Microbial community response to nitrogen deposition in northern forest ecosystems

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.     

Functional and molecular responses of soil microbial communities under differing soil management practices

The effects of soil management on some microbiological properties and soil bacterial community structure were evaluated. Two field sites with the same soil type, located on the same geographic area adjacent to one other, have received different soil management practices and cultivation. One site has been subjected for 20 years to intensive horticulture under conventional tillage and irrigation with low quality salt-rich water; the second field site has been uncultivated for a long period and was turned to organic farming practices over the last 5 years and is currently cultivated with fruit orchard. Total bacterial counts, microbial ATP, microbial community metabolic (BIOLOG^®) profiles, and DNA fingerprinting by PCR-DGGE were determined. Two-way ANOVA revealed that total bacterial counts were not significantly (P>0.3) affected by the two different management practices; ATP content was consistently and significantly (P<0.001) lower in salt-water irrigated soil than in organic soil at the three sampling times. The cluster analysis of community level physiological profiles indicated that microbial communities were much more uniform in organic soil than in irrigated one, suggesting that salt-water irrigation could have affected the size of the microbial population, its metabolic activities, as well as its composition. Molecular patterns fitted the BIOLOG^® profile diversity. In particular, at any sampling time, PCR-DGGE patterns of bacterial DNA, extracted by an indirect method, significantly discriminated irrigated from organic soil samples. The PCR-DGGE patterns of total soil DNA, extracted by a direct method, showed a moderate to significant variation among irrigated and organic soil samples. Biochemical, microbiological and molecular data contributed to evidence a significantly different response of indigenous microflora to soil management by using saline water or organic farming.     

Microbial respiration and biomass (substrate-induced respiration) in soils of old-growth and regenerating forests on northern Vancouver Island,British Columbia

In studying the basal respiration, microbial biomass (substrate-induced respiration, SIR), and metabolic quotient (qCO₂) in western red cedar (Thuja plicata Donn ex D. Don)-western hemlock [(Tsuga heterophylla Raf.) Sarg.] ecosystems (old-growth forests, 3- and 10-year-old plantations) on northern Vancouver Island, British Columbia, Canada, we predicted that (1) soil basal respiration would be reduced by harvesting and burning, reflecting the reduction in microbial biomass and activities; (2) the microbial biomass would be reduced by harvesting and slash-burning, due to the excessive heat of the burning or due to reduced substrate availability; (3) microbial biomass in the plantations would tend to recover to the preharvesting levels with growth of the trees and increased substrate availability; and (4) microbial biomass measured by the SIR method would compare well with that measured by the fumigation-extraction (FE) method. Decaying litter layer (F), woody F (Fw) and humus layer (H) materials were sampled four times in the summer of 1992. The results obtained supported the four predictions. Microbial biomass was reduced in the harvested and slash-burned plots. Both SIR and FE methods provided equally good estimates of microbial biomass in the samples [SIR microbial C (mg g^-1)=0.227+0.458 FE microbial C (mg g^-1), r=0.63, P=0.0001] and proved suitable for microbial biomass measurements in this strongly acidic soil. Basal respiration was significantly greater in the old-growth forests than in the young plantations (P<0.05) in both F and H layers, but not in the Fw layer. For the 3- and 10-year-old plantations, there was no difference in basal respiration in F, Fw, and H layers. Basal respiration was related to changes in air temperature, precipitation, and the soil moisture contant at the time of sampling. The qCO₂ values were higher in the old-growth stands than in the plantations. Clear-cutting followed by prescribed burning did not increase soil microbial respiration, but CO₂ released from slash-burning and that contributed from other sources may be of concern to increasing atmospheric CO₂ concentrations.     

Soil microbial biomass and organic matter composition in soils under cultivation

To determine whether there is a relationship between the composition of soil organic matter and the activity of the soil microbial biomass, the composition of the organic matter in 12 typical arable soils in Northwest Germany was investigated by wet chemical analysis and CPMAS cross polarization magic angle spinning ¹³C-NMR spectroscopy. The data were correlated with the microbial biomass as estimated by substrate-induced respiration. A strong correlation between the microbial biomass and alkylic C compounds was observed (r=-0.960^***). Recalcitrant substances were enriched in this fraction, which were classified as humic acids according to the wet chemical procedure. The microbial decomposition of these humic acids is probably retarded, due to their chemical structure and/or physical bonding, when the soil microbial biomass activity is limited.     

Do same-aged but different height Norway spruce (Picea abies) clones affect soil microbial community?

