Temperature and substrate controls on microbial phospholipid fatty acid composition during incubation of grassland soils contrasting in organic matter quality

Soil incubations are often used to investigate soil organic matter (SOM) decomposition and its response to increased temperature, but changes in the activity and community composition of the decomposers have rarely been included. As part of an integrated investigation into the responses of SOM components in laboratory incubations at elevated temperatures, fungal and bacterial phospholipid fatty acids (PLFAs) were measured in two grassland soils contrasting in SOM quality (i.e. SOM composition), and changes in the microbial biomass and community composition were monitored. Whilst easily-degradable SOM and necromass released from soil preparation may have fuelled microbial activity at the start of the incubation, the overall activity and biomass of soil microorganisms were relatively constant during the subsequent one-year soil incubation, as indicated by the abundance of soil PLFAs, microbial respiration rate (r), and metabolic quotient (qCO₂). PLFAs relating to fungi and Gram-negative bacteria declined relative to Gram-positive bacteria in soils incubated at higher temperatures, presumably due to their vulnerability to disturbance and substrate constraints induced by faster exhaustion of available nutrient sources at higher temperatures. A linear correlation was found between incubation temperatures and the microbial stress ratios of cyclopropane PLFA-to-monoenoic precursor (cy17:0/16:1ω7c and cy19:0/18:1ω7c) and monoenoic-to-saturated PLFAs (mono/sat), as a combined effect of temperature and temperature-induced substrate constraints. The microbial PLFA decay patterns and ratios suggest that SOM quality intimately controls microbial responses to global warming.     

Organic matter dynamics in a temperate forest as influenced by soil frost

In the future, climate models predict an increase in global surface temperature and during winter a changing of precipitation from less snowfall to more raining. Without protective snow cover, freezing can be more intensive and can enter noticeably deeper into the soil with effects on C cycling and soil organic matter (SOM) dynamics. We removed the natural snow cover in a Norway spruce forest in the Fichtelgebirge Mts. during winter from late December 2005 until middle of February 2006 on three replicate plots. Hence, we induced soil frost to 15 cm depth (at a depth of 5 cm below surface up to –5°C) from January to April 2006, while the snow‐covered control plots never reached temperatures < 0°C. Quantity and quality of SOM was followed by total organic C and biomarker analysis. While soil frost did not influence total organic‐C and lignin concentrations, the decomposition of vanillyl monomers (Ac/Ad)_V and the microbial‐sugar concentrations decreased at the end of the frost period, these results confirm reduced SOM mineralization under frost. Soil microbial biomass was not affected by the frost event or recovered more quickly than the accumulation of microbial residues such as microbial sugars directly after the experiment. However, in the subsequent autumn, soil microbial biomass was significantly higher at the snow‐removal (SR) treatments compared to the control despite lower CO₂ respiration. In addition, the water‐stress indicator (PLFA [cy17:0 + cy19:0] / [16:1ω7c + 18:1ω7c]) increased. These results suggest that soil microbial respiration and therefore the activity was not closely related to soil microbial biomass but more strongly controlled by substrate availability and quality. The PLFA pattern indicates that fungi are more susceptible to soil frost than bacteria.     

Microbial communities, biomass, and activities in soils as affected by freeze thaw cycles

Two Finnish agricultural soils (peat soil and loamy sand) were exposed to four freeze-thaw cycles (FTC), with a temperature change from −17.3±0.4 °C to +4.1±0.4 °C. Control cores from both soils were kept at constant temperature (+6.6±2.0 °C) without FTCs. Soil N₂O and CO₂ emissions were monitored during soil thawing, and the effects of FTCs on soil microbes were studied. N₂O emissions were extremely low in peat soil, possibly due to low soil water content. Loamy sand had high N₂O emission, with the highest emission after the second FTC. Soil freeze-thaw increased anaerobic respiration in both soil types during the first 3-4 FTCs, and this increase was higher in the peat soil. The microbial community structure and biomass analysed with lipid biomarkers (phospholipid fatty acids, 3- and 2- hydroxy fatty acids) were not affected by freezing-thawing cycles, nor was soil microbial biomass carbon (MIB-C). Molecular analysis of the microbial community structure with temperature gradient gel electrophoresis (TGGE) also showed no changes due the FTCs. These results show that freezing and thawing of boreal soils does not have a strong effect on microbial biomass or community structure.     

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.     

