PLFA Profiles Research Articles

One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities

Soil microbial communities are regularly exposed to sudden changes in environmental conditions, such as root exudation pulses or freeze-thaw events. As microbial communities have a high potential to adapt to changing conditions, they are expected to be resilient towards this kind of short-term perturbations and return to their pre-perturbed state quickly. Here, we conducted a lab incubation experiment to evaluate the resilience of soil microbial communities to single-pulse perturbations.We incubated temperate forest soil at constant temperature (20 °C) and water content, and exposed it to strong single-pulse perturbations, which nonetheless mimic common pulse-events in temperate soils (glucose addition at 4 mg g−1 soil, or freeze-thawing overnight at −20 °C). We subsequently measured microbial community composition and microbial storage compounds via phospho- and neutral lipid fatty acid (PLFA and NLFA) profiling, as well as C/N stoichiometry of microbial biomass and dissolved organic carbon and nitrogen in the soil solution shortly after (0.4, 1, 4, and 6 days) and after longer time periods (84 and 160 days) following the perturbations.Transferring the soils from their natural environment to the laboratory and incubating them under controlled conditions led to a continuous change of microbial community structure over time, along with an increase in microbial biomass and dissolved N in both perturbed and control soils over the time of the experiment. Against the background of this ‘press-disturbance’, caused by the permanently changed conditions, we see immediate and long-lasting effects of the single pulse events on microbial community composition, C storage and C/N stoichiometry. Both perturbations significantly influenced the microbial community structure (based on PLFA profiles), microbial biomass N and dissolved N up to 160 days, as well as fungal and bacterial biomass and storage (based on absolute PLFA and NLFA concentrations) up to 84 days. Both perturbations increased microbial N (+59.6 µg g−1 dw) and decreased dissolved N (−40.3 µg g−1 dw) after 160 days, and significantly altered C/N ratios in microbial and dissolved pools (particularly in the first 6 days of the experiment).Our results demonstrate that single-pulse perturbations can have long-term legacies in soil microbial ecosystems. In our experiment they led to alternative system states which differed from the unperturbed control in multiple parameters even after 160 days. This indicates that soil microbial communities exhibit a low resistance and resilience towards single-pulse perturbations, and may easily be pushed on alternative trajectories by short but strong environmental pulses.

PLFA Profiling of Coal Mine Spoil: An Integrated Approach for the Assessment of Ecological Restoration

Coal mine overburden spoil created aftermath of mining activities represents disequilibrated geomorphic system. The pedodiversity including its link with biodiversity and landscape ecology describe the spatial diversity has emerged as functional determinants of ecosystem processes. Being the driving force mediating soil processes, ecosystem restoration through mine spoil genesis is monitored based on the shift in microbial community structure in different age series coal mine spoil. Phospholipid fatty acid analysis is culture-independent approach, which provides a set of molecular markers to determine microbial community composition and discriminate microbial communities of different origin. PLFAs are synthesized during microbial growth, rapidly degraded following cell death and reliably reflect living microbial communities. Relative distribution of 51 PLFAs revealed significant variation in microbial community structure across the sites with Shannon diversity index varies from 1.5265 (OB0) to 2.0139 (OB15) and Pielous evenness index from 0.4110 (OB0) to 0.5260 (OB15). Fungal to bacterial ratio exhibited an increasing trend from OB0 (0.055) to OB15 (0.348) over time, which revealed the sign of mine spoil genesis. The principal component analysis and redundancy analysis discriminate different age series coal mine spoil into independent clusters, which evaluated the broad scale patterns of microbial community structure influencing the pace and progress of mine spoil genesis.

Impact of diesel and biodiesel contamination on soil microbial community activity and structure

Soil contamination as a result of oil spills is a serious issue due to the global demand for diesel fuel. As an alternative to diesel, biodiesel has been introduced based on its high degradability rates and potential for reducing of greenhouse gases emissions. This study assessed the impacts diesel and biodiesel contamination on soil microbial community activity and structure. Our results suggest higher microbial activity in biodiesel contaminated soils and analysis of PLFA profiles confirmed shifts in microbial community structure in response to contamination. High-throughput 16S rRNA amplicon sequencing also revealed a lower bacterial richness and diversity in contaminated soils when compared to control samples, supporting evidence of the detrimental effects of hydrocarbons on soil microbiota. Control samples comprised mostly of Actinobacteria, whereas Proteobacteria were predominantly observed in diesel and biodiesel contaminated soils. At genus level, diesel and biodiesel amendments highly selected for Rhodococcus and Pseudomonas spp., respectively. Moreover, predicted functional profiles based on hydrocarbon-degrading enzymes revealed significant differences between contaminated soils mostly due to the chemical composition of diesel and biodiesel fuel. Here, we also identified that Burkholderiaceae, Novosphingobium, Anaeromyxobacter, Pseudomonas and Rhodococcus were the main bacterial taxa contributing to these enzymes. Together, this study supports the evidence of diesel/biodiesel adverse effects in soil microbial community structure and highlights microbial taxa that could be further investigated for their biodegradation potential.

