Contributions of soil biota to C sequestration varied with aggregate fractions under different tillage systems

It is increasingly believed that substantial soil organic carbon (SOC) can be sequestered in conservation tillage system by manipulating the functional groups of soil biota. Soil aggregates of different size provide diverse microhabitats for soil biota and consequently influence C sequestration. Our objective was to evaluate the contributions of soil biota induced by tillage systems to C sequestration among different aggregate size fractions. Soil microbial and nematode communities were examined within four aggregate fractions: large macroaggregates (>2 mm), macroaggregates (2–1 mm), small macroaggregates (1–0.25 mm) and microaggregates (<0.25 mm) isolated from three tillage systems: no tillage (NT), ridge tillage (RT) and conventional tillage (CT) in Northeast China. Soil microbial and nematode communities varied across both tillage systems and aggregate fractions. The activity and abundance of microbes and nematodes were generally higher under NT and RT than under CT. Among the four aggregate fractions, soil microbial biomass and diversity were higher in microaggregates, while soil nematode abundance and diversity were higher in large macroaggregates. Structural equation modelling (SEM) revealed that the linkage between microbial and nematode communities and their contributions to soil C accumulation in >1 mm aggregate fractions were different from those in <1 mm aggregate fractions. Higher abundance of arbuscular mycorrhizal fungi (AMF) could enhance C retention within >1 mm aggregates, while more gram-positive bacteria and plant-parasitic nematodes might increase C accumulation within <1 mm aggregates. Our findings suggested that the increase in microbial biomass and nematode abundance and the alteration in their community composition at the micro-niche within aggregates could contribute to the higher C sequestration in conservation tillage systems (NT and RT).     

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.     

Bacterial community structure in soil microaggregates and on particulate organic matter fractions located outside or inside soil macroaggregates

Soil aggregates and particulate organic matter (POM) are thought to represent distinct soil microhabitats for microbial communities. This study investigated whether organo-mineral (0–20, 20–50 and 50–200 μm) and POM (two sizes: >200 and <200 μm) soil fractions represent distinct microbial habitats. Microbial habitats were characterised by the amount and quality of organic matter, the genetic structure of the bacterial community, and their location outside or inside macroaggregates (>200 μm). The denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial communities structure of organo-mineral soil fractions were significantly different in comparison to the unfractionated soil. Conversely, there were little differences in C concentrations, C:N ratios and no differences in DGGE profiles between organo-mineral fractions. Bacterial communities between soil fractions located inside or outside macroaggregates were not significantly different. However, the bacterial communities on POM fractions were significantly different in comparison to organo-mineral soil fractions and unfractionated soil, and also between the 2 sizes of POM. Thus in the studied soil, only POM fractions represented distinct microhabitats for bacterial community, which likely vary with the state of decomposition of the POM.     

Eubacterial communities in different soil macroaggregate environments and cropping systems

Different positions within soil macroaggregates, and macroaggregates of different sizes, have different chemical and physical properties which could affect microbial growth and interactions among taxa. The hypothesis that these soil aggregate fractions contain different eubacterial communities was tested using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal gene. Communities were characterized from two field experiments, located at the Kellogg Biological Station (KBS), MI, USA and the Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA. Three soil management regimes at each site were sampled and management was found to significantly affect T-RFLP profiles. The soil aggregate erosion (SAE) method was used to isolate aggregate regions (external and internal regions). Differences between eubacterial T-RFLP profiles of aggregate exteriors and interiors were marginally significant at KBS (accounting for 12.5% of total profile variance), and not significant at OARDC. There were no significant differences among macroaggregate size classes at either site. These results are in general agreement with previous studies using molecular methods to examine microbial communities among different soil macroaggregate size fractions, although further study of communities within different aggregate regions is warranted. Analysis of individual macroaggregates revealed large inter-aggregate variability in community structure. Hence the tertiary components of soil structure, e.g. arrangement of aggregates in relation to shoot residue, roots, macropores, etc., may be more important than aggregate size or intra-aggregate regions in the determination of the types of microbial communities present in aggregates. Direct microscopic counts were also used to examine the bacterial population size in aggregate regions at KBS. The proportion of bacterial cells with biovolumes >0.18 μm³ was higher in aggregate interiors than in exteriors, indicating potentially higher activity in that environment. This proportion was significantly related to percent C of the samples, while total bacterial cell counts were not.     

