Fungal PLFA Research Articles

A strategy for marginal semiarid degraded soil restoration: A sole addition of compost at a high rate. A five-year field experiment

This work evaluates the mid-term impact of the addition of large amounts of an organic amendment on the recovery of the physical, chemical and, particularly, the microbiological properties of a marginal semiarid degraded soil and on increasing the soil organic C pool. In order to perform this study, a semiarid degraded soil was treated with composted urban waste at doses equivalent to the addition of 1% (S + CCD1) and 3% (S + CCD2) of organic C (Corg). Changes in soil characteristics in the amended soils were evaluated with respect to a control soil without organic amendment for a period of 5 years after the organic amendment was applied. A spontaneous vegetal cover developed on both amended and unamended soils 3–4 months after the organic amendments were added, yet the level of vegetal biodiversity was lower in the amended plots. Compost-amended soils showed higher concentrations of Corg, water-soluble C and water-soluble carbohydrates than the control soil throughout the experimental period. Furthermore, all of these C fractions were significantly higher (p ≤ 0.05) in S + CCD2 than in S + CCD1 and the control soil. However, compost addition also increased soil electrical conductivity and nitrate content, particularly at the higher dose. Likewise, compost addition produced a 4- to 10-fold increase in soil heavy metal concentrations, although the levels of heavy metal were under the limits allowed in soils. Five years after the organic amendment was added, the soil water holding capacity, stable aggregate percentage, porosity and nutrient and humic substance and humic acid content were greater in amended soils than in control soil, and the higher dose produced greater increases than the lower dose. Soils receiving the highest dose of compost also showed the highest values of basal respiration, dehydrogenase activity and β-glucosidase and phosphatase activity, as well as a greater abundance of total PLFAs, bacterial and fungal PLFAs, and saturated and monounsaturated fatty acids. A greater level of functional diversity was also observed in amended soils, particularly in the soil receiving the higher dose of compost. It can be concluded that the addition of high doses of compost can be a suitable strategy for restoring semiarid degraded soils and for fixing C in these soils, provided that the organic material is of high quality and has a low concentration of heavy metals.

Effects of Different Organic Manures on the Biochemical and Microbial Characteristics of Albic Paddy Soil in a Short-Term Experiment

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile.

Divergent responses of soil microbial communities to water and nitrogen addition in a temperate desert

Increasing precipitation and N deposition are reported in northern China. However, their impacts on soil microorganisms are still unclear. We aimed to elucidate how increasing precipitation and N deposition alone and in combination would affect soil microorganisms in interplant soils and beneath shrubs of Haloxylon ammodendron. A 30% increase in precipitation and 5gNm−2yr−1 addition were applied to simulate precipitation increasing and N deposition in a temperate desert steppe across 2011–2013. Increasing precipitation significantly increased microbial biomass carbon (MBC) and respiration (MR), as well as bacterial and fungal PLFAs. N addition slightly increased MBC, MR, as well as total, bacterial, and fungal PLFAs in interplant, while decreasing all of them beneath shrubs. N addition consistently increased microbial biomass nitrogen (MBN) at both microsites, but only decreased the ratio of MBC to MBN beneath shrubs. Both water and N addition had no impacts on the ratio of fungal to bacterial PLFAs (F:B), suggesting no impacts of water or N addition on microbial community composition. Microbial biomass, respiration, bacterial and fungal PLFAs were positively related to soil water content across treatments, suggesting that the increasing MR under increasing precipitation was mainly contributed by increasing microbial biomass rather than altering microbial community composition. In addition, the interaction of precipitation and N addition on microorganisms is discrepant between interplant and beneath shrubs, with significant effects beneath shrubs and no impacts in interplant. Our results support the hypothesis that water and N are co-limiting factors in desert ecosystems, but the effects are habitat-specific in deserts.

