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Geomorphodiversity is a new emerging topic in earth sciences. Landform diversity influences and interacts with both biodiversity and geodiversity. Hence, there is an increased awareness of the need to understand patterns of geomorphodiversity in different landscapes facing the actual global change. An increasing body of evidence indicates that global climate change is taking place and that it will have important effects on biological processes over the next decades, such as yields and the quality of products, the distribution and outbreak potential of pests in a vast range of crops species, and across all land uses and landscapes.A new approach of landform geodiversity and biodiversity evaluation is proposed, based on the geomorphometric-biogeochemical signature of several geodynamic settings of the Tuscany region. Starting from a geomorphometry approach, the geostatistical and geostochastic modelling enables to quantify, describe, and compare different landforms, providing an objective and useful tool to delineate the signature and the bio-geocomplexity of landforms. The geochemical approach is based on the detection of REEs pattern distribution and fractionation signatures as tools for tracing natural geochemical processes and soil-plant interactions to compare landforms of different origins. Using both REEs and the 87Sr/86Sr ratio it was possible to compare landscapes of different origins and ages. In addition, bioinformatics were used to evaluate species–environment relationships, and to determine factors explaining changes in bacterial composition developed on eleven contrasting lithologies.Whereas most authors have focused on mountainous, coastal and/or continental areas, for the first time a study of this type is applied to different landforms that support a centuries-old Mediterranean olive groves.The general aims of this work is to define a conceptual framework and test a new methodology to improve the knowledge related to the interaction between chemico-physical and biological soil processes able to shape landforms at various spatio-temporal scales. In particular, we will discuss the role of bio-geomorphic interactions influencing the nutrient/mineral content in olive fruit for geographic authentication, healthy food production and a healthy, biodiverse environment.

Soil contamination by SARS-CoV-2 is highly probable because soil can collect several transporters of the virus, such as fallout aerosols, wastewaters, relatively purified sludges, and organic residues. However, the fate and status of SARS-CoV-2 in soil and the possible risks for human health through contaminated food are unknown. Therefore, this perspective paper discusses the challenges of determining the SARS-CoV-2 in soil and the mechanisms concerning its adsorption, movement, and infectivity in soil, considering what has already been reported by perspective papers published up to May 2021. These issues are discussed, drawing attention to the soil virus bibliography and considering the chemical structure of the virus. The mechanistic understanding of the status and behavior of SARS-CoV-2 in soil requires setting up an accurate determination method. In addition, future researches should provide insights into i) plant uptake and movement inside the plant, ii) virus adsorption and desorption in soil with the relative infectivity, and iii) its effects on soil functions. Models should simulate spatial localization of virus in the soil matrix.

Climate change has strongly increased the fire frequency in Mediterranean forests causing changes in soil bacterial, fungal and microarthropod communities. Fire impacts on soil properties depend on vegetation covers. In this framework, the aim of this research was to evaluate the effects of fire on bacterial, fungal communities and microarthropod community in soils under trees and shrubs in a Mediterranean area. Surface soil cores were sampled in unburnt and burnt (three years since fire occurrence) patches in the Vesuvius National Park trees (Quercus ilex L. and Pinus nigra L.) and shrubs (Ginesta sp., Myrtus communis L., Laurus nobilis L.). Samples were analyzed for abiotic (pH, water content and concentrations of C, N, Corg, P, NO2 NH4+ and Pavail) and biotic (bacterial and fungal biomasses, and density, taxa richness, diversity, evenness and QBS-ar of microarthropods) properties. Results showed that, three years since fire, the abiotic properties were recovered in shrub stands but not yet in tree stands. Fire stimulated the development of bacteria only in shrub stands; no effects were observed for the fungal community in both shrub and tree stands; the amount and the taxa richness of microarthropods recovered to the values of the pre-fire conditions in both the stands. In conclusion, in the investigated area, fire differently impacted the vegetation covers, making soils under trees more similar to shrubs with the consequence to reduce the differences between the vegetation covers

In systemic sclerosis (SSc), the gastrointestinal tract (GIT) plays a central role in the patient’s quality of life. The microbiome populates the GIT, where a relationship between the Lactobacillus and gastrointestinal motility has been suggested. In this study, the analysis of oral Lactobacillus species in SSc patients and healthy subjects using culture-independent molecular techniques, together with a review of the literature on microbiota and lactobacilli in SSc, has been carried out. Twenty-nine SSc female patients (mean age 62) and twenty-three female healthy subjects (HS, mean age 57.6) were enrolled and underwent tongue and gum swab sampling. Quantitative PCR was conducted in triplicate using Lactobacillus specific primers rpoB1, rpoB1o and rpoB2 for the RNA-polymerase β subunit gene. Our data show significantly (p = 0.0211) lower LactobacillusspprpoB sequences on the tongue of patients with SSc compared to HS. The mean value of the amount of Lactobacillus ssprpoB gene on the gumsofSSc patients was minor compared to HS. A significant difference between tongue and gums (p = 0.0421) was found in HS but not in SSc patients. In conclusion, our results show a lower presence of Lactobacillus in the oral cavity of SSc patients. This strengthens the hypothesis that Lactobacillus may have both a protective and therapeutic role in SSc patients.

