A metagenomic and amplicon sequencing combined approach reveals the best primers to study marine aerobic anoxygenic phototrophs
Gazulla, Carlota R. (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Cabello, Ana María (Instituto Español de Oceanografía. Centro Oceanográfico de Málaga)
Sánchez, Pablo (Institut de Ciències del Mar)
Gasol, Josep M. (Institut de Ciències del Mar)
Sánchez Martínez, M. Olga (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Ferrera, Isabel (Instituto Español de Oceanografía. Centro Oceanográfico de Málaga)

Data:	2023
Resum:	Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufMsequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.
Ajuts:	Agencia Estatal de Investigación PID2019-110128RB-I00 Ministerio de Ciencia e Innovación CEX2019-000928-S
Nota:	Altres ajuts: acords transformatius de la UAB
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	AAP bacteria ; Amplicon sequencing ; Metagenomics ; Primer evaluation ; Pufm gene
Publicat a:	Microbial Ecology, Vol. 86, Issue 3 (October 2023) , p. 2161-2172, ISSN 1432-184X

DOI: 10.1007/s00248-023-02220-y
PMID: 37148309

12 p, 47.1 MB

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