Endogeic earthworms differentially influence bacterial communities associated with different soil aggregate size fractions

Endogeic earthworm activities can strongly influence soil structure. Although soil microorganisms are thought to be central to earthworm-facilitated aggregate formation, how and where within the soil matrix earthworm-facilitated influences on soil microbial communities are manifested is poorly defined. In this study we used 16S rRNA gene-based terminal restriction fragment polymorphism (T-RFLP) analyses to examine bacterial communities associated with different aggregate size fractions (macroaggregates, microaggregates-within-macroaggregates and inner-microaggregates-within-macroaggregates) of soils incubated for 28 d with and without earthworms. We hypothesized that bacterial communities in different soil aggregate size fractions are differentially influenced by earthworm activities. Our results indicate significantly enhanced aggregate formation (both macroaggregates and microaggregates within macroaggregates) in earthworm-worked soils relative to soils receiving only plant litter. Although significant differences were found between bacterial communities of earthworm and litter-only treatments for all soil fractions, communities associated with earthworm-worked macroaggregate fractions exhibited the least similarity to all other soil fractions regardless of treatment. In addition to differences in terminal restriction fragment (T-RF) size distributions, T-RFLP profiles of earthworm-worked soil macroaggregates had significantly fewer T-RF sizes, further suggesting less species evenness and more extensive alteration of bacterial communities within this fraction. These findings suggest that, due to rapid occlusion of organic materials, microbial communities associated with microaggregates-within-macroaggregates formed during or shortly after passage through the earthworm gut are relatively inactive, and therefore change relatively little over time compared to macroaggregate populations as a whole.     

Sensitivities to nitrogen and water addition vary among microbial groups within soil aggregates in a semiarid grassland

We investigated whether enhanced nitrogen (N) and water inputs would redistribute the microbial community within different soil aggregate size classes in a field manipulation experiment initiated in 2005. Distribution of microbial groups was monitored in large macroaggregates (>2000 μm), small macroaggregates (250–2000 μm), and microaggregates (<250 μm) in a semiarid grassland. Both arbuscular mycorrhizal (AM) fungi and saprophytic fungi were the most abundant in soil macroaggregates. The gram-negative bacteria were more abundant in soil microaggregates. Total phospholipid fatty acid (PLFA) concentration in general and actinomycetes in particular decreased with N addition under ambient precipitation but was unaffected by combined additions of N and water within the three soil aggregate fractions as compared to control plots. In contrast, the abundance of saprophytic fungi decreased with combined N and water addition, but it was not affected by N addition under ambient precipitation. The abundance of gram-positive bacteria increased with N addition under both ambient and elevated water conditions for all soil aggregate fractions. In summary, the higher short-term nutrient and water availabilities provoked a shift in soil microbial community composition and increased total PLFA abundance irrespectively of the level of soil aggregation. In the long term, this could destabilize soil carbon pools and influence the nutrient limitation of soil biota within different soil aggregate size classes under future global change scenarios.     

有机种植对温室土壤肥力质量的影响

利用中国农业大学曲周实验站温室有机种植长期定位试验,研究了不同种植模式下3种土壤物理指标、9种土壤化学指标和4种土壤生物指标,并运用主成分分析方法,对不同种植模式下土壤肥力质量进行综合评分。结果表明:①相比于无公害和常规种植,有机种植有利于降低温室土壤容重,提高温室土壤含水量,温室土壤水稳性大团聚体高达58.02%,改善了温室土壤物理环境条件;②有机种植提高了温室土壤有机质及氮、磷、钾养分含量,对温室土壤pH和EC值影响不大,但增加了温室土壤阳离子交换量,有利于提高温室土壤的保水保肥能力;③相比于无公害和常规种植,有机种植土壤微生物碳含量分别提高了32.84%、109.30%,同时增强了温室土壤脲酶、磷酸酶及过氧化氢酶活性,有利于温室土壤微生物多样性提高;④通过对16个土壤肥力质量指标进行主成分分析,3个主成分累计贡献率达91.052%,主成分综合评分能更敏感反映土壤质量变化,本试验中有机种植、无公害种植和常规种植的主成分综合评分分别为1.514、0.099和–1.613,表明有机种植显著提高了温室土壤的肥力质量。     

