Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.
A Gram-negative, rod-shaped, non-spore-forming and nitrogen-fixing bacterium, designated ICB 89(T), was isolated from stems of a Brazilian sugar cane variety widely used in organic farming. 16S rRNA gene sequence analysis revealed that strain ICB 89(T) belonged to the genus Stenotrophomonas and was most closely related to Stenotrophomonas maltophilia LMG 958(T), Stenotrophomonas rhizophila LMG 22075(T), Stenotrophomonas nitritireducens L2(T), [Pseudomonas] geniculata ATCC 19374(T), [Pseudomonas] hibiscicola ATCC 19867(T) and [Pseudomonas] beteli ATCC 19861(T). DNA-DNA hybridization together with chemotaxonomic data and biochemical characteristics allowed the differentiation of strain ICB 89(T) from its nearest phylogenetic neighbours. Therefore, strain ICB 89(T) represents a novel species, for which the name Stenotrophomonas pavanii sp. nov. is proposed. The type strain is ICB 89(T) ( = CBMAI 564(T)  = LMG 25348(T)).
Ramos
Patrícia L
PL
Department of Pediatrics, University of São Paulo Medical School, São Paulo, Brazil.|Biotechnology Research Center, CPB-USP, University of São Paulo, São Paulo, Brazil.
Van Trappen
Stefanie
S
BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Belgium.
Thompson
Fabiano L
FL
Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Rocha
Rafael C S
RCS
Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
Barbosa
Heloiza R
HR
Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
De Vos
Paul
P
BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, Belgium.
Moreira-Filho
Carlos A
CA
Department of Pediatrics, University of São Paulo Medical School, São Paulo, Brazil.|Biotechnology Research Center, CPB-USP, University of São Paulo, São Paulo, Brazil.
D001938:Brazil; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D009693:Nucleic Acid Hybridization; D058871:Organic Agriculture; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D031786:Saccharum / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D020588:Stenotrophomonas / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S