The influence of individual trees in monocrop forests on soil microbial communities is poorly understood. We measured basal respiration, substrate-induced respiration and phospholipid fatty acids (PLFA), bacterial growth rate with the ³H-thymidine incorporation technique and fungal growth rate as ¹⁴C-acetate incorporation into ergosterol to investigate whether slow- and fast-growing 12-year-old Norway spruce (Picea abies) clones have affected differently on their associated soil microbial communities. Understorey vegetation, soil chemical properties and elemental concentrations of needles were also determined. The slow- and fast-growing spruce clones differed in PLFA profiles, understorey vegetation and elemental concentrations in needles suggesting that spruce clones have directly or indirectly affected soil microbes.     

Microbial biomass in soils of Russia under long-term management practices

 Non-tilled and tilled plots on a spodosol (C_org 0.65–1.70%; pH 4.1–4.5) and a mollisol (C_org 3.02–3.13%, pH 4.9–5.3), located in the European region of Russia, were investigated to determine variances in soil microbial biomass and microbial community composition. Continuous, long-term management practices, including tillage and treatment with inorganic fertilizers or manure, were used on the spodosol (39 years) and mollisol (22 years). Total microbial biomass (C_mic), estimated by the substrate-induced respiration (SIR) method, and total fungal hyphae length (membrane filter technique) were determined seasonally over a 3-year period. Long-term soil management practices (primarily tillage and fertilizer application) led to decreases in total microbial biomass (80–85% lower in spodosol and 20–55% lower in mollisol), decreases in the contribution of C_mic to C_org (2.3- to 3.5-fold lower in spodosol and 1.2- to 2.3-fold lower in mollisol), and 50–87% decreases in total fungal hyphae length compared to non-tilled control plots. The contribution of fungi to total SIR in virgin mollisol and fallow spodosol plots was approximately 30%. However, the contribution of fungi to SIR was approximately two times greater in tilled spodosol plots compared to a fallow plot. In contrast, the contribution of fungi to SIR in tilled plots of mollisol was less (1.4–4.7 times) than for a virgin plot. In summary, long-term soil management practices such as tillage and treatment with organic or inorganic fertilizers are important determinants of soil microbial biomass and the contribution of fungi to total SIR. Received: 28 April 1998     

Microbial biomass and respiratory activity in soil aggregates of different sizes from three beechwood sites on a basalt hill

We studied the effects of aggregates of different sizes on the soil microbial biomass. The distribution of aggregate size classes (<2, 2–4, 4–10, >10 mm) in the upper mineral soil horizon (A_h layer) was very different in three sites (upper, intermediate, lower) in a beechwood (Fagus sylvatica) on a basalt hill (Germany). Aggregates of different sizes (<2, 2–4, 4–10 mm) contained different amounts of C and N but the C:N ratios were similar. C and N contents were generally higher in smaller aggregates. The maximum initial respiratory response by microorganisms in intact aggregates and in aggregates passed through a 1-mm sieve declined with the aggregate size, but the difference was more pronounced in intact aggregates. Disruption of aggregates generally increased this response, particularly in 4- to 10-mm aggregates in the lower site. Basal respiration differed strongly among sites, but was similar in each of the aggregate size classes. Aggregate size did not significantly affect the specific respiration (g O₂ g^–1 microbial C h^–1) nor the microbial: organic C ratio, but these parameters differed among sites. Microbial growth was increased strongly by passing the soil through a 1-mm sieve in each of the aggregate materials. The growth of microorganisms in disrupted aggregates was similar, and the effect of aggregate disruption depended on the growth of microorganisms in intact aggregates.     

Assessment of the influence of phosphate fertilizers on the microbial activity of pasture soils

The objective of the present work was to examine the effects of phosphate fertilizers on the microbial activity of pasture soils. Various microbial characteristics were measured using soils from an existing long-term phosphate fertilizer field trial and a short-term incubation experiment. The measurements included basal respiration, substrate induced respiration, inhibition of substrate-induced respiration by streptomycin sulphate (fungal activity) and actidione (bacterial activity) and microbial biomass C. The long-term field trials was initiated during 1985 to examine the effectiveness of different sources of phosphate fertilizers (single superphosphate, North Carolina phosphate rock, partially acidulated North Carolina phosphate rock, and diammonium phosphate) on pasture yield. The incubation experiment was conducted for 8 weeks using the same soil and the sources of phosphate fertilizers used in the field trial. In the incubation experiment the fertilizer addition caused an initial decrease in basal and substrate-induced respiration but had no effect on total microbial biomass. The initial decline in basal and substrate-induced respiration with the fertilizer addition was restored within 8 weeks after incubation. In the field experiment the fertilizer addtion had no significant effect on basal respiration but increased substrate-induced respiration and microbial biomass C. The short-term and the long-term effects of phosphate fertilizer addition on the microbial characteristies of the soils are discussed in relation to its effects on pH, salt concentration, and the nutrient status of the soils.     

