Showing papers in "Soil Biology & Biochemistry in 2004"

Increased snow depth affects microbial activity and nitrogen mineralization in two Arctic tundra communities

Abstract: Microbial activity in Arctic tundra ecosystems continues through the winter and is an important component of the annual C budget. This activity is sensitive to climatic variation, particularly snow depth because that regulates soil temperature. The influence of winter conditions on soil N cycling is poorly understood. In this study, we used intact core incubations sampled periodically through the winter and following growing season to measure net N mineralization and nitrification in dry heath and in moist tussock tundra under ambient and experimentally increased snow depths (by use of a snowfence). In dry heath, we sampled soils under Dryas octopetela or Arctostaphylos alpine, while in tussock tundra, we sampled Eriophorum vaginatum tussocks and Sphagnum dominated areas between tussocks. Our objectives were to: (1) examine how different winter snow regimes influenced year-round N dynamics in the two tundra types, and (2) evaluate how these responses are affected by dominant species present in each system. In tussock tundra, soils with increased winter snow cover had high net N mineralization rates during the fall and winter, followed by immobilization during thaw. In contrast, N mineralization only occurred during the autumn in soils with ambient snow cover. During the growing season when N immobilization dominated in areas with ambient snow cover, soils with increased winter snow cover had positive net mineralization and nitrification rates. In dry heath tundra, soils with increased snow depth had high late winter net N mineralization rates, but these rates were: (a) comparable to early winter rates in soils under Arctostaphylos plants with ambient snow cover; (b) greater in soils under Arctostaphylos plants than in soils under Dryas plants; and (c) less than the rates found in tussock tundra. Our findings suggest under ambient snow conditions, low soil temperatures limit soil N mineralization, but that deeper snow conditions with the associated warmer winter soil temperatures dramatically increase over-winter N mineralization and thereby alter the amount and timing of plant-available N in tundra ecosystems.

Nitrous oxide emissions as influenced by amendment of plant residues with different C:N ratios

Abstract: To investigate the influence of plant residues decomposition on N2O emission, laboratory incubations were carried out for a period of 21 days using urea and five plant residues with a wide range of C:N ratios from 8 to 118. Incorporation of plant residues enhanced N2O and CO2 emissions. The two gas fluxes were significantly correlated (R2=0.775, p<0.001). Cumulative emissions of N2O and CO2 were negatively correlated with the C:N ratio in plant residues (R2=0.783 and 0.986 for N2O, and 0.854 for CO2, respectively). A negative relationship between the N2O–N/NO3−–N ratio and the C:N ratio was observed (R2=0.867) when residue plus urea was added. We calculated the changes in dissolved organic C (DOC) and the relevant changes in N2O emission. The incorporation of residues increased DOC when compared with the control, while the incorporation of residue plus urea decreased DOC. Cumulative emissions of N2O and CO2 were positively correlated with DOC concentration measured at the end of the incubation. In addition, the N2O emission fraction, defined as N2O–N emissions per unit N input, was not found to be a constant for either residue-N or urea-N amendment but dependent on C:N ratio when plant residue was incorporated.

Non-symbiotic bacterial diazotrophs in crop-farming systems : can their potential for plant growth promotion be better exploited?

Abstract: Biological N2 fixation (BNF) by associative diazotrophic bacteria is a spontaneous process where soil N is limited and adequate C sources are available. Yet the ability of these bacteria to contribute to yields in crops is only partly a result of BNF. A range of diazotrophic plant growth-promoting rhizobacteria participate in interactions with C3 and C4 crop plants (e.g. rice, wheat, maize, sugarcane and cotton), significantly increasing their vegetative growth and grain yield. We review the potential of these bacteria to contribute to yield increases in a range of field crops and outline possible strategies to obtain such yield increases more reliably. The mechanisms involved have a significant plant growth-promoting potential, retaining more soil organic-N and other nutrients in the plant– soil system, thus reducing the need for fertiliser N and P. Economic and environmental benefits can include increased income from high yields, reduced fertiliser costs and reduced emission of the greenhouse gas, N2O (with more than 300 times the global warming effect of CO2), as well as reduced leaching of NO3 –N to ground water. Obtaining maximum benefits on farms from diazotrophic, plant growth promoting biofertilisers will require a systematic strategy designed to fully utilise all these beneficial factors, allowing crop yields to be maintained or even increased while fertiliser applications are reduced. q 2004 Elsevier Ltd. All rights reserved.

Role of dissolved organic nitrogen (DON) in soil N cycling in grassland soils

Abstract: Dissolved organic nitrogen (DON) represents a significant pool of soluble N in many soils and freshwaters. Further, the low molecular weight (LMW) component of DON represents an important source of N for microorganisms and can also be utilized directly by some plants. Our purpose was to determine which of the pathways in the decomposition and subsequent ammonification and nitrification of organic N represented a significant block in soil N supply in three agricultural grassland soils. The results indicate that the conversion of insoluble organic N to LMW-DON and not LMW-DON to NH4+ or NH4+ to NO3− represents a major constraint to N supply. We hypothesize that there are two distinct DON pools in soil. The first pool comprises mainly free amino acids and proteins and is turned over very rapidly by the microbial community, so it does not accumulate in soil. The second pool is a high molecular weight pool rich in humic substances, which turns over slowly and represents the major DON loss to freshwaters. The results also suggest that in NO3− rich soils the uptake of LMW-DON by soil microorganisms may primarily provide them with C to fuel respiration, rather than to satisfy their internal N demand.