Soil microbial biomass and organic matter fractions during transition from conventional to organic farming systems

The aim of this study was to investigate the response of soil microbial biomass and organic matter fractions during the transition from conventional to organic farming in a tropical soil. Soil samples were collected from three different plots planted with Malpighia glaba: conventional plot with 10 years (CON); transitional plot with 2 years under organic farming system (TRA); organic plot with 5 years under organic farming system (ORG). A plot under native vegetation (NV) was used as a reference. Soil microbial biomass C (MBC) and N (MBN), soil organic carbon (SOC) and total N (TN), soil organic matter fractioning and microbial indices were evaluated in soil samples collected at 0–5, 5–10, 10–20 and 20–40 cm depth. SOC and fulvic acids fraction contents were higher in the ORG system at 0–5 cm and 5–10 cm depths. Soil MBC was highest in the ORG, in all depths, than in others plots. Soil MBN was similar between ORG, TRA and NV in the surface layer. The lowest values for soil MBC and MBN were observed in CON plot. Soil microbial biomass increased gradually from conventional to organic farming, leading to consistent and distinct differences from the conventional control by the end of the second year.     

Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil

 Particle-size fractionation of a heavy metal polluted soil was performed to study the influence of environmental pollution on microbial community structure, microbial biomass, microbial residues and enzyme activities in microhabitats of a Calcaric Phaeocem. In 1987, the soil was experimentally contaminated with four heavy metal loads: (1) uncontaminated controls; (2) light (300 ppm Zn, 100 ppm Cu, 50 ppm Ni, 50 ppm V and 3 ppm Cd); (3) medium; and (4) heavy pollution (two- and threefold the light load, respectively). After 10 years of exposure, the highest concentrations of microbial ninhydrin-reactive nitrogen were found in the clay (2–0.1 μm) and silt fractions (63–2 μm), and the lowest were found in the coarse sand fraction (2,000–250 μm). The phospholipid fatty acid analyses (PLFA) and denaturing gradient gel electrophoresis (DGGE) separation of 16S rRNA gene fragments revealed that the microbial biomass within the clay fraction was predominantly due to soil bacteria. In contrast, a high percentage of fungal-derived PLFA 18 : 2ω6 was found in the coarse sand fraction. Bacterial residues such as muramic acid accumulated in the finer fractions in relation to fungal residues. The fractions also differed with respect to substrate utilization: Urease was located mainly in the <2 μm fraction, alkaline phosphatase and arylsulfatase in the 2–63 μm fraction, and xylanase activity was equally distributed in all fractions. Heavy metal pollution significantly decreased the concentration of ninhydrin-reactive nitrogen of soil microorganisms in the silt and clay fraction and thus in the bulk soil. Soil enzyme activity was reduced significantly in all fractions subjected to heavy metal pollution in the order arylsulfatase >phosphatase >urease >xylanase. Heavy metal pollution did not markedly change the similarity pattern of the DGGE profiles and amino sugar concentrations. Therefore, microbial biomass and enzyme activities seem to be more sensitive than 16S rRNA gene fragments and microbial amino-sugar-N to heavy metal treatment. Received: 21 January 2000     

Microbial physiology and necromass regulate agricultural soil carbon accumulation

