Search

We have investigated the effects of genetic modifications to lignin biosynthesis in tobacco on the structural and functional characteristics of the microbial community in the rhizospheres of plants with down-regulations to cinnamyl alcohol dehydrogenase (CAD), caffeic acid O-methyltransferase (COMT) and cinnamoyl-CoA reductase (CCR) singly and in all the double and triple combinations, and corresponding unmodified plants. The mass of root produced was reduced by the down-regulation of enzymes in the phenylpropanoid pathway, but there were no differences in the microbial biomass in the rhizosphere per mass of roots. The composition of the rhizosphere microbial communities differed between modified and unmodified plants, with the modified plants having smaller proportions of fungal biomass as indicated by phospholipid fatty acid. Subtle changes to both root chemistry and rhizosphere microbial community function associated with down-regulation of CAD have the potential to modify carbon cycling processes.

Biological processes in soils are regulated in part by soil temperature, and there is currently considerable interest in obtaining robust information on the temperature sensitivity of carbon cycling process. However, very little comparable information exists on the temperature regulation of specific nitrogen cycling processes. This paper addresses this problem by measuring the temperature sensitivity of nitrogen cycling enzymes in soil. A grassland soil was incubated over a range of temperatures (−2 to 21 °C) reflecting 99 % of the soil temperature range during the previous 50 years at the site. After 7 and 14 days of incubation, potential activities of protease, amidase and urease were determined. Activities of protease and urease were positively related to temperature (activation energy; E a = 49.7 and 73.4 kJ mol−1, respectively, and Q 10 = 2.97 and 2.78, respectively). By contrast, amidase activity was relatively insensitive to temperature, but the activity was significantly increased after the addition of glucose. This indicated that there was a stoichiometric imbalance with amidase activity only being triggered when there was a supply of exogenous carbon. Thus, carbon supply was a greater constraint to amidase activity than temperature was in this particular soil.

The decomposition of tobacco roots with genetic modifications to lignin biosynthesis by the ligninolytic fungus Phanerochaete chrysosporium, by the cellulolytic fungus Chaetomium globosum, and by microbial communities in soil were examined to determine whether the rates of decomposition of the modified and unmodified roots decomposed at different rates, whether the order of colonization by P. chrysosporium and C. globosum facilitated decomposition, and whether the microbial community in soil was conditioned by exposure to roots subsequently so that the subsequent decomposition of the roots was increased. Both P. chrysosporium and C. globosum decomposed the modified roots more rapidly, at least initially, than the unmodified roots. Colonization by P. chrysosporium facilitated the subsequent decomposition by C. globosum, presumably because by degrading lignin, P. chrysosporium increased the susceptibility of the polysaccharide component of root material to attack by C. globosum. Selection of the soil microbial community by exposure to the modified residues accelerated subsequent decomposition of the root modified. Although demonstrating effects of the lignin modification on decomposition, they are relatively subtle and in most cases short-lived (less than 40 days) ones to which the microbial community is able to adapt, and therefore, we conclude that there are unlikely to be any persistent effects of the modified lignin on the soil decomposer community.

Various biologically mediated processes are involved in the turnover of dissolved organic matter (DOM) in soil; however, relatively little is known about the dynamics of either the microbial community or the individual classes of organic molecules during the decomposition of DOM. We examined the net loss of DOC, the mineralisation of C to CO2 and the degradation of DOC from six different soils by soil microorganisms. We also quantified the changes in the concentrations of protein, carbohydrate and amino acid C during microbial biodegradation. Over a 70-day incubation period at 20°C, the mineralisation of DOC to CO2 was described by a double exponential model with a labile pool (half-life, 3–8 days) and a stable pool (half-life, 0.4–6 years). However, in nearly all cases, the mass loss of DOC exceeded the C released as CO2 with significant deviations from the double exponential model. Comparison of mass DOC loss, CO2 production and microbial cell counts, determined by epifluorescence microscopy, showed that a proportion of the lost DOC mass could be accounted for by microbial assimilation. Carbohydrate and protein C concentrations fluctuated throughout the incubation with a net change of between 3 to 13 and −30 to 22.4% initial DOC, respectively. No amino acid C was detected during the incubation period (level of detection, 0.01 mg C l−1).

