Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities.

Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.

Assessing the Ecotoxicity of Eight Widely Used Antibiotics on River Microbial Communities.

Global prevalence of antibiotic residues (ABX) in rivers requires ecotoxicological impact assessment. River microbial communities serve as effective bioindicators for this purpose. We quantified the effects of eight commonly used ABXs on a freshwater river microbial community using Biolog EcoPlates™, enabling the assessment of growth and physiological profile changes. Microbial community characterization involved 16S rRNA gene sequencing. The river community structure was representative of aquatic ecosystems, with the prevalence of Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. Our findings reveal that all ABXs at 100 µg/mL reduced microbial community growth and metabolic capacity, particularly for polymers, carbohydrates, carboxylic, and ketonic acids. Chloramphenicol, erythromycin, and gentamicin exhibited the highest toxicity, with chloramphenicol notably impairing the metabolism of all studied metabolite groups. At lower concentrations (1 µg/mL), some ABXs slightly enhanced growth and the capacity to metabolize substrates, such as carbohydrates, carboxylic, and ketonic acids, and amines, except for amoxicillin, which decreased the metabolic capacity across all metabolites. We explored potential correlations between physicochemical parameters and drug mechanisms to understand drug bioavailability. Acute toxicity effects at the river-detected low concentrations (ng/L) are unlikely. However, they may disrupt microbial communities in aquatic ecosystems. The utilization of a wide array of genetically characterized microbial communities, as opposed to a single species, enables a better understanding of the impact of ABXs on complex river ecosystems.

Microbial Community Response to Various Types of Exogenous Organic Matter Applied to Soil.

Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha-1. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity.

Effects of copper sulfate algaecide on the cell growth, physiological characteristics, the metabolic activity of Microcystis aeruginosa and raw water application.

Harmful cyanobacteria blooms (HCBs) occurred frequently and become a serious scientific challenge. Copper sulfate (CuSO4) is a broad-spectrum chemical algaecide to control algae blooms. Herein, the Microcystis aeruginosa was exposed to different CuSO4 (0.0, 0.2 and 0.5 mg/L) to assess the variations in algal physiological process and metabolic profiles. The results indicated that exposure to CuSO4 of 0.5 mg/L at 72 h could significantly inhibit the cell growth and photosynthetic capacity of M. aeruginosa, including chl-a content and chlorophyll fluorescence parameters. Plasma membrane damage causing cell lysis of M. aeruginosa increased the K+ release. The increase of SOD and CAT suggested that CuSO4 treatment caused oxidative stress in algal cells. Different doses of CuSO4 modified the carbon metabolic potential, algal cells had their unique metabolic mode thereby. Moreover, the research further verified that CuSO4 would also inhibit algal growth and change algal community structure in site-collected water application. Overall, laboratory results of M. aeruginosa to CuSO4 and site-collected water application of algal responses to CuSO4 might be conducive to uncovering the controlling mechanism of algae and the potential effect of carbon cycling in an ecological environment.

Elucidating the microbiome of the sustainable peat replacers composts and nature management residues.

Sustainable peat alternatives, such as composts and management residues, are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. This study examined if and how microbiological characteristics of subtypes of composts and management residues differ from peat-based substrates, and how feedstock and (bio)chemical characteristics drive these characteristics. In addition, microbiome characteristics were evaluated that may contribute to plant growth and health. These characteristics include: genera associated with known beneficial or harmful microorganisms, microbial diversity, functional diversity/activity, microbial biomass, fungal to bacterial ratio and inoculation efficiency with the biocontrol fungus Trichoderma harzianum. Bacterial and fungal communities were studied using 16S rRNA and ITS2 gene metabarcoding, community-level physiological profiling (Biolog EcoPlates) and PLFA analysis. Inoculation with T. harzianum was assessed using qPCR. Samples of feedstock-based subtypes of composts and peat-based substrates showed similar microbial community compositions, while subtypes based on management residues were more variable in their microbial community composition. For management residues, a classification based on pH and hemicellulose content may be relevant for bacterial and fungal communities, respectively. Green composts, vegetable, fruit and garden composts and woody composts show the most potential to enhance plant growth or to suppress pathogens for non-acidophilic plants, while grass clippings, chopped heath and woody fractions of compost show the most potential for blends for calcifuge plants. Fungal biomass was a suitable predictor for inoculation efficiency of composts and management residues.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou's evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3 - was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris).