Strategies for mitigating soil organic carbon (SOC) losses in intensively managed agricultural systems typically draw from traditional concepts of soil organic matter formation, and thus emphasize increasing C inputs, especially from slowly decomposing crop residues, and reducing soil disturbance. However these approaches are often ineffective and do not adequately reflect current views of SOC cycling, which stress the important contributions of microbial biomass (MB) inputs to SOC. We examined microbial physiology as an alternate mechanism of SOC accumulation under organic (ORG) compared to conventional (CT) agricultural management practices, where ORG is accumulating C despite fewer total C inputs and greater soil tillage. We hypothesized that microbial communities in ORG have higher growth rates (MGR) and C use efficiencies (CUE) and that this relates to greater MB production and ultimately higher retention of new C inputs. We show that ORG had 50% higher CUE (±8 se) and 56% higher MGR (±22 se) relative to CT (p < 0.05). From in situ ¹³C substrate additions, we show that higher CUE and MGR are associated with greater rates and amounts of ¹³C glucose and phenol assimilation into MBC and mineral-associated SOC pools in ORG up to 6 mo after field substrate additions (p < 0.05). ORG soils were also enriched in proteins and lipids and had lower abundances of aromatic compounds and plant lipids (p < 0.05). These results illustrate a new mechanism for SOC accumulation under reduced C inputs and intensive soil disturbance and demonstrate that agricultural systems that facilitate the transformation of plant C into MB may be an effective, often overlooked strategy for building SOC in agricultural soils.     

长期施肥对红壤性水稻土团聚体稳定性及固碳特征的影响

施用有机肥是提高土壤有机碳(SOC)含量、促进土壤团聚体形成和改善土壤结构的重要措施。本研究旨在探讨长期作物残留和投入有机物料对水稻土团聚体分布及稳定性的影响,分析不同粒级团聚体的固碳特征及其与团聚体形成的相关性,以及土壤和不同粒级团聚体对累积碳投入的响应。长期定位施肥试验始于1986年,设不施肥(CK)、单施化肥(CF)、秸秆化肥混施(RS)、低量粪肥配施化肥(M1)和高量粪肥配施化肥(M2)5个处理。2009年采集0~10 cm土壤样品,测定总土以及大团聚体(LM,2 mm)、较大团聚体(SM,0.25~2 mm)、微团聚体(MA,0.25~0.053 mm)和黏粉粒(SC,0.053 mm)的质量比例及其SOC浓度,并分析闭蓄于SM内部的颗粒有机物(POM)、微团聚体(MA-SM)和黏粉粒(SC-SM)的质量含量和SOC浓度。结果表明,与CK和CF比较,有机肥混施化肥处理(RS、M1和M2)均显著提高了LM和SM的质量比例和平均当量直径(MWD),降低了SC质量含量;两个粪肥配施化肥处理(M1和M2)的效果优于秸秆化肥混施(RS),但是M1和M2间差异不显著;单施化肥则降低了稳定性团聚体的比例。团聚体的SOC浓度没有随粒级增大而增加,各处理均为LM和SM结合的SOC浓度最高,其次为SC,最小为MA。与CK比较,有机肥混施化肥处理均显著提高了各粒级团聚体的SOC浓度。总土SOC的增加主要取决于SM的SOC含量,而MA-SM组分决定了SM固持SOC的能力。总土、LM和SM的SOC含量以及从SM分离出的POM、MA-SM和SC-SM的SOC含量均与累积碳投入量呈显著正相关,但总土分离出的MA和SC的SOC含量对累积碳投入量反应不敏感,表现出碳饱和迹象。因此,尽管长期大量施用有机物料促进了红壤性水稻土大团聚体的形成和团聚体稳定性,增加了其SOC的固持,但有机质可能不是该土壤水稳性团聚体形成的最主要黏结剂。     

Catabolic response and phospholipid fatty acid profiles as microbial tools to assess soil functioning