A regulatory role for phenol oxidase during decomposition in peatlands

Abstract: Unique peatland properties, such as their ability to preserve intact ancient human remains (bog bodies) and to store globally significant quantities of atmospheric CO2, can be attributed to their low rates of enzymic decomposition. Peatland soils are normally devoid of molecular oxygen in all, but the uppermost layer, and thus enzymes such as phenol oxidase, which require molecular oxygen for their activity, are rarely active. Interestingly, even the activities of enzymes such as hydrolases that have no oxygen requirement, are also extremely limited in peatlands. Here, we show that those low hydrolase activities can be indirectly attributed to oxygen constraints on phenol oxidase. On addition of oxygen, phenol oxidase activity increased 7-fold, P<0.05, a response that allowed phenolic depletion in the peatland soil. Phenolic materials are highly inhibitory to enzymes and their lower abundance allowed higher hydrolase activities (β-glucosidase 26%, P<0.05, phosphatase 18%, P<0.05, sulphatase 47%, P<0.01, xylosidase 16%, P<0.05 and chitinase 22%, P<0.05). Thus, oxygen constraints upon phenol oxidase activity promote conditions that inhibit decomposition. This mechanism has important implications for preservation of archaeological organic materials, sequestration of atmospheric CO2 and potentially in the preservation of food and treatment of water pollution.

Legume seed inoculation technology—a review

Abstract: Inoculation of legume seed is an efficient and convenient way of introducing effective rhizobia to soil and subsequently the rhizosphere of legumes. However, its full potential is yet to be realised. Following widespread crop failures, the manufacture of high quality inoculants revolutionised legume technology in Australia in the 1960s. Many improvements to inoculants and the advent of an inoculant control service ensured that quality was optimised and maintained. Minimum standards for the number of rhizobia per seed were set after consideration of several factors including seed size and loss of viability during inoculation. Despite manufacturers' recommendations for storage and application of inoculants, there is a distinct lack of control over the inoculation process; hence the full potential of high quality products may not always be achieved. The efficacy of inoculation varies depending on several factors, all of which affect the number of viable rhizobia available for infection of legume roots. Increased numbers of viable rhizobia per seed by application of inoculant above the commercially recommended rate, results in a continued linear increase in nodulation and yield. Several studies have reported yield increases of up to 25%. However, applying higher quantities of inoculant is uneconomical and technically difficult. Alternatively, higher numbers of viable rhizobia per seed may be achieved by improving survival during seed inoculation. Despite recognition of the factors affecting survival of rhizobia on seed and a substantial demand for commercially pre-inoculated legume seed, poor survival is still a major concern. Desiccation, temperature and seed coat toxicity all influence survival of rhizobia on seed. Their adverse effects may be ameliorated by selecting tolerant rhizobial strains and legume seed cultivars with low toxicity or artificially, by the use of additives in the seed coating. The accumulation of the desiccant protectant trehalose in strains of rhizobia, may result in better survival under desiccation stress. Similarly, the accumulation of exopolysaccharide (EPS) may act as a barrier reducing excessive water loss. Polymeric adhesives such as gum arabic, methyl cellulose and polyvinyl pyrollidone (PVP) have improved survival. However, studies of additives used in inoculation have been ad hoc and little of their mode of action is understood. A better understanding of the mechanisms involved in the protection of rhizobia from adverse conditions will assist in defining the optimum conditions for seed inoculation and storage to ensure a higher quality product for farmers at the time of sowing.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

Abstract: The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable–cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality.

New indices for quantifying the resistance and resilience of soil biota to exogenous disturbances

Abstract: The stability (resistance and resilience to disturbance) of a soil system is a key factor influencing ecosystem properties and processes. To compare the stability of different systems, it is necessary to have indices that provide a relative quantitative measure of both the resistance and resilience of a response variable in all possible scenarios. However, the indices currently in use are frequently unable to do this, or are difficult to interpret. Here, we present new indices that avoid these problems. We compare our indices with previously published indices of stability, and also test their performance by using a real data set. We show that our indices accurately represent the response of soil properties (e.g. soil microbial biomass) to a disturbance, and that they are capable of determining differences in stability between contrasting soils.

Grazing intensity alters soil respiration in an alpine meadow on the Tibetan plateau

Abstract: Grazing intensity may alter the soil respiration rate in grassland ecosystems. The objectives of our study were to (1) determine the influence of grazing intensity on temporal variations in soil respiration of an alpine meadow on the northeastern Tibetan Plateau; and (2) characterise, the temperature response of soil respiration under different grazing intensities. Diurnal and seasonal soil respiration rates were measured for two alpine meadow sites with different grazing intensities. The light grazing (LG) meadow site had a grazing intensity of 2.55 sheep ha(-1), while the grazing intensity of the heavy grazing (HG) meadow site, 5.35 sheep ha(-1), was approximately twice that of the LG site. Soil respiration measurements - showed that CO2 efflux was almost twice as great at the LG site as at the HG site during the growing season, but the diurnal and seasonal patterns of soil respiration rate were similar for the two sites. Both exhibited the highest annual soil respiration rate in mid-August and the lowest in January. Soil respiration rate was highly dependent on soil temperature. The Q(10) value for annual soil respiration was lower for the HG site (2.75) than for the LG site (3.22). Estimates of net ecosystem CO2 exchange from monthly measurements of biomass and soil respiration revealed that during the period from May 1998 to April 1999, the LG site released 2040 g CO2 m(-2) y(-1) to the atmosphere, which was about one third more than the 1530g CO2 m(-2) y(-1) released at the HG site. The results suggest that (1) grazing intensity alters not only soil respiration rate, but also the temperature dependence of soil CO2 efflux; and (2) soil temperature is the major environmental factor controlling the temporal variation of soil respiration rate in the alpine meadow ecosystem. (C) 2003 Elsevier Ltd. All fights reserved.

