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

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

Linking Microbial Community Dynamics Associated with Rhizosphere Carbon Flow in a Biofuel Crop (Jatropha curcas L.)

Photosynthetically derived rhizodeposits are an important source of carbon (C) for microbes in root vicinity and can influence the microbial community dynamics. Pulse labeling of carbon dioxide (¹³CO₂) coupled with stable isotope probing techniques have potential to track recently fixed photosynthate into rhizosphere microbial taxa. Therefore, the present investigation assessed the microbial community change associated with the rhizosphere and bulk soil in Jatropha curcas L. (a biofuel crop) by combining phospholipid fatty acid (¹³C-PLFA) profiling using a stable isotope ¹³CO₂ labeling approach. The labeling (¹³C) took place after 45 days of germination, PLFAs were extracted from both soils (rhizosphere and bulk) after 1 and 20 days pulse labeling and analyzed by gas chromatography-isotope ratio mass spectrometry. There was no significant temporal effect on the PLFA profiles in the bulk soil, but significantly increased abundance of Gram positive (i15:0) and Gram negative (16:1ω7c and 16:1ω5c) biomarkers was observed in the rhizosphere soil from day 1 to day 20 after labeling. The Gram negative (16:1ω7c) decreased and fungal (18:2ω6,9c) increased significantly in rhizospheric soil compared to bulk soil after day 1 of labeling. Whereas, after 20 days of labeling, the Gram negative biomarker (16:1ω7c and 18:1ω7c) decreased and Gram positive (a15:0) increased significantly in rhizospheric soil compared to bulk soil. One day following labeling, i15:0, a15:0, i16:0, 16:1ω5c, 16:0, i17:0, a17:0, 18:2ω6,9c, 18:1ω9c, and 18:0 PLFAs were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. Twenty days after labeling, 16:1ω5c (Gram negative) and 18:2ω6,9c (fungal) were significantly more enriched in δ¹³C in the rhizosphere than in the bulk soil. These results shows the effectives of PLFA coupled using the pulse chase labeling technique to examine the microbial community changes in response to recently fixed photosynthetic C flow in rhizodeposits.     

Linking dynamics of soil microbial phospholipid fatty acids to carbon mineralization in a C natural abundance experiment: Impact of heavy metals and acid rain

A ¹³C natural abundance experiment including GC-c-IRMS analysis of phospholipid fatty acids (PLFAs) was conducted to assess the temporal dynamics of the soil microbial community and carbon incorporation during the mineralization of plant residues under the impact of heavy metals and acid rain. Maize straw was incorporated into (i) control soil, (ii) soil irrigated with acid rain, (iii) soil amended with heavy metal-polluted filter dust and (iv) soil with both, heavy metal and acid rain treatment, over a period of 74 weeks. The mineralization of maize straw carbon was significantly reduced by heavy metal impact. Reduced mineralization rate of the added carbon likely resulted from a reduction of the microbial biomass due to heavy metal stress, while the efficiency of ¹³C incorporation into microbial PLFAs was hardly affected. Since acid rain did not significantly change soil pH, little impact on soil microorganisms and mineralization rate was found. Temporal dynamics of labelling of microbial PLFAs were different between bacterial and fungal PLFA biomarkers. Utilization of maize straw by bacterial PLFAs peaked immediately after the application (2 weeks), while labelling of the fungal biomarker 18:2ω6,9 was most pronounced 5 weeks after the application. In general, ¹³C labelling of microbial PLFAs was closely linked to the amounts of maize carbon present in the soil. The distinct higher labelling of microbial PLFAs in the heavy metal-polluted soils 74 weeks after application indicated a large fraction of available maize straw carbon still present in the soil.     

