Soil texture affects soil microbial and structural recovery during grassland restoration

Many biotic and abiotic factors influence recovery of soil communities following prolonged disturbance. We investigated the role of soil texture in the recovery of soil microbial community structure and changes in microbial stress, as indexed by phospholipid fatty acid (PLFA) profiles, using two chronosequences of grasslands restored from 0 to 19 years on silty clay loam and loamy fine sand soils in Nebraska, USA. All restorations were formerly cultivated fields seeded to native warm-season grasses through the USDA’s Conservation Reserve Program. Increases in many PLFA concentrations occurred across the silty clay loam chronosequence including total PLFA biomass, richness, fungi, arbuscular mycorrhizal fungi, Gram-positive bacteria, Gram-negative bacteria, and actinomycetes. Ratios of saturated:monounsaturated and iso:anteiso PLFAs decreased across the silty clay loam chronosequence indicating reduction in nutrient stress of the microbial community as grassland established. Multivariate analysis of entire PLFA profiles across the silty clay loam chronosequence showed recovery of microbial community structure on the trajectory toward native prairie. Conversely, no microbial groups exhibited a directional change across the loamy fine sand chronosequence. Changes in soil structure were also only observed across the silty clay loam chronosequence. Aggregate mean weighted diameter (MWD) exhibited an exponential rise to maximum resulting from an exponential rise to maximum in the proportion of large macroaggregates (>2000 μm) and exponential decay in microaggregates (<250 μm and >53 μm) and the silt and clay fraction (<53 μm). Across both chronosequences, MWD was highly correlated with total PLFA biomass and the biomass of many microbial groups. Strong correlations between many PLFA groups and the MWD of aggregates underscore the interdependence between the recovery of soil microbial communities and soil structure that may explain more variation than time for some soils (i.e., loamy fine sand). This study demonstrates that soil microbial responses to grassland restoration are modulated by soil texture with implications for estimating the true capacity of restoration efforts to rehabilitate ecosystem functions.     

Shrub-interspace dynamics alter relationships between microbial community composition and belowground ecosystem characteristics

In desert ecosystems, belowground characteristics are influenced chiefly by the formation and persistence of “shrub-islands of fertility” in contrast to barren plant interspaces. If soil microbial communities are exclusively compared between these two biogeochemically distinct soil types, the impact of characteristics altered by shrub species, especially soil C and N, are likely to be overemphasized and overshadow the role of other characteristics in structuring microbial composition. To determine how belowground characteristics influence microbial community composition, and if the relative importance of these characteristics shifts across the landscape (i.e., between and within shrub and interspace soils), changes in microbial communities across a 3000-year cold desert chronosequence were related to 27 belowground characteristics in surface and subsurface soils. When shrub and interspace communities in surface and subsurface soils were combined across the entire chronosequence, communities differed and were primarily influenced by soil C, NO₃⁻ concentrations, bulk density, pH, and root presence. Within shrub soils, microbial communities were shrub species-specific, especially in surface soils, highlighting differences in soil characteristics created by specific shrub species and/or similarity in stresses structuring shrub species and microbial communities alike. Microbial communities in shrub soils were not influenced by soil C, but by NO₃⁻ and NH₄⁺ concentrations, pH, and silt in surface soils; and Cl, P, soil N, and NO₃⁻ concentrations in subsurface soils. Interspace soil communities were distinct across the chronosequence at both depths and were strongly influenced by dune development. Interspace communities were primarily associated with soil stresses (i.e., high B and Cl concentrations), which decreased with dune development. The distribution of Gram-positive bacteria, Actinobacteria, and fungi highlighted community differences between and within shrub and interspace soils, while Gram-negative bacteria were common in all soils across the chronosequence. Of the 27 belowground characteristics investigated, 13 separated shrub from interspace communities, and of those, only five emerged as factors influencing community composition within shrub and interspace soils. As dunes develop across this cold desert chronosequence, microbial community composition was not regulated primarily by soil C, but by N and P availability and soil stresses in shrub soils, and exclusively by soil stresses in interspace soils.     

