Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences

BACKGROUND: Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. Keeping this in view, the aim was to identify a region of 16S rDNA sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns from these stretches that are specific to the genus. RESULTS: Repeating elements that are highly conserved across different species of Pseudomonas were considered as guiding markers to locate a region within the 16S gene. Four repeating patterns showing more than 80% consistency across fifty different species of Pseudomonas were identified. The sub-sequences between the repeating patterns yielded a continuous region of 495 bases. The sub-sequences after alignment and using Shanon's entropy measure yielded a consensus pattern. A stretch of 24 base positions in this region, showing maximum variations across the sampled sequences was focused for possible genus specific patterns. Nine patterns in this stretch showed nearly 70% specificity to the target genus. These patterns were further used to obtain a signature that is highly specific to Pseudomonas. The signature region was used to design PCR primers, which yielded a PCR product of 150 bp whose specificity was validated through a sample experiment. CONCLUSIONS: The developed approach was successfully applied to genus Pseudomonas. It could be tried in other bacterial genera to obtain respective signature patterns and thereby PCR primers, for their rapid tracking in the environmental samples

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

Metagenomic DNA extracted from polluted as well as control soil sample and electrophoresed on 0.8 % agarosa gel. Lane M is of marker, Lane 1, is for polluted sample (representing pooled metagenomic DNA for P1 + P2 + P3 = P) and Lane 2 is for control soil sample (representing pooled metagenomic DNA for C1 + C2 + C3 = C). Figure S2. Distribution of taxa among bacteria at rank phylum classified according to 16S rDNA using RDP classifier for both polluted as well as control sample. Figure S3. Distribution of taxa among bacteria at rank phylum classified according to lowest common ancestor (LCA) for both polluted as well as control sample. Figure S4. Comparative distribution of taxa among bacteria at rank class classified according to WebCARMA and M5NR datasets for both polluted as well as control sample. Table S1. Enzymes mapped for lipid metabolism pathways in KEEG database. (DOC 300 kb

Effects of softwood biochars on soil biota in medium-term field experiments in Finland

Biochar soil amendment could be used to sequester carbon, enhance soil fertility and potentially increase crop yields. It can have significant impacts on soil organic carbon levels and physicochemical conditions, which consequently affect soil micro- and macro-biota. It is therefore important to understand how key biological components in the soil such as microbial and earthworm communities response to biochar application in the long-term. This study was conducted in Southern Finland in a fertile Stagnosol and a nutrient deficient Umbrisol, four and five years after biochar amendment, respectively. Biochars were produced from spruce (Picea abies (L.) H.Karst.) and pine (Pinus sylvestris L.), and applied at the rates of 10 and 30 t ha-1, respectively. Earthworms and soil samples for microbial analyses were collected in September 2015. Soil microbial communities were studied by using phospholipid fatty acid profiling and 16S rRNA gene amplicon sequencing. Casts from the sampled earthworms were collected to investigate the consumption of biochar and the potential of earthworm bioturbation to affect biochar distribution. Additionally, greenhouse gas emissions from soil were measured. Biochar and fertilizer treatments or their interaction had no statistically significant effects on the earthworm abundance, community composition or greenhouse gas emissions in either field. Earthworms had ingested biochar as earthworm casts from biochar treated-plots contained significantly more black carbon than those in the control plots, demonstrating that earthworm bioturbation is a potentially important factor in the translocation of applied biochar in the soil profile. Microbial community structure data will be presented in the final presentation.Non peer reviewe

3rd Conference on Ecology of Soil Microorganisms

We are pleased to welcome you to the 3rd conference on the Ecology of Soil Microorganisms in Helsinki, Finland. The two previous meetings were organized in Prague in 2011 and 2015 by Petr Baldrian. We are delighted to see that as many participants, 400 are joining us also under the midnight sun. During the meeting, soil science will be linked with traditional microbiology and modern genomic, transcriptomic and proteomic analysis tools, extending from the soil-microbe interphase to their interactions with plants. Indeed, one important goal of the conference is to inspire us to bring forward new dimensions in the characterization of the interplay between soil microbial ecology and larger-scale processes in various ecosystems. In this meeting we will cover not only the role of soil microbiota but also their viruses. We hope that you take a moment to think of recent studies that have begun to unearth relationships found between soil microbes, plant performance and even human health. Sustainability of soils and their role in mitigation of climate change are key challenges for preserving life on Earth. As microbes are living functional components of soils, our focus during the week could not be timelier. The organizers and the host organization Natural Resources Institute Finland wish you a fruitful and invigorating conference. We are excited that you have joined us here in Helsinki to promote state-of-the-art research in soil ecology under the northern midsummer madness!201