Distribution and turnover of recently fixed photosynthate in ryegrass rhizospheres

The cycling of root-deposited photosynthate (rhizodeposition) through the soil microbial biomass can have profound influences on plant nutrient availability. Currently, our understanding of microbial dynamics associated with rhizosphere carbon (C) flow is limited. We used a ¹³C pulse-chase labeling procedure to examine the flow of photosynthetically fixed ¹³C into the microbial biomass of the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam.). To assess the temporal dynamics of rhizosphere C flow through the microbial biomass, plants were labeled either during the transition between active root growth and rapid shoot growth (Labeling Period 1), or nine days later during the rapid shoot growth stage (Labeling Period 2). Although the distribution of ¹³C in the plant/soil system was similar between the two labeling periods, microbial cycling of rhizodeposition differed between labeling periods. Within 24 h of labeling, more than 10% of the ¹³C retained in the plant/soil system resided in the soil, most of which had already been incorporated into the microbial biomass. From day 1 to day 8, the proportion of ¹³C in soil as microbial biomass declined from about 90 to 35% in rhizosphere soil and from about 80 to 30% in bulk soil. Turnover of ¹³C through the microbial biomass was faster in rhizosphere soil than in bulk soil, and faster in Labeling Period 1 than Labeling Period 2. Our results demonstrate the effectiveness of using ¹³C labeling to examine microbial dynamics and fate of C associated with cycling of rhizodeposition from plants at different phenological stages of growth.     

Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs

We combined microbial community phospholipid fatty acid (PLFA) analyses with an in situ stable isotope ¹³CO₂ labelling approach to identify microbial groups actively involved in assimilation of root-derived C in limed grassland soils. We hypothesized that the application of lime would stimulate more rapid ¹³C assimilation and turnover in microbial PLFAs. Four and 8 d after label application, 18:1ω9, 18:2ω6,9 (fungal biomarkers) and 16:1ω7, 18:1ω7, 19:0cy (Gram-negative bacterial biomarkers) showed the most ¹³C enrichment and rapid turnover rates. This suggests that these microorganisms were assimilating recently-photosynthesized root C inputs to soils. Contrary to our hypothesis, liming did not affect assimilation or turnover rates of ¹³C-labelled C. ¹³C stable isotope pulse-labelling technique paired with analyses of PLFA microbial biomarkers shows promise for in situ investigations of microbial function in soils.     

Distinct microbial and faunal communities and translocated carbon in Lumbricus terrestris drilospheres

Lumbricus terrestris is a deep-burrowing anecic earthworm that builds permanent, vertical burrows with linings (e.g., drilosphere) that are stable and long-lived microhabitats for bacteria, fungi, micro- and mesofauna. We conducted the first non-culture based field study to assess simultaneously the drilosphere (here sampled as 0–2 mm burrow lining) composition of microbial and micro/mesofaunal communities relative to bulk soil. Our study also included a treatment of surface-applied ¹³C- and ¹⁵N-labeled plant residue to trace the short-term (40 d) translocation of residue C and N into the drilosphere, and potentially the assimilation of residue C into drilosphere microbial phospholipid fatty acids (PLFAs). Total C concentration was 23%, microbial PLFA biomass was 58%, and PLFAs associated with protozoa, nematodes, Collembola and other fauna were 200-to-300% greater in the drilosphere than in nearby bulk soil. Principal components analysis of community PLFAs revealed that distributions of Gram-negative bacteria and actinomycetes and other Gram-positive bacteria were highly variable among drilosphere samples, and that drilosphere communities were distinct from bulk soil communities due to the atypical distribution of PLFA biomarkers for micro- and mesofauna. The degree of microbial PLFA ¹³C enrichment in drilosphere soils receiving ¹³C-labeled residue was highly variable, and only one PLFA, 18:1ω9c, was significantly enriched. In contrast, 11 PLFAs from diverse microbial groups where enriched in response to residue amendment in bulk soil 0–5 cm deep. Among control soils, however, a significant δ¹³C shift between drilosphere and bulk soil at the same depth (5–15 cm) revealed the importance of L. terrestris for translocating perennial ryegrass-derived C into the soil at depth, where we estimated the contribution of the recent grass C (8 years) to be at least 26% of the drilosphere soil C. We conclude that L. terrestris facilitates the translocation of plant C into soil at depth and promotes the maintenance of distinct soil microbial and faunal communities that are unlike those found in the bulk soil.     