Regional‐scale patterns of soil microbes and nematodes across grasslands on the Mongolian plateau: relationships with climate, soil, and plants

Belowground communities exert major controls over the carbon and nitrogen balances of terrestrial ecosystems by regulating decomposition and nutrient availability for plants. Yet little is known about the patterns of belowground communities and their relationships with environmental factors, particularly at the regional scale where multiple environmental gradients co‐vary. Here, we describe the patterns of belowground communities (microbes and nematodes) and their relationships with environmental factors based on two parallel studies: a field survey with two regional‐scale transects across the Mongolia plateau and a water‐addition experiment in a typical steppe. In the field survey, soils and plants were collected across two large‐scale transects (a 2000‐km east–west transect and a 900‐km south–north transect). At the regional‐scale, the variations in soil microbes (e.g. bacterial PLFA, fungal PLFA, and F/B ratio) were mainly explained by precipitation and soil factors. In contrast, the variation in soil nematodes (e.g. density of trophic groups and the bacterial‐feeding/fungal‐feeding nematode ratio) were primarily explained by precipitation. These variations of microbe or nematode variables explained by environmental factors at regional scale were derived from different vegetation types. Along the gradient from nutrient‐poor to nutrient‐rich vegetation types, the total variation in soil microbes explained by precipitation increased and that explained by plant and soil decreased, while the opposite was true for soil nematodes. Experimental water addition, which increased rainfall by 30% during the growing season, increased biomass or density of belowground communities, with the nematodes being more responsive than the microbes. The different responses of soil microbial and nematode communities to environmental gradients at the regional scale likely reflect their different adaptations to climate, soil nutrients, and plants. Our findings suggest that the soil nematode and microbial communities are strongly controlled by bottom‐up effects of precipitation alone or in combination with soil conditions.

Impact of a woody biochar on properties of a sandy loam soil and spring barley during a two-year field experiment

Biochar is often proposed to increase soil quality and crop yield, while sequestering carbon. Despite the growing number of studies in temperate regions, the claimed positive effects are still unsure for northwestern European soils. Moreover, there is a need to upscale results from lab and pot studies in these soil types to field experiments.The objectives of this study were therefore to investigate the effect of biochar application to a temperate agricultural soil on soil chemical, physical and biological properties, and on crop growth and nutrient uptake under field circumstances. A field trial, located in Merelbeke (Belgium), was established in October 2011 and monitored until August 2013. The biochar applied was produced from a mixture of hard- and softwood at 480°C. The biochar dose was 0 (control) or 20tha−1 (on dry weight basis). Over two years, biochar addition to soil did not affect soil chemical properties, except for organic carbon content and C:N ratios. Effects on bulk density, porosity and soil water retention curves were non-consistent over time, possibly due to interaction with tillage operations. Biochar increased soil water content in 2012, although mostly not significantly. However, in 2013, when soil water content was overall lower compared to 2012, it was not affected by biochar addition. Soil temperature, as measured at a soil depth interval of 8–20cm, was not changed by biochar addition. Furthermore, biochar addition to soil did only slightly influence soil microbiological community structure during the first year after biochar application, as only certain bacterial biomarker PLFAs were significantly affected by biochar addition, but no fungal biomarker PLFAs. Hence, it was not surprising that biochar addition did not affect crop yield, N or P uptake during the first two years after biochar application.

Naphthalene addition to soil surfaces: A feasible method to reduce soil micro-arthropods with negligible direct effects on soil C dynamics

Soil fauna are a key component of soil biodiversity and a driver of soil functioning. While the importance of soil fauna is well recognized, quantitative estimates of the role of soil fauna on soil biogeochemical processes, such as plant litter decomposition, are limited by methodological constraints. The addition of naphthalene, a polycyclic aromatic hydrocarbon (C10H8), to suppress soil fauna has been used for decades in decomposition experiments, but its efficacy remains questioned. In fact, we lack a rigorous field assessment of the efficacy of naphthalene additions for soil fauna suppression and potential non-target effects on the soil microbial community and carbon cycling. We added naphthalene at a high rate (477gm−2) monthly for 23 months on the bare soil surface of a tallgrass prairie. We determined the effect of such additions on the abundance of nematodes and micro-arthropods along the soil profile to a depth of 20cm at 11, 16 and 23 months after initiating naphthalene application. We used the variation in the natural 13C abundance of the naphthalene (δ13C – 25.5‰) as compared to the native soil (δ13C∼−17‰) to quantify naphthalene contribution to soil CO2 efflux and microbial biomarkers (PLFA). Naphthalene addition significantly reduced the abundance of oribatid mites (−45%), predatory mites (−52%) and springtails (−49%), but did not affect nematode abundance. The 13C abundance of a few Gram-negative (cy17:0, 18:1ω7c, 16:1ω7c), Gram-positive (a15:0, i15:0) and Actinobacteria (10Me-16:0, 10Me-18:0) PLFA markers decreased significantly in naphthalene treated plots, indicating bacterial utilization of naphthalene-derived C. Mixing models showed this contribution to be highly variable, with the highest naphthalene-C incorporation for Gram negative bacteria. Naphthalene-C was not incorporated in fungal PLFAs. This microbial utilization did not affect overall microbial abundance, community structure or activity, estimated as soil respiration. This experiment proves that naphthalene addition is a feasible method to reduce soil micro-arthropods in the field, with negligible direct effects on soil nematodes, microbial abundance and C dynamics.