Variations in microbial community composition through two soil depth profiles

Soil profiles are often many meters deep, but with the majority of studies in soil microbiology focusing exclusively on the soil surface, we know very little about the nature of the microbial communities inhabiting the deeper soil horizons. We used phospholipid fatty acid (PLFA) analysis to examine the vertical distribution of specific microbial groups and to identify the patterns of microbial abundance and community-level diversity within the soil profile. Samples were collected from the soil surface down to 2 m in depth from two unsaturated Mollisol profiles located near Santa Barbara, CA, USA. While the densities of microorganisms were generally one to two orders of magnitude lower in the deeper horizons of both profiles than at the soil surface, approximately 35% of the total quantity of microbial biomass found in the top 2 m of soil is found below a depth of 25 cm. Principal components analysis of the PLFA signatures indicates that the composition of the soil microbial communities changes significantly with soil depth. The differentiation of microbial communities within the two profiles coincides with an overall decline in microbial diversity. The number of individual PLFAs detected in soil samples decreased by about a third from the soil surface down to 2 m. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the microbes inhabiting the deeper soil horizons are more carbon limited than surface-dwelling microbes. Using PLFAs as biomarkers, we show that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundances of Gram-negative bacteria, fungi, and protozoa were highest at the soil surface and substantially lower in the subsurface. The vertical distribution of these specific microbial groups can largely be attributed to the decline in carbon availability with soil depth.     

Soil microbial communities in (sub)alpine grasslands indicate a moderate shift towards new environmental conditions 11 years after soil translocation

A change in environmental conditions may result in altered soil microbial communities in alpine grasslands but the extent and direction of the change is largely unknown. The aim of our study was to investigate (i) differences in soil microbial communities across an elevation gradient of (sub)alpine grassland soils in the Swiss Alps, and (ii) the long-term effect of translocation of soil cores from a higher to a lower elevation site. The translocation of undisturbed soil cores from a high alpine site (2525 m asl) to a subalpine site near the timberline (1895 m asl) induced an effective artificial warming of 3.3 °C. We hypothesized that after longer than a decade, soil microbial community in translocated cores would differ from that at the original site but resemble the community at the new site. Results from soil phospholipid fatty acid (PLFA) analysis confirm significant differences in microbial communities between sites and a shift in total microbial biomass (TMB) and proportional distribution of structural groups in the translocated cores towards the lower elevation community. Patterns related to translocation were also observed as shifts in the fractional biomass of ectomycorrhizal and arbuscular fungi, and in relative contents of several structural groups. Hence, soil microbial community activity and diversity indicate a moderate shift towards new site conditions after 11 years and therefore, our data suggest slow responses of microbial communities to environmental changes in alpine soils.     

Experimental warming effects on the microbial community of a temperate mountain forest soil

Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO₂ (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.     

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

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

Physiological, biochemical and molecular responses of the soil microbial community after afforestation of pastures with Pinus radiata

Afforestation and deforestation are key land-use changes across the world, and are considered to be dominant factors controlling ecosystem functioning and biodiversity. However, the responses of soil microbial communities to these land-use changes are not well understood. Because changes in soil microbial abundance and community structure have consequences for nutrient cycling, C-sequestration and long-term sustainability, we investigated impacts of land-use change, age of stand and soil physico-chemical properties on fungal and bacterial communities and their metabolic activities. This study was carried out at four sites in two geographical locations that were afforested on long-established pastures with Pinus radiata D. Don (pine). Two of the sites were on volcanic soils and two on non-volcanic soils and stand age ranged from 5 to 20 y. Microbial communities were analysed by biochemical (phospho-lipid fatty acids; PLFA) and molecular (multiplex-terminal restriction fragment length polymorphism; M-TRFLP) approaches. Both site and stand age influenced microbial properties, with changes being least detectable in the 5-y-old stand. Land use was a key factor influencing soil metabolic activities as measured by physiological profiling using MicroResp. Pasture soils had higher microbial biomass (P < 0.001), and metabolic activities (P < 0.001), and basal respiration rates were up to 2.8-times higher than in the pine soils. Microbial abundance analysis by PLFA showed that the fungal to bacterial ratio was higher in the pine soils (P < 0.01). Community analysis suggested that soil bacterial communities were more responsive to site (principal component 1; P < 0.001) than to land use (principal component 5; P < 0.001). In contrast, the fungal community was more affected by land-use change (principal component 1; P < 0.001) than by site, although site still had some influence on fungal community structure (principal component 2; P < 0.001). Redundancy analysis also suggested that bacterial and fungal communities responded differently to various soil abiotic properties, land-use change and location of sites. Overall, our results indicate that the change in land use from pasture to P. radiata stands had a direct impact on soil fungal communities but an indirect effect, through its effects on soil abiotic properties, on bacterial communities. Most of the changes in bacterial communities could be explained by altered soil physico-chemical properties associated with afforestation of pastures.     

