The influence of soil type and altered lignin biosynthesis on the growth and above and belowground biomass allocation of Populus tremuloides

Plants influence soil carbon (C) formation through the quality and quantity of C released to soil. Soil type, in turn can modify a plant’s influence on soil through effects on plant production, tissue quality and regulation of soil C decomposition and stabilization. Wild-type aspen and three transgenic aspen lines expressing reduced stem lignin concentrations and/or increased syringyl (S) to guaiacyl (G) ratio lignin were grown in greenhouse mesocosms containing a sandy loam, a silt loam, or a clay loam soil for 6 months in order to examine the effects of altered lignin biosynthesis and soil type on biomass partitioning (above vs. belowground) and soil C processes. Results indicated that soil type significantly affected plant performance. Aspen grown in soils with high sand/low clay content accumulated the most total biomass, while aspen grown in soils with high clay content accumulated the least total biomass. These reductions in growth combined with specific soil characteristics led to differences among soil types in soil C formation. Transformed aspen expressing high syringyl/guaiacyl (S/G) lignin accumulated less total plant C and subsequently accumulated less aspen derived C in soil. Reduced lignin content alone in aspen did not affect plant growth or soil C formation. There were significant soil type × genetic line interactions indicating that growth and soil C formation for transgenic and wild type aspen lines varied among the different soil types. Given these interactions, future investigation needs to include long-term field studies across a range of soil types before transgenic aspen are widely planted.     

Plant growth, biomass partitioning and soil carbon formation in response to altered lignin biosynthesis in Populus tremuloides

We conducted a glasshouse mesocosm study that combined (13)C isotope techniques with wild-type and transgenic aspen (Populus tremuloides) in order to examine how altered lignin biosynthesis affects plant production and soil carbon formation. Our transgenic aspen lines expressed low stem lignin concentration but normal cellulose concentration, low lignin stem concentration with high cellulose concentration or an increased stem syringyl to guaiacyl lignin ratio. Large differences in stem lignin concentration observed across lines were not observed in leaves or fine roots. Nonetheless, low lignin lines accumulated 15-17% less root C and 33-43% less new soil C than the control line. Compared with the control line, transformed aspen expressing high syringyl lignin accumulated 30% less total plant C - a result of greatly reduced total leaf area - and 70% less new soil C. These findings suggest that altered stem lignin biosynthesis in Populus may have little effect on the chemistry of fine roots or leaves, but can still have large effects on plant growth, biomass partitioning and soil C formation.     

Physiology and microbial community structure in soil at extreme water content

A sandy loam soil was brought to 6 water contents (13-100% WHC) to study the effects of extreme soil moistures on the physiological status of microbiota (represented by biomass characteristics, specific respiration, bacterial growth, and phospholipid fatty acid, PLFA, stress indicators) and microbial community structure (assessed using PLFA fingerprints). In dry soils, microbial biomass and activity declined as a consequence of water and/or nutrient deficiency (indicated by PLFA stress indicators). These microbial communities were dominated by G+ bacteria and actinomycetes. Oxygen deficits in water-saturated soils did not eliminate microbial activity but the enormous accumulation of poly-3-hydroxybutyrate by bacteria showed the unbalanced growth in excess carbon conditions. High soil water content favored G bacteria.     

Characterization of the rhizosphere microbial community from different Arabidopsis thaliana genotypes using phospholipid fatty acids (PLFA) analysis

Total and culturable rhizosphere microbial communities structure from three different genotypes of Arabidopsis thaliana growing on three different substrates was studied with phospholipid fatty acid analysis (PLFA) and multivariate statistical analyses: correspondence analysis (CA) and distance based redundancy analyses (db-RDA). In addition, microbial biomass from different groups (total bacteria, Gram+, Gram? and fungi) was calculated from biomarkers PLFA peak area, both from total and culturable microbial community. db-RDA analysis showed significant differences between soils but not between plant genotypes for culturable microbial community structure. Total microbial community was significantly different between soils, and also between plant lines in each soil. Biomass of different bacterial groups showed significant higher values in soil two rhizosphere irrespective of the plant line. In addition, significant differences between plant lines were also found for microbial biomass of different bacterial groups both in total and culturable microbial community. Throughout the work we have demonstrated that PLFA analysis has been able to show a different behaviour of total microbial community with regard to the culturable fraction analyzed in this work under the influence of plant roots. Microbial biomass of different microbial groups calculated with PLFA biomarkers was a suitable tool to detect differences between soils irrespective of the plant line, and differences in the same soil between plant lines. According to this data, a previous study should be carried out before GMPs are used in field conditions to evaluate the potential alterations that may take place on rhizosphere microbial communities structure which may further affect soil productivity. In conclusion, based on data presented in this work, GMPs alter rhizosphere microbial communities structure and this effect is different depending on the soil. Furthermore, total microbial community is affected to a greater extent than the culturable fraction analyzed.     