Environmental DNA is made-up of intracellular (iDNA) and extracellular (eDNA) pools. In soils, eDNA can be present up to 40% and could distort the assessment of living microorganisms. Distribution of microbial community is inconsistent among different size-aggregates, and the persistence and turnover of eDNA are thus uneven. Uneven persistence and distribution of eDNA could lead to heterogeneity in community analysis biases that arise due to eDNA sequences at micro-scale distribution. Here, we investigated the diversity and structure of eDNA and iDNA bacterial communities in bulk soil and different size-aggregates. Significant differences were observed between eDNA and iDNA bacterial diversity and composition. Changes in community composition are more important than the amount of eDNA to assess the biases caused by eDNA in community analysis. Furthermore, variations were also observed in aggregates-levels for eDNA and iDNA community which indicates that colonization pattern of iDNA community and protection of eDNA through absorbance on particle surface within soil-matrix is heterogeneous. Our work provides empirical evidence that eDNA presence could mask the detection of aggregates-level spatial dynamics in soil microbial community and have potential to qualitatively baffle observed live effects of given treatment by adequately muting the actual response dynamics of the soil microbiome.

The combined action of physical protection and chemical stabilisation is the main factor regulating the persistence of soil organic matter (SOM). In particular, physical protection refers to the compartmentalization of SOM and microbial biomass within aggregates. Thus, we have investigated the role of (macro-, meso- and micro-) soil aggregates in the protection of SOM and extracellular and intracellular DNA (eDNA vs iDNA) from oxidative stress by treating aggregates with Low Temperature Ashing (LTA) for different durations (0, 5, 24 and 48 h). DNA (exDNA vs iDNA) was sequentially extracted from the different aggregate size classes, and qualitatively (agarose gel electrophoresis) and quantitatively (fluorimetry; spectrophotometry) analysed, discriminating between double stranded (ds) and single stranded (ss) DNA. In addition, comparative PCR-DGGE (exDNA vs iDNA) was performed to assess the bacterial, fungal and archaeal communities of the different aggregate size classes. The use of LTA enabled to determine the amount of physically protected DNA in different aggregate sizes, evidencing the potential involvement of both exDNA and iDNA in the formation of the aggregates. Our results also provided insights into the important role of soil aggregates in protecting the genetic information of the autochthonous soil microbiota. The PCoA of bacterial, archaeal and fungal DGGE patterns displayed contrasting results. While fungal and archaeal fingerprinting patterns revealed direct relationships with aggregate sizes and LTA treatment, the bacterial community was not affected by these factors. This suggests a selective action of the size of aggregates on the dominant soil microbial community members. Our findings indicate that aggregates provide a protective habitat for the soil microbial community against environmental stress conditions, such as oxidative stress. Further, the specific protection of the soil microbiota (bacteria vs archaea vs fungi) is directly correlated to the size distribution of the microbial community and the aggregate size classes.

The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and more evident to the scientific community by the progressive discovery of functions accompanying to natural gene transformation. However, despite the increased number of published articles dedicated to eDNA in soil, so far only few are focused on its single stranded form (eDNAss). The present paper is the first to investigate the quantitative relevance of eDNAss in the total soil eDNA pool, discriminating between its linear (eDNAssl) and circular (eDNAssc) forms and the respective weakly (wa) and tightly (ta) adsorbed fractions. The results showed the prevalence of eDNAss and its linear form in both the total soil eDNA pool and its wa and ta fractions. Both of the eDNAss fractions (linear and circular) were characterized by small fragments.

Cellulose is the most abundant polysaccharide in the dead plant biomass, and its degradation is an important part of global carbon cycle. β-Glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. Genetic potential and expression of β-glucosidase genes were studied in the topsoil of a Picea abies forest in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families GH1 and GH3 amplified from DNA and RNA and amplicon pools were analyzed. Transcript pool were largely corresponded to gene pools, although some abundant transcripts were not found in the gene pool. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and Basidiomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria Acidobacteria and Deinococcus-Thermus. This indicates that a diverse microbial community utilized cellobiose. Seasonality influenced both genetic diversity of β-glucosidase genes and their expression. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in forest soils. Even β-glucosidase genes showing low abundance in DNA may be functionally important as revealed by their high expression especially in basidiomycota. The functional diversity in the studied ecosystem clearly exhibited a seasonal pattern.

In the last decades, many studies were addressed to focus the interplay between plant and microbial community into the soil and especially in the small soil zone in contact to plant root, called rhizosphere, which can be considered as a hotspot for interactions and therefore is a major target for improving nutrient use efficiency in crops. In this regard, unraveling the microbial activities that can be used to improve nutrient use efficiency may be the major challenge considering a sustainable agricultural contest. However, although using different approaches (metabolomics and transcriptomic) it has made it possible to characterize many interaction mechanisms, more remains largely unknown. Here, we summarize and discuss the abiotic and biotic factors that may manage plant-microbe interactions in the rhizosphere as well as in those parts of the soil furthest from the root, focusing on root architecture and nitrate as well.