Soil microbial biomass, activity and nitrogen transformations in a turfgrass chronosequence

Understanding the chronological changes in soil microbial properties of turfgrass ecosystems is important from both the ecological and management perspectives. We examined soil microbial biomass, activity and N transformations in a chronosequence of turfgrass systems (i.e. 1, 6, 23 and 95 yr golf courses) and assessed soil microbial properties in turfgrass systems against those in adjacent native pines. We observed age-associated changes in soil microbial biomass, CO₂ respiration, net and gross N mineralization, and nitrification potential. Changes were more evident in soil samples collected from 0 to 5 cm than the 5 to 15 cm soil depth. While microbial biomass, activity and N transformations per unit soil weight were similar between the youngest turfgrass system and the adjacent native pines, microbial biomass C and N were approximately six times greater in the oldest turfgrass system compared to the adjacent native pines. Potential C and N mineralization also increased with turfgrass age and were three to four times greater in the oldest vs. the youngest turfgrass system. However, microbial biomass and potential mineralization per unit soil C or N decreased with turfgrass age. These reductions were accompanied by increases in microbial C and N use efficiency, as indicated by the significant reduction in microbial C quotient (qCO₂) and N quotient (qN) in older turfgrass systems. Independent of turfgrass age, microbial biomass N turnover was rapid, averaging approximately 3 weeks. Similarly, net N mineralization was ∼12% of gross mineralization regardless of turfgrass age. Our results indicate that soil microbial properties are not negatively affected by long-term management practices in turfgrass systems. A tight coupling between N mineralization and immobilization could be sustained in mature turfgrass systems due to its increased microbial C and N use efficiency.     

Artificial neural network modeling of microbial community structures in the Atlantic Forest of Brazil

Microbial communities vary across the landscape in forest soils, but prediction of their biomass and composition is a difficult challenge due to the large numbers of variables that influence their community structures. Here we examine the use of artificial neural network (ANN) models for extraction of patterns among soil chemical variables and microbial community structures in forest soils from three regions of the Atlantic Forest of Brazil. At each location, variations in soil chemical properties and FAME profiles of microbial community structures were mapped at 20 × 20 m intervals within 10 ha parcels. Geostatistical analyses showed that spatial variability in soil physical and chemical variables could be mapped at scale distances of 20 m, but that FAME profiles representing the microbial communities were highly variable and had no spatial dependence at the same scale in most cases. RDA analysis showed that FAME signatures representing different microbial groups were positively associated with soil pH, OM, P and base cations concentrations, whereas microbial biomass was negatively associated with the same environmental factors. In contrast, ANN models revealed clear relationships between microbial community structures at each parcel location, and generated verifiable predictions of variations in FAME profiles in relation to soil pH, texture, and the relative abundances of base cations. The results suggest that ANN modeling provides a useful approach for describing the relationships between microbial community structures and soil properties in tropical forest soils that were not able to be captured using geostatistical and RDA analyses.     

The seasonal pattern of soil microbial community structure in mesic low arctic tundra