滩涂围垦和土地利用对土壤微生物群落的影响

土壤微生物在生态系统营养物质循环过程,特别是碳、氮循环过程中扮演着重要的角色。上海市崇明岛位于长江入海口,因其土壤发育时间较短、土地利用历史背景清晰、土壤本底均一,不同土壤围垦年代的土壤,代表了土壤发育年代的不同时期。以空间变化代替时间变化,对崇明岛稻田和旱地6个不同围垦年代土壤的磷酸脂肪酸(PLFA)指纹图谱研究表明,湿地滩涂围垦16a后土壤微生物总PLFA、细菌PLFA、革兰氏阳性菌(G+)PLFA和革兰氏阴性菌(G-)PLFA含量显著降低。随着围垦时间的逐步增加,PLFA含量逐步上升。经过长时间的农业种植,G+PLFA在围垦120a和300a稻田和旱地土壤中没有显著性差异;而总PLFA、细菌和G-PLFA在围垦75、120a和300a的土壤中含量趋于稳定且没有显著性差异。围垦16a和40a稻田土壤中总PLFA和G+PLFA显著高于旱地土壤;围垦40a稻田土壤中细菌和G-PLFA显著高于旱地土壤。不同围垦年代土壤总PLFA、细菌PLFA与土壤总氮、粘土含量成显著的正相关关系。河口湿地围垦后微生物数量的变化与土壤营养含量存在强烈相关关系,提示土壤围垦及演替过程中微生物与土壤肥力之间的紧密关系,对探讨土壤演替过程中微生物群落的变化具有重要意义。     

Differential Utilization of Carbon Substrates by Bacteria and Fungi in Tundra Soil

