Symbiosis
Symbiosis has played a key role in the evolution of life on Earth. Symbiotic mergers of once independent species drove the origin of eukaryotes. Moreover, symbiosis has enabled many species to gain novel functions and occupy new ecological niches, thus underpinning the functioning of diverse ecosystems. As endosymbionts, microbes provide their eukaryotic hosts with an array of ecological and physiological innovations, including new metabolic capabilities, such as autotrophy or nitrogen fixation, and protection against infections or environmental stressors. Microbial eukaryotes also commonly host their own endosymbionts, including bacteria and algae. Understanding the stability and resilience of symbioses is key to predicting the response of important ecosystems, such as coral reefs, to global change. Manipulating symbiotic associations also has far-reaching economic, environmental and medical implications, through the potential to improve crop productivity, reduce reliance on fertilisers, and control the insect vectors of infectious diseases.
This collection, guest edited by Professor Michael Brockhurst (University of Manchester) and Dr. Rebecca J Hall (University of Birmingham), will feature microbe-focused studies of symbiosis, ranging from the molecular mechanisms of host-symbiont interactions, their genetic and genomic diversity, to understanding the impacts of symbioses in natural and manmade ecosystems.
Collection Contents
68 results
-
-
Approaching the domesticated plant holobiont from a community evolution perspective
More LessPlants establish a pivotal relationship with their microbiome and are often conceptualized as holobionts. Nonetheless, holobiont theories have attracted much criticism, especially concerning the fact that the holobiont is rarely a unit of selection. In previous work, we discussed how the plant microbiome can be considered to be an ‘ecosystem on a leash’, which is subject to the influence of natural selection acting on plant traits. We proposed that in domesticated plants the assembly of the plant microbiome can usefully be conceptualized as being subject to a ‘double leash’, which encompasses both the effect of artificial selection imposed by the domesticator on plant traits and the leash from the plant to the microbiome. Here we approach the domesticated plant holobiont, simply defined as a community of organisms, from a community evolution point of view, and show how community heritability (a measure of community selection) complements the ‘double-leash’ framework in providing a community-level view of plant domestication and its impact on plant–microbe interactions. We also propose simple experiments that could be performed to investigate whether plant domestication has altered the potential for community selection at the holobiont level.
-
-
-
Symbiont-mediated immune priming in animals through an evolutionary lens
More LessProtective symbionts can defend hosts from parasites through several mechanisms, from direct interference to modulating host immunity, with subsequent effects on host and parasite fitness. While research on symbiont-mediated immune priming (SMIP) has focused on ecological impacts and agriculturally important organisms, the evolutionary implications of SMIP are less clear. Here, we review recent advances made in elucidating the ecological and molecular mechanisms by which SMIP occurs. We draw on current works to discuss the potential for this phenomenon to drive host, parasite, and symbiont evolution. We also suggest approaches that can be used to address questions regarding the impact of immune priming on host-microbe dynamics and population structures. Finally, due to the transient nature of some symbionts involved in SMIP, we discuss what it means to be a protective symbiont from ecological and evolutionary perspectives and how such interactions can affect long-term persistence of the symbiosis.
-
-
-
Microbe Profile: Buchnera aphidicola: ancient aphid accomplice and endosymbiont exemplar
More LessBuchnera aphidicola is an obligate endosymbiont of aphids that cannot be cultured outside of hosts. It exists as diverse strains in different aphid species, and phylogenetic reconstructions show that it has been maternally transmitted in aphids for >100 million years. B. aphidicola genomes are highly reduced and show conserved gene order and no gene acquisition, but encoded proteins undergo rapid evolution. Aphids depend on B. aphidicola for biosynthesis of essential amino acids and as an integral part of embryonic development. How B. aphidicola populations are regulated within hosts remains little known.
