PREMISE: Despite the high functional importance of endophytes, we still have limited understanding of the biotic and abiotic factors that influence colonization of plant hosts along major ecological gradients and lack quantitative estimates of their colonization extent. In this study, we hypothesized that the developmental stage of the ecosystem will affect the levels of bacterial and fungal endophytic assemblages in the foliar endosphere. METHODS: We quantified levels of bacterial and fungal endophytes in leaves of four plant hosts at four stages of vegetation succession using an optimized qPCR protocol with bacteria-specific 16S and fungi-targeting primers. RESULTS: (1) The ecosystem developmental stage did not have a significant effect on the colonization levels of bacterial or fungal endophytes. (2) Colonization levels by bacterial and fungal endophytes were governed by different mechanisms. (3) Endophytic colonization levels and their relationship to foliar tissue stoichiometry were highly host specific. CONCLUSIONS: Quantifying colonization levels is important in the study of endophytic ecology, and the fast, relatively low-cost qPCR-based method can supply useful ecological information, which can significantly enhance the interpretation potential of descriptive data generated, for example, by next-generation sequencing.

• Keywords
• cell counts, ecological succession, foliar endophyte, fungi‐bacteria ratios, qPCR, soil chronosequence,
• MeSH
• Bacteria * genetics   growth & development   isolation & purification   MeSH
• Ecosystem MeSH
• Endophytes * physiology   genetics   MeSH
• Host Specificity * MeSH
• Fungi * genetics   isolation & purification   physiology   MeSH
• Real-Time Polymerase Chain Reaction methods   MeSH
• Plant Leaves * microbiology   MeSH
• Publication type
• Journal Article MeSH

Community-level physiological profiling (CLPP) analyses from very diverse environments are frequently used with the aim of characterizing the metabolic versatility of whole environmental bacterial communities. While the limitations of the methodology for the characterization of whole communities are well known, we propose that CLPP combined with high-throughput sequencing and qPCR can be utilized to identify the copiotrophic, fast-growing fraction of the bacterial community of soil environments, where oligotrophic taxa are usually dominant. In the present work we have used this approach to analyze samples of litter and soil from a coniferous forest in the Czech Republic using BIOLOG GN2 plates. Monosaccharides and amino acids were utilized significantly faster than other C substrates, such as organic acids, in both litter and soil samples. Bacterial biodiversity in CLPP wells was significantly lower than in the original community, independently of the carbon source. Bacterial communities became highly enriched in taxa that typically showed low abundance in the original soil, belonging mostly to the Gammaproteobacteria and the genus Pseudomonas, indicating that the copiotrophic strains, favoured by the high nutrient content, are rare in forest litter and soil. In contrast, taxa abundant in the original samples were rarely found to grow at sufficient rates under the CLPP conditions. Our results show that CLPP is useful to detect copiotrophic bacteria from the soil environments and that bacterial growth is substrate specific.

• MeSH
• Principal Component Analysis MeSH
• Bacteria classification   genetics   MeSH
• Biodiversity * MeSH
• Phylogeny MeSH
• Soil Microbiology * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Environment MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Czech Republic MeSH
• Names of Substances
• RNA, Ribosomal, 16S MeSH