Fluazifop-p-butyl herbicide: Implications for germination, emergence and growth of Australian plant species

Five experiments were implemented to collect information related to the effects of fluazifop-p-butyl (active chemical in grass selective herbicides, Fusilade^® and Fusilade Forte™) on seed germination, seedling emergence, growth and health of species native to southwest Australia (a grass and non-grasses), together with several co-occurring introduced species (grasses and a non-grass). Experiments investigated effects of herbicide concentrations, seed burial depths, seed-sowing times since herbicide application and application locations (foliage versus soil). Both herbicides, at half to quadruple strength of recommended field application concentrations, adversely affected development of native and introduced species, both grasses and non-grasses. Herbicidal effects were observed during the seed germination phase, and if germination had occurred, during seedling emergence and, finally, during plant establishment. However, effects were more pronounced after seed germination, particularly on development of seedlings and plants, with retardation and/or discoloration of either radicles or shoots. Not unexpectedly, seedlings from seeds buried deeper in the sand medium (20 mm) struggled to emerge. Both herbicides demonstrated residual characteristics by impeding seedling emergence and growth from seeds sown at various dates (up to maximum test duration of 3 weeks) following exposure of the sand medium to the herbicides. Further, herbicide application to sand only, produced effects on 5-6 months old plants that were similar as application to foliage only, demonstrating herbicide uptake from sand. While the findings support independent research, they contradict the purported herbicide characteristics by commercial sources - grass selective, post-emergent, non-residual, rapid breakdown and active through foliar application only. Implications of these herbicides for biodiversity conservation are discussed.     

Differences in the activity and bacterial community structure of drained grassland and forest peat soils

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.     

Spatial variations of chemical composition, microbial functional diversity, and enzyme activities in a Mediterranean litter (Quercus ilex L.) profile

Litter decomposition on the forest floor is an essential process in soil nutrient cycles and formation. These processes are controlled by abiotic factors such as climate and chemical litter quality, and by biotic factors such as microbial community diversity and activity. The aim of this study was to investigate the importance of litter depth with respect to (i) chemical litter quality as evaluated by solid-state ¹³C NMR, (ii) enzyme activities, and (iii) microbial functional diversity in four different litter layers (OLn, OLv, OF, and OH). A Mediterranean soil profile under an evergreen oak (Quercus ilex L.) forest was used as a model. The recalcitrant OM fraction, corresponding to the deepest layer, showed low enzyme activities. Peroxidases and fluorescein diacetate hydrolases (FDA) were more active in the OLn layer and probably originated largely from plants. High cellulase activity in the OLn and the OLv layers, which are rich in polysaccharides, corresponded with the high content of O-alkyl carbon compounds. Following polysaccharide degradation, laccases and lipases were much more evident in the intermediate layers. This spatial variation in nutrient demand reflected a preferential degradation of the specific plant polymers. Phosphatases were more active along the three upper layers and probably reflected a P limitation during litter degradation. Alkaline/acid (AcPAlP/AcP) ratio increased in the deepest layer, suggesting an increased participation of bacteria AlP in phosphatase pools. Results of Biolog^TM also indicated spatial variations in microbial functionality. Indeed, FF plates showed the highest functional diversity in the uppermost layer, while ECO plate functional diversity was highest in the intermediate layers. Finally, our results indicated that microbial activity and functional diversity of micro-organisms change with litter depth on a very small scale and vary with chemical organic matter (OM) composition. Thus, the observed increases in the biological variables studied were determined by the evolution of OM chemical structures, the nature and availability in C nutrients, and they ultimately resulted in a progressive accumulation of recalcitrant compounds.     

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.     