Microbial properties may help to provide an integrated view of changes in soil functioning associated with soil management or soil status. The fatty acid profiles of membrane phospholipids (PLFA) can give the composition of ecophysiological groups of soil microbial communities, while catabolic response profiles (CRP) estimate the heterotrophic functional diversity in soils, both relevant to the understanding of the role of micro‐organisms in the functioning of the soil. The objectives of this study were (i) to evaluate the CRP and PLFA as microbial tools to characterize changes in soil functioning and (ii) clarify the relation among these microbial measurements, with other physical, chemical and biochemical soil properties. We compare the same soil subjected to different managements and degrees of erosion. An undisturbed soil (UN), an old pasture soil (OP) and soils under continuous cultivation (NT) with four different depth of A horizon: 25 cm (NT 25), 23 cm (NT 23), 19 cm (NT 19) and 14 cm (NT 14) were tested. Substrate‐induced respiration of most substrates diminished when cropping pressure increased (UN > OP > NT), and soil catabolic evenness, as a diversity index, decreased by increasing production pressure and soil erosion. The correlation found among most of the measured physical, chemical and biochemical soil properties with the catabolic evenness showed the potential of this measurement to provide an integrated view of soil functioning. The PLFA analysis showed that the composition of microbial community denoting a partial recovery after 10 yr under grazed grassland. The stress indicators showed that farming practices increased microbial stress with the highest values found in the most eroded soils.     

Measurements of microbial community activities in individual soil macroaggregates

The functional potential of single soil macroaggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for β-glucosidase, N-acetyl-β-d-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual macroaggregates (250–1000 μm diameter). Across all enzymes, the smallest macroaggregates had the greatest activity and the range of enzyme activities observed in all macroaggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and β-glucosidase on the same macroaggregates suggest the presence of both extracellular β-glucosidase functioning in macroaggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low β-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.     

Rhizosphere isoflavones (daidzein and genistein) levels and their relation to the microbial community structure of mono-cropped soybean soil in field and controlled conditions

Despite an increase in the understanding of the soybean isoflavones involved in root-colonizing symbioses, relatively little is known about their levels in the rhizosphere and their interactions with the soil microbial community. Based on a 13-year experiment of continuous soybean monocultures, in the present study we quantified isoflavones in the soybean rhizosphere and analyzed the soil microbial community structure by examining its phospholipid fatty acid (PLFA) profile. Two isoflavones, daidzein (7, 4′-dihydroxyisoflavone) and genistein (5,7,4′- trihydroxyisoflavone), were detected in the rhizosphere soil of soybean plants, with the concentrations in the field varying with duration of mono-cropping. Genistein concentrations ranged from 0.4 to 1.2 μg g⁻¹ dry soil over different years, while daidzein concentrations rarely exceeded 0.6 μg g⁻¹ dry soil. PLFA profiling showed that the signature lipid biomarkers of bacteria and fungi varied throughout the years of the study, particularly in mono-cropping year 2, and mono-cropping years 6-8. Principal component analysis clearly identified differences in the composition of PLFA during different years under mono-cropping. There was a positive correlation between the daidzein concentrations and soil fungi, whereas the genistein concentration showed a correlation with the total PLFA, fungi, bacteria, Gram (+) bacteria and aerobic bacteria in the soil microbial community. Both isoflavones were easily degraded in soil, resulting in short half-lives. Concentrations as small as 1 μg g⁻¹ dry soil were sufficient to elicit changes in microbial community structure. A discriminant analysis of PLFA patterns showed that changes in microbial community structures were induced by both the addition of daidzein or genistein and incubation time. We conclude that daidzein and genistein released into the soybean rhizosphere may act as allelochemicals in the interactions between root and soil microbial community in a long-term mono-cropped soybean field.     

Pasture degradation impacts soil phosphorus storage via changes to aggregate-associated soil organic matter in highly weathered tropical soils