温度和秸秆质量调节与秸秆分解相关的微生物磷脂脂肪酸（PLFA）组成

Variations in temperature and moisture play an important role in soil organic matter (SOM) decomposition. However, relationships between changes in microbial community composition induced by increasing temperature and SOM decomposition are still unclear. The present study was conducted to investigate the effects of temperature and moisture levels on soil respiration and microbial communities involved in straw decomposition and elucidate the impact of microbial communities on straw mass loss. A 120-d litterbag experiment was conducted using wheat and maize straw at three levels of soil moisture (40%, 70%, and 90% of water-holding capacity) and temperature (15, 25, and 35°C). The microbial communities were then assessed by phospholipid fatty acid (PLFA) analysis. With the exception of fungal PLFAs in maize straw at day 120, the PLFAs indicative of Gram-negative bacteria and fungi decreased with increasing temperatures. Temperature and straw C/N ratio significantly affected the microbial PLFA composition at the early stage, while soil microbial biomass carbon (C) had a stronger effect than straw C/N ratio at the later stage. Soil moisture levels exhibited no significant effect on microbial PLFA composition. Total PLFAs significantly influenced straw mass loss at the early stage of decomposition, but not at the later stage. In addition, the ratio of Gram-negative and Gram-positive bacterial PLFAs was negatively correlated with the straw mass loss. These results indicated that shifts in microbial PLFA composition induced by temperature, straw quality, and microbial C sources could lead to changes in straw decomposition.     

Abundance, production and stabilization of microbial biomass under conventional and reduced tillage

Soil tillage practices affect the soil microbial community in various ways, with possible consequences for nitrogen (N) losses, plant growth and soil organic carbon (C) sequestration. As microbes affect soil organic matter (SOM) dynamics largely through their activity, their impact may not be deduced from biomass measurements alone. Moreover, residual microbial tissue is thought to facilitate SOM stabilization, and to provide a long term integrated measure of effects on the microorganisms. In this study, we therefore compared the effect of reduced (RT) and conventional tillage (CT) on the biomass, growth rate and residues of the major microbial decomposer groups fungi and bacteria. Soil samples were collected at two depths (0-5 cm and 5-20 cm) from plots in an Irish winter wheat field that were exposed to either conventional or shallow non-inversion tillage for 7 growing seasons. Total soil fungal and bacterial biomasses were estimated using epifluorescence microscopy. To separate between biomass of saprophytic fungi and arbuscular mycorrhizae, samples were analyzed for ergosterol and phospholipid fatty acid (PLFA) biomarkers. Growth rates of saprophytic fungi were determined by [¹⁴C]acetate-in-ergosterol incorporation, whereas bacterial growth rates were determined by the incorporation of ³H-leucine in bacterial proteins. Finally, soil contents of fungal and bacterial residues were estimated by quantifying microbial derived amino sugars. Reduced tillage increased the total biomass of both bacteria and fungi in the 0-5 cm soil layer to a similar extent. Both ergosterol and PLFA analyses indicated that RT increased biomass of saprophytic fungi in the 0-5 cm soil layer. In contrast, RT increased the biomass of arbuscular mycorrhizae as well as its contribution to the total fungal biomass across the whole plough layer. Growth rates of both saprotrophic fungi and bacteria on the other hand were not affected by soil tillage, possibly indicating a decreased turnover rate of soil microbial biomass under RT. Moreover, RT did not affect the proportion of microbial residues that were derived from fungi. In summary, our results suggest that RT can promote soil C storage without increasing the role of saprophytic fungi in SOM dynamics relative to that of bacteria.     

两种施肥处理下不同有机质含量农田黑土微生物群落结构PLFA分析

土壤有机质含量和施肥是影响黑土微生物群落结构的重要因素,但是受气候影响,很难单独明确有机质含量或施肥对土壤微生物群落的影响.本研究利用黑土生产力长期定位试验,将有机质含量不同的5个黑土(SOM1.7、SOM3、SOM5、SOM6、SOM11)置于相同气候条件下,通过分析磷脂脂肪酸,系统地研究了施肥与有机质含量对农田黑土...     