It is essential to investigate to which extent and how specifically soil&ndash, plant&ndash, microbe interactions can be conditioned by different agricultural practices. Legumes such as Vicia faba is one of the essential functional group in intercropping and crop rotations due to its higher N fixing capacity. Hence, it is important to study the living microbial community of this legume. Further, it is also expected that fluctuations in soil microbial diversity and composition could be complemented by plant phenological stages and different fertilizer amendments. Thus, we investigated bacterial community composition in soil treated with phosphate-based inorganic and organic fertilizers, in the presence of Vicia faba plants at flowering and fruiting time using NGS 16S rRNA gene amplicon sequencing. Further, the evaluation of plant biomass parameters under different fertilizer treatments was also carried out. The presence of the Vicia faba plant increased the abundance of N fixing bacterial such as Bardyrhizobium, Microvirga (Rhizobiales), Arthrobacter, and Psuedoarthrobacter (Actinomycetales) in soil. Fluctuation in composition and diversity of bacterial community was further supplemented by plant phenological stages. These alterations could be due to changes that occurred in the plant nutrient requirement and varied root exudation patterns at a specific phenological stage. Further, fertilizer treatments also have a profound effect on the diversity and structure of the bacterial community. Organic fertilizers, especially vegetable tanned leather waste (VTLW), have a stronger effect on the composition and diversity of bacterial community compared to inorganic fertilizer (PT&mdash, triple superphosphate). Alpha-diversity was significantly decreased by both organic and inorganic amendments, especially a species evenness because each fertilizer tends to stimulate the growth of distinctive microbes that dominated the community of amended soil. Proteobacteria, Actinobacteria, and Cyanobacteria were the most abundant phyla, and Chelatococcus, Cyanobacteria, Sphingomonas, and Microvirga were a most abundant genus that contributed most in co-occurrence pattern, which suggests that these generalists are adapted to a variety of environments. These indicate that plant presence was a key, dominating factor, followed by fertilizers and time, in affecting soil bacterial diversity and composition. Plant recruits system (fertilization and time) -specific taxa due to differences in available nutrients and energy sources among different treatments during different growth stages. Further, fertilizer treatments did not have a stronger effect on plant production as compared to the effect on microbial community, which highlights that organic fertilizers did not tend to increase plant production. Thus, organic and inorganic amendments with matched macronutrients could have a similar impact on crop yields.

Alpine ecosystems are vulnerable to ever-changing environmental conditions, leading to shifts in vegetation distribution and composition with implications on soil functionality and carbon (C) turnover. Although deadwood represents an important global C stock, scarce information is available on how slope exposure influences the wood-inhabiting microbiota throughout the decomposition process in an Alpine setting. We therefore evaluated the impact of slope exposure (north- vs. south-facing sites) on physicochemical and microbiological properties (microbial abundance based on real-time PCR: fungal 18S rRNA, dinitrogen reductase [nifH]; microbial biomass: double strand DNA; and microbial activity: hydrolytic enzyme activities of the main nutrient cycles) of Picea abies wood blocks and the underlying soil in a field experiment in the Italian Alps during a three-year period. Overall, a higher abundance of fungi and nitrogen-fixing bacteria was recorded in the soil at the north-facing site where cooler and moister conditions were observed. In contrast, no exposure effects were found for these two microbial groups in the wood blocks, while their abundance increased over time, accompanied by more acidic conditions with progressing decay. The impact of exposure was also enzyme specific and time dependent for both the P. abies wood blocks and the underlying soil.

We studied the molecular diversity of β-glucosidase-encoding genes, microbial biomass, cellulase, N-acetyl-glucosaminidase, β-glucosidase, and β-galactosidase activities in the rhizosphere and bulk soil of two maize lines differing in nitrogen use efficiency (NUE). The maize lines had significant differences in diversity of β-glucosidase-encoding genes in their rhizosphere, and Actinobacteria and Proteobacteria were the dominating phyla in all samples, but representatives of Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Cyanobacteria were also detected. Among the Proteobacteria, β-glucosidase genes from α-, β-, and γ-Proteobacteria were dominant in the rhizosphere of the high NUE maize line, whereas δ-Proteobacteria β-glucosidase genes were dominant in the rhizosphere of the low NUE maize line. The high NUE maize line also showed higher glucosidase activities in the rhizosphere than the low NUE maize line. We concluded that plants with high NUE select bacterial communities in the rhizosphere differing in the diversity of β-glucosidase-encoding genes which likely result in higher C-hydrolyzing enzyme activities. These effects on the diversity of β-glucosidase-encoding genes may influence the C dynamics in the agro-ecosystems.

We performed a longitudinal study (repeated observations of the same sample over time) to investigate both the composition and structure of temporal changes of bacterial community composition in soil mesocosms, subjected to three different treatments (water and 5 or 25 mg kg(-1) of dried soil Cd(2+)). By analogy with the pan genome concept, we identified a core bacteriome and an accessory bacteriome. Resident taxa were assigned to the core bacteriome, while occasional taxa were assigned to the accessory bacteriome. Core and accessory bacteriome represented roughly 35 and 50 % of the taxa detected, respectively, and were characterized by different taxonomic signatures from phylum to genus level while 15 % of the taxa were found to be unique to a particular sample. In particular, the core bacteriome was characterized by higher abundance of members of Planctomycetes, Actinobacteria, Verrucomicrobia and Acidobacteria, while the accessory bacteriome included more members of Firmicutes, Clamydiae and Proteobacteria, suggesting potentially different responses to environmental changes of members from these phyla. We conclude that the pan-bacteriome model may be a useful approach to gain insight for modeling bacterial community structure and inferring different abilities of bacteria taxa.