Soil microbial community dynamics and phenanthrene degradation as affected by rape oil application

The effects of rape oil application on soil microbial communities and phenanthrene degradation were characterized by examining phenanthrene concentrations, changes in microbial composition and incorporation of [¹³C] phenanthrene-derived carbon into phospholipid fatty acids (PLFAs). A Haplic Chernozem was incubated with and without rape oil in combination with and without phenanthrene over 60 days. High-performance liquid chromatography (HPLC) analysis showed a net reduction in extractable phenanthrene in the soils treated with rape oil but no net reduction in the soils without rape oil. Rape oil application increased the total PLFA content and changed microbial community composition predominantly due to growth of fungal groups and Gram-positive bacterial groups. Under rape oil and phenanthrene amendment all detected microbial groups grew until day 24 of incubation. The ¹³C PLFA profiles showed ¹³C enrichment for the PLFAs i14:0, 15:0, 18:0, 18:1ω5 and the fungal biomarker 18:2ω6,9 under rape oil application. Fungal PLFA growth was highest among detected all PLFAs, but its ¹³C incorporation was lower compared to the Gram-positive and Gram-negative bacteria PLFAs. Our results demonstrate the effect of rape oil application on the abundance of microbial groups in soil treated with phenanthrene and its impact on phenanthrene degradation.     

外源铬对小白菜(Brassica chinensis L.)根际土壤微生物生物量和磷脂脂肪酸的剖面分布特征的影响

The effects of root activity on microbial response to cadmium （Cd） loading in the rhizosphere are not well understood. A pot experiment in greenhouse was conducted to investigate the effects of low Cd loading and root activity on microbial biomass and community structure in the rhizosphere of pakchoi （Brassica chinensis L.） on silty clay loam and silt loamy soil. Cd was added into soil as Cd（NO3）2 to reach concentrations ranging from 0.00 to 7.00 mg kg-1. The microbial biomass carbon （MBC） and community structure were affected by Cd concentration, root activity, and soil type. Lower Cd loading rates （〈 1.00 mg kg-1） stimulated the growth of pakchoi and microorganisms, but higher Cd concentrations inhibited the growth of microorganisms. The content of phospholipid fatty acids （PLFAs） was sensitive to increased Cd levels. MBC was linearly correlated with the total PLFAs. The content of general PLFAs in the fungi was positively correlated with the available Cd in the soil, whereas those in the bacteria and actinomycetes were negatively correlated with the available Cd in the soil. These results indicated that fungi were more resistant to Cd stress than bacteria or actinomycetes, and the latter was the most sensitive to Cd stress. Microbial biomass was more abundant in the rhizosphere than in the bulk soil. Root activity enhanced the growth of microorganisms and stabilized the microbial community structure in the rhizosphere. PLFA analysis was proven to be sensitive in detecting changes in the soil microbial community in response to Cd stress and root activity.     

Microscale distribution and function of soil microorganisms in the interface between rhizosphere and detritusphere

The rhizosphere and the detritusphere are hot spots of microbial activity, but little is known about the interface between rhizosphere and detritusphere. We used a three-compartment pot design to study microbial community structure and enzyme activity in this interface. All three compartments were filled with soil from a long-term field trial. The two outer compartments were planted with maize (root compartment) or amended with mature wheat shoot residues from a free air CO₂ enrichment experiment (residue compartment) and were separated by a 50 μm mesh from the inner compartment. Soil, residues and maize differed in ¹³C signature (δ¹³C soil −26.5‰, maize roots −14.1‰ and wheat residues −44.1‰) which allowed tracking of root- and residue-derived C into microbial phospholipid fatty acids (PLFA). The abundance of bacterial and fungal PLFAs showed clear gradients with highest abundance in the first 1–2 mm of the root and residue compartment, and generally higher values in the vicinity of the residue compartment. The δ¹³C of the PLFAs indicated that soil microorganisms incorporated more carbon from the residues than from the rhizodeposits and that the microbial use of wheat residue carbon was restricted to 1 mm from the residue compartment. Carbon incorporation into soil microorganisms in the interface was accompanied by strong microbial N immobilisation evident from the depletion of inorganic N in the rhizosphere and detritusphere. Extracellular enzyme activities involved in the degradation of organic C, N and P compounds (β-glucosidase, xylosidase, acid phosphatase and leucin peptidase) did not show distinct gradients in rhizosphere or detritusphere. Our microscale study showed that rhizosphere and detritusphere differentially influenced microbial C cycling and that the zone of influence depended on the parameter assessed. These results are highly relevant for defining the size of different microbial hot spots and understanding microbial ecology in soils.     

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.     