The effect of liming and earthworms on the composition and function of soil microbial communities was investigated in an upland soil from the UK in order to understand interactions between the biotic and abiotic components of soil systems. A factorial experiment was established using soils from the Sourhope Farm, near Kelso, with lime or no lime added, with or without earthworms added and a combined treatment of both lime and earthworm additions. The soils were incubated and destructively sampled after 180 days. Measurements of soil microbial biomass, dehydrogenase activity, phenotypic structure (by phospholipid fatty acid analysis (PLFA) and responses to four carbon substrates (d-glucose, l-arginine, α-ketoglutaric acid, α-cyclodextrin) were determined. Statistically significant results were limited to the litter layers, with no significant observations in either the H or Ah horizons. There were significant decreases in the soil microbial biomass and microbial activity in the litter layers caused by the addition of earthworms; liming reduced microbial biomass only. The addition of earthworms caused a significant difference in the PLFA principle component analysis (PCA) profile, as did liming. For the PLFA PCA profile, earthworm plus lime treatment was indistinguishable from the liming result. Addition of earthworms significantly suppressed the response to glucose; this effect was removed by liming. This indicates that liming may significantly alter the ecological interactions between earthworms and the microbial community.

We have compared properties of roots from different lines (genotypes) of tobacco raised either in tissue culture or grown from seed. The different lines included unmodified plants and plants modified to express reduced activity of the enzyme cinnamoyl-CoA reductase, which has a pivotal role in lignin biosynthesis. The size and structure of the rhizosphere microbial community, characterized by adenosine triphosphate and phospholipid fatty acid analyses, were related to root chemistry (specifically the soluble carbohydrate concentration) and decomposition rate of the roots. The root material from unmodified plants decomposed faster following tissue culture compared with seed culture, and the faster decomposing material had significantly higher soluble carbohydrate concentrations. These observations are linked to the larger microbial biomass and greater diversity of the rhizosphere communities of tissue culture propagated plants.

Application of organic materials to soils to enhance N immobilization into microbial biomass, thereby reducing inorganic N concentrations, was studied as a management option to accelerate the reestablishment of the native vegetation on abandoned arable fields on sandy soils the Kiskunsag National Park, Hungary. Sucrose and sawdust were used at three different topographic sites over 4 years. N availability and extractable inorganic N concentrations were significantly reduced in all sites. Soil microbial biomass C and microbial biomass N increased significantly following C additions, but the microbial C to microbial N ratio remained unaffected. It is concluded that the combined application of the rapidly utilized C source (sucrose) promoted N immobilization, whereas the addition of the slowly utilized C source (sawdust) maintained the elevated microbial biomass C and microbial biomass N in the field.

Changes in microbial community-level physiological profiles (CLPP) were investigated during decomposition of plant materials in maritime Antarctic soils from Alexander Island and Signy Island. For each soil, a series of microcosms were established and half of them amended with Deschampsia antarctica residues and the other half left unamended (controls). Microcosms were destructively sampled at regular intervals and a soil suspension from each microcosm was used to inoculate BIOLOG EcoPlates. The results showed differences between samples due to the treatment (amendment) but no systematic changes due to incubation period. Microbial response in terms of the overall BIOLOG activity in FB soils was greater than in JC and increased in the former during plant decomposition whilst the overall activity of the JC soils remained relatively unchanged. The differences in the microbial community response to plant amendment between FB and JC may be related to the C:N ratio of these soils and to differences in the way in which the different microbial communities respond to sporadic resource inputs.