Microbial assembly and association network in watermelon rhizosphere after soil fumigation for Fusarium wilt control

Soil fumigation is an effective method to control soil-borne diseases like Fusarium wilt, however the processes and mechanisms driving microbial community reestablishment and pathogen suppression in the rhizosphere after fumigation remain poorly understood. In this study, we examined the dynamics of the rhizosphere microbiome and microbial network associations across different watermelon development stages and plant statuses (i.e. healthy and dead) after soil fumigation and organic fertilizer (OF) application in plastic shelters with Fusarium oxysporum f. sp. niveum (FON) heavily infected. Our results showed that fumigation treatments significantly reduced Fusarium wilt disease incidence and pathogen abundance, meanwhile, decreased soil microbial metabolic activity, fungal biomass and diversity. Bacterial community recovered from fumigation suppression in a short period, while fungal suppression was longer lasting, resulting in decreased fungi to actinomycetes (F/A) and fungi to bacteria (F/B) ratios in PLFA profiles. We further found some bacterial families, such as Actinospicaceae within Actinobacteria, Haliangiaceae, Rhizobiaceae and uncultured Rhodospirillales within Proteobacteria, Sporolactobacillaceae and Limnochordaceae within Firmicutes were greatly enriched after fumigation and might potentially contribute to pathogen suppression. The fumigation treatments significantly reduced microbial network complexity and the percentage of fungal nodes in comparison to un-fumigated control treatment. In contrast, a more complex microbial network was observed in the rhizosphere soil of healthy plants than that in the soil surrounding dead plant roots within fumigation treatments. Furthermore, healthy plant rhizosphere significantly enriched potential beneficial and nitrogen cycle-related bacterial phyla like Gemmatimonadetes, Verrucomicrobia, and Nitrospirae. More interestingly, Fusarium were markedly enriched in the rhizosphere soil of healthy plants and mainly represented by non-FON Fusarium like F. verticillioides and F. solani, implying a potential niche competition between FON and nonpathogenic Fusarium species in the rhizosphere of healthy watermelon. Taken together, our results provide vital information on the reconstruction of microbial communities and potential interactions between plant and its beneficial consortium after fumigation, which is instructive to develop more systematic strategies through targeting both beneficial and pathogen-similar taxa to improve disease control and soil suppression.

Effect of halotolerant plant growth promoting rhizobacteria inoculation on soil microbial community structure and nutrients

Halophytes are potential sources of salt-tolerant bacteria with plant growth enhancing abilities. Previously, our group has isolated plant growth promoting rhizobacteria (PGPR) from the roots of a halophyte (Arthrocnemum indicum) and tested for their abilities to enhance the peanut growth. The resilience of native soil microbial community to exogenous inoculation of PGPR is of growing concern as change in microbial community structure impacts on soil-plant-microbe interaction. Therefore, the aim of the present study was to examine the influence of inoculation of PGPR isolated from halophytes on the native soil microbial community in the field grown peanut (Arachis hypogaea L.). The PGPR had significantly influenced and enhanced the availability of nutrients (N, P, K and Fe) in soil. Alkaline phosphatase activity was significantly improved in the bacteria inoculated soils, except MBE03 (Ochrobactrum anthropic), in comparison to the control soil where the highest increase was observed in the soil inoculated with MBE02 (Klebsiella sp.). There was a significant influence of bacterial treatments on the contents of total PLFAs, Gram-positive and actinomycetes PLFAs. The contents of these PLFAs were maximum in soil inoculated with MBE01 (Agrobacierium tumefaciens). The multivariate analysis of PLFA profiles exhibited that the microbial community structure of soil was not significantly affected by the bacterial inoculation. Our results suggest that the inoculation with beneficiary bacteria does not perturb the natural soil microbial community.

