Currently the major challenge of humanity is focused on population growth/ increase through agricultural production in order to meet the demand for food. Overtime, different pests have emerged, with some being of great importance. Among these pests, the nematodes are noted for attacking leguminous plants, grasses, citrus, and other fruits. The main pest species are of the genus Heterodera, Meloidogyne, Pratylenchus, and Globodera. These nematodes cause losses up to 100 %, preventing agriculture of certain areas. Financially, about $100 billion annual damage is caused by nematodes. These amount to 90 % of the yield of cotton, yams, beans, and soybeans, and in citrus damage is estimated at 14 % of production. Alternative methods of control are being studied, and in this context, a bacterium of the genus Bacillus has prominence and importance. Besides Bacillus subtilis, some by pesticides are already marketed for the control of nematodes, such as Bioarc ® the basis of Bacillus megaterium, Bio Zeid ® the basis of Trichoderma album, and also using the brown alga, Ascophyllum nodosum (Algaefol ® ), among others. The objective of this chapter is to report the use of different Bacillus species and some biopesticides used to control nematodes of agricultural importance.

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As the majority of environmental microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomic binning and single cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole genome amplification techniques which are known to be prone to bias. Here we propose a novel approach for the purpose of metagenomic genome reconstructions, that utilizes the potential of fluorescence-activated cell sorting (FACS) for targeted enrichment and depletion of different cell types to create distinct cell fractions of sufficient size circumvent amplification. By distributing sequencing efforts over these fractions as well as the original sample, co-assemblies become highly optimized for co-abundance variation based binning approaches. 'Midi-metagenomics' enables accurate metagenome assembled genome (MAG) reconstruction from individual sorted samples with higher quality than co-assembly of multiple distinct samples and has potential for the targeted enrichment and sequencing of uncultivated organism of interest.

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