The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon's diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.

The microbial metabolic activity on carbohydrates and polymers impact the biodegradability of landfilled solid waste.

Biological waste degradation is the main driving factor for landfill emissions. In a 2-year laboratory experiment simulating different landfill in-situ aeration scenarios, the microbial degradation of solid waste under different oxygen conditions (treatments) was investigated. Nine landfill simulation reactors were operated in triplicates under three distinct treatments. Three were kept anaerobic, three were aerated for 706 days after an initial anaerobic phase and three were aerated for 244 days in between two anaerobic phases. In total, 36 solid and 36 leachate samples were taken. Biolog® EcoPlates™ were used to assess the functional diversity of the microbial community. It was possible to directly relate the functional diversity to the biodegradability of MSW (municipal solid waste), measured as RI4 (respiration index after 4 days). The differences between the treatments in RI4 as well as in carbon and polymer degradation potential were small. Initially, a RI4 of about 6.5 to 8 mg O2 kg-1 DW was reduced to less than 1 mg O2 kg-1 DW within 114 days of treatment. After the termination of aeration, an increase 3 mg O2 kg-1 DW was observed. By calculating the integral of the Gompertz equation based on spline interpolation of the Biolog® EcoPlates™ results after 96 h two substrate groups mainly contributing to the biodegradability were identified: carbohydrates and polymers. The microbial activity of the respective microbial consortium could thus be related to the biodegradability with a multilinear regression model.

Functional Metabolic Diversity of Bacterioplankton in Maritime Antarctic Lakes.

A summer survey was conducted on the bacterioplankton communities of seven lakes from Byers Peninsula (Maritime Antarctica), differing in trophic and morphological characteristics. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The versatility for metabolizing carbon sources was also assessed in three of the lakes using Biolog Ecoplates. Relevant differences among lakes and within lake depths were observed. A total of 23 metabolic activities associated to the main biogeochemical cycles were foreseen, namely, carbon (11), nitrogen (4), sulfur (5), iron (2), and hydrogen (1). The aerobic metabolisms dominated, although anaerobic respiration was also relevant near the lakes' bottom as well as in shallow eutrophic lakes with higher nutrient and organic matter contents. Capacity for using carbon sources further than those derived from the fresh autochthonous primary production was detected. Clustering of the lakes based on metabolic capabilities of their microbial communities was determined by their trophic status, with functional diversity increasing with trophic status. Data were also examined using a co-occurrence network approach, indicating that the lakes and their catchments have to be perceived as connected and interacting macrosystems, where either stochastic or deterministic mechanisms for the assembling of communities may occur depending on the lake's isolation. The hydrological processes within catchments and the potential metabolic plasticity of these biological communities must be considered for future climate scenarios in the region, which may extend the growing season and increase biomass circulation.

Presence of polyethylene terephthalate (PET) fibers in hyporheic zone alters colonization patterns and seasonal dynamics of biofilm metabolic functioning.