Phospholipid Fatty Acid Profiles of Soils under Variable Handling and Storage Conditions

Core Ideas Sample handling had profound and disproportionate effects on PLFA biomarkers. Gram positive and actinobacteria were not significantly affected by storage. Gram negative and fungal biomarkers were dramatically affected by storage. PLFA ratios significantly changed as a result of sample handling and storage. Interpretation of PLFA profiles is highly sensitive to sample handling. ABSTRACTPhospholipid fatty acid (PLFA) analysis is an increasingly popular method for estimating microbial biomass and assessing microbial community structure in soils. In particular, there is a strong interest in the use of PLFA microbial group ratios as benchmarks for soil health assessment and interpretation. Due to the sensitivity of PLFA biomarkers, the recommended procedure for sample handling involves immediate analysis of fresh, field‐moist soil, immediate lyophilization with freezer storage, or storage at –80°C. This protocol may not be practical under all circumstances, yet the effects of handling and storage conditions, and the implications for interpretation of PLFA biomarkers, are not fully understood. The primary objective of this study was to evaluate the effects of multiple sample handling and storage conditions on quantification and interpretation of PLFA biomarkers. A suite of soil properties were measured on 17 prairie soil samples, including PLFA analysis. Multiple processing and handling procedures were evaluated by splitting the soil samples and comparing PLFA profiles from (i) fresh soil, (ii) soil stored air‐dry for 7 and 14 d, (iii) soil stored field‐moist at room temperature for 7 and 14 d, and (iv) soil oven‐dried for 24 h at 105°C. All handling and storage procedures resulted in significant losses of PLFA biomarkers relative to fresh, lyophilized samples and microbial groups were disproportionately affected, leading to significant shifts in biomarker ratios. Overall, this study highlights the sensitivity of PLFA biomarkers, the importance of proper sample handling for PLFA analysis, and the potential for error and misinterpretation of PLFA data.

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices

Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.

Soil hydraulic properties as the main driver in the establishment of biomass crops in contaminated soils

In recent years increasing attention has been given to the potential use of contaminated lands for biofuel production, because these degraded soils cannot be used for food production. To establish these crops in Mediterranean contaminated areas, where the soil quality is usually very poor, the addition of soil amendments might be necessary to improve soil productivity. In addition, the use of crops with low water demands, adapted to these particular conditions of climate and soil contamination, is a key requirement. We studied the development of Cynara cardunculus and Silybum mariamun crops (both suitable for the production of biomass for biofuel uses under a Mediterranean climate) in trace element contaminated soils under field conditions. To our knowledge, this is the first such work under these particular experimental conditions (soil contamination and field trial). Soil physical (hydraulic), chemical, and biochemical properties were monitored for one year in experimental plots, where we tested the effects of the addition of two different amendments (sugar lime and biosolid compost) on soil functioning and crop productivity. Seed germination and plant biomass production were low, although amendment addition improved both parameters. The chemical and biological indicators (enzyme activities, PLFA profiles, and soil respiration) tended to be slightly improved by the amendments, especially sugar lime. The hydraulic properties of the soil in the experimental area were very deficient, and the effect of the amendments was not enough to improve them; this was probably the main cause of the general low productivity of these rain-fed crops, as water infiltrated poorly through the root zone. To improve crop productivity under these soil conditions, certain aspects could be improved: higher doses of amendments should be applied and deeper tillage of the soil after amendment addition should be performed to facilitate water infiltration.

Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.

Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.

Insights into the role of earthworms on the optimization of microbial community structure during vermicomposting of sewage sludge by PLFA analysis

In this study, the influences of earthworms on the structure of microbial community as well as the metabolic function in vermicomposting (VPs, with earthworms) for excess sludge stabilization were investigated. Comparison between the dynamic variation of PLFA profiles in VPs and common composting (CPs, with no earthworms) was conducted. The Shannon index was increased in VPs, while it was decreased in CPs with time, indicating earthworm activity enhanced microbial community diversity. The fungal and protozoal biomasses were significantly increased in VPs compared with CPs. Further researches by principal component analysis (PCA) indicated that earthworms benefited certain microorganisms containing biomarkers of 18:1ω9c, 18:3ω3, 18:3ω6, 20:1ω9, 20:2ω6 and 20:3ω6. Moreover, the ratios of monounsaturated to branched PLFAs in VPs were larger than those in CPs, suggesting the aeration condition was promoted by the burrowing behaviors of earthworms and therefore facilitated the growth and propagation of aerobic microorganisms, such as protozoa. Those results indicated that earthworm activity led to the general optimization of vermicomposting for excess sludge stabilization.