-
-
-
The impact of intra-specific diversity in the rhizobia-legume symbiosis
More LessRhizobia - nitrogen-fixing, root-nodulating bacteria - play a critical role in both plant ecosystems and sustainable agriculture. Rhizobia form intracellular infections within legumes roots where they produce plant accessible nitrogen from atmospheric nitrogen and thus reduce the reliance on industrial inputs. The rhizobia-legume symbiosis is often treated as a pairwise relationship between single genotypes, both in research and in the production of rhizobial inoculants. However in nature individual plants are infected by a high diversity of rhizobia symbionts. How this diversity affects productivity within the symbiosis is unclear. Here, we use a powerful statistical approach to assess the impact of diversity within the Rhizobium leguminosarum - clover symbiosis using a biodiversity-ecosystem function framework. Statistically, we found no significant impact of rhizobium diversity. However this relationship was weakly positive - rather than negative - indicating that there is no significant cost to increasing inoculant diversity. Productivity was influenced by the identity of the strains within an inoculant; strains with the highest individual performance showed a significant positive contribution within mixed inoculants. Overall, inoculant effectiveness was best predicted by the individual performance of the best inoculant member, and only weakly predicted by the worst performing member. Collectively, our data suggest that the Rhizobium leguminosarum - clover symbiosis displays a weak diversity-function relationship, but that inoculant performance can be improved through the inclusion of high performing strains. Given the wide environmental dependence of rhizobial inoculant quality, multi-strain inoculants could be highly successful as they increase the likelihood of including a strain well adapted to local conditions across different environments.
-
-
-
R-type bacteriocins of Xenorhabdus bovienii determine the outcome of interspecies competition in a natural host environment
Xenorhabdus species are bacterial symbionts of Steinernema nematodes and pathogens of susceptible insects. Different species of Steinernema nematodes carrying specific species of Xenorhabdus can invade the same insect, thereby setting up competition for nutrients within the insect environment. While Xenorhabdus species produce both diverse antibiotic compounds and prophage-derived R-type bacteriocins (xenorhabdicins), the functions of these molecules during competition in a host are not well understood. Xenorhabdus bovienii (Xb-Sj), the symbiont of Steinernema jollieti, possesses a remnant P2-like phage tail cluster, xbp1, that encodes genes for xenorhabdicin production. We show that inactivation of either tail sheath (xbpS1) or tail fibre (xbpH1) genes eliminated xenorhabdicin production. Preparations of Xb-Sj xenorhabdicin displayed a narrow spectrum of activity towards other Xenorhabdus and Photorhabdus species. One species, Xenorhabdus szentirmaii (Xsz-Sr), was highly sensitive to Xb-Sj xenorhabdicin but did not produce xenorhabdicin that was active against Xb-Sj. Instead, Xsz-Sr produced high-level antibiotic activity against Xb-Sj when grown in complex medium and lower levels when grown in defined medium (Grace’s medium). Conversely, Xb-Sj did not produce detectable levels of antibiotic activity against Xsz-Sr. To study the relative contributions of Xb-Sj xenorhabdicin and Xsz-Sr antibiotics in interspecies competition in which the respective Xenorhabdus species produce antagonistic activities against each other, we co-inoculated cultures with both Xenorhabdus species. In both types of media Xsz-Sr outcompeted Xb-Sj, suggesting that antibiotics produced by Xsz-Sr determined the outcome of the competition. In contrast, Xb-Sj outcompeted Xsz-Sr in competitions performed by co-injection in the insect Manduca sexta, while in competition with the xenorhabdicin-deficient strain (Xb-Sj:S1), Xsz-Sr was dominant. Thus, xenorhabdicin was required for Xb-Sj to outcompete Xsz-Sr in a natural host environment. These results highlight the importance of studying the role of antagonistic compounds under natural biological conditions.
-
-
-
Identification of Photorhabdus symbionts by MALDI-TOF MS
More LessSpecies of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.
