The Lotus japonicus Genome

whatM. lotiis and the range of bacterial species
to be discussed. Secondly, we describe genome
structures ofM. lotistrains with special emphasis
on symbiosis islands. We then discuss genes
involved in symbiosis and their regulation.
Genetic resources to study M. loti are also
described.

5.2 LotusRhizobia, Definition of
M. lotiand Their Life Cycle

As stated above, this chapter mainly describes
the twoM. lotistrains, MAFF303099 and R7A.
A third strain NZP2037 that has an expanded
host range compared to the other strains is also
discussed. The three strains were all originally
isolated from nodules offield-grownLotusspe-
cies (Jarvis et al. 1982 ; Kaneko et al. 2000 ). The
complete genome sequence of MAFF303099
(Kaneko et al. 2000 ) as well as the symbiosis
island sequences of R7A and NZP2037 has been
reported (Sullivan et al. 2002 ; Kasai-Maita et al.
2013 ), and the complete genomes of R7A and
NZP2037 have recently become available
through the DOE Joint Genome Institute (JGI)
Web site. These strains all belong to the same
Mesorhizobiumspecies. Nevertheless, there are
concerns regarding the taxonomical definition
not only of this species but also of the genus
Mesorhizobium(Turner et al. 2002 ).

5.2.1 Original Definition ofM. loti

Historically, bacterial species that form nitrogen-
fixing nodules on the roots of plants of the genus
Lotuswere calledLotusrhizobia.Lotusrhizobia
were recognized to include fast- and slow-growing
groups with distinguishable features such as pro-
tein and extracellular polysaccharide composi-
tions (Pankhurst et al. 1979 ). At this early stage of
bacterial taxonomy, rhizobial nomenclature was
based on cross-inoculation grouping of rhizobia
and host legumes, although it was also known
that such groups were not mutually exclusive.

In 1982, Jarvis and colleagues proposedRhizo-

bium lotias a new species for fast-growingLotus

rhizobia with a type strain NZP2213 (Jarvis et al.

1982 ). Later, a group of Rhizobium species

includingR. lotiwere transferred from the genus

Rhizobiumto a new genusMesorhizobium(Jarvis

et al. 1997 ). In the second edition of Bergey’s

Manual of Systematic Bacteriology (2005), the

genusMesorhizobiumis described as a member

constituting the familyPhyllobacteriaceaeof the

orderRhizobialesof the classAlphaproteobacte-

ria(Sawada et al. 2003 ).M. loticells are Gram

negative, aerobic, non-spore-forming rods, and

motile. The cells might contain, often as bacter-

oids in nodules, poly-beta-hydroxybutyrate

inclusion bodies. On yeast mannitol agar, they

form colonies greater than 1 mm after seven days

at 28°C, but their growth is inhibited at temper-

atures higher than 42°C. Their growth is also

inhibited by 2 % NaCl. They can grow within the

pH range between 4.0 and 10.0. In addition to

mannitol,M. loticells utilize a number of carbo-

hydrates, including glucose, galactose, arabinose,

and maltose and produce acidic end products

(Jarvis et al. 1982 , 1997 ).

5.2.2 Diverse Nature ofM. lotiStrains

At the time of definition ofRhizobium loti, it was

known that someM. lotistrains have a broader

host range than the type strain NZP2213. They can

form effective nodules on some ofLotusspecies

and non-Lotusplants on which NZP2213 cannot;

such hosts includeLotus pedunculatus(orLotus

uliginosus) and a tree legumeLeucaena leuco-

cephala(Jarvis et al. 1982 ). NZP2037, originally

isolated from a nodule offLotus divaricatus,is the

representative of the broader-host-range strains

(Chua et al. 1985 ; Pankhurst et al. 1987 ). This

strain is also capable of forming effective nodules

on some species ofCarmichaelia,Ornithopus,

Clianthus, andVigna(Chua et al. 1985 ; Pankhurst

et al. 1987 ; Pueppke and Broughton 1999 ).

The strain R7A is afield reisolate of strain

ICMP3153 (also known as NZP2238) and was

42 K. Saeki and C.W. Ronson