Investigations of microbial degradation of polycyclic aromatic hydrocarbons based on 13C-labeled phenanthrene in a soil co-contaminated with trace elements using a plant assisted approach

Co-contaminations of soils with organic and inorganic pollutants are a frequent environmental problem. Due to their toxicity and recalcitrance, the heterogeneous pollutants may persist in soil. The hypothesis of this study was that degradation of polycyclic aromatic hydrocarbons (PAHs) is enhanced if heavy metals in soil are immobilized and their bioavailability reduced. For metal immobilization and enhanced biodegradation, distinct mineral and organic soil amendments (iron oxides, gravel sludge, biochar) were deployed in an incubation batch experiment. The second part of the experiment consisted of a greenhouse pot experiment applying fast-growing and pollution-tolerant woody plants (willow and black locust). Soil amendments initially immobilized NH4NO3-extractable zinc, cadmium, and lead; after 100days of incubation, soil amendments showed reductions only for cadmium and a tendency to enhance arsenic mobility. In order to monitor the remediation success, a 13C-phenanthrene (PHE) label was applied. 13C-phospholipid fatty acid analysis (13C-PLFA) further enabled the identification of PHE-degrading soil microorganisms. Both experiments exhibited a similar PLFA profile. Gram-negative bacteria (esp. cy17:0, 16:1ω7 + 6, 18:1ω7c) were the most significant microbial group taking up 13C-PHE. Plants effectively increased the label uptake by gram-positive bacteria and increased the biomass of the fungal biomarker, although their contribution to the degradation process was minor. Plants tended to prolong PAH dissipation in soil; at the end of the experiment, however, all treatments showed equally low total PAH concentrations in soil. While black locust plants tended not to take up potentially toxic trace elements, willows accumulated them in their leaves. The results of this study show that the chosen treatments did not enhance the remediation of the experimental soil.

Indications that long-term nitrogen loading limits carbon resources for soil microbes

Microbial communities in the organic horizon (O-horizon) of forest soils play key roles in terrestrial nitrogen (N) cycling, but effects on them of long-term high N loading, by N deposition or experimental addition, are not fully understood. Thus, we investigated N-loading effects on soil microbial biomass N, carbon (C) and phosphorus stoichiometry, hydrolytic and oxidative enzymes, community composition (via phospholipid fatty acids, PLFA) and soil chemistry of the O-horizon in study plots of three well-studied experimental Norway spruce (Picea abies) forests in Sweden and the Czech Republic. These forests span substantial gradients in current N deposition, experimental N addition and nitrate (NO3−) leaching. Current N deposition ranges from ∼3 kg ha−1 year−1 of N in central Sweden (Stråsan) to ∼15 kg ha−1 year−1 of N in SW Sweden (Skogaby) and Czech Republic (Čertovo). Furthermore, accumulated historical N loading during 1950–2000 (which include experimental N addition performed at Stråsan and Skogaby) ranged ∼200–∼2000 kg ha−1 of N. Across all sites and treatments, current NO3− leaching ranged from low (∼0.1 kg ha−1 year−1 of N) at Stråsan, to high (∼15 kg ha−1 year−1 of N) at Skogaby and Čertovo. We found significantly lower C/N ratios and greater amounts of extractable inorganic N species in the forest soils’ O-horizons at the high N loading plots. Microbial biomass and basal respiration decreased under experimental N addition treatments and tended to decrease with increased N deposition. Similarly, activities of hydrolytic enzyme activity associated with N acquisition were lower, although differences in activities at specific sites with the highest and intermediate historical N deposition levels failed statistical significance. Conversely, activities of soil hydrolytic enzymes associated with C acquisition were greater in study plots exposed high N loading. PLFA profiles indicated shifts in microbial community composition induced by long-term N load, towards higher and lower relative abundance of Gram-positive and Gram-negative bacteria, respectively (but no changes in fungal relative abundance). Taken together, our results suggest that long-term N loading of N-limited Norway spruce forests aggravates limitation of other resources, likely of C, for soil microbial communities. Although microbial variables in the soil O-horizon differed between plots exposed to low and high current N loading, microbial variables in plots that leached small amounts and large amounts of NO3− exposed to high N load were similar.