Rapid soil fungal community response to intensive management in a bamboo forest developed from rice paddies

Although heavy winter mulch and high rate fertilizer application are commonly practiced in intensively managed bamboo (Phyllostachys praecox) plantations, little is known about the effects of these practices on soil microbial activities. Therefore a field study was conducted to investigate the long term intensive management on the development and composition of soil fungal communities. Fungal biomass (fungal phospholipid fatty acid marker), fungal DNA (18S rDNA real-time qPCR) and fungal community composition (culture-independent methods: DGGE, cloning and sequencing) were determined across a bamboo plantation that included seven stand age-classes (1, 4, 6, 8, 10, 12 and 20 years old). Although soil microbial PLFA biomass and fungal DNA abundance were unaffected during the first two years of intensive management, all increased significantly after three years of intensive management. The total microbial PLFA and bacterial PLFA increase linearly (P < 0.001) with increasing stand age, while soil fungal PLFA and 18S gene abundance increase was best described using a quadratic equation (P < 0.01). The fungal/bacterial ratio generally remained constant, but did increase for the 8 and 12 year stand soils. Sequencing of commonly-occurring bands revealed that the majority of the soil fungi were species of either Sordariomycetes or Chytridiomycetes. Cluster analysis by Ward's method revealed rapid short-term change in fungal communities that returned to its original composition within one to two years when the soils were not disturbed. This indicated a robust original fungal community that was resilient to transient perturbations resulting from intensive land management when allowed breaks from nutrient loading and soil disturbance. Redundancy analysis indicated that soil chemical characteristics, such as pH, Ntot and Corg, could account for 12.7%, 12.1% and 10.3% of the variance in soil fungal community composition, respectively. Stand age contributed to 12.6% of the variance of soil fungal community.

Biochar amendment to soils with contrasting organic matter level: effects on N mineralization and biological soil properties

AbstractFour biochar types, produced by slow pyrolysis of poultry litter (PL) and pine chips (P) at 400 or 500 °C, were added to two adjacent soils with contrasting soil organic matter (SOM) content (8.9 vs. 16.1 g C kg−1). The N mineralization rate was determined during 14‐week incubations and assessments were made of the microbial biomass C, dehydrogenase activity, and the microbial community structure (PLFA‐extraction). The addition of PL biochars increased the net N mineralization (i.e., compared to the control treatment) in both soils, while for treatments with P biochars net N immobilization was observed in both soils. Increasing the pyrolysis temperature of both feedstock types led to a decrease in net N mineralization. The ratio of Bacterial to Fungal PLFA biomarkers also increased with addition of biochars, and particularly in the case of the 500 °C biochars. Next to feedstock type and pyrolysis temperature, SOM content clearly affected the assessed soil biological parameters, viz. net N mineralization or immobilization, MBC and dehydrogenase activity were all greater in the H soil. This might be explained by an increased chance of physical contact between the microbial community activated by SOM mineralization upon incubation and discrete biochar particles. However, when considering the H soil's double C and N content, these responses were disproportionally small, which may be partly due to the L soil's, somewhat more labile SOM. Nonetheless, increasing SOM content and microbial biomass and activity generally appears to result in greater mineralization of biochar. Additionally, higher N mineralization after PL addition to the H soil with lower pH than the L soil can be due to the liming effect of the PL biochars.