Worldwide, the production of plastics is increasing, and plastic pollution in aquatic environments is a major global concern. Under natural conditions, plastic weathers to smaller pieces called microplastics (MP), which come in various shapes, with fibers often being the most common in freshwater sediments. The hyporheic zone, an ecotone between surface and groundwater, is important for the transport and fate of all MP particles. The main metabolic pathways in rivers take place in the hyporheic zone and are driven by a diverse microbial community. The objective of this study was to investigate in situ whether the presence of PET fibers in riverbed sediments affects patterns of colonization and the seasonal dynamics of microbial metabolic activities in the hyporheic zone. The effects of the presence of PET on microbial metabolism were evaluated in situ over a month (colonization study) and over a year (seasonal study) by measuring total protein content (TPC), and microbial respiration as respiratory electron transport system activity (ETSA) and by community-level physiological profiling (CLPP). Additionally, PET fibers were examined under a scanning electron microscope (SEM), and isotopic analysis (δ13C) of PET was performed after one year of exposure to field conditions. The findings demonstrated that during colonization and biofilm formation, and also over the seasons, the date had a large and significant impact on biofilm growth and activity, while PET presence slightly suppressed microbial biomass (TPC) and respiratory activity (ETSA). Overall microbial activity was repressed in the presence of PET fibers but there was a higher capacity for the utilization of complex synthetic polymer substrates (i.e., Tween 40) which have previously been linked to polluted environments. SEM micrographs showed diverse microbial communities adhering to PET fibers but little surface deterioration. Similarly, isotopic analysis suggested little deterioration of PET fibers after one year of in situ conditions. The study indicated that PET fibers present in riverbed sediments could have impacts on the metabolic functioning in rivers and thus affect their self-cleaning ability.

Understanding the Shift in the Microbiome of Composts That Are Optimized for a Better Fit-for-Purpose in Growing Media.

Three characteristics are considered key for optimal use of composts in growing media: maturity, pH and organic matter content. Maturation is a critical step in the processing of composts contributing to compost quality. Blending of composts with chopped heath biomass, sieving out the larger fraction of composts and acidification of composts by adding elemental sulfur may be used either to increase organic matter content or to reduce pH for a better fit in growing media. While several studies have shown the effectiveness of these treatments to improve the use of composts in growing media, the effect of these treatments on the compost microbiome has merely been assessed before. In the present study, five immature composts were allowed to mature, and were subsequently acidified, blended or sieved. Bacterial and fungal communities of the composts were characterized and quantified using 16S rRNA and ITS2 gene metabarcoding and phospholipid fatty acid analysis. Metabolic biodiversity and activity were analyzed using Biolog EcoPlates. Compost batch was shown to be more important than maturation or optimization treatments to determine the compost microbiome. Compost maturation increased microbial diversity and favored beneficial microorganisms, which may be positive for the use of composts in growing media. Blending of composts increased microbial diversity, metabolic diversity, and metabolic activity, which may have a positive effect in growing media. Blending may be used to modify the microbiome to a certain degree in order to optimize microbiological characteristics. Acidification caused a decrease in bacterial diversity and microbial activity, which may be negative for the use in growing media, although the changes are limited. Sieving had limited effect on the microbiome of composts. Because of the limited effect on the microbiome, sieving of composts may be used flexible to improve (bio)chemical characteristics. This is the first study to assess the effects of maturation and optimization treatments to either increase organic matter content or lower pH in composts on the compost microbiome.

Comparison of microbial community structure and function in sediment between natural regenerated and original mangrove forests in a National Nature Mangrove Reserve, South China.

Mangrove has been destroyed and reforestation is often undertaken, but whether a regenerated forest could restore its ecological function is not clear. This study compares microbial community structure and function in sediment of the 17-years old natural regenerated mangrove forest (Y17) with the original forest (Y74). No significant differences in phospholipid fatty acid (PLFA) profiles and microbial metabolism of most carbon substrates were found between these two forests. However, activities of dehydrogenase, protease, cellulase and phosphatase were lower in Y17 than Y74, and some specific microbial functions were also different. Both forests exhibited significant seasonal differences in enzyme activities and microbial characteristics, but such difference was larger in Y17 than Y74, indicating the regenerated forest was more sensitive to season. Correspondence analysis based on PLFA profiles and enzyme activities revealed the microbial community in Y17 was comparable to Y74, suggesting sediment microbial characteristics in natural regenerated mangroves could be restored.

Combination of plant-growth-promoting and fluoranthene-degrading microbes enhances phytoremediation efficiency in the ryegrass rhizosphere.