Introduction of Faba bean in crop rotation: Impacts on soil chemical and biological characteristics

Agricultural practices such as crop rotation affect soil physical, chemical and biological properties. Legumes crop effect has been shown to provide several agro-ecological services as a cereal previous crop. The aim of the present field study was to estimate the middle term effects of introducing faba bean in crop rotation on the structure and function of soil microbial communities. Two experimental rotation systems were tested (i) Wheat-Beet-Faba Bean-Rape-Wheat (Leg+) and (ii) Wheat-Flax-Wheat-Beet-Wheat (Leg−). Soil samples were collected on tilled plots at 0–10cm depth on July 2013 under wheat. Soil microbial biomass and soil enzymatic activities (β-glucosidase, cellulase, urease and arylamidase activities) were assessed. Soil microbial diversity was evaluated with two complementary approaches: Phospholipid fatty acid profiling (PLFA) and the metabolic capabilities of the microbial community (Biolog Ecoplates). Soil organic carbon and total nitrogen were significantly and respectively 1.5 and 1.3 times higher in faba bean's rotation compared to free faba bean rotation. Soil microbial biomass did not differ significantly between the two rotations. In general, Leg+ rotation resulted in the greatest carbon mineralization and β-glucosidase and arylamidase activities. The analysis of Biolog data and PLFA profiling indicated that the rotation including faba bean has modified microbial populations and induced differences in the catabolic capability of soil microbial communities. Our results suggested that changing rotation crop by introducing faba bean two years before wheat modifies the surrounding habitat of microbial communities by providing available carbon and nitrogen as well as suitable soil pH. This new habitat could impact the structure of microbial communities and their functions. Leg + rotation seems to be a suitable practice promoting microbial activities in agricultural plots.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change.

Degradation of S-metolachlor and its Effects on Soil Enzymes and Microbial Communities in Vegetable Field Soil

S-metolachlor is a promising alternative to metolachlor. However, the extensive use of S-metolachlor as herbicide in vegetable fields in China has caused concerns about its environmental fate. Here we investigated the effects of temperature, relative humidity (RH) and PH on the degradation rate of S-metolachlor in vegetable soil. The degradation rates of S-metolachlor increased with increasing temperatures and RH and either acidic or basic PH facilitates S-metolachlor degradation. The degradation of S-metolachlor under these conditions followed the first-order kinetics resulting in the half-lives (T-1/2) ranging from 12.18 d to 70.71 d at 5–35°C, and 27.28 d to 53.72 d at RH 30–90%; and 29.62–19.69 d at pH 6–8. Stronger response of soil enzymes including catalase, dehydrogenase, urease and cellulase to S-metolachlor was detected in soil with high organic matter. PLFA profiles showed that, totally, the microbe populations including actinomycetes, fungi and bacteria increased gradually in the first 14 days after the treatment and decreased from 14d to 28d after the treatment. All the S-metolachlor treatments caused the increase of aerobe and anaerobe. High S-metolachlor concentration, 13.9 mg/kg, could cause significant variation at the first 2 weeks, stimulating growth of the entire soil microbial community. These findings might have practical implications for the fate of S-metolachlor residue in vegetable fields. Environmental factors, especially temperature, relative humidity and pH should be considered in combination with the appropriate application dose of S-metolachlor for achieving satisfactory weed-control efficacy, reducing runoff, and minimizing effects on environmental quality.

Effects of seawater irrigation on soil microbial community structure and physiological function

Irrigation with diluted seawater would be an alternative water resource which can play an important role under scarce resources of freshwater for promoting agricultural production in coastal areas. Salvadora persica Linn. was irrigated with different concentrations of seawater (0, 10, 20, 40, 60, 80 and 100 % seawater), and their effect on plant growth, nutrient contents in soil and plants, shift in soil microbial community structure (phospholipid fatty acid; PLFA) and community-level physiological profiling (CLPP, Biolog ECO MicroPlate) were studied. Plant dry matter was significantly increased with all seawater treatments, and highest increase was at 20 % seawater treatment. Sodium and chloride contents were significantly increased, whereas ratios of K/Na and Ca/Na were significantly decreased in plants with seawater irrigation. Soil electrical conductivity (EC), available K and Na were significantly increased with increasing the concentration of seawater. Total PLFA concentration and PLFA profile of soils were used as indices of total microbial biomass and community composition, respectively. The concentrations of total PLFA, gram-positive, gram-negative and actinomycetes biomarker PLFAs were significantly reduced at 20, 40, 80 and 40 % concentrations of seawater, respectively. The application of different concentrations of seawater induced a clear shift in the soil microbial community structure toward the bacterial abundance. The microbial community structure and community-level physiological profiling in seawater irrigation treatments had significantly differentiated. It can be concluded that irrigation with different concentrations of seawater had significant impact on soil chemical and microbial properties which is attributed due to the salinity stress.