Maintaining the productivity of tropical pastures is a major challenge for the sustainable management of tropical landscapes around the globe. To address this issue, we examined linkages between soil organic matter (SOM), aggregation, and phosphorus (P) dynamics by comparing productive vs. degraded pastures in the deforested Amazon Basin of Colombia. Paired plots of productive (dominated by planted Brachiaria spp.) vs. degraded pasture were identified on nine farms in the Department of Caquetá and sampled during the rainy season of 2011. Aboveground pasture biomass production and nutrient content were measured. Surface soils (0–10 cm) were also fractionated by wet sieving, and C, ¹³C, N and P contents were analyzed for the bulk soil and various aggregate size classes. Productive pastures yielded more than double the aboveground biomass compared to degraded pastures (during a 35 day regrowth period following cutting), with over 60% higher N and P contents in this material. Similar trends were observed for the standing litter biomass and nutrient contents. Soil aggregate stability was found to differ between pasture types, with a mean weight diameter of 3590 vs. 3230 μm in productive vs. degraded pastures, respectively. Productive pastures were found to have 20% higher total soil C and N contents than degraded pastures. While there was no difference in total P content between pasture types, organic P was found to be nearly 40% higher in soils of productive vs. degraded pastures. Differences in total SOM between pasture types were largely explained by a higher C content in the large macroaggregate fraction (>2000 μm), and more specifically in the microaggregates (53–250 μm) occluded within this fraction. These findings confirm the role of microaggregates within macroaggregates as a preferential site for the physical stabilization of SOM, and furthermore, suggest that it may serve as a useful diagnostic fraction for evaluating management impacts on SOM in tropical pasture systems. Similar to trends observed for C and N, total P content was 25% higher in the microaggregates within large macroaggregates of productive vs. degraded pasture soils. This correspondence between C and total P contents in large macroaggregate fractions, along with elevated levels of organic P in productive pastures, suggests that this P is likely in an organic form and that there is a close link between soil structure, SOM dynamics and the maintenance of organic P in these soils. Given the potential relevance of organic P for efficient P cycling in these soils, our findings offer critical new insight for the management of SOM and aggregate-associated P pools in tropical pasture systems.     

Effects of tree identity dominate over tree diversity on the soil microbial community structure

This study investigated the possible effects of tree species diversity and identity on the soil microbial community in a species-rich temperate broad-leaved forest. For the first time, we separated the effects of tree identity and tree species diversity on the link between above and belowground communities in a near-natural forest. We established 100 tree clusters consisting of each three tree individuals represented by beech (Fagus sylvatica L.), ash (Fraxinus excelsior L.), hornbeam (Carpinus betulus L.), maple (Acer pseudoplatanus L.), or lime (Tilia spec.) at two different sites in the Hainich National Park (Thuringia, Germany). The tree clusters included one, two or three species forming a diversity gradient. We investigated the microbial community structure, using phospholipid fatty acid (PLFA) profiles, in mineral soil samples (0–10 cm) collected in the centre of each cluster.The lowest total PLFA amounts were found in the pure beech clusters (79.0 ± 23.5 nmol g⁻¹ soil dw), the highest PLFA amounts existed in the pure ash clusters (287.3 ± 211.3 nmol g⁻¹ soil dw). Using principle components analyses (PCA) and redundancy analyses (RDA), we found only for the variables ‘relative proportion of beech trees’ and ‘living lime fine root tips associated with ectomycorrhiza’ a significant effect on the PLFA composition. The microbial community structure was mainly determined by abiotic environmental parameters such as soil pH or clay content. The different species richness levels in the clusters did not significantly differ in their total PLFA amounts and their PLFA composition. We observed a tendency that the PLFA profiles of the microbial communities in more tree species-rich clusters were less influenced by individual PLFAs (more homogenous) than those from species-poor clusters.We concluded that tree species identity and site conditions were more important factors determining the soil microbial community structure than tree species diversity per se.     

Responses of enzymatic activities within soil aggregates to 9-year nitrogen and water addition in a semi-arid grassland

