土壤微生物群落结构与多样性对农田集约化管理程度降低的响应

Using a scheme of agricultural fields with progressively less intensive management （deintensification）, different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage （CT） or no-tillage （NT）, an organic farming system （OR）, an integrated cropping system with animals （IN）, a successional field （SU）, and a plantation woodlot （WO）. Microbial phospholipid fatty acid （PLFA） profiles and substrate utilization patterns （BIOLOG ECO plates） were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N （P 〈 0.05） were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system （P 〈 0.05）. There were also significant decreases （P 〈 0.05） along with agricultural deintensification for contributions of total bacterial and gram positive （G＋） bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.     

Microbial communities in forest floors under four tree species in coastal British Columbia

We compare forest floor microbial communities in pure plots of four tree species (Thuja plicata, Tsuga heterophylla, Pseudotsuga menziesii, and Picea sitchensis) replicated at three sites on Vancouver Island. Microbial communities were characterised through community level physiological profiles (CLPP), and profiling of phospholipid fatty acids (PLFA).Microbial communities from cedar forest floors had higher potential C utilisation than the other species. The F layer of the forest floor under cedar contained significantly higher bacterial biomass (PLFA) than the F layer under the other three tree species. There were differences in microbial communities among the three sites: Upper Klanawa had the highest bacterial biomass and potential C utilisation; this site also had the highest N availability in the forest floors. Forest floor H layers under hemlock and Douglas-fir contained greater biomass of Gram positive, Gram negative bacteria and actinomycetes than F layers based on PLFA, and H layers under spruce contained greater biomass of Gram negative bacteria than F layers. There were no significant differences in bacterial biomass between forest floor layers under cedar. Fungal biomass displayed opposite trends to bacteria and actinomycetes, being lowest in cedar forest floors, and highest in the F layer and at the site with lowest N availability. There were also differences in community composition among species and sites, with cedar forest floors having a much lower fungal:bacterial ratio than spruce, hemlock and Douglas-fir. The least fertile Sarita Lake site had a much greater fungal:bacterial ratio than the more fertile San Juan and Upper Klanawa sites. Forest floor layer had the greatest effect on microbial community structure and potential function, followed by site, and tree species. The similarity in trends among measures of N availability and microbial communities is further evidence that these techniques provide information on microbial communities that is relevant to N cycling processes in the forest floor.     

Temporal and seasonal change in microbial community structure of an undisturbed,disturbed, and carbon-amended pasture soil

Disturbance and change to C inputs can alter microbial community structure and impact ecosystem function. Particularly in temperate regions, seasonal change also has an effect on microbial communities both directly through climate and indirectly through plant function. The temporal change in microbial communities of an undisturbed pasture, disturbed pasture (similar to a single tillage event) and pasture soil amended with two forms of particulate carbon were monitored over eight consecutive seasons after grass was reestablished. The soil microbial community was assessed by a DNA fingerprinting technique (terminal restriction fragment length polymorphism, TRFLP) of bacterial, fungal and archaeal communities, and also from phospholipid fatty acid (PLFA) analysis. The single disturbance had a significant effect on fungal microbial community structure (by TRFLP) and significantly decreased the fungal:bacterial ratio. Though the change was relatively small, it persisted throughout the sampling period. Nitrate was also higher on the disturbed treatment providing evidence for the theory that changes to fungal:bacterial ratios can alter nutrient cycling and retention. Fungal communities were the most altered by the C amendments, and while bacteria were also affected by the C amendments, seasonal change was a greater cause of variation. Correlation to soil and climatic variables explained more of the total variability for PLFA (78% for all treatments) than bacterial (50%), fungal (35%) and archaeal (14%) restriction fragments. Most climate and soil variables explained significant variation for seasonal patterns in the multivariate community structures but measurements of soil moisture were important for all communities while pH was relatively more important for bacteria, temperature for fungi, and soil C:N ratio for archaea. Autumn was particularly distinct from other seasons for bacteria (less so for the fungal community) and although there was seasonal change in pH suggesting pasture management was a factor, the significant correlation of other soil characteristics suggests that plant physiological changes (most probably root exudates) also played a significant role. The large change in the saprotrophic fungal community due to the particulate C addition but minor seasonal change would tend to suggest that the fungal community may be more responsive to changes in litter inputs rather than root exudates while the reverse is true for bacteria.     