Linking microbial community structure and allocation of plant-derived carbon in an organic agricultural soil using 13CO2 pulse-chase labelling combined with 13C-PLFA profiling

We conducted a ¹³CO₂ pulse-chase labelling experiment in a drained boreal organic (peat) soil cultivated with perennial crop, reed canary grass (RCG; Phalaris arundinacea) to study the flow of carbon from plants to soil microbes. Both limed and unlimed soils were studied, since liming is a common agricultural practice for acidic organic soils. Soil samples taken within three months after the labelling and three times in the following year were used for the δ¹³C analysis of microbial phospholipid fatty acids (PLFAs), root sugars and root lipids. We estimated the contribution of carbon from root exudates to microbial PLFA synthesis. The flow of carbon from plants to microbes was fast as the label allocation in PLFAs had a peak 1–3 days after labelling. The results showed that fungi were important in the incorporation of fresh, plant-derived carbon, including root sugars. None of the main microbial PLFA biomarker groups (fungi, Gram-positive bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi) was completely lacking label over the measurement period. One year after the labelling, when the labelled carbon was widely distributed into plant biomass and soil, bacterial biomarkers increased their share of the label allocation. Liming had a minor effect on the label allocation rate into PLFAs. The mixing model approach used to calculate the root exudate contribution to microbial biomass resulted in a highly conservative estimate of utilization of this important C-source (0–6.5%, with highest incorporation into fungi). In summary, the results of this study provide new information about the role of various microbial groups in the turnover of plant-derived, fresh carbon in boreal organic soil.     

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.     

Microbial community abundance and structure are determinants of soil organic matter mineralisation in the presence of labile carbon

Altered rates of native soil organic matter (SOM) mineralisation in the presence of labile C substrate (‘priming’), is increasingly recognised as central to the coupling of plant and soil-biological productivity and potentially as a key process mediating the C-balance of soils. However, the mechanisms and controls of SOM-priming are not well understood. In this study we manipulated microbial biomass size and composition (chloroform fumigation) and mineral nutrient availability to investigate controls of SOM-priming. Effects of applied substrate (¹³C-glucose) on mineralisation of native SOM were quantified by isotopic partitioning of soil respiration. In addition, the respective contributions of SOM-C and substrate-derived C to microbial biomass carbon (MBC) were quantified to account for pool-substitution effects (‘apparent priming’). Phospholipid fatty acid (PLFA) profiles of the soils were determined to establish treatment effects on microbial community structure, while the ¹³C-enrichment of PLFA biomarkers was used to establish pathways of substrate-derived C-flux through the microbial communities. The results indicated that glucose additions increased SOM-mineralisation in all treatments (positive priming). The magnitude of priming was reduced in fumigated soils, concurrent with reduced substrate-derived C-flux through putative SOM-mineralising organisms (fungi and actinomycetes). Nutrient additions reduced the magnitude of positive priming in non-fumigated soils, but did not affect the distribution of substrate-derived C in microbial communities. The results support the view that microbial community composition is a determinant of SOM-mineralisation, with evidence that utilisation of labile substrate by fungal and actinomycete (but not Gram-negative) populations promotes positive SOM-priming.     

Response of microbial community composition and activity in agricultural and grassland soils after a simulated rainfall

Rainfall in Mediterranean climates may affect soil microbial processes and communities differently in agricultural vs. grassland soils. We explored the hypothesis that land use intensification decreases the resistance of microbial community composition and activity to perturbation. Soil carbon (C) and nitrogen (N) dynamics and microbial responses to a simulated Spring rainfall were measured in grassland and agricultural ecosystems. The California ecosystems consisted of two paired sets: annual vegetable crops and annual grassland in Salinas Valley, and perennial grass agriculture and native perennial grassland in Carmel Valley. Soil types of the respective ecosystem pairs were derived from granitic parent material and had sandy loam textures. Intact cores (30 cm deep) were collected in March 1999. After equilibration, dry soil cores (approx. −1 to −2 MPa) were exposed to a simulated Spring rainfall of 2.4 cm, and then were measured at 0, 6, 24, and 120 h after rewetting. Microbial biomass C (MBC) and inorganic N did not respond to rewetting. N₂O and CO₂ efflux and respiration increased after rewetting in all soils, with larger responses in the grassland than in the agricultural soils. Phospholipid fatty acid (PLFA) profiles indicated that changes in microbial community composition after rewetting were most pronounced in intensive vegetable production, followed by the relict perennial grassland. Changes in specific PLFA markers were not consistent across all sites. There were more similarities among microbial groups associated with PLFA markers in agricultural ecosystems than grassland ecosystems. Differences in responses of microbial communities may be related to the different plant species composition of the grasslands. Agricultural intensification appeared to decrease microbial diversity, as estimated from numbers of individual PLFA identified for each ecosystem, and reduce resistance to change in microbial community composition after rewetting. In the agricultural systems, reductions in both the measures of microbial diversity and the resistance of the microbial community composition to change after a perturbation were associated with lower ecosystem function, i.e. lower microbial responses to increased moisture availability.     