Exotic earthworms alter soil microbial community composition and function

Exotic earthworms can profoundly alter soil carbon (C) and nitrogen (N) dynamics in northern temperate forests, but the mechanisms explaining these responses are not well understood. We compared the soil microbial community (SMC) composition (measured as PLFAs) and enzyme activity between paired earthworm-invaded and earthworm-free plots in northern hardwood forests of New York, USA. We hypothesized that differences in SMCs and enzyme activity between plots would correspond with differences in soil C content and C:N ratios. Relative abundance of several bacterial (mostly gram-positive) PLFAs was higher and that of two fungal PLFAs was lower in earthworm compared to reference plots, largely because of earthworm incorporation of the organic horizon into mineral soil. In surface mineral soil earthworms increased arbuscular mycorrhizal fungi (AMF) and gram-positive bacterial PLFAs, and decreased fungal (mostly saprotrophic) and several bacterial (gram-negative and non-specific) PLFAs. Earthworms also increased the activities of cellulolytic relative to lignolytic enzymes in surface mineral soil, and the relationships between enzyme activities and components of the SMC suggest a substrate-mediated effect on the SMC and its metabolism of C. A highly significant relationship between components of the SMC and soil C:N also suggests that earthworms reduce soil C:N through functional and compositional shifts in the SMC. Finally, changes in AMF abundances were linked to phosphatase activity, suggesting that earthworms do not necessarily inhibit P-acquisition by AMF-associated plants in our study system. We conclude that the combined influence of earthworm-related changes in physical structure, accessibility and chemistry of organic matter, and relative abundance of certain groups of fungi and bacteria promote C metabolism, in particular by increasing the activities of cellulolytic vs. lignolytic enzymes.

Long-term copper application in an organic vineyard modifies spatial distribution of soil micro-organisms

Organic viticulturists utilize copper to prevent and reduce downy mildew (Plasmopara viticola) within the vineyard. Being a heavy metal, copper either builds up in the soil or is leached into the groundwater or taken up by living organisms. Therefore, its use impacts the environment. In organic farming there are currently no copper substitutes available and, therefore, it is necessary to understand the depth of damage that copper is inflicting on soil microbial communities over the long-term. Here a field-scale grid, 4 m by 5 m, was analyzed within a 17 year practicing organic vineyard in Southwestern Germany. Copper fractions, enzyme analyses (phosphatase, arylsulfatase, invertase, urease, xylanase), fungal analyses (ergosterol, fungal PLFA), bacterial analyses (bacterial PLFA), and microbial biomass were measured and spatial distribution maps were interpolated. Readily available and exchangeable copper fractions were higher within the vine rows and lower between them. Total copper ranged from 43 mg kg−1 to 142 mg kg−1, which is above prevention levels for Germany. In areas of high copper, a negative effect on total carbon, ergosterol, as well as phosphatase and invertase enzyme activities was observed. Tillage practices were found to be more important than copper for the distribution of carbon, nitrogen and xylanase activity within the vineyard.

Effects of manure composts on soil biota and root-rot disease incidence of ginseng (Panax ginseng)

Some saprophytic fungi are pathogenic to ginseng, and input of organic materials may influence these pathogens. The objective of this study was to investigate the application effects of manure composts on soil-borne pathogenic fungi and the responses of soil organisms in relation to root rot disease. Manure composts from 3 different organisms, namely, chicken, cow, and pig, were applied at 20Mgha−1. We compared these effects between paddy-converted fields and upland fields. Despite the input of manure composts, the root yield did not increase because of root loss and growth disorder caused by root rot disease. We isolated Cylindrocarpon destructans and Fusarium solani from the diseased roots, which suggested that these 2 fungi were the main causal pathogens. Hyphal growth of the 2 fungi increased in soils of both fields treated with manure composts, but the promoting effect was high in paddy-converted fields. These findings suggest that the application of manure composts may accelerate root rot disease by promoting pathogenic fungi. Microflora was estimated by analysing phospholipid fatty acids, and non-metric multidimensional scaling analysis showed that the responses of microflora were different between the two fields. Aerobic bacterial PLFAs were greatly increased in the upland field, which indicated that influences of manure compost might differ according to soil type. Fungal PLFAs showed correlations with fungivorous nematodes but not with abundance of Collembola and Oribatida. It seemed that the suppressive effect of fungivorous fauna promoted by manure compost is minor and restricted to some organisms. Our study suggests that increased substrates in the soil might promote the growth of C. destructans and F. solani, and suppression of these pathogenic fungi is required in relation to the application of manure composts.

