Phylogenetic distribution of bacteria isolated from the floodwater of a Japanese paddy field

Figures & data

Table 1 Phylogenetic distribution of 119 Gram-negative isolates at the family or genus level

Phylogenetic group	Family or genus
Gram-negative bacteria
Proteobacteria
Alpha group	Rhodobacter (4), Rhodoplanes (2), Methylobacterium (2), Sphingomonas (41), Rhizobium (2), Afipia (2), Azospirllum (3), Azorhizobium (1)
Beta group	Ralstonia (4), Herbaspirillum (1), other (4)
Gamma group	Stenotrophomonas (1), Pseudomonas (2), Acinetobacter (1), Klebsiella (2), Enterobacter (2), Pantoea (1), Rahnella (3), Luteimonas (2)
Cytophaga–Flavobacterium–  Bacteroides group	Flavobacteriaceae (4), Cytophaga (7), Chryseobacterium (3), Pedobacter (1), other (1)
Gram-positive bacteria
High-GC Gram-positive bacteria	Nocadioides (3), Mycobacterium (3), Arthrobacter (3), Streptomyces (1), Agromyces (1), Terracoccus (1), Microbacterium (2), Blastcoccus (2), other (2)
Low-GC Gram-positive bacteria	Bacillus (4), other (1)
Figures in parentheses show the number of isolates belonging to each family or genus.

Figure 1  Seasonal changes in the composition of Gram-negative bacteria in floodwater during the rice cultivation period. Figures at the top of the columns indicate the number of Gram-negative bacteria examined for their 16S rDNA sequences. (

) α-Proteobacteria; (

) β-Proteobacteria; (

) γ-Proteobacteria; (

) Cytophaga–Flavobacterium–Bacteroides.

Table 2 Changes in the phylogenetic composition of bacterial isolates during the rice cultivation period

Family or Genus	6 May	23 May	12 June	4 July	28 July	16 August
Proteobacteria
Alpha group
Methylobacterium (2)	+
Sphingomonas (41)	+	+	+	+	+	+
Rhizobium (2)	+		+
Rhodoplanes (2)	+					+
Rhodobacter (4)	+				+	+
Afipia (2)					+	+
Azospirllum (3)						+
Rhodospirillum (1)						+
Beta group
Ralstonia (4)	+
Herbaspirillum (1)						+
Other (4)	+			+		+
Gamma group
Stenotrophomonas (1)	+
Pseudomonas (2)	+					+
Acinetobacter (1)		+
Klebsiella (2)		+
Enterobacter (2)			+
Pantoea (1)				+
Rahnella (3)				+
Luteimonas (2)						+
CFB group
Flavobacteriaceae (4)	+			+		+
Cytophaga (7)	+					+
Chryseobacterium (3)	+
Pedobacter (1)						+
Other (1)				+
Figures in parentheses show the number of isolates belonging to each family or genus.

Figure 2  Phylogenetic relationships between Gram-negative isolates from floodwater and DNA clones obtained from various sites in paddy fields. (•) isolates (present study); CP, composting process of rice straw; FW, floodwater; MC, microcrustaceans; PW, percolating water; RS, rice straw; RR, rice roots. The scale bar represents 0.1 substitutions per nucleotide. Bootstrap values are shown at branch points when the values exceed 50%.