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Sour cherry (Prunus cerasus L.) is one of the most important fruit crops in Poland and 'Łutówka' is the dominant cultivar in commercial orchards. The experiment was carried out in 2007–2013 in three orchards; in each of them, three levels of fertilization were applied: 0 N kg ha−1, 60 kg N ha−1, and 120 kg N ha−1. The activity of dehydrogenase and protease in the soil was studied depending on nitrogen fertilization. The abundance of soil microorganisms was assessed: bacteria, fungi, actinomycetes, and nitrogenous bacteria (Azospirillum and Azotobacter) in the years during the experiments carried out with fertilization of 60 kg N ha−1 in all orchards. The enzyme activity of dehydrogenases increased after the use of 60 kg N ha−1 from 3.8 to 6.7 (cm3 H2 24 h−1 kg−1 DW soil), but a further increase in the dose to 120 kg N ha−1 caused a decrease in activity to 5.1 (cm3 H2 24 h−1 kg−1 DW soil). The activity of proteases was dependent on nitrogen fertilization, but to a large extent it was related to the course of climatic conditions. There is no relationship between the growth and the activity of proteases. The yield and selected quality parameters of the cherry fruits were associated with both dehydrogenases and proteases. The use of lower doses of nitrogen fertilizers allows for maintaining biological balance in the soil and a more efficient use of nutrients, contributing to less environmental pollution. [ABSTRACT FROM AUTHOR]

Despite emergent research initiatives, significant knowledge gaps remain of soil microbiology-associated cadaver decomposition. Nevertheless, preliminary studies have shown that the vast diversity and complex interactions of soil microbial communities have great potential for forensic applications such as clandestine grave location and postmortem interval estimation. This study investigated changes in soil bacterial communities during pig (Sus scrofa domesticus) leg decomposition. 16S rRNA, instead of the usually applied 16S rDNA marker, was used to compare the metabolically active bacteria. Total bacterial RNA was extracted from soil samples of three different layers on day 3,28 and 77 after the shallow burial of a pig leg. The V3 region of the 16S rRNA was amplified, analysed by RT-PCR DGGE, and compared with control soil bacterial community profiles. Statistically significant differences in soil bacterial biodiversity were observed. For the control, bacterial diversity (H0) and species richness (S) of the three layers averaged 2.48 ± 0.14 (H0) and 18.8 ± 2 .5 (S), respectively, while for the test soil increases (p = 0.027) were recorded between day 3 (H0 = 2.71 ±0.02; S = 21.3 ± 2 . 0 ) and 28 (H0 = 3.46±0.32; S = 60.3 ±16.9), particularly in the middle (10-20 cm) and bottom (20-30 cm) soil layers. Between day 28 and 77 the diversity and richness then decreased on average for all three layers (H0 = 3.43 ±0.20; S = 60.0 ±17.3) but remained higher than on day 3. Thus, responses in soil bacterial profiles and activity to carcass decomposition, detected and characterised by RNA-based DGGE, could be used together with RNA sequencing data, changes in physico-chemical variables (carbon, nitrogen, phosphorus, temperature, redox potential, water activity and pH) and conventional macroecology markers (e.g. insects and vegetation), to develop a suite of analytical protocols for different forensic scenarios. [ABSTRACT FROM AUTHOR]

The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV) disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage). We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages). Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the introduced gene is derived from a virus. [ABSTRACT FROM AUTHOR]

Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity. [ABSTRACT FROM AUTHOR]

The relationship between total and metabolically active soil microbial communities can change drastically with environment. In dry lands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active Archaea and Bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16 S r RNA genes (total community) and their r RNA (active community) amplified by PCR or RT- PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for Archaea and Bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7-19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by the analysis of active communities are not as robust as those drawn from total communities. [ABSTRACT FROM AUTHOR]

Highlights: [•] Changes of soil microbiota in relation to abiotic and biotic environment in a forest reserve are shown. [•] Mutual links between the above- and belowground components of a forest ecosystem exist. [•] Beta diversity of microorganisms is higher in an old growth than in a commercial stand. [•] Microclimate affects soil microorganisms less than the availability of organic material. [•] Soil microbiota prefers a diverse ground-layer vegetation rather than a diverse tree layer. [Copyright &y& Elsevier]

The use of short rotation forest tree species is increasing worldwide. The hybrid aspen (Populus tremuloides Michx. x P. tremula L.) is one of the suitable tree species under the climatic conditions of the Baltic region. The cultivation of these trees on former agricultural soils differs from agricultural practices with reduced soil tillage and is characterized by increased demand of nutrients, which in long term can cause changes in the soil microbial populations. The aim of our investigation was to compare soil microbial populations in hybrid aspen and European aspen (P. tremula L.) stands in four sampling plots with aspen age ranging from 10 to 46 years. The abundance and diversity of soil microbial populations were estimated by enumeration of microorganisms (plate counts on three microbiological media) and by molecular methods (PCR, ARDRA, molecular identification of fungal isolates). Results showed that during long cultivation periods hybrid aspens reduced the number of culturable bacteria. The number of culturable filamentous fungi was statistically significantly increased only in one sampling plot in soil samples from hybrid aspen clones at a depth of 16.30 cm and only on one microbiological cultivation medium. The same was detected also with molecular methods in the case of fungal diversity estimated by Shannon. Weaver diversity indices in this sampling plot. None of the other characteristics of soil microbial populations, such as the number of yeasts and maltose utilizing bacteria on MEA, the number of yeasts and filamentous fungi on RBA, the total amount of soil DNA, fungal and bacterial diversity estimated by molecular biology methods, and species composition of filamentous fungi, was significantly affected by hybrid aspen. The identified filamentous fungi represented the following genera: Acremonium, Exophiala, Geomyces, Gibellulopsis, Gibberella, Hypocrea/Trichoderma, Leptosphaeria, Metarhizium, Mortierella, Nectria, Paecilomyces, Penicillium, Trichosporon, and others. The main conclusion was that cultivation of hybrid aspen as a short rotation forest tree in the Baltic region would not significantly affect the abundance and diversity of saprophytic soil microorganisms. [ABSTRACT FROM AUTHOR]