Ascorbic acid is a bacteriostatic agent; one of the many ways by which ascorbic acid hampers bacterial growth is by the production of hydrogen peroxide, which further converts into hydroxyl free radicals. Certain amino acids can counteract the inhibitory effect of hydroxyl free radicals by checking their oxidizing effect. Though ascorbic acid is bacteriostatic in nature, it facilitates prokaryotic respiration by decarboxylation. This study was carried out to understand how microbes from different horizons of the forest soil respond to the addition of a bacteriostatic agent (ascorbic acid) and growth promoting agent (amino acids), with respect to the soil respiration. We observed that the addition of either ascorbic acid or a combination of it with amino acid consistently results in increased soil respiration, and this increase is different for different soil types depending on soil composition and origin. Furthermore, we also found that beta alanine-induced maximum respiration in basic soils and L-glutamic in acidic soils. This study is significant because it can be used to explain how a strong reducing sugar, i.e., ascorbic acid, affects the soil respiration mediated via soil microbes. To the best of our knowledge, it is the first report that demonstrates the effect of bacteriostatic and the growth promoting agent together on microbe-mediated soil respiration.

We set up a simple, culture independent, low-cost and high-throughput method for DNA-based quantitative assessment of soil microbial biomass using eight soils covering a wide range of physico-chemical properties. DNA was extracted with a 0.12 M, pH 8 Na2HPO4 buffer using bead beating; double stranded DNA (dsDNA) was quantified in a crude (not purified) extract using PicoGreen reagent. In contrast to yields obtained by using a commercial standard method (FastDNA Kit for soil, MP-Biomedicals), our yields of dsDNA were generally higher, most probably because any purification method for obtaining highly pure DNA for downstream analyses leads to DNA loss. These results suggest the new method provides more reliable quantitative data; thus it is a good environmental indicator, as an underestimation of the soil microbial biomass due to DNA loss during purification can be excluded. The ratio between microbial C (Cmic) obtained by the traditional, widely used fumigation-extraction method and dsDNA ranged from 12.0 to 63.5 μg Cmic per μg dsDNA. Crude DNA obtained by the new method as well as purified DNA obtained by using the commercial kit were compared in terms of quantity (fluorometry; spectrophotometry) and quality (purity indices: A260/A280, A260/A230; PCR compatibility; gel electrophoresis: molecular weight and molecular integrity). Our results suggest that the new method provides a high-throughput estimator of microbial biomass (expressed as μg dsDNA g−1 soil) in soils having widely different properties without the need for high-cost commercial extraction kits and/or cumbersome individual methods. Due to its simplicity, speed and low-cost, our method is capable for routine quantitative assessments of soil microbial biomass, assessable also for soil scientists with laboratories that are otherwise not equipped for molecular analyses.

International audience; Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physicochemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.

Olive trees play an important role in cultural, ecological, environmental and social fields, constituting in large part the Mediterranean landscape. In Tuscany, an important economic activity is based on olive. Unfortunately, the Verticillium wilt affects this species and causes vascular disease. In the present study, a real-time quantitative PCR approach has been used to detect and quantify Verticillium dahliae in soil and in olive tree tissues both in micropropagated and in seedling olives. The minimum amounts of V. dahliae DNA sequences detected in soil were 11.4 fg which is equivalent to less than one fungal haploid genome. In micropropagated olive the pathogen was detected in the leaves after 43 days, showing a vertical upward movement of the fungus from the culture medium to stem and leaves. A similar fungal behaviour was observed in inoculated olive stem where after 15 days the fungal DNA was detected from symptomless stem tissue above 8 cm the inoculation site. The described molecular approach is expected to provide a more sensitive and less time-consuming alternative detection method for V. dahliae than plating assay procedures, which were traditionally proposed as an early diagnosis method for Verticillium wilt to farmers and tree nursery growers.

This study was carried out to understand the interplay of plant Nitrogen Utilizing Efficiency (NUE) with protease activity and microbial proteolytic community composition in the rhizosphere and bulk soils. Protease activity, diversity and abundance of protease genes (using DGGE and qPCR respectively of two key bacterial protease encoding genes: alkaline metallo-peptidase ( apr ) and neutral-metallopeptidases ( npr )) were monitored in both rhizosphere and bulk soils from two maize in-bred lines L05 and T250 with higher and lower NUE respectively, using a rhizobox approach. Illumina sequencing was employed to assess the diversity of proteolytic communities encoding for the above-mentioned protease genes. Our results show higher enzyme activity, higher abundance and diversity of proteolytic genes in L05 maize rhizosphere, with higher NUE than in T250 maize rhizosphere.

We performed screening of bacteria inhabiting soil organic (O) layers vs mineral (A) layers. Community level and group-specific genetic fingerprinting was used to assess changes in bacterial structures of dry woodlands of Argentina as function of regional climate, season and land use. Multiple factor effects and correlations of soil organic matter, microbial biomass and bacterial structures were found, indicating substrate, soil moisture and moderate temperature as favorable conditions. Fingerprinting data showed distinct soil bacteria inhabiting O vs A layers. At the community level, lower similarities were found in the O layer (28%) than in the A layer (47%); this phenomenon was not always reflected at the group level, providing more accurate insights into environmental change induced shifts in soil bacterial structures (i.e., higher similarities among actinomycetes and ammonium oxidizers inhabiting the O layer with respect to the A layer). Specific bacterial groups were more affected in O than A layers, in wet summer and under moderate regional climate (moisture effect). N2 fixers were found to be the most sensitive community members (i.e., to grazing induced disturbances) and predominate in the O layer. Discrimination of soil bacteria provided evidences about the role of organic layer bacteria in overall organic matter dynamics.