Soil microbial dynamics in maize-growing soil under different tillage and residue management systems

Abstract: The long-term impact of tillage and residue management on soil microorganisms was studied over the growing season in a sandy loam to loamy sand soil of southwestern Quebec, growing maize ( Zea mays L.) monoculture. Tillage and residue treatments were first imposed on plots in fall 1991. Treatments consisted of no till, reduced tillage, and conventional tillage with crop residues either removed from (−R) or retained on (+R) experimental plots, laid out in a randomized complete block design. Soil microbial biomass carbon (SMB-C), soil microbial biomass nitrogen (SMB-N) and phospholipid fatty acid (PLFA) contents were measured four times, at two depths (0–10 and 10–20 cm), over the 2001 growing season. Sample times were: May 7 (preplanting), June 25, July 16, and September 29 (prior to corn harvest). The effect of time was of a greater magnitude than those attributed to tillage or residue treatments. While SMB-C showed little seasonal change (160 μg C g −1 soil), SMB-N was responsive to post-emergence mineral nitrogen fertilization, and PLFA analysis showed an increase in fungi and total PLFA throughout the season. PLFA profiles showed better distinction between sampling time and depth, than between treatments. The effect of residue was more pronounced than that of tillage, with increased SMB-C and SMB-N (61 and 96%) in +R plots compared to −R plots. This study illustrated that measuring soil quality based on soil microbial components must take into account seasonal changes in soil physical and chemical conditions.

Trophic niche differentiation in soil microarthropods (Oribatida, Acari): evidence from stable isotope ratios (15N/14N)

Abstract: The large number of animals that coexist in soil without any clear niche differentiation has puzzled biologists for a long time. We investigated stable isotope ratios (15N/14N) in a diverse group of soil microarthropods, oribatid mites, to evaluate trophic niche differentiation. The natural variation of the stable isotopes 15N/14N was measured in 36 species/taxa from four beech and beech-oak forests. Signatures of δ15N formed a gradient spanning over 12 δ units suggesting that (a) different species occupy different trophic niches and (b) oribatid mites span three to four trophic levels. This study for the first time documented strong trophic niche differentiation in decomposer microarthropods. The results suggest that trophic niche differentiation within taxonomic groups significantly contributes to the high diversity of soil animal taxa.

Nitrous oxide production by nitrification and denitrification in soil aggregates as affected by O2 concentration

Abstract: Nitrous oxide emitted by soils can be produced either by denitrification in anoxic conditions or by nitrification in presence of O2. The relative importance of the two processes, particularly under varied partial pressures of O2, is not always known. This paper focuses on the influence of O2 concentration on N2O production by nitrification and denitrification in an arable Orthic Luvisol. Soil aggregates (2–3 mm size), water unsaturated, received 116 mg N kg−1 as ammonium sulphate labelled with 15N and were incubated during 14 days at different O2 partial pressures: 0, 0.35, 0.76, 1.5, 4.3 and 20.4 kPa. A 15N tracing technique was used to quantify nitrification and denitrification rates. 15N2O and 15N2 were measured. Oxygen pressure appeared to strongly influence both nitrification and denitrification rates and also N2O emissions. Nitrification rates were reduced by a factor of 6–9 when O2 decreased from 20.4 to 0.35 kPa. They were highly correlated with O2 consumption rates. Denitrification mainly occurred in complete anoxic conditions. The proportion of N2O emitted by denitrification was estimated by two independent methods: one based on 15N tracing using isotope composition of NH4, NO3 and N2O, the other based on the measurement of the 15N2O:15N2 ratio. The two methods gave close results. The highest N2O emissions were obtained under complete anoxic conditions and were due to denitrification. However, N2O emissions almost as important were obtained at day 14 with 1.5 kPa O2 pressure, and they were due to nitrification. Nitrification was the main source of N2O at O2 concentrations greater than 0.35 kPa. The amounts of N2O-N emitted by nitrification were linearly related to the amounts of N nitrified, but the slope of the regression was highly dependent on O2 concentration: it varied from 0.16 to 1.48% when O2 concentration was reduced from 20.4 to 0.76 kPa. Emissions of N2O by nitrification may then be quite significant if nitrification occurs at a reduced O2 concentration.

Freeze–thaw regime effects on carbon and nitrogen dynamics in sub-arctic heath tundra mesocosms

Abstract: Freeze – thaw fluctuations in soil temperature may be critical events in the annual pattern of nutrient mobilisation that supplies plant growth requirements in some temperate, and most high latitude and high altitude ecosystems. We investigated the effects of two differing freeze – thaw regimes, each of which is realistic of in situ spatial and temporal variation in field conditions, on C and N dynamics in sub-arctic heath tundra mesocosms. In addition, 15 N isotopic label was used to follow the partitioning of a labile N pool between major ecosystem components, both during the freeze – thaw treatments phase, and in a subsequent equilibration phase. A single deep freeze treatment phase enhanced dissolved total and labelled N pools in the soil solution at initial thaw, and resulted in reduced pool sizes at the end of the equilibration phase. By contrast, a multiple freeze – thaw cycling treatment directly enhanced the dissolved labelled N pool, but did not significantly affect dissolved total N. Furthermore, both dissolved labelled N and dissolved total N pools were significantly enhanced in the equilibration period following multiple freeze – thaw, the latter due to a marked increase in soil solution NH4 . Microbial biomass C was not significantly affected by either of the freezing treatments upon final thaw, but was significantly reduced over the combined treatment and equilibration phases of the multiple freeze – thaw regimes. Furthermore, the treatments had no significant effects on total or labelled N within the microbial biomass over either phase. Total mesocosm CO2 efflux rates remained closely correlated with soil temperature throughout the experiment in both regimes, suggesting that respiratory flushes associated with treatment-induced microbial cell lysis were negligible. Together, these results indicate that moderate freeze – thaw fluctuations may have minimal influences on microbial biomass pools, but nevertheless can have strong contrasting effects on the amounts, forms, and timing of N and organic C supply into the soil solution. Ecosystem losses via N2O effluxes were of greatest magnitude immediately upon thawing in both treatments, and were of similar total magnitude to inorganic N leachates in throughflow. Herb leaves, total fine roots, and vascular stems accumulated some 15 N label in one or both of the freezing treatments by the end of the experiment. Together, these results indicating very small N losses relative to the magnitudes of internal transfers, suggest tight ecosystem N cycling both during and after freeze – thaw events. Furthermore, our small and subtle effects on microbial and soluble C and N pools relative to previous studies using more severe regimes, suggests that periods of moderate freeze – thaw fluctuations may have only a minor influence on the annual pattern of C and nutrient dynamics in seasonally cold ecosystems. q 2004 Elsevier Ltd. All rights reserved.

Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA

Abstract: We studied the distribution of the indigenous bacterial and fungal communities in a forest soil profile. The composition of bacterial and fungal communities was assessed by denaturing gradient gel electrophoresis (DGGE) of total and extracellular DNA extracted from all the soil horizons. Microbial biomass C and basal respiration were also measured to assess changes in both microbial biomass and activity throughout the soil profile. The 16S rDNA-DGGE revealed composite banding patterns reflecting the high bacterial diversity as expected for a forest soil, whereas 18S rDNA-DGGE analysis showed a certain stability and a lower diversity in the fungal communities. The banding patterns of the different horizons reflected changes in the microbial community structure with increasing depth. In particular, the DGGE analysis evidenced complex banding patterns for the upper A1 and A2 horizons, and a less diverse microflora in the deeper horizons. The low diversity and the presence of specific microbial communities in the B horizons, and in particular in the deeper ones, can be attributed to the selective environment represented by this portion of the soil profile. The eubacterial profiles obtained from the extracellular DNA revealed the presence of some bands not present in the total DNA patterns. This could be interpreted as the remainders of bacteria not any more present in the soil because of changes of edaphic conditions and consequent shifting in the microbial composition. These characteristic bands, present in all the horizons with the exception of the A1, should support the concept that the extracellular DNA is able to persist within the soil. Furthermore, the comparison between the total and extracellular 16S rDNA-DGGE profiles suggested a downwards movement of the extracellular DNA.

Ligninolytic fungi in bioremediation: extracellular enzyme production and degradation rate

Abstract: Ligninolytic fungi can be used for remediation of pollutants in water and soil. Extracellular peroxidases and laccases have been shown to oxidize recalcitrant compounds in vitro but the likely significance of individual enzyme levels in vivo remains unclear. This study documents the amounts and activities of Mn-dependent peroxidase (MnP), lignin peroxidase and laccase (LAC) in various species of ligninolytic fungi grown in liquid medium and soil and their effect on degradation of polycyclic aromatic hydrocarbons (anthracene and pyrene), a polychlorinated biphenyl mixture (Delor 106) and a number of synthetic dyes. Stationary cultures of a highly degradative strain Irpex lacteus exhibited 380-fold and 2-fold increase in production of MnP and LAC, respectively, compared to submerged cultures. Addition of Tween 80 to the submerged culture increased MnP levels 260-fold. High levels of MnP correlated with efficient decolorization of Reactive Orange 16 azo dye but not of Remazol Brilliant Blue R anthraquinone dye. Degradation of anthracene and pyrene in spiked soil by straw-grown explorative mycelium of Phanerochaete chrysosporium, Trametes versicolor and Pleurotus ostreatus showed the importance of MnP and LAC levels secreted into the soil. The importance of high fungal enzyme levels for efficient degradation of recalcitrant compounds was better demonstrated in liquid media compared to the same strains growing in soil.

Microbial community response to nitrogen deposition in northern forest ecosystems

Abstract: The productivity of temperate forests is often limited by soil N availability, suggesting that elevated atmospheric N deposition could increase ecosystem C storage. However, the magnitude of this increase is dependent on rates of soil organic matter formation as well as rates of plant production. Nonetheless, we have a limited understanding of the potential for atmospheric N deposition to alter microbial activity in soil, and hence rates of soil organic matter formation. Because high levels of inorganic N suppress lignin oxidation by white rot basidiomycetes and generally enhance cellulose hydrolysis, we hypothesized that atmospheric N deposition would alter microbial decomposition in a manner that was consistent with changes in enzyme activity and shift decomposition from fungi to less efficient bacteria. To test our idea, we experimentally manipulated atmospheric N deposition (0, 30 and 80 kg NO3−-N) in three northern temperate forests (black oak/white oak (BOWO), sugar maple/red oak (SMRO), and sugar maple/basswood (SMBW)). After one year, we measured the activity of ligninolytic and cellulolytic soil enzymes, and traced the fate of lignin and cellulose breakdown products (13C-vanillin, catechol and cellobiose). In the BOWO ecosystem, the highest level of N deposition tended to reduce phenol oxidase activity (131±13 versus 104±5 μmol h−1 g−1) and peroxidase activity (210±26 versus 190±21 μmol h−1 g−1) and it reduced 13C-vanillin and 13C-catechol degradation and the incorporation of 13C into fungal phospholipids (p<0.05). Conversely, in the SMRO and SMBW ecosystems, N deposition tended to increase phenol oxidase and peroxidase activities and increased vanillin and catechol degradation and the incorporation of isotope into fungal phospholipids (p<0.05). We observed no effect of experimental N deposition on the degradation of 13C-cellulose, although cellulase activity showed a small and marginally significant increase (p<0.10). The ecosystem-specific response of microbial activity and soil C cycling to experimental N addition indicates that accurate prediction of soil C storage requires a better understanding of the physiological response of microbial communities to atmospheric N deposition.

