Broad Distribution and Phylogeny of Anaerobic Endophytes of Cluster XIVa Clostridia in Plant Species Including Crops

Abstract

Endophytic clostridia present on various plants as obligate anaerobes were surveyed by terminal restriction fragment length polymorphism (TRFLP) analysis specific to the clostridial 16S rRNA gene. Endophytic clostridia were detected in 10 plant types: sugarcane, cultivated rice, corn, tobacco, soybean, bermuda grass, tall fescue, and three mangrove species. Phylogenetically, cluster XIVa clostridia were detected more frequently than cluster I clostridia in aerial parts. Isolation of clostridia from surface-sterilized sugarcane stem validated the TRFLP results. Plant-derived clostridia occupied two unique phylogenetic positions (groups I and II) within cluster XIVa. Most of cluster XIVa clostridia from other sources (e.g., human, animal, and insect intestines) were located outside these groups. Thus two unique groups of cluster XIVa clostridia are widely distributed in plants, including crops. In field-grown soybeans, TRFLP analysis revealed clostridia only in a non-nodulating mutant. Ribosomal intergenic spacer analysis (RISA) showed that the bacterial community in soybean shoot depended partly on the soybean nodulation genotype.Key words: Clostridium, cluster XIVa, endophyte, sugarcane, soybean Endophytes are microorganisms that can colonize living plant tissues without causing any apparent damage to the host 3,23,24,35) . Several diazotrophs have been isolated and characterized as nitrogen-fixing endophytes in plants, including Gluconacetobacter diazotrophicus 3,22) , Herbaspirillum spp. 9,33,38,48) , and Azoarcus sp.19,31) . Novel anaerobic endophytic clostridia and their anaerobic nitrogen-fixing consortium (ANFICO) were recently isolated and characterized in grasses during attempt to overcome a problem with culturing nitrogen-fixing microbes 26) . ANFICO consists of nitrogenfixing clostridia and diverse non-diazotrophic bacteria and expresses nitrogen-fixing activity associated with low oxygen tension and interspecies inducers 26) . Phylogenetic analysis indicated that the endophytic clostridia fell exclusively into clusters XIVa and I, as defined by Collins et al. 8) , and were further subdivided into five groups 26) . Miyamoto et al.27) developed a terminal restriction fragment length polymorphism (TRFLP) detection system specific for these clusters and groups of plant clostridia, and demonstrated that the group II clostridia in cluster XIVa 8)dominated the populations of diazotrophs and clostridia in a gramineous grass, Miscanthus sinensis. Inoculation examinations indicate that endophytic clostridia colonize plant tissues, alleviating the damage caused by salt stress 47) and potentially fixing nitrogen in the plant 34) . Thus, more attention should be paid to the endophytic clostridia in terms of their distribution, phylogeny, and function.Recently, cluster XIVa clostridia have been detected and isolated from human faeces 12,18,28) , animal intestines 2,20,21,25,44) , termite guts 40,41) , soil 7,17,45) , and plants 26,27) using culture-independent and culture-dependent methods. However, the relations...

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…Table 1 lists the DDBJ/GenBank/EMBL accession numbers for the 16S rRNA genes and ITS sequences between 16S-and 23S-rRNA that are used in this study. For the phylogenetic analysis, the neighborjoining method and Clustal W were used as described earlier (Saito et al, 2008).…”

Nitrogen Fixation and Translocation in Young Sugarcane (Saccharum officinarum L.) Plants Associated with Endophytic Nitrogen-Fixing Bacteria

“…In addition, the sites of colonization and the movement through xylem vessels of G. diazotrophicus within sugarcane plants are controversial (10,11,13). Recently, Saito et al (29) reported a broad distribution and phylogeny of anaerobic endophytes of cluster XIVa clostridia in various plant species including the leaves, stems, stem cuttings and roots of sugarcane. The fixation of N2 by endophytic bacteria has also been suggested in other crops, eg.…”

The Genotype of the Calcium/Calmodulin-Dependent Protein Kinase Gene ( CCaMK ) Determines Bacterial Community Diversity in Rice Roots under Paddy and Upland Field Conditions

“…3A). Obligate anaerobic bacteria have been found as endophytes in several plant species (37). Under upland conditions, an actinobacterial population belonging to the Actinosynnemataceae was greatly increased in UR plants (Fig.…”