We have measured the rates of respiration over a period of 13 days (304.5 h) at 90-min intervals for two contrasting soils amended with nothing, d-glucose, l-alanine, albumin, starch, d-glucose plus l-alanine, d-glucose plus albumin, l-alanine plus starch or albumin plus starch at 2 mg each individual substrate per gram soil. These treatments represent simple and complex model substrate additions with widely different C:N ratios and enable investigation of the interaction between substrates as they induce microbial respiratory responses. When added singly, the times taken for the maximum respiratory response to occur were less than 15 h for d-glucose, approximately 50 h for l-alanine and approximately 120 h for albumin. Addition of starch alone did not lead to a respiratory response within 304.5 h (13 days). The peak respiratory response from soils amended with l-alanine plus d-glucose was advanced by between 6 and 13 h depending on the soil compared with either substrate added singly. The patterns of respiratory response from soil amended with d-glucose plus albumin were similar to that predicted by the summed data, implying no interaction. The addition of l-alanine plus starch and of albumin plus starch led to increased respiratory responses, implying that the nitrogenous substrate facilitated the utilisation of starch by the soil micro-organisms.

The denitrifying enzyme activity (DEA), denitrification potential (DP) and anaerobic respiration (RESP) together with chemical characteristics were measured in three contrasting soils collected from experimental arable plots that had been subjected to long-term (21–23 years) fertilizer treatments. The plots sampled were either unfertilized or had received either annual inorganic NPK, manure and lime, or inorganic NPK and manure treatments. Addition of inorganic NPK, manure and lime led to large increases in the DEA for two of the three soils, but in the absence of lime, inorganic NPK and manure caused only small increases in DEA compared to unfertilized soils. Both DP and RESP were increased by the addition of inorganic NPK, manure and lime, but were substantially decreased by fertilizer treatments without lime. In most cases there was a simple relationship between soil pH and either DEA and DP, with those treatments that reduced soil pH also leading to reduced denitrification and vice versa. The effects of artificially increasing the pH to a value close to the pH in unfertilized soils (6.3) by addition of NaOH to the soils that had received inorganic NPK, and which had the lowest soil pH values, were to increase substantially DEA, DP and RESP. In soil from one of the sites that had been stored for 5 weeks, the DP values responded differently between the fertilizer treatments. The DP value was lowest in the soil that had inorganic NPK and manure, higher in the soil that received inorganic NPK, manure and lime and it was the highest in unfertilized (control) soil. The soil pH values for these treatments were 4.47, 5.79 and 6.58, respectively. However, when the soil pHs were adjusted by addition of either H2SO4 or NaOH to give a range between pH 2 and 12, the DP values from all three fertilizer treatments showed almost identical responses. The optimum pH value for DP was between 7 and 8 for all three fertilizer treatments. Substrate-induced respiration values from all fertilizer treatments showed a similar trend to DP when the soil pHs were modified. The results show that soil pH was an important factor which in the studied soils controls the microbial community in general and the community of denitrifiers in particular. However, denitrifiers showed a high pH resilience leading to no marked change of the pH optimum for potential denitrification.

Using soils from field plots in four different arable crop experiments that have received combinations of manure, lime and inorganic N, P and K for up to 20 years, the effects of these fertilizers on soil chemical properties and estimates of soil microbial community size and activity were studied. The soil pH was increased or unaffected by the addition of organic manure plus inorganic fertilizers applied in conjunction with lime, but decreased in the absence of liming. The soil C and N contents were greater for all fertilized treatments compared to the control, yet in all cases the soil samples from fertilized plots had smaller C:N ratios than soil from the unfertilized plots. The soil concentrations of all the other inorganic nutrients measured were greater following fertilizer applications compared with the unfertilized plots, and this effect was most marked for P and K in soils from plots that had received the largest amounts of these nutrients as fertilizers. Both biomass C determined by chloroform fumigation and glucose-induced respiration tended to increase as a result of manure and inorganic fertilizer applications, although soils which received the largest additions of inorganic fertilizers in the absence of lime contained less biomass C than those to which lime had been added. Dehydrogenase activity was lower in soils that had received the largest amounts of fertilizers, and was further decreased in the absence of lime. This suggests that dehydrogenase activity was highly sensitive to the inhibitory effects associated with large fertilizer additions. Potential denitrification and anaerobic respiration determined in one soil were increased by fertilizer application but, as with both the microbial biomass and dehydrogenase activity, there were significant reductions in both N2O and CO2 production in soils which received the largest additions of inorganic fertilizers in the absence of lime. In contrast, the size of the denitrifying component of the soil microbial community, as indicated by denitrifying enzyme activity, was unaffected by the absence of lime at the largest rate of inorganic fertilizer applications. The results indicated differences in the composition or function of microbial communities in the soils in response to long-term organic and inorganic fertilization, especially when the soils were not limited.