The aim of the study was to evaluate the impact of cattle overwintering husbandry on composition of upland grassland soil archaeal, bacterial, and fungal communities by comparative fingerprinting (SSU rRNA denaturing gradient gel electrophoresis (DGGE)) of total (tDNA) and extracellular DNA (eDNA) extracted from three differently impacted soils (severely, moderately, and non-impacted soil) and cattle excrements. Cattle excrements carried a significant amount of viable microorganisms and eDNA, and as a result of its high external returns, the amounts of extractable eDNA in soil increased with cattle impact, being positively correlated with soil microbial biomass and activity. The soil eDNA fraction (2.8 to 5.7 μg g−1 dw) significantly contributed to the soil metagenome, representing 18–31 % of soil tDNA. The largest shift in soil community structure was observed for Archaea, followed by fungi and bacteria, indicating that soil bacteria possess the highest resilience to cattle-induced changes. Cattle excrements showed more diverse bacterial than archaeal and fungal communities. The specific DGGE bands of cattle excrements were also observed in community profiles of cattle-impacted soils, confirming the effect of cattle husbandry on composition of soil microbial communities, probably as a result of introduced rumen-borne microbes. Similar changes were also reflected in the eDNA-derived DGGE profiles, suggesting a higher contribution of bacteria to soil extracellular metagenome than Archaea and fungi. This study provided first evidences about the extracellular mobilome in cattle-impacted soils, carrying also genetic information of Archaea, and its susceptibility to impact by outdoor cattle husbandry.

This study focuses on the biological and morphological development of humus profiles in forested Italian Alpine soils as a function of climate. Humus form description, systematic investigation of microannelid communities and polyphasic biochemical fingerprinting of soil microbial communities (denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid analysis (PLFA)) were performed to compare sites differing in mean annual temperature due to different altitude and exposure. Although the soil biota showed complex responses, several differences in soil biological properties seem to be due to thermal differences. Although soil acidity also determines biological properties, it is not a state factor but rather influenced by them. The thickness of the organic layer and the acidification of the subjacent mineral horizon increased under cooler conditions (north-exposure; higher altitude), whereas the thickness of the A horizon inversely decreased. Species richness of microannelid assemblages was higher under warmer conditions (south-exposure; lower altitude) and the vertical distribution of microannelids shifted along the gradient to lower temperatures from predominant occurrence in the mineral soil to exclusive occurrence in the organic layer. Microbial biomass (total PLFA) was higher at the cooler sites; the prevalence of Gram-negative bacteria could be ascribed to their better adaptation to lower temperature, pH and nutrient contents. The δ13C signatures of the PLFA markers suggested a lower decomposition rate at the cooler sites, resulting in a lower respiratory loss and an accumulation of weakly decomposed organic material. DGGE data supported the PLFA results. Both parameters reflected the expected thermal sequence. This multidisciplinary case study provided indications of an association of climate, mesofauna and microbiota using the humus form as an overall link. More data are however needed and further investigations are encouraged.

International audience; Beringite (B) and zerovalent iron grit (Z), singly and in combination (BZ), were added to a loamy sand soil contaminated by trace elements (Reppel, Belgium), mainly by arsenic (As), to reduce As labile fractions and phytoavailability. An uncontaminated sandy soil was studied for comparison. Soils were placed in large lysimeters cultivated with maize and vegetables for 6 years. pH, organic C and total N content increased in amended soils. The Z and BZ treatments reduced the Ca(NO3)2− extractable soil As and As uptake by lettuce. The BZ lettuces had also the lowest foliar Pb, Cd, Zn, and Mn concentrations. All amendments had positive effects on the soil microbial biomass and reduced the qCO2. Glucose mineralization was increased in Z and BZ amended soils. Acid phosphomonoesterase activity was higher in the untreated soil than in the other soils; the alkaline phosphomonoesterase, phosphodiesterase and protease activities were increased by Z and BZ treatments, whereas B amendment had less positive effects. Genetic fingerprinting using Denaturing Gradient Gel Electrophoresis (DGGE) revealed shifts in the composition of eubacterial and fungal communities of the amended soils. Microbial species richness decreased rather than increased in the treated soils, regardless of reduced trace element availability and increased soil microbial biomass and activity.

