The effect of biotic and physical factors on the competitive ability of Rhizobium leguminosarum

Planted Citrus Regulates the Community and Networks of phoD-Harboring Bacteria to Drive Phosphorus Availability Between Karst and Non-Karst Soils

The phosphorus (P) availability in soils is influenced by microbes, particularly those containing the gene responsible for phosphate solubilization. The present study investigated the community structure, diversity, and co-occurrence networks of phoD-harboring bacteria in karst and non-karst citrus orchard soils across a planting duration gradient, natural forests, and abandoned land, as well as the soil total P (TP) and available P (AP) contents and enzyme activities. The soil AP contents were lower in the karst regions than in the non-karst regions, while the soil organic carbon (C; SOC), exchangeable calcium, and microbial biomass nitrogen (N) contents; alkaline phosphatase (ALP) and β-Glucuronidase activities; and pH had the opposite trends. In addition, the soil AP and SOC contents and the ALP and acid phosphatase (ACP) activities in the karst regions decreased with an increase in the planting years, whereas the AP, TP, and microbial biomass P contents and ACP activities in the non-karst regions increased. The diversity indices and network complexity of phoD-harboring bacteria were higher in the karst regions than in the non-karst regions, with marked community differences between different planting years in the non-karst regions. The soil AP was significantly and positively correlated with the rare genera Pelagicola, Methylobacter, Streptomyces, and Micromonospora in the karst regions and Roseivivax, Collimonas, Methylobacterium, Ralstonia, and Phyllobacterium in the non-karst regions. Structural Equation Modeling showed that citrus cultivation altered the soil pH, SOC, and total N, and, in turn, the phoD-harboring bacterial community structure and diversity, which led to changes in the ALP activity and P availability. Thus, the rare genera of the phoD-harboring bacteria, influenced by the pH and SOC, highly regulated the availability of P in the karst and non-karst citrus orchard soils.

Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture

Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 107 mL-1) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 108 VLP mL-1; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.

Enhancing the Efficiency of Soybean Inoculant for Nodulation under Multi-Environmental Stress Conditions

The development of rhizobial inoculants with increased resistance to abiotic stress is critical to mitigating the challenges related to climate change. This study aims at developing a soybean stress-tolerant Bradyrhizobium inoculant to be used under the mixed stress conditions of acidity, high temperature, and drought. Six isolates of Bradyrhizobium with high symbiotic performance on soybean were tested to determine their growth or survival abilities under in vitro conditions. The representative stress-tolerant Bradyrhizobium isolates 184, 188, and 194 were selected to test their ability to promote soybean growth under stress conditions compared to the type strain Bradyrhizobium diazoefficiens USDA110. The plant experiment indicated that isolate 194 performed better in symbiosis with soybean than other Bradyrhizobium strains under stress conditions. Based on the stress tolerance index, soybeans inoculated with isolate 194 showed a high growth performance and significantly better nodulation competition ability than USDA110 under several stress conditions. Interestingly, supplementation of sucrose in the culture medium significantly enhances the survival of the isolate and leads to improved plant biomass under various stress conditions. Analysis of the intra-cellular sugars of isolate 194 supplemented with sucrose showed the accumulation of compatible solutes, such as trehalose and glycerol, that may act as osmoprotectants. This study indicates that inoculation of stress-tolerant Bradyrhizobium together with sucrose supplementation in a medium could enhance bacterial survival and symbiosis efficiency under stress conditions. Although it can be applied for inoculant production, this strategy requires validation of its performance in field conditions before adopting this technology.

Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence

Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N₂)-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient. We collected nodules from plants grown in soils from five chronosequence stages ranging from very young (10s of years; associated with strong N limitation for plant growth) to very old (> 2,000,000 years; associated with strong P limitation), and sequenced the nifH gene in root nodules to determine the composition and diversity of N₂-fixing bacterial symbionts. A total of 335 unique nifH gene operational taxonomic units (OTUs) were identified. Community composition of N₂-fixing bacteria within nodules, but not diversity, changed with increasing soil age. These changes were attributed to pedogenesis-driven shifts in edaphic conditions, specifically pH, exchangeable manganese, resin-extractable phosphate, nitrate and nitrification rate. A large number of common N₂-fixing bacteria genera (e.g. Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium) belonging to the Rhizobiaceae family (α-proteobacteria) comprised 70% of all raw sequences and were present in all nodules. However, the oldest soils, which show some of the lowest soil P availability ever recorded, harboured the largest proportion of unclassified OTUs, suggesting a unique set of N₂-fixing bacteria adapted to extreme P limitation. Our results show that N₂-fixing bacterial composition varies strongly during long-term ecosystem development, even within the same host, and therefore rhizobia show strong edaphic preferences.