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.     

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.     

干旱热带地区土地利用变化对土壤微生物群落组成及有机碳含量的影响

Restoration of forests poses a major challenge globally,particularly in the tropics,as the forests in these regions are more vulnerable to land-use change.We studied land-use change from natural forest (NF) to degraded forest (DF),and subsequently to either Jatropha curcas plantation (JP) or agroecosystem (AG),in the dry tropics of Uttar Pradesh,India,with respect to its impacts on soil microbial community composition as indicated by phospholipid fatty acid (PLFA) biomarkers and soil organic carbon (SOC) content.The trend of bacterial PLFAs across all land-use types was in the order:NF ＞ JP ＞ DF＞ AG.In NF,there was dominance of gram-negative bacterial (G-) PLFAs over the corresponding gram-positive bacterial (G+) PLFAs.The levels of G-PLFAs in AG and JP differed significantly from those in DF,whereas those of G+ PLFAs were relatively similar in these three land-use types.Fungal PLFAs,however,followed a different trend:NF ＞ JP ＞ DF =AG.Total PLFAs,fungal/bacterial (F/B) PLFA ratio,and SOC content followed trends similar to that of bacterial PLFAs.Across all land-use types,there were strong positive relationships between SOC content and G-,bacterial,fungal,and total microbial PLFAs and F/B PLFA ratio.Compared with bacterial PLFAs,fungal PLFAs appeared to be more responsive to land-use change.The F/B PLFA ratio,fungal PLFAs,and bacterial PLFAs explained 91％,94％,and 73％ of the variability in SOC content,respectively.The higher F/B PLFA ratio in JP favored more soil C storage,leading to faster ecosystem recovery compared to either AG or DF.The F/B PLFA ratio could be used as an early indicator of ecosystem recovery in response to disturbance,particularly in relation to land-use change.     

Atmospheric nitrate deposition and the microbial degradation of cellobiose and vanillin in a northern hardwood forest

Human activity has increased the amount of N entering terrestrial ecosystems from atmospheric NO₃⁻ deposition. High levels of inorganic N are known to suppress the expression of phenol oxidase, an important lignin-degrading enzyme produced by white-rot fungi. We hypothesized that chronic NO₃⁻ additions would decrease the flow of C through the heterotrophic soil food web by inhibiting phenol oxidase and the depolymerization of lignocellulose. This would likely reduce the availability of C from lignocellulose for metabolism by the microbial community. We tested this hypothesis in a mature northern hardwood forest in northern Michigan, which has received experimental atmospheric N deposition (30 kg NO₃⁻-N ha⁻¹ y⁻¹) for nine years. In a laboratory study, we amended soils with ¹³C-labeled vanillin, a monophenolic product of lignin depolymerization, and ¹³C-labeled cellobiose, a disaccharide product of cellulose degradation. We then traced the flow of ¹³C through the microbial community and into soil organic carbon (SOC), dissolved organic carbon (DOC), and microbial respiration. We simultaneously measured the activity of enzymes responsible for lignin (phenol oxidase and peroxidase) and cellobiose (β-glucosidase) degradation. Nitrogen deposition reduced phenol oxidase activity by 83% and peroxidase activity by 74% when compared to control soils. In addition, soil C increased by 76%, whereas microbial biomass decreased by 68% in NO₃⁻ amended soils. ¹³C cellobiose in bacterial or fungal PLFAs was unaffected by NO₃⁻ deposition; however, the incorporation of ¹³C vanillin in fungal PLFAs extracted from NO₃⁻ amended soil was 82% higher than in the control treatment. The recovery of ¹³C vanillin and ¹³C cellobiose in SOC, DOC, microbial biomass, and respiration was not different between control and NO₃⁻ amended treatments. Chronic NO₃⁻ deposition has stemmed the flow of C through the heterotrophic soil food web by inhibiting the activity of ligninolytic enzymes, but it increased the assimilation of vanillin into fungal PLFAs.     

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes β-glucosidase, β-xylosidase, N-acetyl-β-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C_org, N_t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G⁻ to a more G⁺, and from a fungal to a more bacteria-dominated community. Rhizosphere β-xylosidase, N-acetyl-β-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, β-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G⁻, G⁺/G⁻). The activities of β-glucosidase, β-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microflora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply.     