-
-
-
Genetic regulation, biochemical properties and physiological importance of arginase from Sinorhizobium meliloti
In bacteria, l-arginine is a precursor of various metabolites and can serve as a source of carbon and/or nitrogen. Arginine catabolism by arginase, which hydrolyzes arginine to l-ornithine and urea, is common in nature but has not been studied in symbiotic nitrogen-fixing rhizobia. The genome of the alfalfa microsymbiont Sinorhizobium meliloti 1021 has two genes annotated as arginases, argI1 (smc03091) and argI2 (sma1711). Biochemical assays with purified ArgI1 and ArgI2 (as 6His-Sumo-tagged proteins) showed that only ArgI1 had detectable arginase activity. A 1021 argI1 null mutant lacked arginase activity and grew at a drastically reduced rate with arginine as sole nitrogen source. Wild-type growth and arginase activity were restored in the argI1 mutant genetically complemented with a genomically integrated argI1 gene. In the wild-type, arginase activity and argI1 transcription were induced several fold by exogenous arginine. ArgI1 purified as a 6His-Sumo-tagged protein had its highest in vitro enzymatic activity at pH 7.5 with Ni2+ as cofactor. The enzyme was also active with Mn2+ and Co2+, both of which gave the enzyme the highest activities at a more alkaline pH. The 6His-Sumo-ArgI1 comprised three identical subunits based on the migration of the urea-dissociated protein in a native polyacrylamide gel. A Lrp-like regulator (smc03092) divergently transcribed from argI1 was required for arginase induction by arginine or ornithine. This regulator was designated ArgIR. Electrophoretic mobility shift assays showed that purified ArgIR bound to the argI1 promoter in a region preceding the predicted argI1 transcriptional start. Our results indicate that ArgI1 is the sole arginase in S. meliloti , that it contributes substantially to arginine catabolism in vivo and that argI1 induction by arginine is dependent on ArgIR.
-
-
-
Photorhabdus: a tale of contrasting interactions
More LessDifferent model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus Photorhabdus comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore Photorhabdus has three distinct and obligate roles to play during this life-cycle: (1) Photorhabdus must kill the insect host; (2) Photorhabdus must be capable of supporting nematode growth and development; and (3) Photorhabdus must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between Photorhabdus and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.
-
-
-
Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid (Euprymna scolopes)
More LessMany microorganisms engaged in host-microbe interactions pendulate between a free-living phase and a host-affiliated stage. How adaptation to stress during the free-living phase affects host-microbe associations is unclear and understudied. To explore this topic, the symbiosis between Hawaiian bobtail squid (Euprymna scolopes) and the luminous bacterium Vibrio fischeri was leveraged for a microbial experimental evolution study. V. fischeri experienced adaptation to extreme pH while apart from the squid host. V. fischeri was serially passaged for 2000 generations to the lower and upper pH growth limits for this microorganism, which were pH 6.0 and 10.0, respectively. V. fischeri was also serially passaged for 2000 generations to vacillating pH 6.0 and 10.0. Evolution to pH stress both facilitated and impaired symbiosis. Microbial evolution to acid stress promoted squid colonization and increased bioluminescence for V. fischeri , while symbiont adaptation to alkaline stress diminished these two traits. Oscillatory selection to acid and alkaline stress also improved symbiosis for V. fischeri , but the facilitating effects were less than that provided by microbial adaptation to acid stress. In summary, microbial adaptation to harsh environments amid the free-living phase may impact the evolution of host-microbe interactions in ways that were not formerly considered.