Plant- and/or microbe-based systems can provide a cost-effective, sustainable means to remove contaminants from soil. Microbe-assisted phytoremediation has potential utility for polycyclic aromatic hydrocarbons such as fluoranthene (Flu) removal from soils; however, the efficiency varies with the plant and microbes used. This study evaluated the Flu removal efficiency in a system with ryegrass (Lolium multiflorum), an IAA-producing Arthrobacter pascens strain (ZZ21), and/or a Flu-degrading Bacillus cereus strain (Z21). Strain ZZ21 significantly enhanced the growth of ryegrass. Ryegrass in combination with both strains (FIP) was the most effective method for Flu removal. By day 60, 74.9% of the Flu was depleted in the FIP treatment, compared with 21.1% in the control (CK), 63.7% with ryegrass alone (P), 69.0% for ryegrass with ZZ21 (IP), and 72.6% for ryegrass with Z21 (FP). FIP treatment promoted ryegrass growth, accelerated Flu accumulation in plants, and increased soil microbial counts. Microbial carbon utilization was significantly higher in soil in the FIP than with the CK treatment. Principal component analysis of the distribution of carbon substrate utilization showed that microbial functional profiles diverged among treatments, and this divergence became more profound at day 60 than day 30. Microbial inoculation significantly enhanced microbial utilization of phenols. Microbes in the FIP soil dominantly utilized amines/amides and phenols at day 30 but shifted to carbohydrates by day 60. Together, the combination of IAA-producing microbes and Flu-degrading microbes could promote plant growth, facilitate Flu degradation, and change soil microbial functional structure.

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure - A mesocosm study.

Bauxite residues (BR), commonly named red muds, are the saline-sodic waste produced during the extraction of alumina from bauxite. In this study, four kinds of BR were mixed at increasing concentrations with two soils in a mesososm experiment. Unamended BR from Provence (PRO) and Guinea (GUI) bauxite were selected, and Modified Bauxite Residues from PRO and GUI (MBR-PRO and MBR-GUI) were obtained by gypsum application and repeated leaching, in order to reduce their pH, electrical conductivity (EC) and exchangeable sodium percentage (ESP). Several indicators of microbial community functions and structure (growth of culturable bacteria; enzymatic activities; C-sourced substrates degradation (Biolog®); bacteria and fungi PCR-RFLP fingerprints) were measured after 35 days of incubation. Results showed that PRO residue had stronger negative effects than GUI on all the tested indicators. Residues modified by gypsum addition (MBR-PRO, MBR-GUI) were equally or sometimes less harmful compared to unamended residues. Microbial activities (bacterial growth and enzyme activities) were more inhibited than the diversity of microbial functions (Biolog®), and the structure of bacterial and fungal communities was not affected by increasing concentrations of bauxite residues. EC and ESP were the main factors explaining the inhibition of microbial activities, although the origin of bauxite residue is of great importance too.

Liming and Nitrogen Fertilization Effects on Soil Microbial Community in Long Term No-till

Abstract Soil management influences organic matter decomposition rates as well soil microbial community functional behavior. No-till (NT) is the most used management system by farmers due to its conservation practices and high productivity. The main objective of this study was to evaluate the impact of surface-applied lime, nitrogen (N) application, and black oat residues on soil microbial community of a Typic Hapludox under continuous NT. Therefore, soil chemical attributes, microbial biomass carbon, basal respiration, metabolic quotient, most probable number of diazotrophs, as well as bacterial functional analysis were performed. The effect of liming and N fertilization amendments inputs were saw in soil respiration and metabolic quotient measurements, showing them to be good indicators of soil quality. Further studies should be carried out in order to molecularly identify microbial communities present in soils with different liming and N fertilization management to evaluate the behavior of specific bacterial taxa under such conditions.

Disentangling natural and anthropogenic impacts on groundwater by hydrogeochemical, isotopic and microbiological data: Hints from a municipal solid waste landfill.