The review discusses origin, state and function of extracellular DNA in soils and sediments. Extracellular DNA can be released from prokaryotic and eukaryotic cells and can be protected against nuclease degradation by its adsorption on soil colloids and sand particles. Laboratory experiments have shown that DNA adsorbed by colloids and sand particles can be taken up by prokaryotic competent cells and be involved in natural transformation. Most of these experiments have been carried out under artificial conditions with pure DNA molecules and pure adsorbing matrices, but in soils and sediments, pure surface-reactive colloids are not present and DNA is present with other cellular components (wall debris, proteins, lipids, RNA, etc.) especially if released after cell lysis. The presence of inorganic compounds and organic molecules on both soil particles and DNA molecules can influence the DNA adsorption, degradation and transformation of competent cells. Extracellular DNA can be used as C, N and P sources by heterotrophic microorganisms and plays a significant role in bacterial biofilm formation. The nucleotides and nucleosides originated from the degradation of extracellular DNA can be re-assimilated by soil microorganisms. Extracellular DNA in soil can be leached and moved by water through the soil profile by capillarity. In this way, the extracellular DNA secreted by a cell can reach a competent bacterial cell far from the donor cell. Finally, the characterisation of extracellular DNA can integrate information on the composition of the microbial community of soil and sediments obtained by analysing intracellular DNA.

The aim of this work was to study variations in the composition of eubacteria and ammonia-oxidizing populations of soil, both determined by denaturing gradient gel electrophoresis (DGGE), after the addition of a pharmaceutical fungal biomass, treated to degrade its DNA. This waste can be used as an amendment. The fungal biomass waste was added at three rates: 0.05, 0.1, and 1% per dry weight of soil. Control soil, without any amendment, was also investigated. Total DNA was extracted, purified, and amplified by using either universal (eubacteria) or specific (amoA) primers. Amplicons were separated by DGGE. Sequencing was also carried out to better assess the diversity of ammonia oxidizing bacteria. Changes in the composition of eubacterial community were detected after 3 days only in the soil treated with the highest dose, while the ammonia oxidizing population responded more promptly (after 1 day) with evident modifications at level of Nitrosolobus like sequences.

Several studies have investigated the adsorption of pure DNA on soil particles and its transformation ability. However, the presence of not purified (dirty) rather than pure DNA is more common in the extracellular soil environment. For this reason, we have investigated the adsorption and binding of dirty DNA on montmorillonite (M) and kaolinite (K) and their transforming ability in comparison to pure DNA. After lysis of Bacillus subtilis cells, induced by KCl, dirty DNA was characterized by the presence of cellular wall debris (cwd) and other constitutional organic components (coc). The dirty DNA was then divided into two fractions, one with cellular wall debris (DNA +cwd) and the other without cellular wall debris (DNA −cwd). B. subtilis BD 1512 (Cmr) and BD 170 (Cms) were selected as donor and recipient bacteria, respectively, for adsorption and transformation studies. Both cwd and coc seem to facilitate the adsorption of DNA to clay minerals, whereas only cwd promote the DNA binding on clays, protecting also the DNA fragments below 400 bp against nucleases. Both dirty DNA fractions adsorbed and bound on clay minerals were able to transform competent cells.

The application of pig slurry, high in ammonia-nitrogen concentration, to agricultural land is a practice whose effect on soil microbial communities is poorly understood. The autotrophic ammonia-oxidising bacteria are an integral component of the nitrogen cycle in soil, and their activity will be affected by addition of nitrogenous fertilizer. Molecular biological techniques were applied to the direct detection and identification of ammonia-oxidiser populations in cultivated soil plots treated with different amounts of pig slurry. Members of the genus Nitrosospira were shown by 16S rDNA-directed PCR to be present in both unamended and amended soils, regardless of the quantity of pig slurry applied. In contrast, members of the genus Nitrosomonas were detected by the same approach only in those soil plots that had received high loadings of slurry. The fidelity of amplification products was always confirmed by oligonucleotide probing. In addition, we used high stringency PCR and confirmatory gene probing to detect the presence of the ammonia monooxygenase gene (amoA) of Nitrosomonas europaea directly in all amended soil samples, with hybridization signal intensities that increased with the amount of pig slurry applied to plots. Nitrosomonas europaea amoA DNA could not be detected in soil from the untreated plot. These data support the view that nitrosospiras are ubiquitous as important members of nitrifying populations in the environment. The direct detection of nitrosomonad DNA only in amended soils supports the hypothesis that these nitrosomonads become highly competitive under conditions analogous to laboratory enrichment cultures.

We studied the distribution of the indigenous bacterial and fungal communities in a forest soil profile. The composition of bacterial and fungal communities was assessed by denaturing gradient gel electrophoresis (DGGE) of total and extracellular DNA extracted from all the soil horizons. Microbial biomass C and basal respiration were also measured to assess changes in both microbial biomass and activity throughout the soil profile. The 16S rDNA-DGGE revealed composite banding patterns reflecting the high bacterial diversity as expected for a forest soil, whereas 18S rDNA-DGGE analysis showed a certain stability and a lower diversity in the fungal communities. The banding patterns of the different horizons reflected changes in the microbial community structure with increasing depth. In particular, the DGGE analysis evidenced complex banding patterns for the upper A1 and A2 horizons, and a less diverse microflora in the deeper horizons. The low diversity and the presence of specific microbial communities in the B horizons, and in particular in the deeper ones, can be attributed to the selective environment represented by this portion of the soil profile. The eubacterial profiles obtained from the extracellular DNA revealed the presence of some bands not present in the total DNA patterns. This could be interpreted as the remainders of bacteria not any more present in the soil because of changes of edaphic conditions and consequent shifting in the microbial composition. These characteristic bands, present in all the horizons with the exception of the A1, should support the concept that the extracellular DNA is able to persist within the soil. Furthermore, the comparison between the total and extracellular 16S rDNA-DGGE profiles suggested a downwards movement of the extracellular DNA.