-
-
-
Defining the requirements for the conjugative transfer of Rhizobium leguminosarum plasmid pRleVF39b
More LessRhizobium leguminosarum strain VF39 contains a plasmid, pRleVF39b, which encodes a distinctive type of conjugation system (rhizobial type IVa) that is relatively widespread among rhizobial genomes. The cluster of genes encoding the transfer functions lacks orthologs to genes such as traCD, traF and traB, but contains 15 conserved genes of unknown function. We determined the importance of these genes in conjugation by constructing marked and unmarked mutations in each gene, and established that six genes, now designated trcA-F, played a significant role in plasmid transfer. Like the relaxase gene, traA, and the genes encoding the MPF system (trb genes), five of these genes, located in two divergently transcribed operons, are regulated by the Xre family repressor TrbR. The other gene, trcF encodes a protein with similarity to histidinol phosphatases, and its role in conjugation is unclear, but mutations in trcF are severely impaired for conjugation. TrcF does not play a role in regulation of other conjugation genes.
-
-
-
Polyamines produced by Sinorhizobium meliloti Rm8530 contribute to symbiotically relevant phenotypes ex planta and to nodulation efficiency on alfalfa
More LessIn nitrogen-fixing rhizobia, emerging evidence shows significant roles for polyamines in growth and abiotic stress resistance. In this work we show that a polyamine-deficient ornithine decarboxylase null mutant (odc2) derived from Sinorhizobium meliloti Rm8530 had significant phenotypic differences from the wild-type, including greatly reduced production of exopolysaccharides (EPS; ostensibly both succinoglycan and galactoglucan), increased sensitivity to oxidative stress and decreased swimming motility. The introduction of the odc2 gene borne on a plasmid into the odc2 mutant restored wild-type phenotypes for EPS production, growth under oxidative stress and swimming. The production of calcofluor-binding EPS (succinoglycan) by the odc2 mutant was also completely or mostly restored in the presence of exogenous spermidine (Spd), norspermidine (NSpd) or spermine (Spm). The odc2 mutant formed about 25 % more biofilm than the wild-type, and its ability to form biofilm was significantly inhibited by exogenous Spd, NSpd or Spm. The odc2 mutant formed a less efficient symbiosis with alfalfa, resulting in plants with significantly less biomass and height, more nodules but less nodule biomass, and 25 % less nitrogen-fixing activity. Exogenously supplied Put was not able to revert these phenotypes and caused a similar increase in plant height and dry weight in uninoculated plants and in those inoculated with the wild-type or odc2 mutant. We discuss ways in which polyamines might affect the phenotypes of the odc2 mutant.
-
-
-
Bacteriophage acquisition restores protective mutualism
More LessInsects are frequently infected with inherited facultative symbionts known to provide a range of conditionally beneficial services, including host protection. Pea aphids (Acyrthosiphon pisum) often harbour the bacterium Hamiltonella defensa , which together with its associated bacteriophage A. pisum secondary endosymbiont (APSE) confer protection against an important natural enemy, the parasitic wasp Aphidius ervi. Previous studies showed that spontaneous loss of phage APSE resulted in the complete loss of the protective phenotype. Here, we demonstrate that APSEs can be experimentally transferred into phage-free (i.e. non-protecting) Hamiltonella strains. Unexpectedly, trials using injections of phage particles alone failed, with successful transfer occurring only when APSE and Hamiltonella were simultaneously injected. After transfer, stable establishment of APSE fully restored anti-parasitoid defenses. Thus, phages associated with heritable bacterial symbionts can move horizontally among symbiont strains facilitating the rapid transfer of ecologically important traits although natural barriers may preclude regular exchange.