Within human-impacted areas, high levels of inorganic compounds in groundwater are broadly and preventively attributed to local anthropogenic pollution, thoroughly disregarding geogenic natural background levels. Particularly in landfills, a proper evaluation of the significant adverse environmental effects should be completed through a detailed groundwater characterization, and appropriate reference values established prior to landfill onset. However, the monitoring network may lack a full hydrogeological representativeness of the site and of the background conditions of groundwater. This study aimed at disentangling natural and anthropogenic impacts through a synoptic analysis of hydrogeochemical, isotopic and microbiological characteristics of groundwaters from a municipal solid waste landfill area in Central Italy. Samples were collected during four seasonal monitoring surveys from the mostly anoxic aquifer underlying the target area. Field parameters, inorganic and organic compounds, environmental isotopes, faecal contamination, and microbial community characteristics were determined, along with a detailed hydrogeological conceptual model. Key inorganic contaminants (As, Fe and Mn) exceeded the local threshold values in most of the sampling points, while organic contamination was generally very low. Stable isotopes suggested that groundwater originated mainly from local rainfall, except at one monitoring points where tritium levels might indicate moderate impact. Microbiological data and the microbial community characterization, assessed by flow cytometry and BIOLOG assays, provided further supportive information, also highlighting fundamental effects of groundwater quality alterations. Overall, an integrated multi-parametric approach proved suitable to distinguish geogenic and anthropogenic impacts, thus improving strategies and schemes for protection and management of groundwaters in landfills and waste related industrial areas.

Residue management alters microbial diversity and activity without affecting their community composition in black soil, Northeast China.

Residue management is an important agricultural practice for improving soil fertility. To reveal the impact of residue management on soil microbial community, we conducted a field experiment with three treatments: no straw returning (control, CK), straw returning (SR), and straw returning combined with cow manure (SM). Our results indicated that soil organic matter content was significantly higher in SR treatment than CK in both seedling and jointing stages. In seedling stage, the lowest total nitrogen content was observed in CK treatment, and significantly lower than that in SM and SR treatment. Furthermore, soil available phosphorus content was significantly higher in SM and SR treatment than CK in jointing stage. In the seedling stage, the soil microbial average wellcolor development (AWCD) value, microbial McIntosh index, and Shannon index of CK and SM treatments were significantly higher than those in SR treatment. The AWCD value and McIntosh index in the jointing stage showed similar patterns: SM > CK > SR. Permutational multivariate analysis of variance indicated that soil microbial community was significantly affected by growth stage, but unaffected by residue management. The partial Mantel test revealed that the available potassium and the C/N ratio had independent effects on soil microbial community. Overall, our results indicated that straw returning combined with cow manure had a beneficial effect on soil fertility, microbial activity and diversity.

Genetic and Functional Diversity of Bacterial Microbiome in Soils With Long Term Impacts of Petroleum Hydrocarbons.

Soil contamination with petroleum, especially in the area of oil wells, is a serious environmental problem. Restoring soil subjected to long-term pollution to its original state is very difficult. Under such conditions, unique bacterial communities develop in the soil that are adapted to the contaminated conditions. Analysis of the structure and function of these microorganisms can be a source of valuable information with regard to bioremediation. The aim of this study was to evaluate structural and functional diversity of the bacterial communities in soils with long-term impacts from petroleum. Samples were taken from the three oldest oil wells at the Crude Oil Mine site in Weglówka, Poland; the oldest was established in 1888. They were collected at 2 distances: (1) within a radius of 0.5 m from the oil wells, representing soil strongly contaminated with petroleum; and (2) 3 m from the oil wells as the controls. The samples were analyzed by 16S rRNA sequencing and the community level physiological profiling (CLPP) method in order to better understand both the genetic and functional structure of soil collected from under oil wells. Significant differences were found in the soil samples with regard to bacterial communities. The soils taken within 0.5 m of the oil wells were characterized by the highest biodiversity indexes. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria were strongly correlated with biological activity in these soils. Families of Alphaproteobacteria were also dominant, including: Bradyrhizobiaceae, Rhizobiaceae, Rhodobacteraceae, Acetobacteraceae, Hyphomicrobiaceae, and Sphingomonadaceae. The study showed that the long term contamination of soil changes bacterial communities and their metabolic activity. Even so, natural bioremediation leads to the formation of specific groups of bacteria that actively grow at the site of contamination in the soil.

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.

Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management.

Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional diversity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less diverse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.