Soil microorganisms secrete enzymes used to metabolize carbon (C), nitrogen (N), and phosphorus (P) from the organic materials typically found in soil. Because of the connection with the active microbial biomass, soil enzyme activities can be used to investigate microbial nutrient cycling including the microbial response to environmental changes, transformation rates and to address the location of the most active biomass. In a 9-year field study on global change scenarios related to increasing N inputs (ambient to 15 g N m⁻² yr⁻¹) and precipitation (ambient to 180 mm yr⁻¹), we tested the activities of soil β-glucosidase (BG), N-acetyl-glucosaminidase (NAG) and acid phosphomonoesterase (PME) for three soil aggregate classes: large macroaggregates (>2000 μm), small macroaggregates (250–2000 μm) and microaggregates (<250 μm). Results showed higher BG and PME activities in micro-vs. small macroaggregates whereas the highest NAG activity was found in the large macroaggregates. This distribution of enzyme activity suggests a higher contribution of fast-growing microorganisms in the micro-compared with the macroaggregates size fractions. The responses of BG and PME were different from NAG activity under N addition, as BG and PME decreased as much as 47.1% and 36.3%, respectively, while the NAG increased by as much as 80.8%, which could imply better adaption of fungi than bacteria to lower soil pH conditions developed under increased N. Significant increases in BG and PME activities by as much as 103.4 and 75.4%, respectively, were found under water addition. Lower ratio of BG:NAG and higher NAG:PME underlined enhanced microbial N limitation relative to both C and P, suggesting the repression of microbial activity and the accompanied decline in their ability to compete for N with plants and/or the accelerated proliferation of soil fungi under elevated N inputs. We conclude that changes in microbial activities under increased N input and greater water availability in arid- and semi-arid grassland ecosystems where NPP is co-limited by N and water may result in substantial redistribution of microbial activity in different-sized soil particles. This shift will influence the stability of SOM in the soil aggregates and the nutrient limitation of soil biota.     

Microbial biogeography at the soil pore scale

Microbial communities exist and are active in a complex 3-D physical framework which can cause a variety of micro-environments to develop that are more or less suitable for microbial growth, activity and survival. If there is a significant microbial biogeography at the pore scale in soil, then the relationship between microbial diversity and ecosystem function is likely to be affected by micro-environmental variations at the pore scale. In this laboratory study we show that there is a significant pore-scale microbial biogeography by labelling microbial communities in different pore size classes of undisturbed soil cores with ¹³C-labelled fructose (a soluble, labile substrate). This was achieved by adding the substrate solution to the samples at different matric potentials (−100 kPa, −3.15 kPa and −1 kPa; placing the substrate in pores with maximum diameter of 0.97, 9.7 and 97 μm, respectively) and incubating the samples for two weeks. The mineralisation of soil organic carbon and fructose was measured as CO₂ and ¹³C-CO₂, respectively, in the jar headspace throughout the incubation. At the end of incubation we analysed the total microbial community structure using PLFA. The structure of microbial communities in different pore size classes was measured by PLFA stable isotope probing. Total PLFA profiles suggested that there was little effect of the incubation conditions on microbial community structure. However, labelled PLFA profiles showed that microbial community structure differed significantly among pore size classes, the differences being due primarily to variations in the abundance of mono-unsaturated lipids (Gram-biomarkers) and of the fungal biomarker (C18:2(9,12)). This is the first evidence for a significant microbial biogeography at the pore scale in undisturbed soil cores.     

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.     

Microbial community structure varies in different soil zones of a potato field

Analyses of phosholipid fatty acids (PLFA) and phospholipid etherlipids (PLEL) revealed differences in size and structure of microbial communities in the three soil zones of a potato field: ridge (RS), uncompacted interrow (IS), and tractor‐compacted interrow soil (CS). The quantity of phosholipid biomarker concentrations (= microbial biomass) showed large differences among different zones, when lipid contents were related to fresh soil volume instead of soil dry matter. Compaction of interrow soil caused an increase in bacterial and eukaryotic biomass, expressed as total PLFA concentration, as well as an increase in total archaeal biomass, expressed as total PLEL concentration and caused a decrease in the fungi‐to‐bacteria ratio. Due to the higher waterfilled pore space (an indirect measure for reduced O₂ availability) in CS, a more pronounced anaerobic microbial community was estimated than in IS, which serves as an explanation for the elevated N₂O fluxes in this soil zone. Apart from the effect of O₂ availability, microbial communities, especially populations of aerobic bacteria, ascinomycetes, fungi, algae, protozoa, and aerobic archaea responded to organic matter composition in the individual zones. Only in RS PLEL derived cyclic isoprenoids were found, which presumably indicate root‐colonizing archaea. Following principal component analyses of specific biomarker profiles, the assumed substrate effect had the strongest influence on the differences in microbial community structure between the three soil zones.