Oxytetracycline (OTC) and sulfamethoxazole (SMX) are two of most widely used antibiotics in livestock and poultry industry. After consumption of antibiotics, a major portion of these compounds is excreted through the feces and urine of animals. Land application of antibiotic-treated animal wastes has caused increasing concern about their adverse effects on ecosystem health. In this regard, inconsistent results have been reported regarding the effects of antibiotics on soil microbial activities. This study was conducted based on the completely randomized design to the measure microbial biomass carbon, cumulative respiration and iron (III) reduction bioassays. Concentrations of OTC and SMX including 0, 1, 10, 25, 50, and 100 mg/kg were spiked in triplicate to a sandy loam soil and incubated for 21 days at 25°C. Results showed that the effects of OTC and SMX antibiotics on cumulative respiration and microbial biomass carbon were different. SMX antibiotic significantly affected soil microbial biomass carbon and cumulative respiration at different treatments compared to control with increasing incubation time. OTC antibiotic, on the other hand, negatively affected cumulative respiration compared to control treatment throughout the incubation period. Although OTC antibiotic positively affected microbial biomass carbon at day one of incubation, there was no clear trend in microbial biomass carbon between different treatments of this antibiotic after that time period. Nevertheless, sulfamethoxazole and oxytetracycline antibiotics had similar effects on iron (III) reduction such that they considerably affected iron (III) reduction at 1 and 10 mg/kg, and iron (III) reduction was completely inhibited at concentrations above 10 mg/kg. Hence, according to our results, microbial biomass carbon and cumulative respiration experiments are not able alone to exhibit the effect of antibiotics on soil microbial activity, but combination of these two experiments with iron (III) reduction test could well display the effects of sulfamethoxazole (SMX) and oxytetracycline (OTC) antibiotics on soil biochemical activities.

To evaluate the effects of management practices and seasons on a soil bacterial community and the composition of ammonia-oxidizing bacteria (AOB), molecular screenings were compared among Mediterranean (Sardinia) soils with different plant covers and different agricultural practices, namely cork oak forest, tilled/non-tilled vineyard, hay crop and pasture. We compared the fingerprints from both independent replicates and pooled samples to ascertain the best approach for studying the environmental effects on bacterial composition. The soil microbial biomass, which was estimated from the amounts of extracted soil dsDNA, was 2 to 3 folds higher in the spring than in the autumn; in the spring, it was negatively correlated with the intensity of land use. A 16S rDNA DGGE experiment confirmed that both the land use and season markedly affect the composition of the soil bacterial community. Tilled vineyard soil exhibited the lowest similarities in community structures, suggesting that tillage induced the most marked disturbance among the tested land management methods. Distinct AOB populations were found for each type of land use; among these types, the cork oak forest proved to be a protective habitat for AOB against environmental changes. Our results suggest that the comparative community level and group-specific fingerprinting enabled an accurate evaluation of multiple factors in soil bacterial structures when performed with both independent and pooled replicates.

Study of the changes in soil microbial biomass, enzyme activity and the microbial community structure in the rhizosphere of two contrasting maize lines differing in the nitrogen use efficiency (NUE). The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soil and solution. We also determined microbial biomass, enzyme activities involved in the C, N, P and S cycles, and the microbial community structure using a phylogenetic group specific PCR-DGGE approach in the rhizosphere and bulk soil of both Lo5 and T250 maize lines. High NUE Lo5 maize induced faster inorganic N depletion in the rhizosphere and larger changes in microbial biomass and enzyme activities than the low NUE T250 maize line. The two maize lines induced differences in the studied microbial groups in the rhizosphere, with the larger modifications induced by the high NUE Lo5 maize line. The Lo5 maize line with higher NUE induced larger changes in soil chemical properties and in the enzyme activity, soil microbial biomass and community structure than the low NUE T250 maize line, probably due to differences in the root exudates of the two maize lines.

Probes for the detection of Azospirillum strains were obtained from DNA fragments generated by random amplification of polymorphic DNA (RAPD) and tested to assess their specificity towards DNA extracted from pure cultures. The most specific probe, referred to as α4, produced a hybridization signal only with amplified DNA of A. lipoferum ATCC29731. This strain was inoculated, together with two other Azospirillum strains, in soil microcosms of different complexity and its presence tested with the probe α4. This probe confirmed its high specificity with amplified DNA extracted from the soil microcosm and in the presence of other A. lipoferum strains, indicating that the strategy for bacterial detection, based on RAPD markers, is useful for monitoring the presence of a particular strain under environment-like conditions. Other RAPD-derived probes, when tested on soil samples, did not show the same level of specificity as that shown on DNA from pure cultures. This result suggests that some precautions are necessary in the choice of a really specific RAPD marker. In a further development of this strategy, the α4 probe was sequenced and two pairs of “nested” primers were designed, which enabled a diagnostic polymerase chain reaction from soil samples that was specific for the A. lipoferum species.