Soil microorganisms are critical to carbon and nutrient fluxes in terrestrial ecosystems. Understanding the annual pattern of soil microbial community structure and how it corresponds to soil nutrient availability and plant production is a fundamental first step towards being able to predict impacts of environmental change on ecosystem functioning. We investigated the composition, structure and nutrient stoichiometry of the soil microbial community in mesic arctic tundra on 9 sample dates in 6 months from winter to fall using phospholipid fatty acid analysis (PLFA), quantitative polymerase chain reaction (qPCR), epifluorescent microscopy and chloroform-fumigation–extraction (CFE). PLFA analysis indicates that the winter microbial community was fungal-dominated, cold-adapted and associated with high C, N and P in the soil solution and microbial biomass. The microscopy data suggest that both bacteria and fungi were active and growing in soils between −5 °C and 0 °C. A significant shift occurred in the PLFA data, qPCR patterns, microscopy and microbial biogeochemistry after the thaw period, resulting in a distinct community that persisted through our spring, summer and fall sample dates, despite large changes in plant productivity. This shift was characterised by increasing relative abundances of certain bacteria (especially Gram +ves) as well as a decline in fungal biomass, and corresponded with decreasing C, N and P in the soil solution. The summer period of low substrate availability (plant–microbe competition) was associated with microbial indicators of nutritional stress. Overall, our results indicate that tundra microbial communities are clearly differentiated according to the changes in soil nutrient status and environmental conditions that occur between winter and post-thaw, and that those changes reflect functionally important adaptations to those conditions.     

Long-term exclusion of plant-inputs to soil reduces the functional capacity of microbial communities to mineralise recalcitrant root-derived carbon sources

Microbial communities in soil are highly species-rich, recognition of which has led to the view that functional redundancy within communities may buffer many impacts of altered community structure on soil functions. In this study we investigated the impact of long-term (>50 years) exclusion of plant-inputs (bare-fallow treatment) on soil microbial community structure and on the ability of the microbial biomass to mineralise tracer additions of ¹³C-labelled plant-derived C-substrates. Exclusion of plant-inputs resulted in depletion of soil organic matter (SOM) and a reduction in microbial biomass size. The microbial community structure was also strongly affected, as indicated by the distinct phospholipid fatty acid (PLFA) profiles in bare-fallow and grassland soils. Mineralisation of labile plant-derived substrates was not perturbed by the bare-fallow treatment. The incorporation of labile plant-derived C into PLFA biomarkers was found to differ between soils, reflecting the distinct community structures of the soils and indicating that these substrates were utilised by a broad range of microbial groups. In contrast, the mineralisation of recalcitrant plant-derived substrates was reduced in bare-fallow soil and the fate of substrate-derived C within PLFA biomarkers was, initially, similar between the soils. These results indicate that utilisation of these recalcitrant substrates was a function restricted to specific groups, and that exclusion of plant-derived inputs to soil had reduced the capacity of bare-fallow microbial communities to utilise this substrate type. Therefore, the study suggests that long-term selective pressure on microbial communities, resulting in altered community structure, may also result in altered functional attributes. This structure-function relationship was apparent for utilisation of recalcitrant plant-derived substrates, but not for the more widely distributed attribute of labile C-substrate utilisation.     

Microbial community composition on native and drastically disturbed serpentine soils

During construction of roads, entire hillsides can be cut away, dramatically disturbing the ecosystem. Microbial communities play important, but poorly understood roles in revegetating roadcuts because of the many functions they perform in nutrient cycling, plant symbioses, decomposition, and other ecosystem processes. Our objective was to determine relationships among microbial community composition, soil chemistry, and disturbance on a serpentine soil disturbed by a roadcut and then partially revegetated. We hypothesized that the adjacent undisturbed serpentine soil would have a different microbial community composition from barren and revegetated sections of the roadcut and that undisturbed soils would have the greatest microbial biomass and diversity. We measured phospholipid fatty acids (PLFA) and soil nutrient concentrations on barren and revegetated sections of the roadcut and on adjacent undisturbed serpentine and nonserpentine soils. Most roadcut samples had soil chemistry similar to the serpentine reference soil. The microbial biomass and diversity of barren sites was lower than that of revegetated or the serpentine reference site. The nonserpentine reference site had significantly (P≤0.05) greater microbial biomass than serpentine or disturbed sites but significantly lower relative proportions of actinomycetes, and slow growth biomarkers. The Barren site had the lowest microbial biomass and a significantly (P≤0.05) greater proportion of that biomass was fungi. Barren, revegetated, and serpentine sites all had dissimilar microbial community composition. The composition of the revegetated communities, however, was intermediate between the serpentine reference and barren soils, suggesting that community composition of revegetated soils is approaching that of an undisturbed site with similar soil chemistry.     