BIOLOG在土壤微生物群落功能多样性研究中的应用

微生物功能多样性信息对于明确不同环境中微生物群落的作用具有重要意义 ,而微生物群落的定量描述一直是微生物学家面临的最艰巨的任务之一。目前 ,以群落水平碳源利用类型为基础的BIOLOG氧化还原技术为研究土壤微生物群落功能多样性提供了一种简单、快速的方法 ,并得以广泛应用。但它仍然是一种以培养为基础的方法 ,显示的代谢多样性类型也不一定反映整个土壤微生物群落的功能多样性。因此 ,这种方法优点明显 ,缺陷也存在 ,并且在应用过程中还有很多关键的操作要点与技巧。本文综述了BIOLOG研究土壤微生物群落功能多样性的原理、BIOLOG研究土壤微生物群落功能多样性的方法与技巧、应用过程中容易产生的问题及可能克服的办法 ,同时还提出了值得进一步研究的问题。旨在促进对BIOLOG测定土壤微生物群落功能多样性的了解 ,为正确运用这种方法开展土壤微生物群落功能多样性研究提供科学依据和理论指导。     

温室菜园土壤氮矿化和微生物群落对水分的响应

Soil drying and wetting impose significant influences on soil nitrogen (N) dynamics and microbial communities. However, effects of drying-wetting cycles, while common in vegetable soils, especially under greenhouse conditions, have not been well studied. In this study, two greenhouse vegetable soils, which were collected from Xinji (XJ) and Hangzhou (HZ), China, were maintained at 30% and 75% water-holding capacity (WHC), or five cycles of 75% WHC followed by a 7-day dry-down to 30% WHC (DW). Soil inorganic N content increased during incubation. Net N mineralization (Nmin), microbial activity, and microbial biomass were significantly higher in the DW treatment than in the 30% and 75% WHC treatments. The higher water content (75% WHC) treatment had higher Nmin, microbial activity, and microbial biomass than the lower water content treatment (30% WHC). Multivariate analyses of community-level physiological profile (CLPP) and phospholipid fatty acid (PLFA) data indicated that soil moisture regime had a significant effect on soil microbial community substrate utilization pattern and microbial community composition. The significant positive correlation between Nmin and microbial substrate utilization or PLFAs suggested that soil N mineralization had a close relationship with microbial community.     

Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques

We have compared the total microbial biomass and the fungal/bacterial ratio estimated using substrate-induced respiration (SIR) in combination with the selective inhibition technique and using the phospholipid fatty acid (PLFA) technique in a pH gradient (3.0-7.2) consisting of 53 mature broad-leaved forest soils. A fungal/bacterial biomass index using the PLFA technique was calculated using the PLFA 18:2ω6,9 as an indicator of fungal biomass and the sum of 13 bacterial specific PLFAs as indicator of the bacterial biomass. Good linear correlation (p<0.001) was found between the total microbial biomass estimated with SIR and total PLFAs (totPLFA), indicating that 1 mg biomass-C was equivalent to 130 nmol totPLFA. Both biomass estimates were positively correlated to soil pH. The fungal/bacterial ratio measured using the selective inhibition technique decreased significantly with increasing pH from about 9 at pH 3 to approximately 2 at pH 7, while the fungal/bacterial biomass index using PLFA measurements tended to increase slightly with increasing soil pH. Good correlation between the soil content of ergosterol and of the PLFA 18:2ω6,9 indicated that the lack of congruency between the two methods in estimating fungal/bacterial ratios was not due to PLFA 18:2ω6,9-related non-fungal structures to any significant degree. Several PLFAs were strongly correlated to soil pH (R² values >0.8); for example the PLFAs 16:1ω5 and 16:1ω7c increased with increasing soil pH, while i16:0 and cy19:0 decreased. A principal component analysis of the total PLFA pattern gave a first component that was strongly correlated to soil pH (R²=0.85, p<0.001) indicating that the microbial community composition in these beech/beech-oak forest soils was to a large extent determined by soil pH.     