-
-
-
Regulation of hsnT, nodF and nodE genes in Rhizobium tropici CIAT 899 and their roles in the synthesis of Nod factors and in the symbiosis
Rhizobium tropici strain CIAT 899 possesses outstanding agronomic properties as it displays tolerance to environmental stresses, a broad host range and high effectiveness in fixing nitrogen with the common bean (Phaseolus vulgaris L.); in addition, it carries intriguing features such as five copies of the regulatory nodD gene, and the capacity to synthesize a variety of nodulation factors (NFs), even in a flavonoid-independent manner, when submitted to abiotic stresses. However, the roles of several nod genes of the repertoire of CIAT 899 remain to be determined. In this study, we obtained mutants for the hsnT, nodF and nodE genes of CIAT 899 and investigated their expression, NF structures and symbiotic properties. Either in the presence of the flavonoid apigenin, or of salt the expression of hsnT, nodF and nodE in wild-type CIAT 899 was highly up-regulated in comparison to the mutants of all five copies of nodD, indicating the roles that regulatory nodD genes play in the activation of hsnT, nodF and nodE; however, NodD1 was recognized as the main inducer. In total, 29 different NF structures were synthesized by wild-type CIAT 899 induced by apigenin, and 36 when induced by salt, being drastically reduced by mutations in hsnT, nodF and nodE, especially under osmotic stress, with specific changes related to each gene, indicating that the three genes participate in the synthesis of NFs. Mutations in hsnT, nodF and nodE affected differently symbiotic performance (nodule number and shoot dry weight), according to the host plant. Our results indicate that the expression of hsnT, nodF and nodE genes of CIAT 899 is mediated by nodD genes, and although these three genes do not belong to the main set of genes controlling nodulation, they contribute to the synthesis of NFs that will impact symbiotic performance and host specificity.
-
-
-
Rhizobium tropici CIAT 899 copA gene plays a fundamental role in copper tolerance in both free life and symbiosis with Phaseolus vulgaris
Rhizobium tropici CIAT 899 is a facultative symbiotic diazotroph able to deal with stressful concentrations of metals. Nevertheless the molecular mechanisms involved in metal tolerance have not been elucidated. Copper (Cu2+) is a metal component essential for the heme-copper respiratory oxidases and enzymes that catalyse redox reactions, however, it is highly toxic when intracellular trace concentrations are surpassed. In this study, we report that R. tropici CIAT 899 is more tolerant to Cu2+ than other Rhizobium and Sinorhizobium species. Through Tn5 random mutagenesis we identify a R. tropici mutant strain with a severe reduction in Cu2+ tolerance. The Tn5 insertion disrupted the gene RTCIAT899_CH17575, encoding a putative heavy metal efflux P1B-1-type ATPase designated as copA. Phaseolus vulgaris plants inoculated with the copA::Tn5 mutant in the presence of toxic Cu2+ concentrations showed a drastic reduction in plant and nodule dry weight, as well as nitrogenase activity. Nodules induced by the copA::Tn5 mutant present an increase in H2O2 concentration, lipoperoxidation and accumulate 40-fold more Cu2+ than nodules formed by the wild-type strain. The copA::Tn5 mutant complemented with the copA gene recovered the wild-type symbiotic phenotypes. Therefore, the copA gene is essential for R. tropici CIAT 899 to survive in copper-rich environments in both free life and symbiosis with P. vulgaris plants.
-
-
-
ngrA-dependent natural products are required for interspecies competition and virulence in the insect pathogenic bacterium Xenorhabdus szentirmaii
More LessXenorhabdus species are symbionts of entomopathogenic nematodes and pathogens of susceptible insects. Nematodes enter insect hosts and perforate the midgut to invade the haemocoel where Xenorhabdus bacteria are released transitioning to their pathogenic stage. During nematode invasion microbes from the insect gut translocate into the haemocoel. Different species of nematodes carrying specific strains of Xenorhabdus can also invade the same insect. Xenorhabdus species thereby compete for nutrients and space with both related strains and non-related gut microbes. While Xenorhabdus species produce diverse antimicrobial compounds in complex media, their functions in insect hosts are not well understood. We show that Xenorhabdus szentirmaii produced ngrA-dependent antibiotics that were active against both gut-derived microbes and Xenorhabdus nematophila whereas antibiotics of X. nematophila were not active against X. szentirmaii . X. nematophila growth was inhibited in co-cultures with wild-type X. szentirmaii in medium that mimics insect haemolymph. An antibiotic-deficient strain of X. szentirmaii was created by inactivating the ngrA gene that encodes the enzyme that attaches the 4′ phosphopantetheinyl moiety to non-ribosomal peptide synthetases involved in antibiotic biosynthesis. X. nematophila growth was not inhibited in co-cultures with the ngrA strain. The growth of X. nematophila was suppressed in Manduca sexta co-injected with wild-type X. szentirmaii and X. nematophila . In contrast, growth of X. nematophila was not suppressed in M. sexta co-injected with the ngrA strain. Two unique compounds were detected by MALDI-TOF MS analysis in haemolymph infected with the wild-type but not with the ngrA strain. Finally, killing of M. sexta was delayed in insects infected with the ngrA strain. These findings indicate that in the insect host X. szentirmaii produces ngrA-dependent products involved in both interspecies competition and virulence.