Effects of pine roots on microorganisms,fauna, and nitrogen availability in two soil horizons of a coniferous forest spodosol

Summary We investigated the effects of pitch pine seedling roots on extractable N, microbial growth rate, biomass C and N, and nematodes and microarthropods in microcosms with either organic (41% C, 1.14% N) or mineral (0.05% C, 0.01% N) horizon soils of a spondosol. Root quantity was manipulated by varying plant density (0, 1, 2, or 4 seedlings) and rhizosphere soil was separated from non-rhizosphere soil by a 1.2 m mesh fabric. In the rhizosphere of organic soil horizons, moisture, microbial growth rate, biomass C and N, and extractable N declined as root density was increased, but there was little effect on nematodes or microarthropods. High levels of extractable N remained after 5 months, suggesting that N mineralization was stimulated during the incubation. In the rhizosphere of mineral soil horizons, microbial growth rate, and nematode and microarthropod abundances increased at higher root density, and in the absence of roots faunal abundance approached zero. Faunal activity was concentrated in the rhizosphere compared to non-rhizosphere soil. In organic soil horizons, roots may limit microbial activity by reducing soil moisture and/or N availability. However, in mineral soil horizons, where nutrient levels are very low, root inputs can stimulate microbial growth and faunal abundance by providing important substrates for microbial growth. Our results demonstrate a rhizosphere effect for soil fauna in the mineral soil, and thus extends the rhizosphere concept to components of the soil community other than microbes for forest ecosystems. Although our results need to be verified by field manipulations, we suggest that the effects of pine roots on nutrient cycling processes in coniferous forests can vary with soil nutrient content and, therefore, position in the soil profile.     

Development of soil microbial communities during tallgrass prairie restoration

Soil microbial communities were examined in a chronosequence of four different land-use treatments at the Konza Prairie Biological Station, Kansas. The time series comprised a conventionally tilled cropland (CTC) developed on former prairie soils, two restored grasslands that were initiated on former agricultural soils in 1998 (RG₉₈) and 1978 (RG₇₈), and an annually burned native tallgrass prairie (BNP), all on similar soil types. In addition, an unburned native tallgrass prairie (UNP) and another grassland restored in 2000 (RG₀₀) on a different soil type were studied to examine the effect of long-term fire exclusion vs. annual burning in native prairie and the influence of soil type on soil microbial communities in restored grasslands. Both 16S rRNA gene clone libraries and phospholipid fatty acid analyses indicated that the structure and composition of bacterial communities in the CTC soil were significantly different from those in prairie soils. Within the time series, soil physicochemical characteristics changed monotonically. However, changes in the microbial communities were not monotonic, and a transitional bacterial community formed during restoration that differed from communities in either the highly disturbed cropland or the undisturbed original prairie. The microbial communities of RG₉₈ and RG₀₀ grasslands were also significantly different even though they were restored at approximately the same time and were managed similarly; a result attributable to the differences in soil type and associated soil chemistry such as pH and Ca. Burning and seasonal effects on soil microbial communities were small. Similarly, changing plot size from 300 m² to 150 m² in area caused small differences in the estimates of microbial community structure. In conclusion, microbial community structure and biochemical properties of soil from the tallgrass prairie were strongly impacted by cultivation, and the microbial community was not fully restored even after 30 years.     

Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia

Soil horizons below 30 cm depth contain about 60% of the organic carbon stored in soils. Although insight into the physical and chemical stabilization of soil organic matter (SOM) and into microbial community composition in these horizons is being gained, information on microbial functions of subsoil microbial communities and on associated microbially-mediated processes remains sparse. To identify possible controls on enzyme patterns, we correlated enzyme patterns with biotic and abiotic soil parameters, as well as with microbial community composition, estimated using phospholipid fatty acid profiles. Enzyme patterns (i.e. distance-matrixes calculated from these enzyme activities) were calculated from the activities of six extracellular enzymes (cellobiohydrolase, leucine-amino-peptidase, N-acetylglucosaminidase, chitotriosidase, phosphatase and phenoloxidase), which had been measured in soil samples from organic topsoil horizons, mineral topsoil horizons, and mineral subsoil horizons from seven ecosystems along a 1500 km latitudinal transect in Western Siberia. We found that hydrolytic enzyme activities decreased rapidly with depth, whereas oxidative enzyme activities in mineral horizons were as high as, or higher than in organic topsoil horizons. Enzyme patterns varied more strongly between ecosystems in mineral subsoil horizons than in organic topsoils. The enzyme patterns in topsoil horizons were correlated with SOM content (i.e., C and N content) and microbial community composition. In contrast, the enzyme patterns in mineral subsoil horizons were related to water content, soil pH and microbial community composition. The lack of correlation between enzyme patterns and SOM quantity in the mineral subsoils suggests that SOM chemistry, spatial separation or physical stabilization of SOM rather than SOM content might determine substrate availability for enzymatic breakdown. The correlation of microbial community composition and enzyme patterns in all horizons, suggests that microbial community composition shapes enzyme patterns and might act as a modifier for the usual dependency of decomposition rates on SOM content or C/N ratios.     

Long-term effects of mineral fertilizers on soil microorganisms – A review

Increasing nutrient inputs into terrestrial ecosystems affect not only plant communities but also associated soil microbial communities. Studies carried out in predominantly unmanaged ecosystems have found that increasing nitrogen (N) inputs generally decrease soil microbial biomass; less is known about long-term impacts in managed systems such as agroecosystems. The objective of this paper was to analyze the responses of soil microorganisms to mineral fertilizer using data from long-term fertilization trials in cropping systems. A meta-analysis based on 107 datasets from 64 long-term trials from around the world revealed that mineral fertilizer application led to a 15.1% increase in the microbial biomass (C_mic) above levels in unfertilized control treatments. Mineral fertilization also increased soil organic carbon (C_org) content and our results suggest that C_org is a major factor contributing to the overall increase in C_mic with mineral fertilization. The magnitude of the effect of fertilization on C_mic was pH dependent. While fertilization tended to reduce C_mic in soils with a pH below 5 in the fertilized treatment, it had a significantly positive effect at higher soil pH values. Duration of the trial also affected the response of C_mic to fertilization, with increases in C_mic most pronounced in studies with a duration of at least 20 years. The input of N per se does not seem to negatively affect C_mic in cropping systems. The application of urea and ammonia fertilizers, however, can temporarily increase pH, osmotic potential and ammonia concentrations to levels inhibitory to microbial communities. Even though impacts of fertilizers are spatially limited, they may strongly affect soil microbial biomass and community composition in the short term. Long-term repeated mineral N applications may alter microbial community composition even when pH changes are small. How specific microbial groups respond to repeated applications of mineral fertilizers, however, varies considerably and seems to depend on environmental and crop management related factors.     

Development of microbial community during primary succession in areas degraded by mining activities

Together with plants, soil microbial communities play an essential role in the development of stable ecosystems on degraded lands, such as postmining spoil heaps. Our study addressed concurrent development of the vegetation and soil fungal and bacterial communities in the course of primary succession in a brown coal mine spoil deposit area in the Czech Republic across a chronosequence spanning 54 years. During succession, the plant communities changed from sparse plants over grassland and shrubland into a forest, becoming substantially more diverse with time. Microbial biomass increased until the 21st year of ecosystem development and later decreased. Although there was a close association between fungi and vegetation, with fungi mirroring the differences in plant community assemblages, the development of the bacterial community was different. The early succession community in the barren nonvegetated soil largely differed from that in the older sites, especially in its high abundance of autotrophic and free‐living N₂‐fixing bacteria. Later in succession, bacterial community changes were minor and reflected the chemical parameters of the soil, including pH, which also showed a minor change with time. Our results show that complex forest ecosystems developed over 54 years on the originally barren soil of the temperate zone and indicate an important role of bacteria in the initial stage of soil development. Although the arrival of vegetation affects substantially fungal as well as bacterial communities, it is mainly fungi that respond to the ongoing development of vegetation.     

