Companion planting is one of the most common and effective planting methods in modern agriculture. White clover (Trifolium repens L.) and orchard grass (Dactylis glomerata L.) are two typical pastures planted together to promote each other's growth. However, the detailed biological foundations of companion planting remain unclear. In this study, we screened typical microbiome profiles under separate and combination planting conditions using 16s RNA gene sequencing techniques. We identified the typical distinctive microorganism subtypes based on the microbiome profiles and recognized the enriched functions of top abundant microorganisms in soil using different planting strategies with the help of Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups annotation. This analysis confirmed that the optimal microorganisms and screened functional annotations are correlated with nitrogen fixation; thus, companion planting may improve the yield and efficacy of plants by improving the efficiency of nitrogen fixation.

Gut microbiomes are integral microflora located in the human intestine with particular symbiosis. Among all microorganisms in the human intestine, bacteria are the most significant subgroup that contains many unique and functional species. The distribution patterns of bacteria in the human intestine not only reflect the different microenvironments in different sections of the intestine but also indicate that bacteria may have unique biological functions corresponding to their proper regions of the intestine. However, describing the functional differences between the bacterial subgroups and their distributions in different individuals is difficult using traditional computational approaches. Here, we first attempted to introduce four effective sets of bacterial features from independent databases. We then presented a novel computational approach to identify potential distinctive features among bacterial subgroups based on a systematic dataset on the gut microbiome from approximately 1,500 human gut bacterial strains. We also established a group of quantitative rules for explaining such distinctions. Results may reveal the microstructural characteristics of the intestinal flora and deepen our understanding on the regulatory role of bacterial subgroups in the human intestine.

Background The gossypol, as an antinutritional factor or natural plant toxin, has antifertility effects on humans and animals, exists in cottonseed oil and meal, and is a typical food or feed contaminant. It is the classic screening method to using acetate gossypol as the sole carbon sources to prepare selective medium and screening gossypol-degrading microorganisms. By the classic screening strategy, many researchers have discovered that some microorganisms, and Aspergillus niger is the most reported microorganism. A strain of A. niger which can grow in an agar solid medium with gossypol as the sole carbon source is isolated from cattle rumen liquid was obtained by classic screening strategy. The effectiveness of the classic screening strategy was verified, by duplicating and verifying the degradation of gossypol by the A. niger. Results the A. niger can reduce the free gossypol (FG) content through biosorption but has no effect on the total gossypol (TG) content. And it can secrete agarase, utilise agar as carbon source. Conclusions The A. niger can secrete agarase, but cannot effectively degrade gossypol, In this case, it will mislead researchers and lead them to make wrong judgments. The usual methods of previous screening strategies are not rigorous enough, the classic screening method has defect in screening toxin-degrading strain, so agar control group should be added.

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The effectiveness of the classic screening strategy was verified, by duplicating and verifying the degradation of gossypol by the Aspergillus niger. It can reduce the free gossypol content through biosorption but has no effect on the total gossypol content and cannot effectively degrade gossypol. And the most interesting thing we found the strain can secrete agarase, utilise agar as carbon source. In this case, that will mislead researchers and lead them to make wrong judgments. That turns out the usual methods of previous screening strategies are not rigorous enough, the classic screening method has defect in screening toxin-degrading strain, so agar control group should be added. In this study, some suggestions are put forward to optimise the same type of experiments and broaden the idea of detoxification by microorganisms and provide reference for screening effective toxin-degrading microorganisms.