Abstract: Soils are currently being degraded at an alarming rate due to increasing pressure from different sources of environmental degradation. Consequently, we carried out a 4-month microcosm experiment to measure the impact of different sources of environmental degradation (biodiversity loss, nitrogen deposition and climate change) on soil health in a non-polluted (non-degraded) and a heavily metal-polluted (degraded) soil, and to compare their responses. To this aim, we determined a variety of soil microbial properties with potential as bioindicators of soil health: basal respiration; β-glucosaminidase and protease activities; abundance (Q-PCR) of bacterial, fungal and chitinase genes; richness (PCR-DGGE) of fungal and chitinase genes. Non-polluted and metal-polluted soils showed different response microbial dynamics when subjected to sources of environmental degradation. The non-polluted soil appeared resilient to “biodiversity loss” and “climate change” treatments. The metal-polluted soil was probably already too severely affected by the presence of high levels of toxic metals to respond to other sources of stress. Our data together suggests that soil microbial activity and biomass parameters are more sensitive to the applied sources of environmental degradation, showing immediate responses of greater magnitude, while soil microbial diversity parameters do not show such variations. [Copyright &y& Elsevier]

Abstract: Bioturbation is known to stimulate microbial communities, especially in macrofaunal burrows where the abundance and activities of bacteria are increased. Until now, these microbial communities have been poorly characterized and an important ecological question remains: do burrow walls harbor similar or specific communities compared with anoxic and surface sediments? The bacterial community structure of coastal sediments inhabited by the polychaete worm Hediste diversicolor was investigated. Surface, burrow wall and anoxic sediments were collected at the Carteau beach (Gulf of Fos, Mediterranean Sea). Bacterial diversity was determined by analyzing small subunit ribosomal RNA (16S rRNA) sequences from three clone libraries (168, 179 and 129 sequences for the surface, burrow wall and anoxic sediments, respectively). Libraries revealed 306 different operational taxonomic units (OTUs) belonging to at least 15 bacterial phyla. Bioinformatic analyses and comparisons between the three clone libraries showed that the burrow walls harbored a specific bacterial community structure which differed from the surface and anoxic environments. More similarities were nevertheless found with the surface assemblage. Inside the burrow walls, the bacterial community was characterized by high biodiversity, which probably results from the biogeochemical heterogeneity of the burrow system. [Copyright &y& Elsevier]

The contribution of chemotaxis to the competitive colonization of the rhizosphere for the vast majority of the soil community is unknown. We have developed and applied a molecular diagnostic tool, based on a gene encoding the central regulator of bacterial chemotaxis ( cheA), to characterize and temporally track specific populations of native microbes with chemotaxis potential that are present in soil exposed to two rhizospheres: wheat and cowpea. The data show that the chemotactic-competent communities present in the rhizospheres of the two plants are distinct and less diverse than the bulk soil, indicating the development of unique microbial communities. Consistent with the supposition that selection and recruitment of specific soil microbes takes place in the rhizosphere, the dynamics of specific cheA phylotypes provides support for the hypothesis that chemotaxis provides a competitive advantage to some soil microbes. This is the first study to examine and profile the genetic diversity of chemotaxis genes in natural populations. As such, it illustrates our limited understanding of microbial chemotaxis for the majority of soil microbes. It also highlights the value of a culture-independent approach for examining chemotaxis populations in order to build empirical lines of evidence for its role in structuring of microbial assemblages. [ABSTRACT FROM AUTHOR]

Abstract: This study aimed at testing the capability of microbial community structure and abundance to be used as bioindicators of the origin of earthworm cast aggregates. Compact surface casts produced by Amynthas khami and surrounding aggregates lacking visible signs of biological activity (control) were left to disaggregate by natural rainfall and separated into four size classes (5–2, 2–0.5, 0.5–0.25 and <0.25 mm). The genetic structure and the abundance of the bacterial and fungal communities were characterized using B- and F-ARISA fingerprinting approach and quantitative PCR directly from DNA extracted from soil. Bacteria and to a lesser extent fungi were more abundant in casts than in control aggregates for all the size fractions. In addition, PCA carried out from B- and F-ARISA confirmed the different microbial properties between cast and control aggregates for all the aggregate size fractions. In conclusion, this study confirms the cryptic properties of earthworm casts when fragmented by the rain and the relevance of bacterial and fungal abundance and diversity as biological indicators of the origin of soil aggregates. [Copyright &y& Elsevier]