Rates of decomposition of plant residues and available nitrogen in soil, related to residue composition through simulation of carbon and nitrogen turnover

Abstract: The dynamics of inorganic N in soil following the application of plant residues depends on their composition We assumed that all plant materials are composed of similar components, each decomposing at a specific rate, but differ in the proportions of the various components The NCSOIL model that simulates C and N turnover in soil was used to link the rates of residue decomposition to their composition, defined as soluble, cellulose-like and lignin-like C and N, and thereby integrate short and long-term effects of residues on available N dynamics in soil Five plant residues in a wide range of C:N ratios were incubated in soil for 24 weeks at 30 °C, during which C and N mineralization were measured The materials with large C:N ratios (corn, rice hulls and wheat straw) were also incubated with NH 4 + –N to avoid N deficiency The residues were analyzed for total and soluble C and N The partitioning of insoluble C and N between cellulose- and lignin-like pools was optimized by best fit of simulated C and N mineralization to measured results The decomposition rate constants of the soluble and lignin-like pools were assumed to be 10 and 10 −5 d −1 , respectively, and that of the cellulose-like pool, obtained by model optimization against mineralization of cellulose with NH 4 + –N in soil, was 0051 d −1 The optimized, kinetically defined lignin-like pool of all residues was considerably larger than lignin contents normally found in plant residues by the Van Soest procedure Gross N mineralization of tobacco and rape residues was similar, but N recovery from tobacco was larger, because a larger fraction of its C was in the lignin-like pool N in rice hulls, corn and wheat residues was mostly recalcitrant, yet rice hulls did not cause N deficiency, because most of its C was recalcitrant too The soluble components of the residues had strong short-term effects on available N in soil, but the cellulose-like pool was equally important for short and medium-term effects Soluble and cellulose-like C were 29 and 42% of total C, respectively, in corn and 7 and 50% in wheat Maximal net inorganic N losses, measured in both residue treatments after 2 weeks, were 42 mg g −1 C applied as corn and 31 mg g −1 C applied as wheat, or 84 and 110 mg g −1 decomposed C of corn and wheat, respectively Rice hulls immobilized N slowly, but by the end of 24 weeks all three residues immobilized 26–27 mg N kg −1 C applied The different dynamics of N immobilization demonstrated the need to determine the decomposability of C and N rather than their total contents in plant residues

Amino sugars and muramic acid—biomarkers for soil microbial community structure analysis

Abstract: Characterizing functional and phylogenetic microbial community structure in soil is important for understanding the fate of microbially-derived compounds during the decomposition and turn-over of soil organic matter. This study was conducted to test whether amino sugars and muramic acid are suitable biomarkers to trace bacterial, fungal, and actinomycetal residues in soil. For this aim, we investigated the pattern, amounts, and dynamics of three amino sugars (glucosamine, mannosamine and galactosamine) and muramic acid in the total microbial biomass and selectively cultivated bacteria, fungi, and actinomycetes of five different soils amended with and without glucose. Our results revealed that total amino sugar and muramic acid concentrations in microbial biomass, extracted from soil after chloroform fumigation varied between 1 and 27 mg kg−1 soil. In all soils investigated, glucose addition resulted in a 50–360% increase of these values. In reference to soil microbial biomass-C, the total amino sugar- and muramic acid-C concentrations ranged from 1–71 g C kg−1 biomass-C. After an initial lag phase, the cultivated microbes revealed similar amino sugar concentrations of about 35, 27 and 17 g glucosamine-C kg−1 TOC in bacteria, fungi, and actinomycetes, respectively. Mannosamine and galactosamine concentrations were lower than those for glucosamine. Mannosamine was not found in actinomycete cultures. The highest muramic acid concentrations were found in bacteria, but small amounts were also found in actinomycete cultures. The concentrations of the three amino sugars studied and muramic acid differed significantly between bacteria and the other phylogenetic microbial groups under investigation (fungi and actinomycetes). Comparison between the amino sugar and muramic acid concentrations in soil microbial biomass, extracted after chloroform fumigation, and total concentrations in the soil showed that living microbial biomass contributed negligible amounts to total amino sugar contents in the soil, being at least two orders of magnitude greater in the soils than in the soil inherent microbial biomass. Thus, amino sugars are significantly stabilized in soil.

Heavy metal accumulation by two earthworm species and its relationship to total and DTPA-extractable metals in soils

Abstract: The concentrations of Zn, Cd, Pb and Cu in earthworm tissues were compared with the total and DTPA-extractable contents of these heavy metals in contaminated soils. Samples were taken from a pasture polluted by waste from a metallurgic industry over 70 y ago. Three individuals of Aporrectodea caliginosa and Lumbricus rubellus and soil samples were collected at six points along a gradient of increasing pollution. Total metal contents of earthworms, soil, and metals extracted by DTPA from the soil were measured. Total heavy metal contents of the soils ranged from 165.7 to 1231.7 mg Zn kg 21 , 2.7 to 5.2 mg Cd kg 21 , 45.8 to 465.5 mg Pb kg 21 and 30.0 to 107.5 mg Cu kg 21 . Their correlations with metals extracted by DTPA were highly significant. Contents of the metals in earthworm tissues were higher in A. caliginosa than in L. rubellus, with values ranging from 556 to 3381 mg Zn kg 21 , 11.6 to 102.9 mg Cd kg 21 , 1.9 to 182.8 mg Pb kg 21 and 17.9 to 35.9 mg Cu kg 21 in A. caliginosa, and from 667.9 to 2645 mg Zn kg 21 , 7.7 to 26.3 mg Cd kg 21 , 0.5 to 37.9 mg Pb kg 21 and 16.0 to 37.6 mg Cu kg 21 in L. rubellus, respectively. Correlations between body loads in earthworms with either total or DTPA-extractable contents of soil metals were significant, except for Cd in L. rubellus and Cu in A. caliginosa. Considering its simple analytical procedure, DTPAextractable fraction may be preferable to total metal content as a predictor of bio-concentrations of heavy metals in earthworms. Biota-to-Soil Accumulation Factor (BSAF) of these four metals are Cd . Zn . Cu . Pb, with range of mean values between: Cd (6.18‐ 17.02), Zn (1.95‐ 7.91), Cu (0.27‐ 0.89) and Pb (0.08‐ 0.38) in A. caliginosa, and Cd (3.64‐ 6.34), Zn (1.5‐ 6.35), Cu (0.29‐ 0.87) and Pb (0.04‐ 0.13) in L. rubellus. The BSAF of Ca, Fe and Mn are Ca . Mn . Fe, with mean values of: Ca (0.46‐ 1.31), Mn (0.041‐ 0.111), Fe (0.017‐ 0.07) in A. caliginosa and Ca (0.98‐ 2.13), Mn (0.14‐ 0.23), Fe (0.019‐ 0.048) in L. rubellus, respectively. Results of principal component analysis showed that the two earthworm species differ in the pattern of metal bioaccumulation which is related to their ecological roles in contaminated soils. q 2003 Elsevier Ltd. All rights reserved.