Little is known about the contribution of bacteria and fungi to decomposition of different carbon compounds in arctic soils, which are an important carbon store and possibly vulnerable to climate warming. Soil samples from a subarctic tundra heath were incubated with ¹³C-labeled glucose, acetic acid, glycine, starch, and vanillin, and the incorporation of ¹³C into different phospholipid fatty acids (PLFA; indicative of growth) and neutral lipid fatty acids (NLFA; indicative of fungal storage) was measured after 1 and 7 days. The use of ¹³C-labeled substrates allowed the addition of substrates at concentrations low enough not to affect the total amount of PLFA. The label of glucose and acetic acid was rapidly incorporated into the PLFA in a pattern largely corresponding to the fatty acid concentration profile, while glycine and especially starch were mainly taken up by bacteria and not fungi, showing that different groups of the microbial community were responsible for substrate utilization. The ¹³C-incorporation from the complex substrates (starch and vanillin) increased over time. There was significant allocation of ¹³C into the fungal NLFA, except for starch. For glucose, acetic acid, and glycine, the allocation decreased over time, indicating use of the storage products, whereas for vanillin incorporation into fungal NLFA increased during the incubation. In addition to providing information on functioning of the microbial communities in an arctic soil, our study showed that the combination of PLFA and NLFA analyses yields additional information on the dynamics of substrate degradation.Bacteria and fungi comprise more than 90% of the soil microbial biomass and are the main agents for decomposition of organic matter in soil. Until recently it was thought that these two organism groups could be lumped together in this respect, and total microbial biomass or total activity (respiration) was often the only variable included in soil microbiology studies of decomposition and soil organic matter turnover (39). However, there is increasing evidence suggesting that whether decomposition is performed by bacteria or fungi, thereby channeling energy through the bacterial or the fungal food web, has profound effects on the ecosystem. Such effects can have direct influence on the higher trophic levels in the food web (30) or indirect effects on nutrient mineralization rates (14) and nutrient transfer (19, 20), and they can even determine the extent of carbon sequestration in the soil (37). The situation becomes even more complex when the impact of changes in climate, nitrogen availability, and litter input on the balance between bacteria and fungi is taken into account. The Arctic region has been identified as an area that will be especially vulnerable to these changes (3).Little is known about the contribution of bacteria and fungi to the utilization of plant-derived carbon substrates in arctic soils. Differentiation of the bacterial and fungal contributions to decomposition has hitherto relied to a large extent on changes in bacterial and fungal biomasses, for example, by analysis of patterns of phospholipid fatty acids (PLFA) (40). PLFA are components of the cell membrane, and some of the PLFA extracted from the soil are characteristic for a certain microbial group in the environment. However, for changes in PLFA concentrations after the addition of substrates to be detected, substrates often have to be added at unrealistically large amounts. Even then only small changes in the PLFA concentrations will often be detected (35).One way of overcoming these problems is to follow the incorporation of ¹³C label from added substrates into specific fatty acids (8, 17). This approach adds a new dimension—metabolic function—to the study of soil microbial communities without the need of cultivation. It also increases the sensitivity in tracing responses of organism groups to different substrates as the addition of substrates at low and more realistic concentrations with high specific ¹³C label will induce large changes in the ¹³C concentration of the PLFA without changing the total amount of PLFA.Carbon-13 labeling has been used to follow uptake of recent photosynthates (11, 13, 27), pure substrates (10, 12, 32, 33, 41), and complex labeled plant material (28, 41, 43, 44) into PLFA although seldom in arctic soils. However, microorganisms incorporate carbon not only into phospholipids (indicating growth) but also into storage products, for example, when a nutrient other than carbon is limiting growth or under growth-restricting conditions. Thus, with excess carbon both bacteria and fungi will store carbon for later need, for example, as polyhydroxyalkanoate or glycogen (bacteria) and triacylglycerols (fungi). Thus, neutral lipid fatty acids (NLFA) of fungal origin can be used to indicate storage in fungi (4). Degraded PLFA, resulting in diacylglycerols, will also end up in the corresponding NLFA fraction, and NLFA has thus been suggested as an indicator of recently dead bacterial biomass (42). Therefore, the NLFA/PLFA ratio serves two purposes: for fungal lipids a higher NLFA/PLFA ratio would indicate allocation of lipids to energy storage while for bacterial lipids it would indicate turnover of this bacterial group. However, the latter will probably be of minor importance during short incubations. As far as we know, no studies on soil microorganisms have used incorporation of ¹³C from substrates to indicate both effects on growth (incorporation into PLFA) and storage (incorporation into NLFA).We assessed the uptake of ¹³C-labeled substrates into lipid biomarkers of different microbial groups in a laboratory incubation experiment using soil from an arctic tundra heath. The selected substrates represented carbon sources present in soil. Glucose, acetic acid, and glycine are simple compounds common in plant root exudates, and glycine is also a nitrogen source. Starch is a very common polysaccharide in plant residues. Vanillin is a common product of lignin depolymerization (18) containing a phenol ring and is often used as a model substance to indicate lignin degradation. Starch and vanillin are therefore examples of more complex substrates and are supposedly more difficult to decompose. We followed the incorporation of the label into different PLFA and NLFA over time. We hypothesized that ¹³C from the simple compounds would be more rapidly incorporated into microbial PLFA than ¹³C from the more complex substrates (more rapid growth), and thus we expected ¹³C emanating from the complex substrates to increase in concentration in the PLFA and NLFA over time. We also hypothesized that bacteria would be better than fungi in utilizing simple compounds while the label from the more complex substrates would preferentially be incorporated into PLFA, indicating fungi (6, 29). We also expected ¹³C from the C-rich substrates to be incorporated into NLFA (fungal storage) to a larger extent than C from glycine, which also serves as a nitrogen source (4). However, with time the carbon in storage structures would decrease as it would be used for growth or maintenance energy.     

Fungi Benefit from Two Decades of Increased Nutrient Availability in Tundra Heath Soil

If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover of complex organic compounds such as vanillin, while warming has had no such effects. Furthermore, the NLFA-to-PLFA ratio for ¹³C-incorporation from acetate increased in warmed plots but not in fertilized ones. Thus, fertilization cannot be used as a proxy for effects on warming in arctic tundra soils. Furthermore, the different functional responses suggest that the biomass increase found in both fertilized and warmed plots was mediated via different mechanisms.     