Changes in microbial community structure following herbicide (glyphosate) additions to forest soils

Glyphosate applied at the recommended field rate to a clay loam and a sandy loam forest soil resulted in few changes in microbial community structure. Total and culturable bacteria, fungal hyphal length, bacterial:fungal biomass, carbon utilization profiles (BIOLOG), and bacterial and fungal phospholipid fatty acids (PLFA) were unaffected 1, 3, 7, or 30 days after application of a commercial formulation (Roundup^®). In contrast, a high concentration of glyphosate (100× field rate) simulating an undiluted chemical spill substantially altered the bacterial community in both soils. Increases in total bacteria, culturable bacteria, and bacterial:fungal biomass were rapid following application. Culturable bacteria increased from about 1% of the total population in untreated soil to as much as 25% at the high concentration by day 7, indicating enrichment of generalist bacteria. Community composition in both soils shifted from fungal dominance to an equal ratio of bacteria to fungi. Functional diversity of culturable bacteria, estimated by C substrate utilization, also increased at the high glyphosate concentration, particularly in the clay loam soil. Unlike the other bacterial indices, only minor changes in bacterial PLFA resulted after the third day following the 100× field rate application. Apparently the herbicide resulted in an across-the-board stimulation of bacteria that was not reflected by the finer-scale PLFA community structure. Changes in fungal properties (hyphae, propagules, PLFA biomarkers) were few and transient. We conclude that the commercial formulation of glyphosate has a benign affect on community structure when applied at the recommended field rate, and produces a non-specific, short-term stimulation of bacteria at a high concentration.     

Response of soil microbial community and diversity to increasing water salinity and nitrogen fertilization rate in an arid soil

The scarcity of fresh water has forced farmers to use saline water (SW) for irrigation. It is important to understand the response of the soil microbial community and diversity to saline irrigation water. The objective of this study was to determine the effects of irrigation water salinity and nitrogen fertilization rates on soil physicochemical properties, microbial activity, microbial biomass, and microbial functional diversity. The field experiment consisted of a factorial design with three levels of irrigation water salinity (electrical conductivities (ECs) of 0.35, 4.61 or 8.04?dS?m^?1) and two nitrogen rates (0 and 360?kg?N?ha^?1). The results showed that the 4.61 and 8.04?dS?m^?1 treatments both reduced soil microbial biomass C (MBC), microbial biomass N (MBN), basal respiration, total phospholipid fatty acid (PLFA), bacterial PLFA, fungal PLFA, and fungal:bacterial ratios. In contrast, the SW treatments increased the MBC:MBN ratio. Nitrogen fertilization increased soil MBC, MBN, basal respiration, total PLFA, bacterial PLFA, and gram-negative bacterial PLFA. In contrast, N fertilization decreased gram-positive bacterial PLFA, fungal PLFA, and fungal:bacterial ratios. Average well color development, Richness, and Shannon's Index were always lowest in the 8.04?dS?m^?1 treatment. Carbon utilization patterns in the 8.04?dS?m^?1 treatment were different from those in the 0.35?dS?m^?1 treatment. In conclusion, five years of irrigation with brackish or SW reduced the soil microbial biomass, activity, and functional diversity, which may cause the deterioration of soil quality. Thus, the high-salinity water (EC?>?4.61?dS?m^?1) is not appropriate as a single irrigation water resource. Proper N fertilizer input may overcome some of the negative effects of salinity on soil microbial.     