Soil moisture pre-treatment effects on enzyme activities as indicators of heavy metal-contaminated and reclaimed soils

Abstract: Heavy metal contamination can inhibit soil functions but it is often difficult to determine the degree of pollution or when soil reclamation is complete. Enzyme assays offer potential as indicators of biological functioning of soils. However, antecedent water content of soil samples may affect the outcome of biological measurements. In Mediterranean regions, for much of the year ‘field moist’ surface soil can have water content similar to that of air-dry samples. The objectives of this study were to: (1) determine the sensitivity of a range of enzyme assays to detect the degree of pollution from a heavy metal mine spill; (2) evaluate rewetting field-dry soil as a pre-treatment for enzyme assays; and (3) test multivariate analysis for improving discrimination between polluted, reclaimed and non-polluted soils. The Aznalcollar mining effluent spill provided a unique opportunity to address these objectives. This accident released toxic, heavy metal-contaminated (As, Bi, Cd, Cu, Pb, Tl, Zn…) and acid tailings into the Guadiamar watershed (SW Spain) in 1998, severely affecting the riparian zone along more than 4000 ha. Contaminated soils were collected from the highly polluted upper watershed and less polluted lower watershed along with reclaimed soil at both sites. Enzyme activities (phosphatases, arylsulfatase, β-glucosidase, urease and dehydrogenase) were assessed on both field-moist samples and soils rewetted to 80% of water-holding capacity and then incubated at 21 °C for 7 d prior to the assay. The reclaimed soils had higher activities than polluted soils but, typically, 1.5–3 times lower levels of activity than the non-polluted soil. Regardless of the moisture pre-treatment, all enzymes showed significant effects due to pollution, with urease and β-glucosidase showing the greatest discrimination between degrees of contamination. In general, rewetting field-dried soils increased activities on non-polluted and reclaimed soils which improved discrimination with polluted soils. Another method to increase the potential of soil enzyme activities to detect soil contamination could be to combine them in multivariate analysis, which provides a more holistic representation of the biochemical and microbial functionality of a soil.

Dynamics of soil microbial biomass C and soil fertility in cropland mulched with plastic film in a semiarid agro-ecosystem

Abstract: Microbial biomass C (MBC) is one of the soil properties used as an indicator for the fertility status of a soil. A study was conducted on a semi-arid Loess Plateau in China. The field was planted with spring wheat and mulched with plastic film for various lengths of time. Our primary objectives were to (i) explore the influence of film mulching on soil MBC and soil fertility, and (ii) seek an effective approach of maintaining and improving sustainability of cropland mulched with plastic film in two growing seasons. Four treatments were tested, non-mulching (M0), mulching for 30 days after sowing (M30), mulching for 60 DAS (M60) and mulching for the whole growing period (Mw). An increasing air temperature with time within the growing season promoted soil MBC in the two growing seasons, but a severe drought led to a lower MBC in 2000 compared with the wet year of 1999. Film mulching promoted MBC significantly in the 2 years, but decreased soil organic carbon (SOC). SOC is very low in the experimental soil, accounting for the higher MBC/SOC ratio compared with ratios reported by others. The SOC is greatly reduced in the non-mulched and the Mw treatments compared to the M30 and M60 treatments. In conclusion, the benefits of film mulching in semi-arid agricultural systems are enormous but realizing their full potential depends on how long the mulching material is maintained during the growing season. In the system tested, it is desirable to mulch the plots for 30–60 DAS in order to enhance microbial biomass and cycling of nutrients and also to provide a more stable soil micro-environment that generates more residues in the rhizosphere.

Estimation of conversion factors for fungal biomass determination in compost using ergosterol and PLFA 18 : 2 omega 6,9

Abstract: Eleven species of common fungi from compost were analysed for their content of ergosterol and phospholipid fatty acids (PLFAs) after growth on agar media. Mean content of ergosterol was 3.1 mg g(-1) dw of fungal mycelium (range 1-24 mg g(-1) dw). Total amount of PLFAs varied between 2.6 and 43.5 mumol g(-1) dw of fungi (mean 14.9 mumol g(-1) dw). The most common PLFAs were 16:0,18:2omega6,9 and 18:1omega9 comprising between 79 and 97 mol% of the total amount of PLFAs. The PLFA 18:2omega6,9, suggested as a marker molecule for fungi, comprised between 36 and 61 mol% of the total PLFAs in the Ascomycetes, between 45 and 57 mol% in the Basidiomycetes and 1222 mol% in the Zygomycetes. There was a good correlation between the content of the two fungal marker molecules, ergosterol and the PLFA 18:2omega6,9, with a mean content of 1 mg ergosterol being equivalent to 2.1 mumol of 18:2omega6,9. Based on results from the fungal isolates, conversion factors were calculated (5.4 mg ergosterol g(-1) biomass C and 11.8 mumol 18:2omega6,9 g(-1) biomass Q and applied to compost samples in which both the ergosterol and the PLFA 18:2omega6,9 content had been measured. This resulted in similar estimates of fungal biomass C using the two marker molecules, but was three to five times higher than total microbial biomass C calculated using ATP content in the compost. This could partly be explained by the fact that both of the markers used for fungal biomass are cell membrane constituents. Thus, the ergosterol and the PLFA content were related to the hyphal diameter of the fungi, where fungi with thinner hyphae had higher ergosterol concentrations than fungi with thicker hyphae. This could also partly explain the large interspecific variation in content of the two marker molecules. (C) 2003 Elsevier Ltd. All rights reserved. (Less)