Comparing PLFA and amino sugars for microbial analysis in an Upper Michigan old growth forest

Phospholipid fatty acid (PLFA) analysis and amino sugars analysis were compared with respect to their capacity to reliably indicate microbial biomass and gross community structure (e.g. fungi to bacteria ratio). We sampled three sets of soils beneath dominant canopy-tree species in an old growth forest and extracted them using both PLFA and amino sugars procedures. Amino sugars data had a lower coefficient of variation among sample replicates and therefore may be better for quantitative application compared to PLFA data. However, when considering microbial community structure, PLFA had an advantage over amino sugars due to its more straightforward interpretation. Finally, because each biomarker derives from different portions of the microbial biomass, a conversion factor between cell membrane PLFA and cell wall amino sugars may be valuable in understanding soil carbon cycling.     

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.     

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.     

陕西靖边花豹湾聚湫坝地土壤微生物群落结构 特征及其影响因子

以黄土高原天然形成的花豹湾聚湫为研究对象,系统分析了3个剖面中土壤的机械组成、有机碳(SOC)、全氮(TN)、微生物生物量碳(MBC)和微生物生物量氮(MBN),并利用磷脂脂肪酸法(PLFA)测定了土壤中细菌、真菌和放线菌的数量,重点讨论了微生物数量和群落结构与碳、氮含量及机械组成之间的相关性。结果表明:1砂粒含量沿着坝尾-坝前的方向有逐渐降低的趋势,粉砂粒和黏粒含量则有逐渐升高的趋势,在垂直方向上可划分出5个明显的沉积旋回(深度分别为0~40、50~60、70~80、100~120和240~260 cm);2聚湫坝地土壤微生物主要含有脂肪酸(15:0 iso、18:1 w9c、18:1 w7c、16:0 10-methyl),约占PLFA总量的54%,土壤微生物以细菌为主,约占65%~75%,放线菌约占15%~25%,真菌约占5%~10%;33种多样性指数的变化趋势基本一致,依次为A剖面B剖面C剖面,3个剖面的土壤微生物群落结构存在比较明显的差异,其中A剖面分化明显;4土壤微生物总量、细菌数量和真菌数量与土壤中粉粒和黏粒含量以及MBC、MBN、SOC和TN均呈显著(P0.05)或极显著(P0.01)的正相关关系;5土壤中细颗粒组分可能是影响微生物数量和群落结构的主要因子。     

Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils

In this study we used compound specific ¹³C and ¹⁴C isotopic signatures to determine the degree to which recent plant material and older soil organic matter (SOM) served as carbon substrates for microorganisms in soils. We determined the degree to which plant-derived carbon was used as a substrate by comparison of the ¹³C content of microbial phospholipid fatty acids (PLFA) from soils of two sites that had undergone a vegetation change from C3 to C4 plants in the past 20-30 years. The importance of much older SOM as a substrate was determined by comparison of the radiocarbon content of PLFA from soils of two sites that had different ¹⁴C concentrations of SOM.The ¹³C shift in PLFA from the two sites that had experienced different vegetation history indicated that 40-90% of the PLFA carbon had been fixed since the vegetation change took place. Thus PLFA were more enriched in ¹³C from the new C4 vegetation than it was observed for bulk SOM indicating recent plant material as preferentially used substrate for soil microorganisms. The largest ¹³C shift of PLFA was observed in the soil that had high ¹⁴C concentrations of bulk SOM. These results reinforce that organic carbon in this soil for the most part cycles rapidly. The degree to which SOM is incorporated into microbial PLFA was determined by the difference in ¹⁴C concentration of PLFA derived from two soils one with high ¹⁴C concentrations of bulk SOM and one with low. These results showed that 0-40% of SOM carbon is used as substrate for soil microorganisms. Furthermore a different substrate usage was identified for different microorganisms. Gram-negative bacteria were found to prefer recent plant material as microbial carbon source while Gram-positive bacteria use substantial amounts of SOM carbon. This was indicated by ¹³C as well as ¹⁴C signatures of their PLFA. Our results find evidence to support ‘priming’ in that PLFA indicative of Gram-negative bacteria associated with roots contain both plant- and SOM-derived C. Most interestingly, we find PLFA indicative of archeobacteria (methanothrophs) that may indicate the use of other carbon sources than plant material and SOM to a substantial amount suggesting that inert or slow carbon pools are not essential to explain carbon dynamics in soil.     

Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities

Phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME), both lipid-based approaches used to characterize microbial communities, were compared with respect to their reliable detection limits, extraction precision, and ability to differentiate agricultural soils. Two sets of soil samples, representing seven crop types from California's Central Valley, were extracted using PLFA and TSFAME procedures. PLFA analysis required 10 times more soil than TSFAME analysis to obtain a reliable microbial community fingerprint and total fatty acid content measurement. Although less soil initially was extracted with TSFAME, total fatty acid (FA) content g⁻¹ soil (DW) was more than 7-fold higher in TSFAME- versus PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than PLFA analysis, with the coefficient of variation between replicates being as much as 4-fold higher with TSFAME extraction. There were significant differences between PLFA- and TSFAME-extracted samples when biomarker pool sizes (mol% values) for bacteria, actinomycetes, and fungi were compared. Correspondence analysis (CA) of PLFA and TSFAME samples indicated that extraction method had the greatest influence on sample FA composition. Soil type also influenced FA composition, with samples grouping by soil type with both extraction methods. However, separate CAs of PLFA- and TSFAME extracted samples depicted strong differences in underlying sample groupings. Recommendations for the selection of extraction method are presented and discussed.     

Seven years of enhanced water availability influences the physiological,structural, and functional attributes of a soil microbial community

Water availability is known to influence many aspects of microbial growth and physiology, but less is known about how complex soil microbial communities respond to changing water status. To understand how long-term enhancement of soil water availability (without flooding) influences microbial communities, we measured the seasonal dynamics of several community-level traits following >7 years of irrigation in a drought-prone tallgrass prairie soil. From late May to mid-September, water was supplied to the irrigated treatments based on calculated plant water demand. Phospholipid fatty acids (PLFA) were used to assess changes in microbial community structure and physiology. To assess the community-level physiological profile, microbial utilization of BIOLOG substrates was determined. After incubation for 2 days, the distribution of added ¹³C-glucose in microbial and respired pools was used as an index of substrate utilization efficiency. We also measured the relative contribution of fungi and bacteria to soil microbial biomass via substrate-induced respiration (SIR). Multivariate analysis of mol% PLFA and BIOLOG substrate utilization indicated that both water availability and sampling time influenced both the physiological and structural characteristics of the soil microbial community. Specific change in biomarker PLFA revealed a decreased ratio of cyclopropyl to ω7-precursors due to water addition, suggesting community-level stresses were reduced. Over the growing season, continuously greater water availability resulted in a 53% greater ratio of fungal to bacterial biomass using SIR, and a 65% increase in fungal PLFA. The number of substrates utilized by the cultivable microbial community tended to be greater in continuously wetted soil, especially during periods of low rainfall. While water dynamics appeared to be associated with some of the shifts in microbial community activity, structural and functional changes in the community appeared to be more closely linked to the cumulative effects of water regime on ecosystem properties. Seasonality strongly influenced microbial communities. The environmental factors associated with seasonal change need to be more closely probed to better understand the drivers of community structure and function.     

The impact of long-term CO2 enrichment and moisture levels on soil microbial community structure and enzyme activities

Soil organic matter is the most important reservoir of terrestrial organic C and minor changes in the balance may have a significant impact on the climate. However, the response of microbial decomposers of soil C to global changes is not fully apprehended. This is particularly the case with regard to the interactive effects of the various climatic changes. Here, we present data from the Giessen Free Air CO₂ Experiment (Gi-FACE, University of Giessen, Germany) in which the CO₂ concentration at a grassland site was increased by 20% relative to atmospheric levels during a period of 10 years. The site included a slope that resulted in differences in average soil moisture. The effects of CO₂ and soil moisture on soil microbial community structure, measured by Denaturing Gradient Gel Electrophoresis (DGGE), PhosphoLipid Fatty Acids (PLFA) and enzyme activity profiles were determined. Total carbon, nitrogen and phosphorous contents were also determined. Soil moisture explained a large part of the variance in the microbial community structure data, by affecting fungi and bacteria. Furthermore, the CO₂ treatment had no significant effect on either overall PLFA or DGGE profiles, despite the fact that the fungal:bacterial PLFA ratio was altered. Overall enzyme activity profiles were also only affected by soil moisture levels, although the CO₂ treatment induced a significant increase of the acid phosphatase activity. Finally, neither soil moisture nor elevated CO₂ induced changes in the soil C stock.     

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.