Shifting microbial community structure across a marine terrace grassland chronosequence, Santa Cruz, California

Changes in the biomass and structure of soil microbial communities have the potential to impact ecosystems via interactions with plants and weathering minerals. Previous studies of forested long-term (1000s - 100,000s of years) chronosequences suggest that surface microbial communities change with soil age. However, significant gaps remain in our understanding of long-term soil microbial community dynamics, especially for non-forested ecosystems and in subsurface soil horizons. We investigated soil chemistry, aboveground plant productivity, and soil microbial communities across a grassland chronosequence (65,000-226,000 yrs old) located near Santa Cruz, CA. Aboveground net primary productivity (ANPP) initially increased to a maximum and then decreased for the older soils. We used polar lipid fatty acids (PLFA) to investigate microbial communities including both surface (<0.1 m) and subsurface (≥0.2 m) soil horizons. PLFAs characteristic of Gram-positive bacteria and actinobacteria increased as a fraction of the microbial community with depth while the fungal fraction decreased relative to the surface. Differences among microbial communities from each chronosequence soil were found primarily in the subsurface where older subsurface soils had smaller microbial community biomass, a higher proportion of fungi, and a different community structure than the younger subsurface soil. Subsurface microbial community shifts in biomass and community structure correlated with, and were likely driven by, decreasing soil P availability and Ca concentrations, respectively. Trends in soil chemistry as a function of soil age led to the separation of the biological (≤1 m depth) and geochemical (>1 m) cycles in the old, slowly eroding landscape we investigated, indicating that this separation, commonly observed in tropical and subtropical ecosystems, can also occur in temperate climates. This study is the first to investigate subsurface microbial communities in a long-term chronosequence. Our results highlight connections between soil chemistry and both the aboveground and belowground parts of an ecosystem.     

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.     

Soil Microbial Community Diversity and Its Relationships with Geochemical Elements under different Farmlands in Shouguang,China

The aims of this study were to investigate soil microbial community characteristics and their interrelationships with soil geochemistry under different farmlands in Shouguang, China. The traditional dilution plate counts, BIOLOG system, and fatty acid methyl ester (FAME) analyses were used to assess microbial populations, substrate utilization, and fatty acid profiles. The number of aerobic heterotrophic bacteria varied significantly among untilled land, maize, and mungbean fields. The amounts of actinomycetes, fungal fatty acids, and Gram-positive/Gram-negative bacteria ratios varied greatly among celery, tomato, and aubergine fields. In the tomato field, the soil microbial community characteristics were significantly different from other fields. Principal component analysis of BIOLOG and FAME data revealed differences in the catabolic capability and fatty acid profiles of soil microbial communities among different farmlands. Spearman correlation analyses showed that in these sand clay soils of Shouguang, microbial communities in different farmlands were closely correlated with soil geochemical elements, moisture, and organic matter.     

Multivariate approach to characterizing soil microbial communities in pristine and agricultural sites in Northwest Argentina

Land use effects on microbial communities may have profound impacts on agricultural productivity and ecosystem sustainability as they are critical in soil quality and health. The main aim of this study was to characterize the microbial communities of pristine and agricultural soils in the central Yungas region in Northwest Argentina. As a first step in the development of biological indicators of soil quality in this region, a comprehensive approach involving a structural and functional evaluation of microbial communities was used to detect changes in soil as consequence of land use. The sites selected included two pristine montane forest sites (MF1 and MF2), two plots under sugarcane monoculture for 40 and 100 years (SC40 and SC100), one plot under 20 years of soybean monoculture (SB20), a recently deforested and soybean cropped site (RC), and two reference sites of native forest adjacent to the sugarcane and soybean plots (PF1 and PF2). We used three microbial community profiling methods: denaturing gradient gel electrophoresis (DGGE) analysis of PCR amplified 16S rRNA genes, community-level physiological profiling (CLPP) using a BD oxygen biosensor system (BDOBS-CLPP) and phospholipid fatty acid (PLFA) analysis. Deforestation and agriculture caused expected increases in pH and decreases in organic carbon and microbial biomass. Additionally, shifts in the microbial community structure and physiology were detected with disturbance, including reduced diversity based on PLFA data. The higher respiratory response to several carbon substrates observed in agricultural soils suggested the presence of microbial communities with lower growth yield efficiency that could further reduce carbon storage in these soils.Using an integrated multivariate analysis of all data measured in this study we propose a minimum data set of variables (organic carbon, pH, sucrose and valeric acid utilizations, a17:0 and a15:0 PLFA biomarkers and the value of impact on microbial diversity) to be used for future studies of soil quality in Northwest Argentina.     

