title: Biogeography of wetland rice methanotrophs.
abstract: We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10-20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community.
authors.affiliation: Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., D-35043 Marburg, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Lüke
authors.forename: Sascha
authors.initials: S
authors.lastname: Krause
authors.forename: Stefano
authors.initials: S
authors.lastname: Cavigiolo
authors.forename: Diego
authors.initials: D
authors.lastname: Greppi
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Lupotto
authors.forename: Peter
authors.initials: P
authors.lastname: Frenzel
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D005843:Geography; D008772:Methylococcaceae / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D015999:Multivariate Analysis; D012275:Oryza / Q000382:microbiology*; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D053833:Wetlands
chemical_list: D004269:DNA, Bacterial