Carbon flow from C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions

To better understand how residue quality and seasonal conditions influence the flow of C from both root and straw residues into the soil microbial community, we followed the incorporation of ¹³C-labeled crimson clover (Trifolium incarnatum) and ryegrass (Lolium multiflorum) root and straw residues into the phospholipid fatty acids (PLFA) of soil microbial biomass. After residue incorporation under field conditions in late summer (September), the ¹³C content of soil PLFA was measured in September, October, and November, 2002, and April and June, 2003. Multivariate non-metric multidimensional scaling techniques showed that the distribution of ¹³C among microbial PLFA differed among the four primary treatments (ryegrass straw and roots, clover straw and roots). Regardless of treatment, some PLFA remained poorly labeled with ¹³C throughout much of the study (16:1ω5, 10Me17:0; 0-5%), whereas other PLFA consistently contained a larger percentage of residue-derived C (16:0; 18:1ω9, 18:2ω6,9; 10-25%). The distribution of residue ¹³C among individual PLFA differed from the relative contributions of individual PLFA (mol%) to total PLFA-C, suggesting that a subset of the soil biomass was primarily responsible for assimilating residue-derived C. The distribution of ¹³C among soil PLFA differed between the sampling times, indicating that residue properties and soil conditions influenced which members of the community were assimilating residue-derived C. Our findings will provide the foundation for further studies to identify the nature of the community members responsible for residue decomposition at different times of the year, and what factors account for the dynamics of the community involved.     

Microbial phospholipid biomarkers and stable isotope methods help reveal soil functions

This review targets microbial phospholipid biomarkers, their isotope analysis and their ability to reveal soil functions. The amount and composition of phospholipid fatty acids (PLFAs) measured in environmental samples strongly depend on the methodology. To achieve comparable results the extraction, separation and methylation method must be kept constant. PLFAs patterns are sensitive to microbial community shifts even though the taxonomic resolution of PLFAs is low. The possibility to easily link lipid biomarkers with stable isotope techniques is identified as a major advantage when addressing soil functions. Measurement of PLFA isotopic ratios is sensitive and enables detecting isotopic fractionation. The difference between the carbon isotopic ratio of single PLFAs and their substrate (Δ¹³C) can vary between −6 and +11‰. This difference derives from the fractionation during biosynthesis and from substrate inhomogeneity. Consequently, natural abundance studies are restricted to quantifying substrate uptake of the total microbial biomass. In contrast, artificial labelling enables quantifying carbon uptake into single PLFAs, but labelling success depends on homogeneous and undisturbed label application. Current developments in microbial ecology (e.g. ¹³C and ¹⁵N proteomics) and isotope techniques (online monitoring of CO₂ isotope ratios) will likely improve soil functional interpretations in the future. ¹³C PLFA analysis will continue to contribute because it is affordable, sensitive and allows frequent sampling combined with the use of small amounts of ¹³C label.     

Seasonal Patterns of Microbial Community Structure and Enzyme Activities in Coastal Saline Soils of Perennial Halophytes

Perennial halophytes are known to be one of the most influential parameters in coastal ecosystem affecting ecosystem processes. The aim of this study was to investigate the changes in soil microbial community structure and enzyme activities in different halophyte‐covered soils (Arthrocnemum indicum , Aeluropus lagopoides , Heleochloa setulosa and Suaeda nudiflora ) with control soil (un‐vegetated) that were collected in three seasons (rainy, winter and summer) from intertidal coastal soils of Gujarat, India. Soil microbial community structure was assessed using phospholipid fatty acid (PLFA) profiling. Halophytes influenced significantly soil micro‐environment by exerting effects on the soil chemical characteristics, enzyme activities and microbial community structure. The activities of β‐glucosidase, urease and alkaline phosphatase were significantly higher in halophyte‐covered soils than in control soil. Among four halophyte‐covered soils, the highest amounts of total, bacterial, actinomycetes and fungal PLFAs were observed in Arthrocnemum soil. The concentrations of total, bacterial, actinomycetes and fungal PLFAs were also significantly higher in summer and winter seasons than in rainy season, whereas enzyme activities also vary with seasons. The non‐metric multidimensional scaling analysis PLFA profiling revealed that the structure of microbial community significantly differed in all seasons as well as between control and halophyte‐covered soils. These shifts in microbial community were due to the higher abundance of Gram‐positive, total bacterial and actinomycetes PLFAs in summer and winter seasons than in rainy season, whereas abundance of fungal biomarker was significantly higher in rainy season than in other seasons. Among halophytes, significantly higher abundance of Gram‐positive, Gram‐negative and total bacteria was observed in Arthrocnemum , Heleochloa and Suaeda whereas the lowest in control soil. Halophytes exhibited improved soil microbial activities, which is important for healthy ecosystem. Copyright © 2017 John Wiley & Sons, Ltd.     