The transformations of the indigenous 13C and the 13C from either uniformly enriched 13C-D-glucose or 13C-glycine added to an organic soil were followed during a 28-day incubation using cross polarization (CP) magic angle spinning (MAS) 13C nuclear magnetic resonance (NMR) spectroscopy and dipolar dephased (DDP) MAS 13C NMR. The C mineralization was determined from 13C remaining by mass spectrometry and from CO2 evolution by gas chromatography. DDP MAS 13C NMR of the unamended soil indicated a transient increase in molecularly mobile 13C in the alkyl- and methyl-C over 5 days, which may be due to redistribution of 13C in the microbial biomass in response to perturbation. The added glucose-13C remaining declined to 43% after 7 days and 34% after 28 days. After 28 days the amount of added glucose-13C remaining was 6 times greater than the biomass C at the outset, while the microbial activity (CO2 production) was 38% greater, indicating that a significant proportion of added glucose-13C was not in microorganisms. Added glycine-13C declined faster, such that 29% and 8% remained after 7 and 28 days, respectively. After 28 days’ incubation with 13C-glucose, the O-alkyl-C, the acetal- and ketal-C, and the methyl- and alkyl-C resonances in CP MAS 13C NMR spectra were all enhanced compared with the unamended soil. The calculated T1ρH values of the O-alkyl-C and the acetal- and ketal-C resonances were less than those of crystalline glucose, indicating that there was no substantial reservoir of unreacted glucose. After 7 days’ incubation with 13C-glycine, none of the signals in the CP MAS 13C NMR spectra were enhanced when compared with the unamended soil, indicating that the added 13C remaining was distributed in undetectable quantities in a range of functionalities. The calculated T1ρH values indicated that glycine 13C was in O-alkyl-C, acetal- and ketal-C and carbonyl-C. T1ρH values may be more sensitive to changes in the distribution of 13C when 13C content is low. The DDP MAS 13C NMR spectra of both the 13C-glucose- and the 13C-glycine-amended soil showed that the molecularly mobile alkyl- and methyl-C increased compared with the unamended soil.

Nitrous oxide emissions from a sandy-loam textured soil wetted to matric potentials of either-1.0 or-0.1 kPa were determined in laboratory experiments in which the soil was incubated in air (control), air plus 10 Pa C2H2 (to inhibit nitrification), 100 kPa O2 (to suppress denitrification), 10 kPa C2H2 (to inhibit N2O reduction to N2 in denitrification) or following autoclaving. The total N2O production, consumption and net N2O emission from the soils together with the contributions to N2O emission from different processes of N2O production were estimated. The rate of N2O production was significantly greater in the wetter soil (282 pmol N2O g-1 soil h-1) than in the drier soil (192 pmol N2O g-1 soil h-1), but because N2O consumption by denitrifiers was also greater in the wetter soil, the net N2O emissions from the wetter and the drier soils did not differ significantly. Non-biological sources made no significant contribution to N2O emission under either moisture regime and biological processes other than denitrification and nitrification made only a small contribution (1% of the total N2O production) in the wetter soil. Denitrifying nitrifiers were the predominant source of N2O emitted from the drier soil and other (non-nitrifying) denitrifiers were the predominant source of N2O emitted from the wetter soil.