Sheep-urine-induced changes in soil microbial community structure

Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.     

Seasonal Dynamics of Microbial Community Composition and Function in Oak Canopy and Open Grassland Soils

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (¹³C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and ¹³C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function.     

转抗菌肽D烟草对土壤微生物群落的影响

采用RAPD分子标记技术研究了种植转抗菌肽D烟草的土壤环境中微生物群落遗传多样性的变化,同时用传统平板培养法研究了土壤中可培养微生物在数量上的变化。RAPD分析结果表明,转抗菌肽D烟草与非转基因烟草根围微生物的遗传多样性相关指数并没有显著差异。培养计数结果表明,转抗菌肽D烟草与非转基因烟草根围可培养细菌在数量上有极显著差异,可培养真菌数量有显著减少,可培养放线菌的数量没有显著差异。说明转抗菌肽D烟草可能抑制了病原细菌及其根围相关的微生物,但是不影响微生物的遗传多样性。     

Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (Resp_POM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.     

Response of Microbial Community Composition and Function to Soil Climate Change

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak–grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying ¹³C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their “life history” envelopes.     

Field‐grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry,microbiology, and carbon storage potential

Cell wall recalcitrance poses a major challenge on cellulosic biofuel production from feedstocks such as switchgrass (Panicum virgatum L.). As lignin is a known contributor of recalcitrance, transgenic switchgrass plants with altered lignin have been produced by downregulation of caffeic acid O‐methyltransferase (COMT). Field trials of COMT‐downregulated plants previously demonstrated improved ethanol conversion with no adverse agronomic effects. However, the rhizosphere impacts of altering lignin in plants are unknown. We hypothesized that changing plant lignin composition may affect residue degradation in soils, ultimately altering soil processes. The objective of this study was to evaluate effects of two independent lines of COMT‐downregulated switchgrass plants on soils in terms of chemistry, microbiology, and carbon cycling when grown in the field. Over the first two years of establishment, we observed no significant differences between transgenic and control plants in terms of soil pH or the total concentrations of 19 elements. An analysis of soil bacterial communities via high‐throughput 16S rRNA gene amplicon sequencing revealed no effects of transgenic plants on bacterial diversity, richness, or community composition. We also did not observe a change in the capacity for soil carbon storage: There was no significant effect on soil respiration or soil organic matter. After five years of establishment, δ¹³C of plant roots, leaves, and soils was measured and an isotopic mixing model used to estimate that 11.2 to 14.5% of soil carbon originated from switchgrass. Switchgrass‐contributed carbon was not significantly different between transgenic and control plants. Overall, our results indicate that over the short term (two and five years), lignin modification in switchgrass through manipulation of COMT expression does not have an adverse effect on soils in terms of total elemental composition, bacterial community structure and diversity, and capacity for carbon storage.     

Two Invasive Plants Alter Soil Microbial Community Composition in Serpentine Grasslands

Plant invasions pose a serious threat to native ecosystem structure and function. However, little is known about the potential role that rhizosphere soil microbial communities play in facilitating or resisting the spread of invasive species into native plant communities. The objective of this study was to compare the microbial communities of invasive and native plant rhizospheres in serpentine soils. We compared rhizosphere microbial communities, of two invasive species, Centaurea solstitialis (yellow starthistle) and Aegilops triuncialis (barb goatgrass), with those of five native species that may be competitively affected by these invasive species in the field (Lotus wrangelianus, Hemizonia congesta, Holocarpha virgata, Plantago erecta, and Lasthenia californica). Phospholipid fatty acid analysis (PLFA) was used to compare the rhizosphere microbial communities of invasive and native plants. Correspondence analyses (CA) of PLFA data indicated that despite yearly variation, both starthistle and goatgrass appear to change microbial communities in areas they invade, and that invaded and native microbial communities significantly differ. Additionally, rhizosphere microbial communities in newly invaded areas are more similar to the original native soil communities than are microbial communities in areas that have been invaded for several years. Compared to native plant rhizospheres, starthistle and goatgrass rhizospheres have higher levels of PLFA biomarkers for sulfate reducing bacteria, and goatgrass rhizospheres have higher fatty acid diversity and higher levels of biomarkers for sulfur-oxidizing bacteria, and arbuscular mycorrhizal fungi. Changes in soil microbial community composition induced by plant invasion may affect native plant fitness and/or ecosystem function.     

Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium

Poplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g., selenium (Se) from poor quality soils. Soil microorganisms may play a vital role in sustaining health of soil and/or tolerance of these trees grown in poor quality soils by contributing to nutrient cycling, soil structure, overall soil quality, and plant survival. The effect of naturally occurring salts boron (B) and Se on soil microbial community composition associated with poplar trees is not known for bioremediation strategies. In this study, three Populus clones 13–366, 345–1, and 347–14 were grown in spring 2006 under highly saline, B, and Se clay-like soils in the west side of the San Joaquin Valley (SJV) of CA, as well as in non-saline sandy loam soils located in the east side of the SJV. After 7 years of growing in the respective soils of different qualities, soil samples were collected from poplar clones grown in saline and non-saline soils to examine and compare soil quality effects on soil microbial community biomass and composition. The phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition in soils from trees grown at both locations. This study showed that microbial biomass and the amount and proportion of arbuscular mycorrhizal fungal (AMF) community were lower in all three poplar clones grown in saline soil compared to non-saline soil. Amounts of Gram + bacterial and actinomycetes PLFAs were significantly lower in poplar clone 13–366 grown in saline soil compared to non-saline soil; however, they did not differ significantly in poplar clones 347–14 and 345–1. Additionally, amounts of saprophytic fungal, Gram ? bacterial and eukaryotic PLFA remained similar at saline and non-saline sites under poplar clones 347–14, 345–1, and 13–366. Therefore, this study suggested that salinity and B do have an impact on microbial biomass and AMF; however, these poplar clones still recycled sufficient amount of nutrients to support and protect saprophytic fungal and bacterial communities from the effects of poor quality soils.     

Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent

The seasonal and spatial variations of microbial communities in Arctic fjelds of Finnish Lapland were studied. Phospholipid fatty acid analysis (PLFA) and terminal restriction fragment analysis (T-RFLP) of amplified 16S rRNA genes were used to assess the effect of soil conditions and vegetation on microbial community structures along different altitudes of two fjelds, Saana and Jehkas. Terminal restriction fragments were additionally analysed from c. 160 cloned sequences and isolated bacterial strains and matched with those of soil DNA samples. T-RFLP and PLFA analyses indicated relatively similar microbial communities at various altitudes and under different vegetation of the two fjelds. However, soil pH had a major influence on microbial community composition. Members of the phylum Acidobacteria dominated especially in the low pH soils (pH 4.6-5.2), but above pH 5.5, the relative amount of terminal restriction fragments corresponding to acidobacterial clones was substantially lower. Both T-RFLP and PLFA analysis indicated stable microbial communities as the DNA and fatty acid profiles were similar in spring and late summer samples sampled over 3 years. These results indicate that differences in microbial community composition could be explained primarily by variation in the bedrock materials that cause variation in the soil pH.     

Seasonal carbon allocation to arbuscular mycorrhizal fungi assessed by microscopic examination, stable isotope probing and fatty acid analysis

Background and Aim

Climate change models are limited by lack of baseline data, in particular carbon (C) allocation to – and dynamics within – soil microbial communities. We quantified seasonal C-assimilation and allocation by plants, and assessed how well this corresponds with intraradical arbuscular mycorrhizal fungal (AMF) storage and structural lipids (16:1ω5 NLFA and PLFA, respectively), as well as microscopic assessments of AMF root colonization.

Methods

Coastal Hypochoeris radicata plants were labeled with ¹³CO₂ in February, July and October, and ¹³C-allocation to fine roots and NLFA 16:1ω5, as well as overall lipid contents and AM colonization were quantified.

Results

C-allocation to fine roots and AMF storage lipids differed seasonally and mirrored plant C-assimilation, whereas AMF structural lipids and AM colonization showed no seasonal variation, and root colonization exceeded 80 % throughout the year. Molecular analyzes of the large subunit rDNA gene indicated no seasonal AMF community shifts.

Conclusions

Plants allocated C to AMF even at temperatures close to freezing, and fungal structures persisted in roots during times of low C-allocation. The lack of seasonal differences in PLFA and AM colonization indicates that NLFA analyses should be used to estimate fungal C-status. The implication of our findings for AM function is discussed.     