Determination of the fate of C labelled maize and wheat rhizodeposit-C in two agricultural soils in a greenhouse experiment under C-CO2-enriched atmosphere

A deeper understanding of the contribution of carbon (C) released by plant roots (rhizodeposition) to soil organic matter (SOM) can help to increase our knowledge of global C-cycling. These insights can eventually lead to sustainable management of SOM especially in agricultural systems. This study was conducted to determine the fate of ¹³C labelled rhizodeposit-C of maize and wheat plants. They were grown in a greenhouse in permeable nylon bags filled with upper soil material from two agricultural soils of the same location, but with different crop yields. The bags were placed into pots, which were also filled with soil surrounding the bags. Soil inside the bags was considered as rhizosphere soil, wheras the one outside the bags represented bulk soil. The contributions of rhizodeposits to water extractable organic carbon (WEOC), microbial biomass-C (MB-C), CO₂-C evolution, and total organic carbon (C_org) were investigated during a 7-week growing period. The WEOC, MB-C, CO₂-C, C_org contents and the respective δ¹³C values were determined regularly, and a newly developed method for determining δ¹³C values in soil extracts was applied.In both soils, regardless of crop yield potential, significant incorporation of rhizodeposition-derived C was observed in the MB-C, CO₂-C, and C_org pool, but not in the WEOC. The pattern of C incorporation into the different pools was the same for both soils with both plants, and rhizodeposit-derived C was recovered in the order MB-C<C_org<CO₂-C. This showed that rhizodeposits were mainly respired, but since C_org was the second largest pool of the overall balances, they were also stabilized in the soils at least in the short term. It is suggested that the increased SOM mineralization observed in this study (positive priming effects) was probably induced by C exchange processes between the soil matrix and soluble rhizodeposits. Moreover, soluble rhizodeposit-C was detected in MB-C and CO₂-C evolved outside the direct root zone, showing the availability of these C-components in the bulk soil.     

Soil nitrogen availability alters rhizodeposition carbon flux into the soil microbial community

Purpose

Soil microorganisms are important in the cycling of plant nutrients. Soil microbial biomass, community structure, and activity are mainly affected by carbon substrate and nutrient availability. The objective was to test if both the overall soil microbial community structure and the community-utilizing plant-derived carbon entering the soil as rhizodeposition were affected by soil carbon (C) and nitrogen (N) availability.

Materials and methods

A ¹³C-CO₂ steady-state labeling experiment was conducted in a ryegrass system. Four soil treatments were established: control, amendment with carboxymethyl cellulose (CMC), amendment with ammonium nitrate (NF), combined CMC and NF. Soil phospholipid fatty acid (PLFA) and ¹³C labeling PLFA were extracted and detected by isotope ratio mass spectrometer.

Results and discussion

The combined CMC and NF treatment with appropriate C/N ratio (20) significantly enhanced soil microbial biomass C and N, but resulted in lower soil inorganic N concentrations. There was no significant difference in soil PLFA profile pattern between different treatments. In contrast, most of the ¹³C was distributed into PLFAs 18:2ω6,9c, 18:1ω7c, and 18:1ω9c, indicative of fungi and gram-negative bacteria. The inorganic-only treatment was distinct in ¹³C PLFA pattern from the other treatments in the first period of labeling. Factor loadings of individual PLFAs confirmed that gram-positive bacteria had relatively greater plant-derived C contents in the inorganic-only treatment, but fungi were more enriched in the other treatments.

Conclusions

Amendments with CMC can improve N transformation processes, and the ryegrass rhizodeposition carbon flux into the soil microbial community is strongly modified by soil N availability.