Responses of soil microbial biomass and community composition to biological soil crusts in the revegetated areas of the Tengger Desert

As a key component of desert ecosystems, biological soil crusts (BSCs) play an important role in dune fixation and maintaining soil biota. Soil microbial properties associated with the colonization and development of BSCs may indicate soil quality changes, particularly following dune stabilization. However, very little is known about the influence of BSCs on soil microbes in sand dunes. We examined the influence of BSCs on soil microbial biomass and community composition in revegetated areas of the Tengger Desert. BSCs increased soil microbial biomass (biomass C and N), microbial phospholipid fatty acid (PLFA) concentrations and the ratio of fungal to bacterial PLFAs. The effects varied with crust type and crust age. Moss crusts had higher microbial biomass and microbial PLFA concentrations than cyanobacteria-lichen crusts. Crust age was positively correlated with microbial biomass C and N, microbial PLFA concentrations, bacterial PLFA concentrations, fungal PLFA concentrations and the ratio of fungal to bacterial PLFAs. BSCs significantly affected microbial biomass C and N in the 0–20 cm soil layers, showing a significant negative correlation with soil depth. The study demonstrated that the colonization and development of BSCs was beneficial for soil microbial properties and soil quality in the revegetated areas. This can be attributed to BSCs increasing topsoil thickness after dunes have been stabilized, creating suitable habitats and providing an essential food source for soil microbes.     

Impact of coloniser plant species on the development of decomposer microbial communities following deglaciation

The effects of coloniser plant species on microbial community growth and composition were investigated on recently deglaciated terrain at Glacier Bay, south-east Alaska. Analysis of microbial communities using phospholipids fatty acid analysis (PLFA) revealed that Alnus and Rhacomitrium had the greatest impact on microbial growth, increasing total PLFA by some 6-7 fold relative to bare soil, whereas Equisetum led to a 5.5 fold increase in total PLFA relative to bare soil. These coloniser species also had significant effects on the composition of their associated microbial communities. Rhacomitrium, Alnus, and Equisetum increased bacterial PLFA, a measure of bacterial biomass, relative to bare soil. Rhacomitrium and Alnus also dramatically increased the concentration of the fungal fatty 18:2ω6 in soil relative to bare soil, by 12-fold and 8-fold, respectively. The net effect of the above changes was a significant increase in the ratio of fungal: bacterial fatty acids in soil associated with Alnus and Rhacomitrium, but not Equisetum. Possible reasons for these effects of particular plants on microbial communities are discussed, as is their significance in relation to the development of microbial communities in relatively sterile, recently deglaciated ground.     

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.     

Structure and function of microbial communities in the rhizosphere of Scots pine after tree-felling

We evaluated changes occurring in the rhizosphere microbial communities of Scots pine (Pinus sylvestris L.) due to tree-felling and decrease of the photosynthetic C flow into the soil under field conditions over one growing season. Samples were taken from tree rhizospheres, freshly felled stump rhizospheres and bulk soil. We used culture dependent (CFU counts, community level physiological profiles, CLPPs) and independent methods (fluorogenic MUF-substrates, PLFA pattern and PCR-DGGE) to monitor the microbial communities in soil samples. The numbers of cultivable bacteria and amounts of phosphatase activity in the rhizosphere of trees were significantly higher compared with those in the bulk soil. The organic C consuming community measured by CLPP was stimulated directly after the tree-felling in stump rhizospheres; utilization of the disintegration components of cellulose, hemicellulose and chitin increased. Furthermore, bacterial and fungal biomass as well as chitin decomposers (CFU) increased in the stump rhizosphere. After 11 weeks of tree-felling the stump rhizosphere soluble PO₄-P and NH₄-N as well as amounts of total C and N began to resemble the concentrations measured in the bulk soil. However, the stump rhizosphere community structure detected by PLFA and PCR-DGGE still resembled that of the tree rhizosphere.     

