -hydroxy fatty acids, both of which were much more abundant in the OF layer of the forest soil than in the remaining samples. A relatively low proportion of monomethyl branched-chain saturated fatty acids was obtained in the forest OF horizon, these being indicators for Gram-positive bacteria and actinomycetes. Various subclasses of proteobacteria produce and mid-chain hydroxy fatty acids, which occur primarily in agricultural soils. The ratios between monounsaturated fatty acids and saturated fatty acids seem to be very useful parameters of soil environmental conditions. In addition, on the basis of the differences in composition of the NEL-PLFA and hydroxy fatty acids of lipopolysaccharides, clear indications for the community structure of various soils were obtained. In the forest soils much more abundant anaerobic micro-organisms and relatively less abundant proteobacteria were present than in the other soils. In the cultivated soils, however, the proportion of Gram-negative bacteria was considerably higher. Furthermore, eukaryotes appeared to be pre-dominant in the soils once used for a manure deposit site.     

Surface cast production by the earthworm Aporrectodea nocturna in a pre-alpine meadow in Switzerland

Field and laboratory experiments were carried out to describe the effects of Aporrectodea nocturna on soil characteristics in a pre-alpine meadow and to support the development of a model of cast production. In the prealpine meadow, increased cast production, first observed about 20 years ago around a newly planted hedge, was recorded to a distance of maximal 170 m from the hedge. Numbers of A. nocturna between 130 and 165 m from the hedge decreased from 164 to 16 individuals m^-2. In the same area cast production steadily decreased from about 1.5 kg m^-2 week^-1 to nil, the plant community structure changed and the microbial biomass decreased, but the root biomass and the moisture content did not change. Laboratory experiments demonstrated that high cast production was not a specific feature of the A. nocturna population nor of the soil in the meadow. Diapause of A. nocturna was terminated in the laboratory during September. A model of cast production potential by the earthworm A. nocturna was established using laboratory determinations of the relationships with body weight, temperature, and water potential. The model was shown to predict cast production in the field given the assumption that the water potential was 0 MPa. According to the model, 81% of surface cast production was by juveniles, and 19% by adults of A. nocturna.     

Microbial community changes in heathland soil communities along a geographical gradient: interaction with climate change manipulations

Climate change constitutes a serious threat for European heathlands as unlike other sources of damage, such as over-grazing, local remediation is not a possibility. Within the large pan-European projects, CLIMOOR and VULCAN, the effect of periodic drought and increased temperature were investigated in four heathland ecosystems along a geographical and climatic gradient across Europe. Fluorogenically labelled substrates for four enzymes (glucosidase, sulphatase, phosphatase, leucine amino peptidase) were used to measure extra-cellular enzyme activity in soil samples from each of the CLIMOOR sites. Microbial extra-cellular enzyme production is linked to microbial activity as well as soil physico-chemical properties, making soil enzymes one of the more reactive components of terrestrial ecosystems and potentially excellent indicators of soil microbial functional status and diversity.Across all sites and over all the substrates, organic matter content was exponentially, inversely related to enzyme activity. Although the increase in temperature produced by the CLIMOOR roofs was small (on average 0.9 °C), this was sufficient to increase enzyme activity in all sites (on average by 45%). The increase was within the range of seasonal variability at each of the sites. The effect of drought on enzyme activity was more pronounced in the Northern European sites than the southern European, and most moisture limited, site. This suggests that the effect of temperature increases may be observed across all regions; however, the soils of northern Europe may be more sensitive to changes in rainfall patterns than more moisture limited Southern European soils.