Bioinformatics resources for microbial research in biological systems

Bioinformatics is a continuously evolving field since it came into existence and contributing significantly in all major areas of biological sciences. Advanced sequencing technologies and exponential growth in computational resources have facilitated the high-end bioinformatics application in various research areas such as microbiome research in biological system. Bioinformatics contributed significantly in the development of powerful methods and tools in metagenomics research through direct inspection of targeted and nontargeted DNA in environmental samples. Advances in metagenomics, high-throughput methods, tools, software, pipelines, databases and analysis products for the microbes and microbiome-related studies have shifted the field of microbiology from culturing and microscopy studies to DNA sequencing and bioinformatics analyses. In the last decade, various long-term research projects and studies have flooded the microbiome sequencing data and analyses. Now, microbial community is realized that the next decade of microbial research will need data management, sharing, mining and networking skills to enhance knowledge discovery and regulation of microbial communities in ecosystem. Here, we are describing the microbiome researches in different biological domains, microbial databases and tools, which can be useful for application of microbes in emerging applied fields

Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing

Soil fungal pathogens are the most common cause of diseases in commercial strawberry crops worldwide. Since simultaneous infections by different pathogens can severely damage the crop, understanding the associated fungal communities can be helpful to mitigate crop loss. Herein, we used Illumina metabarcoding to assess the structure of fungal communities in five strawberry production areas in Estonia. Our analysis revealed 990 to 1430 operational taxonomic units (OTUs) per soil sample (pools of eight soil samples per production area). Based on our analyses, Ascomycota (55.5%) and Basidiomycota (25.0%) were the most OTUs-rich. Amongst the 24 most abundant OTUs, Geomyces, Rhodotorula, Verticillium and Microdochium were the most abundant genera, which were found across nearly all the soil samples. The OTUs were also clustered into three distinct groups, corresponding to different functional guilds of fungi. In addition, Fusarium solani, V. dahliae, Rhizoctonia solani and Colletotrichum truncatum were enormously abundant in the fields with disease symptoms, whereas arbuscular mycorrhizal fungi especially Rhizophagus irregularis were considerably more abundant in the fields with healthy plants. These findings provide support that mycorrhizal fungi may play an important role in suppressing pathogens. Our study for the first time shows the usefulness of Illumina technology in surveying the communities of soil fungi in strawberry fields effectively, which may improve available disease management strategies against strawberry diseases