Nitrogen Addition and Warming Independently Influence the Belowground Micro-Food Web in a Temperate Steppe

Climate warming and atmospheric nitrogen (N) deposition are known to influence ecosystem structure and functioning. However, our understanding of the interactive effect of these global changes on ecosystem functioning is relatively limited, especially when it concerns the responses of soils and soil organisms. We conducted a field experiment to study the interactive effects of warming and N addition on soil food web. The experiment was established in 2006 in a temperate steppe in northern China. After three to four years (2009–2010), we found that N addition positively affected microbial biomass and negatively influenced trophic group and ecological indices of soil nematodes. However, the warming effects were less obvious, only fungal PLFA showed a decreasing trend under warming. Interestingly, the influence of N addition did not depend on warming.Structural equation modeling analysis suggested that the direct pathway between N addition and soil food web components were more important than the indirect connections through alterations in soil abiotic characters or plant growth. Nitrogen enrichment also affected the soil nematode community indirectly through changes in soil pH and PLFA. We conclude that experimental warming influenced soil food web components of the temperate steppe less than N addition, and there was little influence of warming on N addition effects under these experimental conditions.

A closeup study of early beech litter decomposition: potential drivers and microbial interactions on a changing substrate.

AimsLitter decomposition and subsequent nutrient release play a major role in forest carbon and nutrient cycling. To elucidate how soluble or bulk nutrient ratios affect the decomposition process of beech (Fagus sylvatica L.) litter, we conducted a microcosm experiment over an 8 week period. Specifically, we investigated leaf-litter from four Austrian forested sites, which varied in elemental composition (C:N:P ratio). Our aim was to gain a mechanistic understanding of early decomposition processes and to determine microbial community changes.MethodsWe measured initial litter chemistry, microbial activity in terms of respiration (CO2), litter mass loss, microbial biomass C and N (Cmic and Nmic), non purgeable organic carbon (NPOC), total dissolved nitrogen (TDN), NH4 +, NO3 - and microbial community composition (phospholipid fatty acids – PLFAs).ResultsAt the beginning of the experiment microbial biomass increased and pools of inorganic nitrogen (N) decreased, followed by an increase in fungal PLFAs. Sites higher in NPOC:TDN (C:N of non purgeable organic C and total dissolved N), K and Mn showed higher respiration.ConclusionsThe C:N ratio of the dissolved pool, rather than the quantity of N, was the major driver of decomposition rates. We saw dynamic changes in the microbial community from the beginning through the termination of the experiment.

Nematode and microbial communities in a rapidly changing compost environment: How nematode assemblages reflect composting phases

The microbial community (fungi and bacteria) is the main decomposer of organic matter during composting. Its composition is sometimes used as a proxy to assess compost maturity. Although nematodes are probably its most important grazers, only one previous study has highlighted clear shifts in nematode species composition during composting, and the assumption that nematodes reflect changes in the microbial community in compost has not yet been formally tested. Here, the microbial and nematode communities of a single composting process are analyzed together for the first time. Although both displayed broadly similar patterns, the abundance of fungal-feeding nematodes showed a distinct delay as compared to the increase in fungal PLFA. We argue that the nematode community may be a more promising tool to use in assessing compost maturity because it allows to discriminate between the three composting phases. First, during the thermophilic phase, bacterial-feeding nematodes dominate; during cooling, the bacterial-feeding/predators bloom; and during maturation, the abundance of fungal-feeding nematodes increases. Based solely on the microbial community, it was only possible to discriminate between the thermophilic phase and the rest of the process. Bacteria dominated during the thermophilic phase, while bacterial and fungal PLFA had more-or-less equal shares during cooling and maturation.

Soil microbial food web responses to free-air ozone enrichment can depend on the ozone-tolerance of wheat cultivars

Soil processes are driven by soil organisms and their interactions with plants and soil abiotic conditions. Climate changes may directly or indirectly alter soil processes and the organisms mediating these processes. Although aboveground influences of ozone have been studied widely on agroecosystems, the effects on belowground processes are poorly understood. This study aimed to investigate the effects of elevated ozone concentration [O3] on the components of soil microbial food webs and compare their responses between ozone-sensitive and ozone-tolerant wheat cultivars. The responses of soil biota to elevated [O3] varied between the two wheat cultivars. Fungal PLFA and the fungi to bacteria ratio decreased following elevated [O3], especially in the rhizospheric soil of ozone-tolerant wheat. Nematode functional guilds were sensitive to elevated [O3] and cultivar effects. At wheat jointing stage, bacterivores belonging to K-strategies decreased following elevated [O3], while fungivores exhibited a reverse trend. The abundance of flagellates decreased in ozone-tolerant wheat, but increased in ozone-sensitive wheat following elevated [O3]. However, an opposite trend was found in the bacterivores belonging to r-strategies. In conclusion, wheat cultivars play an important role in determining the effects of elevated [O3] on soil food web. The responses of soil biota to elevated [O3] were greater in ozone-tolerant wheat than in ozone-sensitive wheat, which may in turn have influenced soil organic matter decomposition and nutrient turnover.