Decomposition dynamics of plant materials in relation to nitrogen availability and biochemistry determined by NMR and wet-chemical analysis

Abstract: Improved understanding of the interactive relationships of plant material decomposition kinetics to biochemical characteristics and nitrogen availability is required for terrestrial C accounting and sustainable land management. In this study, 15 typical and/or native Australian plant materials were finely ground and incubated with a sandy soil at 25 °C and 55% water holding capacity without nitrogen (−N) or with nitrogen (+N) addition (77 mg N kg−1 soil as KNO3). The C mineralisation dynamics were monitored for 356 days and the initial biochemical characteristics of the plant materials were determined by NMR and wet-chemical analyses. Under the −N treatment, C mineralisation rates of the plant materials were positively correlated with their initial N contents during the first several weeks, and then negatively correlated with lignin and polyphenols contents during the late stages of incubation. Thus the ratios of lignin/N, polyphenols/N and (lignin+polyphenols)/N had more consistent correlation with the cumulative amounts of C mineralised throughout the incubation than did any single component. In terms of the C types determined by NMR analysis, the C mineralisation rates were initially related positively to carbonyl C contents, and then negatively to aryl and O-aryl C contents from day 3 onwards. Addition of NO3−–N accelerated C mineralisation during the early stages, but resulted in lower cumulative C mineralisation at the end of the incubation for most plant materials. Under the +N treatment, the decomposition rates were correlated with the contents of lignin and the sum of cellulose+acid detergent-extractable non-phenolic compounds, or with aryl, O-aryl and N-alkyl+methoxyl C contents. Regardless of the N treatment, the ratios of aryl/carbonyl, O-aryl/carbonyl and (aryl+O-aryl)/carbonyl C had the closest and most consistent correlations with the cumulative C mineralisation among all biochemical indices examined. A double exponential model with defined mineralisation rate constants for the active and slow pools was used to describe the C mineralisation dynamics. The biological meanings of the kinetically estimated active and slow pool sizes are interpreted and their relationships to the initial chemical/biochemical composition of the plant materials are explored.

Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

Abstract: We combined microbial community phospholipid fatty acid (PLFA) analyses with an in situ stable isotope 13 CO 2 labelling approach to identify microbial groups actively involved in assimilation of root-derived C in limed grassland soils. We hypothesized that the application of lime would stimulate more rapid 13 C assimilation and turnover in microbial PLFAs. Four and 8 d after label application, 18:1ω9, 18:2ω6,9 (fungal biomarkers) and 16:1ω7, 18:1ω7, 19:0cy (Gram-negative bacterial biomarkers) showed the most 13 C enrichment and rapid turnover rates. This suggests that these microorganisms were assimilating recently-photosynthesized root C inputs to soils. Contrary to our hypothesis, liming did not affect assimilation or turnover rates of 13 C-labelled C. 13 C stable isotope pulse-labelling technique paired with analyses of PLFA microbial biomarkers shows promise for in situ investigations of microbial function in soils.

Controls on soil respiration in semiarid soils

Abstract: Soil respiration in semiarid ecosystems responds positively to temperature, but temperature is just one of many factors controlling soil respiration. Soil moisture can have an overriding influence, particularly during the dry/warm portions of the year. The purpose of this project was to evaluate the influence of soil moisture on the relationship between temperature and soil respiration. Soil samples collected from a range of sites arrayed across a climatic gradient were incubated under varying temperature and moisture conditions. Additionally, we evaluated the impact of substrate quality on short-term soil respiration responses by carrying out substrate-induced respiration assessments for each soil at nine different temperatures. Within all soil moisture regimes, respiration rates always increased with increase in temperature. For a given temperature, soil respiration increased by half (on average) across moisture regimes; Q10 values declined with soil moisture from 3.2 (at −0.03 MPa) to 2.1 (−1.5 MPa). In summary, soil respiration was generally directly related to temperature, but responses were ameliorated with decrease in soil moisture.

Maturity indices for composted dairy and pig manures

Abstract: Bulking agents and bedding materials used on farms for composting manures affect the time required for composts to mature. The effects of these materials on guidelines for the use of composted manures in potting mixes are not fully known. Several chemical and biological compost characteristics were mentioned and a cucumber plant growth greenhouse bioassay was performed on samples removed from windrows during composting of: (i) dairy manure amended with wheat straw; (ii) dairy manure amended with sawdust (mostly Quercus spp.); and (iii) pig manure amended with sawdust and shredded wood (mostly Quercus spp.). Dry weights of cucumber seedlings grown in fertilized and unfertilized potting mixes amended with composts (30%, v/v) having stability values of , 1m g CO 2 –C g –1 dw d 21 , did not differ significantly from those in a control peat mix. Only the most mature dairy manure-wheat straw compost samples consistently established sufficient N concentrations in cucumber shoots in unfertilized treatments. For the dairy manure-wheat straw compost, all possible subset regression analyses of compost characteristics versus cucumber plant dry weight revealed that any of several compost characteristics (electrical conductivity-EC, compost age, total N, organic C, C-to-N ratio, ash content, CO2 respirometry, Solvita CO2 index and the Solvita w Compost Maturity Index) predicted growth of cucumber in the unfertilized treatments, and thus maturity. In contrast, at least two characteristics of the dairy manure-sawdust compost were required to predict growth of cucumber in the unfertilized treatments. Effective combinations were EC with compost age and the Solvita w maturity index with total N. Even five compost characteristics did not satisfactorily predict growth of cucumber in the non-fertilized pig manure-wood compost. Nutrient analysis of cucumber shoots indicated N availability was the principal factor limiting growth in potting mixes amended with the dairy manure-sawdust compost, and even more so in the pig manure-wood compost even though the compost had been stabilized to a high degree (, 1m g CO 2 –C g 21 dw d 21 ). Maturity of the composted manures, which implies a positive initial plant growth response of plants grown without fertilization, could not be predicted by compost characteristics alone unless the bulking agent or bedding type used for the production of the composts was also considered. q 2004 Elsevier Ltd. All rights reserved.