No-till soil management increases microbial biomass and alters community profiles in soil aggregates

Aggregation is important for soil functioning, providing physical protection of organic matter and microbial inhabitants. Tillage disrupts aggregates, increases wind and water erosion of soils and exposes formerly protected organic matter to decomposition and losses. Microbial biomass and community dynamics in dry-sieved aggregate-size classes from long-term no-till (NT) and conventionally tilled (CT) soils were examined using phospholipid fatty acid analysis (PLFA). Bacterial, fungal, and total biomass were up to 32% greater in NT compared to CT aggregates. Aggregate size also affected microbial biomass, which was highest in the 1–2 mm size class. Arbuscular mycorrhizal fungi (AMF) were particularly affected by tillage disturbance with increases of 40–60% among aggregate-size classes in NT vs. CT, but glomalin related soil protein concentration was not different between tillage treatments or among aggregate-size classes. Bacterial stress biomarkers were higher in CT than NT aggregates but were not significantly correlated with total C, total N or C:N ratio, indicating that the physiological status of bacteria within aggregates was not simply governed by the quantity of available resources. Ordination analysis of PLFA profiles demonstrated a shift in microbial community structure between NT and CT aggregates, correlated with AMF abundance in NT aggregates and increased bacterial stress biomarkers in CT aggregates. Our results demonstrated greater microbial biomass and altered microbial community structure in NT vs. CT aggregates. This work demonstrates that tillage management influences microbial community structure within aggregates and may provide a potential explanation for differences in process rates observed in NT vs. CT soils. Further research into the processes that govern community structure in aggregates from NT and tilled soils is needed to better understand how the interaction of microorganisms with their physical environment affects nutrient turnover and availability.     

Soil microbial community composition as affected by restoration practices in California grassland

Agricultural practices have strong impacts on soil microbes including both the indices related to biomass and activity as well as those related to community composition. In a grassland restoration project in California, where native perennial bunchgrasses were introduced into non-native annual grassland after a period of intensive tillage, weeding, and herbicide use to reduce the annual seed bank, microbial community composition was investigated. Three treatments were compared: annual grassland, bare soil fallow, and restored perennial grassland. Soil profiles down to 80 cm in depth were investigated in four separate layers (0-15, 15-30, 30-60, and 60-80 cm) using both phospholipid ester-linked fatty acid (PLFAs) and ergosterol as biomarkers in addition to microbial biomass C by fumigation extraction. PLFA fingerprinting showed much stronger differences between the tilled bare fallow treatment vs. grasslands, compared to fewer differences between restored perennial grassland and annual grassland. The presence or absence of plants over several years clearly distinguished microbial communities. Microbial communities in lower soil layers were little affected by management practices. Regardless of treatment, soil depth caused a strong gradient of changing habitat conditions, which was reflected in Canonical Correspondence Analysis of PLFAs. Fungal organisms were associated with the presence of plants and/or litter since the total amount and the relative proportion of fungal markers were reduced in the tilled bare fallow and in lower layers of the grassland treatments. Total PLFA and soil microbial biomass were highly correlated, and fungal PLFA biomarkers showed strong correlations to ergosterol content. In conclusion, microbial communities are resilient to the grassland restoration process, but do not reflect the change in plant species composition that occurred after planting native bunchgrasses.     