Identification and characterization of phages parasitic on bradyrhizobia nodulating groundnut (Arachis hypogaea L.) in South Africa

In this study, three lytic phages (namely, PRSA-1, PRSA-2 and PRSA-26) were isolated and characterized for their morphology, host range, profile and restriction endonuclease banding pattern of genome size. The susceptible rhizobial isolates were identified by nifH and glnII sequence analysis. The results showed that all phages had polyhedral head with non-contractile tail which confirmed their relationship with the Siphoviridae family. All the three phages produced highly distinct plaques on their host bradyrhizobial lawn, and were highly sensitive to chloroform. The phage genome sizes ranged from 34.7 to 53.1 kbp. The phages were tested against groundnut-nodulating bradyrhizobial strains TUTAHSA75, TUTAHSA155 and TUTAHSA126 isolated from South African soils. The results revealed different bacterial susceptibilities to phages. Bradyrhizobial isolate TUTAHSA126 was susceptible to all three phages (i.e. PRSA-1, PRSA-2 and PRSA-26), TUTAHSA155 to two phages (i.e. PRSA-1, PRSA-2), and TUTAHSA75 to only one phage (i.e. PRSA-1). Phylogenetic analysis of nifH and glnII gene sequences of the phage-susceptible bradyrhizobial isolates revealed their close relatedness to a diverse group of Bradyrhizobium species. Phage PRSA-1 could parasitize on all three bradyrhizobial strains, which indicates its potential role in horizontal gene transfer through lysogenic conversion, and/or genetic transduction in soil microbial environments.

Homoserine catabolism by Rhizobium leguminosarum bv. viciae 3841 requires a plasmid-borne gene cluster that also affects competitiveness for nodulation

Homoserine represents a substantial component of pea root exudate that may be important for plant-microbe interactions in the rhizosphere. We identified a gene cluster on plasmid pRL8JI that is required for homoserine utilization by Rhizobium leguminosarum bv. viciae. The genes are arranged as two divergently expressed predicted operons that were induced by L-homoserine, pea root exudate, and were expressed on pea roots. A mutation in gene pRL80083 that prevented utilization of homoserine as a sole carbon and energy source affected the mutant's ability to nodulate peas and lentils competitively. The homoserine gene cluster was present in approximately 47% of natural R. leguminosarum isolates (n = 59) and was strongly correlated with homoserine utilization. Conjugation of pRL8JI to R. leguminosarum 4292 or Agrobacterium tumefaciens UBAPF2 was sufficient for homoserine utilization. The presence of L-homoserine increased conjugation efficiency of pRL8JI from R. leguminosarum to a pRL8JI-cured derivative of R. leguminosarum 1062 and to A. tumefaciens UBAPF2, and induced expression of the plasmid transfer gene trbB; however, there was no difference in conjugation efficiency or trbB expression with A. tumefaciens UBAPF2pRL8-Gm as the donor suggesting that other genes in R. leguminosarum may contribute to regulating conjugation of pRL8 in the presence of homoserine.

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

The term ‘Rhizobium-legume symbiosis’ refers to numerous plant-bacterial interrelationships. Typically, from an evolutionary perspective, these symbioses can be considered as species-to-species interactions, however, such plant-bacterial symbiosis may also be viewed as a low-scale environmental interplay between individual plants and the local microbial population. Rhizobium-legume interactions are therefore highly important in terms of microbial diversity and environmental adaptation thereby shaping the evolution of plant-bacterial symbiotic systems. Herein, the mechanisms underlying and modulating the diversity of rhizobial populations are presented. The roles of several factors impacting successful persistence of strains in rhizobial populations are discussed, shedding light on the complexity of rhizobial-legume interactions.