The isotopic composition at natural abundance levels of nitrous oxide emitted from a sandy loam, neutral pH soil under a range of soil water contents (matric potentials of-0.1,-1.0 and-5.0 kPa), from soil amended with sodium succinate and sodium ethanoate, and produced by pure cultures of the nitrifying bacteria Nitrosomonas europaea and Nitrosolobus multiformis, and by the denitrifying bacterium Pseudomonas putida, has been determined in laboratory experiments. N2O from all sources was depleted in the 15N and 18O isotopes relative to the conventional references [atmospheric N2 and standard mean ocean water (SMOW), respectively]. N2O from soil was depleted in 15N and 18O to increasing extents with increasing soil water content. The isotopic composition of N2O produced by N. europaea and N. multiformis was similar to that emitted from drier soil (matric potential of-1.0 kPa) and the N2O produced by P. putida was similar to that emitted from wetter soil (matric potential of-0.1 kPa). N2O emitted from the wetter soil was enriched in 15N and 18O compared with that emitted from the drier soil. The differences in isotopic composition between N2O from the wetter and drier soil were attributed principally to isotopic fractionation during N2O reduction to N2 in the terminal step of denitrification. The effect of both sodium succinate and sodium ethanoate amendment was to increase the overall rate of N2O emission, much of which arose from denitrification, as revealed by incubation in 100 kPa O2. In addition, in the sodium ethanoate amended soil N2O reduction to N2 did not occur, as revealed by incubation in 10 kPa C2H2. The N2O from the sodium ethanoate amended soil was depleted in 15N to a greater extent than the sodium succinate amended soil, which is consistent with the observation that N2O reduction to N2 leaves residual N2O relatively enriched in 15N.

We determined the size, activity, and affinity of the microbial community for glucose in soils from long-term experimental grassland plots. The plots had been treated annually with either farmyard manure, inorganic NPK fertilizers, farmyard manure+inorganic NPK fertilizers, (NH4)2SO4 only, or no experimental amendment sine 1897. The largest biomass and activity differences were between the (NH4)2SO4-treated soil, which was very acid, and the rest, which were nearer neutral. In the (NH4)2SO4-treated soil, the biomass C to organic C ratio was small, but overall the community had high respiratory activity per unit of biomass (qCO2) and high overall affinity for glucose (low K m). The effects of the manure treatment were a greater biomass C and a lower overall glucose affinity than in the control plot. In the presence farmyard manure, NPK led to smaller biomass and a lower biomass to organic C ratio while having no significant effect on either glucose K m or qCO2. In the absence of farmyard manure, NPK led to significantly greater glucose affinity but had no significant effect on the biomass, the biomass C to organic C ratio or qCO2.

Soil nitrification was compared in soils from 89-year-old grassland experimental plots with diverse chemical characteristics. Measurements of NaClO3-inhibited short-term nitrifier activity (SNA) and deamination of 1,2-diamino-4-nitrobenzene were used to study nitrification and deamination activities, respectively, in soil from each of 12 plots. Using multiple regression analysis, an expression for the relationship between SNA, soil pH and fertiliser N additions was derived which indicated that both the frequency and the quantity of farmyard manure additions were important in determining the rate of nitrification. SNA was greatest where there were large and frequent additions of farmyard manure. In soil with pH below 5.2 SNA was very low or insignificant. The effect of (NH4)2SO4 additions could not be assessed because they acidified the soil. We suggest that additions of farmyard manure increase the potential for NO3− leaching or for denitrification. Deaminase assays indicated that soils with a higher pH showed greater N mineralisation than soils with a lower pH, except at the low extreme. There was no obvious relationship between SNA and deaminase activity at higher levels of pH.

Three different nitrification assays (short-term nitrifier activity, assimilatory nitrate reductase activity of Lolium perenne, and nitrate accumulation in the absence of plants) were performed either on soil from a naturally acidic stagnohumic-gley or on leaves from L. perenne grown in this soil. Before the investigation the soil was limed and fertilised in a manner consistent with established agricultural pasture improvement strategies. Short-term nitrifier activity was only detected in soils above pH 5.6. However, nitrate reductase activity and nitrate accumulation both showed a near linear increase between soil pH 3.8 and 6.8. These findings are attributed to the nature of the assays, each of which considers a different component of the soil nitrifier population.