Soil morphology,depth and grapevine root frequency influence microbial communities in a Pinot noir vineyard

The composition of microbial communities responds to soil resource availability, and has been shown to vary with increasing depth in the soil profile. Soil microorganisms partly rely on root-derived carbon (C) for growth and activity. Roots in woody perennial systems like vineyards have a deeper vertical distribution than grasslands and annual agriculture. Thus, we hypothesized that vineyard soil microbial communities along a vertical soil profile would differ from those observed in grassland and annual agricultural systems. In a Pinot noir vineyard, soil pits were excavated to ca. 1.6–2.5 m, and microbial community composition in ‘bulk’ (i.e., no roots) and ‘root’ (i.e., roots present) soil was described by phospholipid ester-linked fatty acids (PLFA). Utilization of soil taxonomy aided in understanding relationships between soil microbial communities, soil resources and other physical and chemical characteristics. Soil microbial communities in the Ap horizon were similar to each other, but greater variation in microbial communities was observed among the lower horizons. Soil resources (i.e., total PLFA, or labile C, soil C and nitrogen, and exchangeable potassium) were enriched in the surface horizons and significantly explained the distribution of soil microbial communities with depth. Soil chemical properties represented the secondary gradient explaining the differentiation between microbial communities in the B-horizons from the C-horizons. Relative abundance of Gram-positive bacteria and actinomycetes did not vary with depth, but were enriched in ‘root’ vs. ‘bulk’ soils. Fungal biomarkers increased with increasing depth in ‘root’ soils, differing from previous studies in grasslands and annual agricultural systems. This was dependent on the deep distribution of roots in the vineyard soil profile, suggesting that the distinct pattern in PLFA biomarkers may have been strongly affected by C derived from the grapevine roots. Gram-negative bacteria did not increase in concert with fungal abundance, suggesting that acidic pHs in lower soil horizons may have discouraged their growth. These results emphasize the importance of considering soil morphology and associated soil characteristics when investigating effects of depth and roots on soil microorganisms, and suggest that vineyard management practices and deep grapevine root distribution combine to cultivate a unique microbial community in these soil profiles.     

Changes in microbial communities in an apple orchard and its adjacent bush soil in response to season,land-use,and violet root rot infestation

Soil microbial communities in an apple orchard and its adjacent boundary bush with or without infestation by violet root rot were investigated for 2 years. Effects of season (spring, summer, and fall), land-use (apple orchard and boundary bush), and violet root rot (infested and healthy) on soil microbial populations, microbial activity, and microbial community structures were determined using physiological, cytochemical, and molecular (PCR-DGGE) approaches. Seasonal fluctuations were significant (P<0.05) in viable bacteria and fungal populations, bacterial FAME, fluorescein diacetate (FDA) hydrolysis, and diversity (H′) and evenness (J′) of community-level physiological profile (CLPP) in both years. However, seasonal differences of soil microbial guilds that utilize carbon substrate groups observed in the first year were not reproduced in the second year. The land-use factor differentiated the apple orchard from the boundary bush where viable bacterial population, bacterial FAME and FDA hydrolysis were significantly greater in both years. Infestation status of violet root rot, on the other hand, significantly increased bacterial FAME and FDA hydrolysis in both years. In addition, neither the land-use nor the disease infestation factor significantly influenced the utilization patterns of individual substrate guilds for the 2 years. In both years, saturated fatty acids were significantly more abundant in the orchard than in the bush soil, and monosaturated fatty acids vice versa. Principal component analyses for CLPP, FAME, and denaturing gradient gel electrophoresis (DGGE) consistently exhibited that, although the violet root rot influenced the soil microbial community structures both in the apple orchard and the boundary bush, overall magnitude of the difference in communities between the violet root rot infested and non-infested sites in the bush were greater than in the orchard, irrespective of the season. These results suggested that the seasonal and the land-use factors affected soil microbial community both quantitatively and qualitatively, whereas the impact of the violet root rot on the soil microbial community was mainly qualitative and more pronounced in the adjacent bush than in the orchard.