Growth and competitive infection behaviors of two sets of Bradyrhizobium spp. strains were examined at different temperatures to explain strain-specific soybean nodulation under local climate conditions. Each set consisted of three strains—B. japonicum Hh 16-9 (Bj11-1), B. japonicum Hh 16-25 (Bj11-2), and B. elkanii Hk 16-7 (BeL7); and B. japonicum Kh 16-43 (Bj10J-2), B. japonicum Kh 16-64 (Bj10J-4), and B. elkanii Kh 16-7 (BeL7)—which were isolated from the soybean nodules cultivated in Fukagawa and Miyazaki soils, respectively. The growth of each strain was evaluated in YM liquid medium at 15, 20, 25, 30, and 35 °C with shaking at 125 rpm for one week while measuring their OD660 daily. In the competitive infection experiment, each set of the strains was inoculated in sterilized vermiculite followed by sowing surface-sterilized soybean seeds, and they were cultivated at 20/18 °C and 30/28 °C in a 16/8 h (day/night) cycle in a phytotron for three weeks, then nodule compositions were determined based on the partial 16S-23R rRNA internal transcribes spacer (ITS) gene sequence of the isolates from the nodules. The optimum growth temperatures were at 15–20 °C for all B. japonicum strains, while they were at 25–35 °C for all B. elkanii strains. In the competitive experiment with the Fukagawa strains, Bj11-1 and BeL7 dominated in the nodules at the low and high temperatures, respectively. In the Miyazaki strains, BjS10J-2 and BeL7 dominated at the low and high temperatures, respectively. It can be assumed that temperature of soil affects rhizobia growth in rhizospheres and could be a reason for the different competitive properties of B. japonicum and B. elkanii strains at different temperatures. In addition, competitive infection was suggested between the B. japonicum strains.

A species-specific latitudinal distribution of soybean rhizobia has been reported; Bradyrhizobium japonicum and B. elkanii dominate in nodules in northern and southern areas, respectively. The aim of this study was to elucidate whether temperature-dependent proliferation in soil or infection is more reliable for determining the latitudinal characteristic distribution of soybean-nodulating rhizobia under local climate conditions. Three study locations, Fukagawa (temperate continental climate), Matsue and Miyazaki (humid sub-tropical climate), were selected in Japan. Each soil sample was transported to the other study locations, and soybean cv. Orihime (non-Rj) was pot-cultivated using three soils at three study locations for two successive years. Species composition of Bradyrhizobium in the nodules was analyzed based on the partial 16S rRNA and 16S–23S rRNA ITS gene sequences. Two Bradyrhizobium japonicum (Bj11 and BjS10J) clusters and one B. elkanii (BeL7) cluster were phylogenetically sub-grouped into two (Bj11-1-2) and four clusters (BjS10J-1-4) based on the ITS sequence. In the Fukagawa soil, Bj11-1 dominated (80–87%) in all study locations. In the Matsue soil, the composition was similar in the Matsue and Miyazaki locations, in which BeL7 dominated (70–73%), while in the Fukagawa location, BeL7 decreased to 53% and Bj11-1 and BjS10J-3 increased. In the Miyazaki soil, BeL7 dominated at 77%, and BeL7 decreased to 13% and 33% in the Fukagawa and Matsue locations, respectively, while BjS10J-2 and BjS10J-4 increased. It was supposed that the B. japonicum strain preferably proliferated in the Fukagawa location, leading to its nodule dominancy, while in the Miyazaki location, temperature-dependent infection would lead to the nodule dominancy of B. elkanii, and both factors would be involved in the Matsue location.

Colonization of a biofertilizer Bacillus sp. OYK strain, which was isolated from a soil, was compared with three rhizospheric and endophytic Bacillus sp. strains to evaluate the colonization potential of the Bacillus sp. strains with a different origin. Surface-sterilized seeds of tomato (Solanum lycopersicum L. cv. Chika) were sown in the sterilized vermiculite, and four Bacillus sp. strains were each inoculated onto the seed zone. After cultivation in a phytotron, plant growth parameters and populations of the inoculants in the root, shoot, and rhizosphere were determined. In addition, effects of co-inoculation and time interval inoculation of Bacillus sp. F-33 with the other endophytes were examined. All Bacillus sp. strains promoted plant growth except for Bacillus sp. RF-37, and populations of the rhizospheric and endophytic Bacillus sp. strains were 1.4–2.8 orders higher in the tomato plant than that of Bacillus sp. OYK. The plant growth promotion by Bacillus sp. F-33 was reduced by co-inoculation with the other endophytic strains: Klebsiella sp. Sal 1, Enterobacter sp. Sal 3, and Herbaspirillum sp. Sal 6., though the population of Bacillus sp. F-33 maintained or slightly decreased. When Klebsiella sp. Sal 1 was inoculated after Bacillus sp. F-33, the plant growth-promoting effects by Bacillus sp. F-33 were reduced without a reduction of its population, while when Bacillus sp. F-33 was inoculated after Klebsiella sp. Sal 1, the effects were increased in spite of the reduction of its population. Klebsiella sp. Sal 1 colonized dominantly under both conditions. The higher population of rhizospheric and endophytic Bacillus sp. in the plant suggests the importance of the origin of the strains for their colonization. The plant growth promotion and colonization potentials were independently affected by the co-existing microorganisms.

Sweet potato (Ipomoea batatas L.) grows well even in infertile and nitrogen-limited fields, and endophytic bacterial communities have been proposed to be responsible for this ability. Plant-growth-promoting bacteria are considered eco-friendly and are used in agriculture, but their application can interact with endophytic communities in many ways. In this study, a commercial biofertilizer, OYK, consisting of a Bacillus sp., was applied to two cultivars of sweet potato, and the effects on indigenous endophytic bacterial communities in field conditions were examined. A total of 101 bacteria belonging to 25 genera in 9 classes were isolated. Although the inoculated OYK was not detected and significant plant-growth-promoting effects were not observed, the inoculation changed the endophytic bacterial composition, and the changes differed between the cultivars, as follows: Novosphingobium in α-Proteobacteria was dominant; it remained dominant in Beniharuka after the inoculation of OYK, while it disappeared in Beniazuma, with an increase in Sphingomonas and Sphingobium in α-Proteobacteria as well as Chryseobacterium and Acinetobacter in Flavobacteria. The behavior of Bacilli and Actinobacteria also differed between the cultivars. The Shannon diversity index (H) increased after inoculation in all conditions, and the values were similar between the cultivars. Competition of the inoculant with indigenous rhizobacteria and endophytes may determine the fates of the inoculant and the endophytic community.

Beyond the nodule symbiosis process, some endophytic bacteria can convert the atmospheric nitrogen to available form for their own and the inhabiting host plants. These bacteria possess a nitrogenase enzyme complex involved in producing ammonia from atmospheric dinitrogen. The nitrogenase reductase subunit of the enzyme complex is governed by the nifH gene and is being used as a suitable marker. In the present study, the nifH gene containing endophytic bacteria had been identified from two sweet potato cultivars grown in different locations. Both the cultureindependent and culture-dependent methods were used to identify the nitrogen-fixing bacteria in sweet potatoes. The nifH sequences closest to Azospirillum, Bradyrhizobium, Herbaspirillum, Klebsiella, Kluyvera, Paenibacillus, Pseudacidovorax, Rhizobium and Sphingomonas were identified in this study. It was supposed that soils and varieties have more effects than climatic factors on nitrogen-fixing bacteria of sweet potato. These nitrogen-fixing bacteria could be utilized to develop biofertilizers helpful for sustainable agriculture.