Tracking Collembola feeding strategies by the natural 13C signal of fatty acids in an arable soil with different fertilizer regimes

Abstract Compound specific stable isotope analysis (13C/12C ratio of fatty acids) was used to assess the allocation of plant carbon in soil microbiota, and to identify the trophic links to microbial grazers in an arable field with long-term mineral and organic fertilizer amendments. The feeding strategy of two dominant Collembola species, epedaphic Isotoma viridis and euedaphic Willemia anophthalma was determined. The investigation was conducted following a shift to amaranth, a C4 plant, after 27 years of continuous C3 crop rotation. The influence of new C4 plant carbon was observed in microbial phospholipids (PLFAs) with higher δ13C recorded in C4 amaranth than in C3 clover soils. The strongest enrichment occurred in the fungal PLFA 18:2ω6,9c and bacterial PLFA 18:1ω9t with 11.2‰ and 6.6‰, respectively. However, other bacterial PLFAs showed no isotopic change, suggesting that the microbial community simultaneously utilized “new” and “old” plant carbon. The δ13C of Collembola fatty acids displayed species specific lipid pattern, which was affected by crop type, but not fertilizer amendments. Isotopic separation of Collembola lipids from amaranth and clover plots was more distinct in I. viridis than W. anophthalma. With up to 18‰, the enrichment in Collembola lipids was stronger than in microbial PLFAs, pointing to a distinct incorporation of carbon resources originating from the actual plant residues. The δ13C pattern in I. viridis indicated trophic links with bacteria, saprotrophic fungi and plant tissues, while saprotrophic fungi and plant tissues were accountable for the patterns observed in W. anophthalma.

Long-term plant growth legacies overwhelm short-term plant growth effects on soil microbial community structure

Plant–soil feedbacks are gaining attention for their ability to determine plant community development. Plant–soil feedback models and research assume that plant–soil interactions occur within days to weeks, yet, little is known about how quickly and to what extent plants change soil community composition. We grew a dominant native plant ( Pseudoroegneria spicata ) and a dominant non-native plant ( Centaurea diffusa ) separately in both native- and non-native-cultivated field soils to test if these species could overcome soil legacies and create new soil communities in the short-term. Soil community composition before and after plant growth was assessed in bulk and rhizosphere soils using phospholipid fatty acid analyses. Nematode abundance and mycorrhizal colonization were also measured following plant growth. Field-collected, native-cultivated soils showed greater bacterial, Gram (−), fungal, and arbuscular mycorrhizal PLFA abundance and greater PLFA diversity than field-collected, non-native-cultivated soils. Both plant species grew larger in native- than non-native-cultivated soils, but neither plant affected microbial composition in the bulk or rhizosphere soils after two months. Plants also failed to change nematode abundance or mycorrhizal colonization. Plants, therefore, appear able to create microbial legacies that affect subsequent plant growth, but contrary to common assumptions, the species in this study are likely to require years to create these legacies. Our results are consistent with other studies that demonstrate long-term legacies in soil microbial communities and suggest that the development of plant–soil feedbacks should be viewed in this longer-term context. ► Plants appear to require several years to cultivate typical microbial communities. ► Short-term plant growth fails to alter microbial structure. ► Rhizosphere soils were more similar to historic than current plant growth. ► Plant–soil feedback processes likely to be slower than thought.

Short-term stabilization of grape marc through earthworms

The winery industry generates vast amounts of organic waste during the various stages of wine production. Among the possible methodological alternatives available for its treatment, vermicomposting is one of the best-known processes for the biological stabilization of solid organic wastes by transforming them into safer and more stabilized materials suitable for application to soil. In this study we carried out a mesocosm experiment to evaluate the effectiveness of the active phase of vermicomposting for the stabilization of grape marc, an enriched lignocellulosic by-product obtained after the grape crushing and pressing stages in wine production. For this we analysed the chemical, biochemical and microbiological properties of the product resulting from this phase, in comparison with those in a control treatment. Earthworm activity reduced the abundance of both bacterial and fungal PLFA biomarkers. Decreases in microbial activity and in protease and cellulase activities were also attributed to the presence of earthworms. The differences in microbial communities were accompanied by a reduction in the labile C pool and the cellulose content. These results indicate that earthworms played a key role in the stabilization of the grape marc in the short-term, via its effects on organic matter decomposition and microbial biomass and activity.

Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle

Abstract Overwintering cattle outdoors causes soil surface disturbance, substantial increases of soil Ntot, Corg, and P and a shift in pH to alkaline levels. Since fungi predominate in unfertilized soils with acidic pH and have filamentous hyphae, we hypothesized that changes caused by overwintering cattle outdoors (trampling, excreta returns, and changes in soil chemistry) will lead to suppressed species richness, lower biomass, and alter the structure of fungal communities. The research was conducted on an upland pasture used more than 10 years for cattle overwintering. Both culture-dependent and -independent methods were used for the determination of either fungal species composition (cultivation; DGGE) or biomass (numbers of CFU; concentration of fungal PLFA marker 18:2ω6,9). Soils under three different levels of cattle disturbance (S – severe, M – moderate, C – no disturbance/control) were investigated during three subsequent years. In addition, the DGGE analysis of soils was completed by comparison with analysis of fresh cattle excrements (Ex). The composition of fungal communities showed significantly higher richness and a substantial shift in species composition in cattle-disturbed soils (S, M) in comparison to the non-disturbed soil (C). The number of separated DGGE bands was significantly higher in S (30.67 ± 1.63; mean ± SD) and M (25.50 ± 1.64) soils than in the C soil (19.33 ± 1.75). Sequencing of typical bands revealed common fungal genera – Alternaria, Penicillium, Fusarium, Rhizopus, Isaria, and Metarhizium. Profiles of the S soil were enriched by bands of rumen-born anaerobic fungi (Neocallimastix, Cyllamyces) occurring mainly in profiles of excrements, where relatively low band richness (14.33 ± 1.15) was observed. The increasing level of cattle disturbance induced an increase in the biomass of complex fungal community over the three-year experimental period from 3.39 ± 2.11 (mean ± SD) nmol of fungal PLFA per gram of the C soil to 5.87 ± 3.16 in the M soil and 9.21 ± 4.69 in the S soil. Concentrations of soil Ntot and Corg were evaluated as the parameters significantly correlating with biomass as well as composition of the fungal community.

Effects of organic amendment and tillage on soil microorganisms and microfauna

Soil microorganisms (bacteria, fungi) and microfauna (nematodes, protozoa) have been shown to be sensitive to organic amendments, but few experiments have investigated the responses of all these organisms simultaneously and across the soil profile. We investigated the impact of organic amendment and tillage on the soil food web at two depths in a field experiment. Over three growing seasons, field plots received seasonal organic amendment that was either incorporated into the soil (tilled) or not (no-till) as part of a tomato/soybean/corn cropping system. Un-amended, control plots that were either tilled or no-till were also included. We hypothesized that the addition of amendments would have a bottom–up effect on the soil food web, positively influencing the abundance of microorganisms, protozoa, and nematodes, primarily in the surface layers of the soil, but that this effect could be extended into deeper layers via tillage. Organic amendment had positive effects on most measured variables, including organic matter, respiration, protozoan and nematode density, and the abundance of PLFA biomarkers for bacteria and fungi. These effects were more pronounced in the 0–5 cm depth, but most variables increased with amendment in the deeper layer as well, especially with tillage. Denaturing Gradient Gel Electrophoresis (DGGE) of bacterial rDNA fragments indicated that distinct bacterial communities were selected for among tillage and amendment treatments and depths. Nematode faunal indices were not influenced by amendment, however. Increased nematode density in amended soils encompassed all trophic groups of free-living nematodes, with the greatest response among fungal-feeders, particularly with tillage. Increased biomass of microorganisms and decomposer microfauna in amended, tilled soils (0–5 cm depth) corresponded with a decline in the abundance of plant-parasitic nematodes. In control soils (0–5 cm depth), tillage reduced the relative abundance of fungal-feeding nematodes and increased the density of bacterial-feeding nematodes, in particular nematode species contributing to the Enrichment Index. When combined with organic amendment however, tillage was associated with increases in fungal-feeding nematodes and fungal biomarker PLFA. The results of this study suggest that when combined with amendment, tillage enhances the soil food web beyond the effect of amendment alone and is associated with declines in plant-parasitic nematodes.