The Use of Neutral Lipid Fatty Acids to Indicate the Physiological Conditions of Soil Fungi

The usefulness of measuring neutral lipid fatty acids (NLFAs) and phospholipid fatty acids (PLFAs) separately in order to interpret perturbation effects on soil and compost microorganisms has been studied. Initially the NLFA/PLFA ratios were studied in different soils. Low ratios were found for fatty acids common in bacteria, especially for cyclopropane fatty acids. Higher ratios were found for fatty acids common in eukaryotic organisms such as fungi (18:1omega9 and 18:2omega6,9) or in saturated fatty acids, common to many types of organisms. Adding glucose to a forest soil increased the amounts of the fungal NLFAs 18:1omega9 and 18:2 omega6,9 up to 60 and 10 times, respectively, after 10 days, followed by a gradual decrease. After 3 months incubation, higher levels of these NLFAs were still found compared with the control samples. Adding glucose together with nitrogen (N) and phosphorus (P) resulted in no increase in NLFAs but a 10-fold increase in the PLFAs 18:1omega9 and 18:2omega6,9. Thus, the NLFA/PLFA ratios for these fatty acids were lower than in the no-addition control when glucose was added together with N and P, but higher when glucose was added alone, even 3 months after the addition. Adding N+P without glucose did not affect the NLFA/PLFA ratio for any fatty acid. Increasing NLFA/PLFA ratios for the fungal fatty acids were also found with time after the thermophilic phase in a compost, indicating increased availability of easily available carbon.     

Soil warming alters microbial substrate use in alpine soils

Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C‐rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007–2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO₂ enrichment experiment using depleted ¹³CO₂ (δ¹³C = ?30‰, 2001–2009). We traced this depleted ¹³C label in phospholipid fatty acids (PLFA) of the organic layer (0–5 cm soil depth) and in C mineralized from root‐free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 (‘old’), from 2001 to 2009 (‘new’) or in 2010 (‘recent’). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root‐free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem.     

Microbial Community Structure and Oxidative Enzyme Activity in Nitrogen-amended North Temperate Forest Soils

Large regions of temperate forest are subject to elevated atmospheric nitrogen (N) deposition which can affect soil organic matter dynamics by altering mass loss rates, soil respiration, and dissolved organic matter production. At present there is no general model that links these responses to changes in the organization and operation of microbial decomposer communities. Toward that end, we studied the response of litter and soil microbial communities to high levels of N amendment (30 and 80 kg ha^–1 yr^–1) in three types of northern temperate forest: sugar maple/basswood (SMBW), sugar maple/red oak (SMRO), and white oak/black oak (WOBO). We measured the activity of extracellular enzymes (EEA) involved directly in the oxidation of lignin and humus (phenol oxidase, peroxidase), and indirectly, through the production of hydrogen peroxide (glucose oxidase, glyoxal oxidase). Community composition was analyzed by extracting and quantifying phospholipid fatty acids (PLFA) from soils. Litter EEA responses at SMBW sites diverged from those at oak-bearing sites (SMRO, BOWO), but the changes were not statistically significant. For soil, EEA responses were consistent across forests types: phenol oxidase and peroxidase activities declined as a function of N dose (33–73% and 5–41%, respectively, depending on forest type); glucose oxidase and glyoxal oxidase activities increased (200–400% and 150–300%, respectively, depending on forest type). Principal component analysis (PCA) ordinated forest types and treatment responses along two axes; factor 1 (44% of variance) was associated with phenol oxidase and peroxidase activities, factor 2 (31%) with glucose oxidase. Microbial biomass did not respond to N treatment, but nine of the 23 PLFA that formed >1 mol% of total biomass showed statistically significant treatment responses. PCA ordinated forest types and treatment responses along three axes (36%, 26%, 12% of variance). EEA factors 1 and 2 correlated negatively with PLFA factor 1 (r = –0.20 and –0.35, respectively, n = 108) and positively with PLFA factor 3 (r = +0.36 and +0.20, respectively, n = 108). In general, EEA responses were more strongly tied to changes in bacterial PLFA than to changes in fungal PLFA. Collectively, our data suggests that N inhibition of oxidative activity involves more than the repression of ligninase expression by white-rot basidiomycetes.This revised version was published online in November 2004 with corrections to Volume 48.