Carbon cycling in rice field ecosystems in the context of input, decomposition and translocation of organic materials and the fates of their end products (CO2 and CH4)

Abstract: Rice fields are intensively managed, unique agroecosystems, where soil flooding is general performance for rice cultivation. Flooding the field results in reductive soil conditions, under which decomposition of organic materials proceeds during the period of rice cultivation. A large variety of organic materials are incorporated into rice soils according to field management. In this review, the kind and abundance of organic materials entering carbon cycling in the rice field ecosystem are evaluated first. Then, decomposition of plant residues and soil organic matter in rice fields is reviewed quantitatively. Decomposition of plant residues is shown to be the active process in carbon cycling in rice fields. Rice releases photosynthates into the rhizosphere (rhizodeposition), and they follow a different avenue of decomposition in soil from that of plant residues. Incorporation of rhizodeposition into microbial biomass and soil organic matter during the period of rice cultivation, and their fates after harvesting are evaluated quantitatively from 13C pulse labeled experiments. Percolating water transports inorganic and organic carbon from the plow layer to the subsoil layer. The amounts of their transport and accumulation in the subsoil layer are evaluated in relation to the amounts of soil organic C in the plow layer. Not only CO2 but also CH4 are produced in the decomposition process of organic materials in flooded rice fields. CH4 evolution from rice fields is of global concern from the viewpoint of global warming. Origins of CH4 evolved from rice fields are estimated first, followed by the fates of CH4 in rice field ecosystems. Rhizodeposition is shown to be the main origin of CH4 evolved from rice fields. Evolution to the atmosphere is not the sole pathway of CH4 produced in rice fields. The amounts of CH4 retained in soil, percolated to the subsoil layer and decomposed in soil are evaluated in the context of the amounts of CH4 efflux. Thus, this review focuses on carbon cycling in the rice field ecosystem from the viewpoints of input, decomposition, and translocation of organic materials and the fates of their end products (CO2 and CH4).

Microbial community composition and substrate use in a highly weathered soil as affected by crop rotation and P fertilization

Abstract: A better understanding of soil microbial processes is required to improve the synchrony between nutrient release from plant residues and crop demand. Phospholipid fatty acid analysis was used to investigate the effect of two crop rotations (continuous maize and maize–crotalaria rotation) and P fertilization (0 and 50 kg P ha−1 yr−1, applied as triple superphosphate) on microbial community composition in a highly weathered soil from western Kenya. Microbial substrate use in soils from the field experiment was compared in incubation experiments. Higher levels of soil organic matter and microbial biomass in the maize–crotalaria rotation were connected with higher total amounts of phospholipid fatty acids and an increase in the relative abundances of indicators for fungi and gram-negative bacteria. P fertilization changed the community profile only within the continuous maize treatment. The decomposition of glucose, cellulose and three plant residues (all added at 2.5 g C kg−1 soil) proceeded faster in soil from the maize–crotalaria rotation, but differences were mostly transient. Microbial P and N uptake within one week increased with the water-soluble carbon content of added plant residues. More P and N were taken up by the greater microbial biomass in soil from the maize–crotalaria rotation than from continuous maize. Re-mineralization of nutrients during the decline of the microbial biomass increased also with the initial biological activity of the soil, but occurred only for a high quality plant residue within the half year incubation period. Compared to the effect of crop rotation, P fertilization had a minor effect on microbial community composition and substrate use.

Effects of municipal solid waste compost amendments on soil enzyme activities and bacterial genetic diversity

Abstract: Municipal solid waste (MSW) composts have been used to maintain the long-term productivity of agroecosystems and to protect the soil environment from overcropping, changes in climatic conditions and inadequate management; they also have the additional benefit of reducing waste disposal costs. Since MSW may contain heavy metals and other toxic compounds, amendments cannot only influence soil fertility, but may also affect the composition and activity of soil microorganisms. The effects of MSW compost and mineral N amendments in a 6-year field trial on some physical–chemical properties, enzyme activities and bacterial genetic diversity of cropped plots (Beta vulgaris–Triticum turgidum rotation) and uncropped plots were investigated. The compost was added at the recommended and twice the recommended dosage (12, 24 t ha−1). Amendments of cropped plots with MSW compost increased the contents of organic C from 13.3 to 15.0 g kg−1 soil and total N from 1.55 to 1.65 g kg−1 soil. There were significant increases in dehydrogenase (9.6%), β-glucosidase (13.5%), urease (15.4%), nitrate reductase (21.4%) and phosphatase (9.7%) activities. A significant reduction in protease activity (from 3.6 to 2.8 U g−1 soil) was measured when a double dose of compost was added to the cropped plots. No dosage effect was detected for the other enzymes. Changes in the microbial community, as a consequence of MSW amendment, were minimal as determined using denaturing gradient gel electrophoresis, rDNA internal spacer analysis and amplified ribosomal DNA restriction analysis of bacteria, archaea, actinomycetes, and ammonia oxidizers. This indicates that there was no significant variation in the overall bacterial communities nor in selected taxonomic groups deemed to be essential for soil fertility.