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data

The aim of this work was to check whether a methodology based on the analysis of data that contain the entire phospholipid fatty acid, PLFA, compositions of water samples can be successfully used to interpret spatial and temporal changes in the microbial communities in water reservoirs. The proposed methodology consists of the construction of a modified weighted multivariate mixture model for the PLFA profiles of the water samples collected in a given monitoring campaign and the identification of latent PLFA components through a comparison with the known PLFA profiles of some cultivated or non-cultivated microbial communities. A 16S rDNA analysis of some of the selected water samples in the monitoring campaign was performed in order to verify the results of the PLFA analysis.The results showed that the proposed methodology can be useful for a dynamic and sensitive evaluation of changes in the microbial quality of water before and after flash flooding and can help in taking a decision regarding further risk assessment.

Pastures to woodlands: changes in soil microbial communities and carbon following reforestation

Reforestation of agricultural lands has the potential to sequester C, while providing other environmental benefits. It is well established that reforestation can have a profound impact on soil physicochemical properties but the associated changes to soil microbial communities are poorly understood. Therefore, the objective of this study was to quantify changes in soil physicochemical properties and microbial communities in soils collected from reforested pastures and compare then to remnant vegetation and un-reforested pastures. To address this aim, we collected soil from two locations (pasture and its adjacent reforested zone, or pasture and its adjacent remnant vegetation) on each of ten separate farms that covered the range of planting ages (0–30 years and remnant vegetation) in a temperate region of southeastern Australia. Soils were analysed for a range of physicochemical properties (including C and nutrients), and microbial biomass and community composition (PLFA profiles). Soil C:N ratios increased with age of tree planting, and soil C concentration was highest in the remnant woodlands. Reforestation had no clear impact on soil microbial biomass or fungal:bacterial ratios (based on PLFA’s). Reforestation was associated with significant changes in the molecular composition of the soil microbial community at many farms but similar changes were found within a pasture. These results indicate that reforestation of pastures can result in changes in soil properties within a few decades, but that soil microbial community composition can vary as much spatially within pastures as it does after reforestation.

Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management

Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method—PLFA), activity (fluorescein diacetate hydrolysis—FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices—the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides.Electronic supplementary materialThe online version of this article (doi:10.1007/s10646-016-1661-7) contains supplementary material, which is available to authorized users.

Monitoring the changes in a bacterial community in petroleum-polluted soil bioaugmented with hydrocarbon-degrading strains

Bioaugmentation is a strategy used to enhance degradation of petroleum compounds in contaminated soils, however little is known about the interactions between introduced bacteria and autochthonous microflora. Therefore the objective of the study was to assess any changes in the structure and metabolic activity of the soil bacterial communities as a result of the introduction of Bacillus subtilis T′-1 or Pseudomonas sp. P-1, as well their consortium, into petroleum-contaminated soil. The bioaugmentation experiment was carried out under laboratory conditions using soil taken from an industrial area located around a refinery in Czechowice-Dziedzice. After the bioaugmentation process, a significant (P<0.05) decrease in the TPH content was reported in all inoculated soils. Inoculation of the soil with the bacterial consortium resulted in a three times greater removal of TPH compared to soils inoculated with single strains. It has been reported that all of the strains had an ability to survive in the environment during the experimental period. The introduction of bacterial strains led to increase in the number of 16S rRNA gene copies in soil on 1 and 7days of the experiment as well as alkB gene copies during 91days of the study compared to the non-treated soil. Analysis of the 16S rRNA and alkB genes-based DGGE fingerprints showed that introduced bacteria changed the genetic diversity of the total bacterial communities as well as the communities that have the genes involved in the degradation of hydrocarbons. Analysis of the PLFA profiles showed that the bacterial strains caused short-term changes in the amounts of fatty acids characteristic for Gram-positive and Gram-negative bacteria. The CLPPs indicated differences in soil metabolic activity between the inoculated and non-inoculated soils after the bioaugmentation process.