Microbial biomass and activity in pine litter in the presence of Tomocerus minor (Insecta,Collembola)

Summary Laboratory microcosms were used to study microbial populations and biomasses developing in fragmented litter of Pinus nigra Arnold var. nigra (A. et G.). Direct observations (fungal standing crop and fluorescein-stainable mycelia), litter enzyme analyses (cellulase and dehydrogenase), and measurements by physiological methods (microbial CO₂ production and total microbial, fungal, and bacterial viable biomasses) were made at 3-week intervals for 15 weeks. Most variables showed great changes during this period, which were ascribed to a rise in litter moisture content during the initial phase of the experiment, and to substrate depletion towards its final phase. The addition of the collembolan Tomocerus minor (Lubbock) for 1 week enhanced cellulase activities by 4%. When the animals were introduced after 6 weeks, the fungal standing crop was enhanced, and the percentage of fluorescein-stainable mycelia was reduced. Dehydrogenase activity was increased by grazing when the microbial population had been established for 9 weeks or longer. Eucaryotic and procaryotic substrate-induced respiration were positively correlated, which was explained by partial segregation of resources for the two groups. Litter cellulase and dehydrogenase activity showed correlations by other techniques, indicating their suitability as parameters for microbial activity in general, and for the collembolan grazing impact on microbial activity in particular.     

Microbial community composition and rhizodeposit-carbon assimilation in differently managed temperate grassland soils

Rhizodeposit-carbon provides a major energy source for microbial growth in the rhizosphere of grassland soils. However, little is known about the microbial communities that mediate the rhizosphere carbon dynamics, especially how their activity is influenced by changes in soil management. We combined a ¹³CO₂ pulse-labeling experiment with phospholipid fatty acid (PLFA) analysis in differently managed Belgian grasslands to identify the active rhizodeposit-C assimilating microbial communities in these grasslands and to evaluate their response to management practices. Experimental treatments consisted of three mineral N fertilization levels (0, 225 and 450 kg N ha⁻¹ y⁻¹) and two mowing frequencies (3 and 5 times y⁻¹). Phospholipid fatty acids were extracted from surface (0-5 cm) bulk (BU) and root-adhering (RA) soil samples prior to and 24 h after pulse-labeling and were analyzed by gas chromatography-combustion-isotope ratio mass spectrometry (GC-c-IRMS). Soil habitats significantly differed in microbial community structure (as revealed by multivariate analysis of mol% biomarker PLFAs) as well as in gram-positive bacterial rhizodeposit-C uptake (as revealed by greater ¹³C-PLFA enrichment following pulse-labeling in RA compared to BU soil in the 450N/5M treatment). Mowing frequency did not significantly alter the relative abundance (mol%) or activity (¹³C enrichment) of microbial communities. In the non-fertilized treatment, the greatest ¹³C enrichment was seen in all fungal biomarker PLFAs (C16:1ω5, C18:1ω9, C18:2ω6,9 and C18:3ω3,6,9), which demonstrates a prominent contribution of fungi in the processing of new photosynthate-C in non-fertilized grassland soils. In all treatments, the lowest ¹³C enrichment was found in gram-positive bacterial and actinomycetes biomarker PLFAs. Fungal biomarker PLFAs had significantly lower ¹³C enrichment in the fertilized compared to non-fertilized treatments in BU soil (C16:1ω5, C18:1ω9) as well as RA soil (all fungal biomarkers). While these observations clearly indicated a negative effect of N fertilization on fungal assimilation of plant-derived C, the effect of N fertilization on fungal abundance could only be detected for the arbuscular mycorrhizal fungal (AMF) PLFA (C16:1ω5). On the other hand, increases in the relative abundance of gram-positive bacterial PLFAs with N fertilization were found without concomitant increases in ¹³C enrichment following pulse-labeling. We conclude that in situ¹³C pulse-labeling of PLFAs is an effective tool to detect functional changes of those microbial communities that are dominantly involved in the immediate processing of new rhizosphere-C.     

Fumigation-extraction and substrate-induced respiration derived microbial biomass C,and respiration rate in limed soil of Scots pine sapling stands

The effect of liming on microbial biomass C and respiration activity was studied in four liming experiments on young pine plantations. One of the experimental sites had been limed and planted 12 years before, two 5 years before, and one a year before soil sampling. The youngest experimental site was also treated with ash fertilizer. Liming raised the pH_KCl of the humus layer by 1.5 units or less. Microbial biomass was measured using the fumigation-extraction and substrate-induced respiration methods. Liming did not significantly affect microbial biomass C, except in the experiment which had been limed 11 years ago, where there was a slight biomass increase. Basal respiration, which was measured by the evolution of CO₂, increased in the limed soils, except for the youngest experiment, where there was no effect. Ash fertilization raised the soil pH_KCl by about 0.5 unit, but did not influence microbial biomass C or basal respiration. Fumigation-extraction and substrate-induced respiration derived microbial biomass C values were correlated positively with each other (r=0.65), but substrate-induced respiration gave approximately 1.3 times higher results. In addition, the effect of storing the soil samples at +6 and -18°C was evaluated. The effects were variable but, generally, the substrate-induced respiration derived microbial biomass C decreased, and the fumigation-extraction derived microbial biomass C and basal respiration decreased or were not affected by storage.     