Microbial communities of Lumbricus terrestris L. middens: structure, activity, and changes through time in relation to earthworm presence

Background, aim, and scope  Earthworms make a major contribution to decomposition in ecosystems where they are present, mainly acting in the drilosphere, that is, galleries, burrows, casts, and middens. Earthworm middens are hot-spots of microbial activity and nutrient dynamics and represent a suitable model for studying earthworm-mediated influences on soil microbial communities by alteration of the patch structure of the microbial environment. We studied the structure and activity of the microbial communities in the soil system formed by middens of Lumbricus terrestris and the soil below and surrounding them and the role of earthworms in maintaining these structures through time. Material and methods  We set up an experiment in which middens were either left (control) or removed from their original place (translocated) and left in a nearby area free of earthworm activity for 2 months. After 1 and 2 months we sampled middens, soil below them, and surrounding soil. We analyzed the phospholipid fatty acid (PLFA) profiles and measured respiratory fluxes of CO₂ and CH₄. Results  Microbial communities of middens clearly differed from those of soil below and surrounding soil samples, showing higher bacterial and fungal PLFAs (p < 0.0001 and p < 0.01, respectively); furthermore, changes in microbial communities were stronger in control middens than in translocated middens. Moreover, gram positive and negative bacterial PLFAs were greater in translocated than control middens (p < 0.0001 and p < 0.001, respectively), as well as total organic carbon (p < 0.001). Microbial activity was higher in middens than in soil below and surrounding soil samples both for CO₂ (p < 0.0001) and CH₄ (p < 0.0001). Discussion  Soil bioturbation by the earthworm L. terrestris was strong in their middens, but there was not any effect on soil below and surrounding soil. Microbial communities of middens maintain their biomass and activity when earthworms were not present, whereas they decreased their biomass and increased their activity when earthworms were present. Conclusions  Earthworms strongly enhanced microbial activity measured as CO₂ production in middens, which indicates that there are hot spots for soil microbial dynamics and increasing habitat heterogeneity for soil microorganisms. Moreover, our data strongly support the fact that the impact of this earthworm species in this soil is restricted to their middens and increasing soil heterogeneity. Recommendations and perspectives  Our data indicate that it is not clear if earthworms enhance or depress microbial communities of middens since the microbial activity increased, but did not modify their biomass and this was not dependent on soil organic C content. These results indicate no competence for C pools between this anecic earthworm and microorganisms, which has been found for other earthworm species, mainly endogeics. Conversely, they suggest some type of facilitation due to the release of additional nutrient pools in middens when earthworms are present, through the digestion of middens' material or the addition of casts produced from other food sources.     

Elevated CO2 differentially alters belowground plant and soil microbial community structure in reed canary grass-invaded experimental wetlands

Several recent studies have indicated that an enriched atmosphere of carbon dioxide (CO₂) could exacerbate the intensity of plant invasions within natural ecosystems, but little is known of how rising CO₂ impacts the belowground characteristics of these invaded systems. In this study, we examined the effects of elevated CO₂ and nitrogen (N) inputs on plant and soil microbial community characteristics of plant communities invaded by reed canary grass, Phalaris arundinacea L. We grew the invasive grass under two levels of invasion: the invader was either dominant (high invasion) at >90% plant cover or sub-dominant (low invasion) at <50% plant cover. Experimental wetland communities were grown for four months in greenhouses that received either 600 or 365 μl l⁻¹ (ambient) CO₂. Within each of three replicate rooms per CO₂ treatment, the plant communities were grown under high (30 mg l⁻¹) or low (5 mg l⁻¹) N. In contrast to what is often predicted under N limitation, we found that elevated CO₂ increased native graminoid biomass at low N, but not at high N. The aboveground biomass of reed canary grass did not respond to elevated CO₂, despite it being a fast-growing C3 species. Although elevated CO₂ had no impact on the plant biomass of heavily invaded communities, the relative abundance of several soil microbial indicators increased. In contrast, the moderately invaded plant communities displayed increased total root biomass under elevated CO_2, while little impact occurred on the relative abundance of soil microbial indicators. Principal components analysis indicated that overall soil microbial community structure was distinct by CO₂ level for the varying N and invasion treatments. This study demonstrates that even when elevated CO₂ does not have visible effects on aboveground plant biomass, it can have large impacts belowground.     

The effect of earthworms and liming on soil microbial communities

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.