Soil aggregates, the basic structural unit of soil, provide special microhabitats and are assumed to protect both soil organic matter and microbiota against negative effects of harsh environmental conditions. Challenging to assess this protective effect on soil microbiota and soil DNA, we have calibrated in laboratory three different sizes of aggregates (0.5-1mm, 500-100µm and

The 16S rDNA of 17 strains of Azospirillum , 14 assigned to one of the known species A. amazonense A. brasilense A. halopraeferens A. irakense and A. lipoferum , and the other three of uncertain taxonomic position, was sequenced after polymerase chain reaction amplification and analysed in order to investigate the phylogenetic relationships at the intra-generic and super-generic level. The phylogenetic analysis confirms that the genus Azospirillum constitutes a phylogenetically separate entity within the a subclass of Proteobacteria and that the five species are well defined. A. brasilense and A. lipoferum are closely related species and form one cluster together with A. halopraeferens ; the pair of species A. amazonense and A. irakense forms a second cluster in which Rhodospirillum centenum is also placed.

There is a growing interest in the links between humus forms and soil biota, and little is known about these links in Mediterranean ecosystems. Culture-independent techniques, such as DNA extraction followed by DGGE and enzyme activities, allowed us to compare microbial communities in two horizons of a forest soil in different seasonal conditions. Direct in situ lysis was applied for extraction of DNA from soil; intracellular DNA was separated from extracellular and used to represent the composition of microflora. The aims were to describe how biochemical and microbiological parameters correlate with topsoil properties in typical Mediterranean Moder humus. Changes in bacterial and fungal community composition were evident from DGGE profiles. Degrees of similarity and clustering correlation coefficients showed that the seasonal conditions may affect the composition and activity of bacterial and fungal communities in the OH horizon, while in the E horizon the two communities were hardly modified. In the same season, OH and E horizons showed a different composition of bacterial and fungal communities and different enzyme activities, suggesting similar behaviour of eubacteria and fungi relatively to all the variables analysed. Evidently, different organic carbon content in soil horizons influenced microflora composition and microbial activities involved in the P and N cycles. © 2011 Springer-Verlag.

International audience; The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up to 4 years. Total DNA was extracted from soil and the number of transgenes (aadA, which confers resistance to both spectinomycin and streptomycin) was quantified by quantitative PCR. The biological activity of these transgenes was assessed by transformation in the bacterial strain Acinetobacter sp. BD413(pBAB2) in vitro. While the proportion of transgenes recovered increased with the increasing amount of transplastomic DNA added, plant DNA was rapidly degraded over time. The number of transgenes recovered decreased about 10,000 fold within 2 weeks. Data reveal, however, that a small fraction of the plant DNA escaped degradation. Transgene sequences were still detected after 4 years and transformation assays showed that extracted DNA remained biologically active and could still transform competent cells of Acinetobacter sp. BD413(pBAB2). The approach presented here quantified the number of transgenes (based on quantitative PCR of 50% of the gene) released and persisting in the environment over time and provided new insights into the fate of transgenic plant DNA in soil. (C) 2010 Elsevier Masson SAS. All rights reserved.

Unsaturated soil columns were used to examine the transport of the plasmid pLEPO1 and plant DNA (transplastomic tobacco DNA), both carrying an antibiotic resistance gene (aadA gene), and the capacity of bacteria to incorporate the gene in their genome after its passage through the soil. Soil columns containing a top leaf layer had sterile water percolated through them at a rate of 0.5 mL h(-1). DNA from column leachate water was extracted and analyzed. Quantitative measurements included total DNA concentrations in the water and the transformation frequencies of Acinetobacter sp. BD413 by DNA in the column effluent. Qualitative measurements included the relative degradation of DNA after passage in the columns by agarose gel electrophoresis and the potential of effluent DNA to transform bacteria, leading to the production of anti biotic-resistant bacteria. The presence of aadA gene in the leachate water of soil columns suggests the mobility of DNA in unsaturated soil medium. The extent of DNA degradation was found to be proportional to its residence time in the soil column while a fraction of DNA was always able to incorporate into the Acinetobacter genome under all conditions studied. These results suggest that biologically active transgenic DNA might be transported downward by rain in unsaturated soils. (C) 2009 Elsevier Inc. All rights reserved.

The soil DNA pool consists of an intracellular (iDNA) and extracellular fraction (eDNA). Challenging to improve the extraction efficiency of soil DNA, and to quantitatively and qualitatively characterize both DNA fractions, we set up a molecular approach consisting of sequential and comparative DNA extraction and microbial community fingerprinting. eDNA was extracted by alkaline soil washings (ASW); iDNA by mechanical chemical cell lysis (MCCL) of the residual soil pellet after the extraction of eDNA (ASW–MCCL). The molecular approach was compared in terms of quantity (fluorometer) and quality (agarose gel electrophoresis; small subunit rRNA-denaturing gradient gel electrophoresis) to directly extracted soil DNA comprising both eDNA and iDNA (tDNA; FastDNA Spin Kit for Soil, BIO101). The proposed method appeared to be a potential tool to separately extract and analyze eDNA (6.07 μg g−1 soil) and iDNA (11.46 μg g−1 soil) and to obtain a greater amount of DNA from soil with broader genetic information about eubacterial and fungal communities with respect to directly extracted tDNA (8.79 μg g−1 soil). Our results revealed the extracellular fraction to be quantitatively and qualitatively important of the soil metagenome. As the sequential DNA extraction method not only increased the total amount of extractable soil DNA (17.53 μg g−1 soil) but also that of iDNA, it is suggested to be suitable for extracting the soil metagenome.