Forest floor microbial communities in relation to stand composition and timber harvesting in northern Alberta

With the growing interest in silvicultural techniques that more closely emulate natural disturbance regimes, there is a need to better understand how partial harvesting affects the soil microbial community in stands with varying ecological characteristics, e.g., tree species composition. Four and a half and 5.5 years post-harvest, we used phospholipid fatty acid (PLFA) and substrate-induced respiration (SIR) analyses to compare the microbial biomass and microbial community structure of forest floors from stands dominated by white spruce (Picea glauca; SPRUCE) or by trembling aspen (Populus tremuloides; ASPEN) and from mixed-species (MIXED) stands in northern Alberta, Canada, that had been clearcut, partial-cut with 20% retention, partial-cut with 50% retention or left uncut (controls). PLFA and SIR analyses revealed that ASPEN forest floors supported a larger microbial biomass with a very different community structure than MIXED or SPRUCE forest floors. The microbial community structure of these soils appeared to be strongly affected by the presence of white spruce and the composition of the understory vegetation. There were no effects of timber harvesting detected within or across stand types on any of the variables measured, with the exception of the PLFA 16:1ω5, which was relatively more abundant in the clearcuts and 50% retention treatments than in the uncut controls, perhaps in response to an increased forest floor pH and grass cover in the disturbed areas. The resilience to timber harvesting of the forest floors from these stands may be the result of efforts to minimize soil disturbance during harvesting and to allow vegetation to regenerate naturally. From the perspective of the forest floor microbial community, partial harvesting does not appear to have any benefit over clearcut harvesting at these boreal forest sites.     

Effects of water amendment on basal and substrate-induced respiration rates of mineral soils

Summary We studied the effects of amending soils with different volumes of water or glucose solution on respiration rates measured as CO₂ evolution. Basal respiration was not significantly affected by the volume of water amendment, but substrate-induced respiration in static soil solutions was significantly reduced by increasing water contents. Inhibition of substrate-induced respiration was removed by continuously agitating the incubation vessels. Estimates of substrate-induced respiration rates for six soils differed markedly, depending on whether the vessels were stationary or agitated during the incubation. Agitation allowed increased discrimination between substrate-induced respiration rates for the soils, while static incubation only differentiated the soil with the highest substrate-induced respiration rate from the other soils.     

Additions of maize root mucilage to soil changed the structure of the bacterial community

The organic compounds released from roots (rhizodeposits) stimulate the growth of the rhizosphere microbial community. They may be responsible for the differences in the structure of the microbial communities commonly observed between the rhizosphere and the bulk soil. Rhizodeposits consists of a broad range of compounds including root mucilage. The aim of this study was to investigate if additions of maize root mucilage, at a rate of 70 μg C g⁻¹ day⁻¹ for 15 days, to an agricultural soil could affect the structure of the bacterial community. Mucilage additions moderately increased microbial C (+23% increase relative to control), which suggests that the turnover rate of microorganisms consuming this substrate was high. Consistent with this, the number of cultivable bacteria was enhanced by +450%. Catabolic (Biolog^® GN2) and 16S-23S intergenic spacer fingerprints exhibited significant differences between control and mucilage treatments. These data indicate that mucilage can affect both the metabolic and genetic structure of the bacterial community as shown by a greater catabolic potential for carbohydrates. We concluded that mucilage is likely to significantly contribute to differences in the structure of the bacterial communities present in the rhizosphere compared to the bulk soil.     

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems

This study coupled stable isotope probing with phospholipid fatty acid analysis (¹³C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced ¹³C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g⁻¹ soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g⁻¹ soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.     

Substrate utilisation profiles of microbial communities in peat are depth dependent and correlate with whole soil FTIR profiles

A multiple substrate induced respiration (SIR) assay, using ¹⁴C-labelled carbon sources, was used to evaluate community level physiological profiles (CLPP) of the microbial community in peat horizons of differing degrees of humification. The separation and grouping of the peat horizons by CLPP was similar to the pattern produced by analysis of the organic carbon chemistry of the peat horizons by Fourier Transform Infrared (FTIR) spectroscopy and therefore reflected the level of decomposition. Partial redundancy analysis showed that a large proportion (68.7%) of the variability in the CLPP data could be attributed to the ratio of polysaccharide to ‘carboxylate’ FTIR bands alone. The multiple substrate SIR technique may, therefore, be a powerful technique to further elucidate the influence of the microbial constituent of peat on the potential activity and patterns of cycling of labile carbon in peatlands.