Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

Abstract

Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens: A review

“…On the contrary, caecum microbiota showed higher diversity and 24 unclassified bacterial species were found to be differentially expressed between high and low performing birds. In a recent study, three families, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae, have been associated with the phenotypic expression of high FE [ 36 ]. In these birds, higher abundance of Ruminococcus , Faecalibacterium , Clostridium and two unknown genera from the Lachnospiraceae family was also observed.…”

“…In these birds, higher abundance of Ruminococcus , Faecalibacterium , Clostridium and two unknown genera from the Lachnospiraceae family was also observed. Even if some strains of Lactobacillus are aimed to improve broilers performance, Stanley et al [ 36 ] identified others which have an undesirable outcome on the overall performance mainly through a stimulation of feed consumption. In another study, Mignon-Grasteau et al [ 37 ] reported that birds selected for a low FCR showed lower cecal counts of Lactobacillus , L. salivarius and E. coli compared to the high ones.…”

Identification of new microbial functional standards for soil quality assessment

“…This applies even more when certain taxa are closely linked to very specific functions, including nitrifiers, methanogens, and arbuscular-and ecto-mycorrhizal fungi and biocontrol microorganisms like Trichoderma (e.g. Hartmann et al, 2009;Hayat et al, 2010;Lugtenberg and Kamilova, 2009;Peng et al, 2008;Singh et al, 2007;Xia et al, 2011). Therefore, the interpretation of the outcomes from microbial community-based testing tends to be straightforward and closely linked to Function 4 and Function 5.…”

“…Among the microorganisms in soil that substantially govern pest control and plant growth promotion (Function 5), arbuscular mycorrhizae and ectomycorrhizal fungi are of high relevance. These microorganisms are especially abundant in the rhizosphere (Hartmann et al, 2009;Hayat et al, 2010;Lugtenberg and Kamilova, 2009). Methods related to Function 5 are listed in Table 3.…”

Chemical compound isolated from antioxidant active extract of endophytic fungus Cladosporium tenuissimum in Swietenia mahagoni leaf stalks

“…The PCR amplicon was sequenced and blasted by using National Center for Biotechnology Information (NCBI) (Mishra et al 2017). Fungal DNA with the highest similarity selected and grouped using ClustalW program (Hannula and Veen 2016) in txt, MSF, and PHYLIP formats (Felsenstein 1989). File PHYLIP opened with SEQBOOT program by entering 1000 times replication.…”