Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys

Achievements and new knowledge unraveled by metagenomic approaches

Metagenomics has paved the way for cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. In recent years, significant progress has been made in this research area. A major breakthrough was the improvement and development of high-throughput next-generation sequencing technologies. The application of these technologies resulted in the generation of large datasets derived from various environments such as soil and ocean water. The analyses of these datasets opened a window into the enormous phylogenetic and metabolic diversity of microbial communities living in a variety of ecosystems. In this way, structure, functions, and interactions of microbial communities were elucidated. Metagenomics has proven to be a powerful tool for the recovery of novel biomolecules. In most cases, functional metagenomics comprising construction and screening of complex metagenomic DNA libraries has been applied to isolate new enzymes and drugs of industrial importance. For this purpose, several novel and improved screening strategies that allow efficient screening of large collections of clones harboring metagenomes have been introduced

Aphid-host plant interactions: Does aphid honeydew exactly reflect the host plant amino acid composition?

peer reviewedPlants provide aphids with unbalanced and low concentrations of amino acids. Likely, intracellular symbionts improve the aphid nutrition by participating to the synthesis of essential amino acids. To compare the aphid amino acid uptakes from the host plant and the aphids amino acid excretion into the honeydew, host plant exudates (phloem + xylem) from infested and uninfested Vicia faba L. plants were compared to the honeydew produced by two aphid species (Acyrthosiphon pisum Harris and Megoura viciae Buckton) feeding on V. faba. Our results show that an aphid infestation modifies the amino acid composition of the infested broad bean plant since the global concentration of amino acids significantly increased into the host plant in response to aphid infestations. Specifically, the concentrations of two amino acids glutamine and asparagine were strongly enhanced. The amino acid profiles from honeydews were similar for the two aphid species, but the concentrations found into the honeydews were generally lower than those measured in the exudates of infested plants (aphids uptakes). This work also highlights that aphids take large amounts of amino acids into the host plant, especially glutamine and asparagine which are converted into glutamic and aspartic acids but also into other essential amino acids. The amino acid profiles differed between the host plant exudates and the aphid excretion product. Finally, this study highlights that the pea aphid - a “specialist” for the V. faba host plant - induced more important modifications into the host plant amino acid composition than the “generalist” aphid M. viciae.Solaphi