-
-
-
Phylogenetic analyses of antibiotic-producing Streptomyces sp. isolates obtained from the stingless-bee Tetragonisca angustula (Apidae: Meliponini)
Many insects have been associated with actinobacteria in protective symbiosis where antimicrobial metabolites inhibit host pathogens. However, the microbiota of neotropical insects such as the stingless-bee Tetragonisca angustula is poorly explored. T. angustula is a meliponid bee widely distributed in Latin America, its honey is traditionally exploited because of its ethno-pharmacological properties and its antimicrobial activity has been demonstrated. Also, the well-structured nest of this species allows exploration of the microbiota of its different components. Even though Streptomyces spp. have been cultured from stingless-bees, little is known about their role in this insect–microbe relationship. In this study, we examined the association between culturable actinobacteria and T. angustula, and evaluated the isolates’ potential as antimicrobial producers. We isolated 51 actinobacteria from adult bees and different substrates of the hive of T. angustula (pollen and honey storage, garbage pellets and cerumen). We then performed a 16S rRNA phylogenetic analysis that clusters the bacteria to previously described lineages of host-associated Streptomyces . In addition, all the isolates were classified according to their antibacterial activity against human pathogens, measured by a growth inhibition test based on diffusion in agar. More than 50 % of our isolates exhibit antimicrobial activity, mainly to Gram-positive bacteria and fungi and only two against Gram-negative bacteria. Additionally, we obtained electron micrographs of adult bees with what appears to be patches of hyphae with Streptomyces -like cell morphology on their body surface. Our results suggest that T. angustula possibly uptakes and transfers actinobacteria from the environment, acting as vectors for these potentially beneficial organisms. This research provides new insights regarding the microbiota associated with T. angustula and justify future studies exploring the full diversity of the microbial community associated with the hive and the possible exchange of microbes with the crops they pollinate.
-
-
-
Symbiont evolution during the free-living phase can improve host colonization
More LessFor micro-organisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether evolution during the free-living stage can be positively pleiotropic to microbial fitness in a host environment. To address this topic, the squid host Euprymna tasmanica and the marine bioluminescent bacterium Vibrio fischeri were utilized. Microbial ecological diversification in static liquid microcosms was used to simulate symbiont evolution during the free-living stage. Thirteen genetically distinct V. fischeri strains from a broad diversity of ecological sources (e.g. squid light organs, fish light organs and seawater) were examined to see if the results were reproducible in many different genetic settings. Genetic backgrounds that are closely related can be predisposed to considerable differences in how they respond to similar selection pressures. For all strains examined, new mutations with striking and facilitating effects on host colonization arose quickly during microbial evolution in the free-living stage, regardless of the ecological context under consideration for a strain’s genetic background. Microbial evolution outside a host environment promoted host range expansion, improved host colonization for a micro-organism, and diminished the negative correlation between biofilm formation and motility.
-
-
-
Polyamines are required for normal growth in Sinorhizobium meliloti
More LessPolyamines (PAs) are ubiquitous polycations derived from basic l-amino acids whose physiological roles are still being defined. Their biosynthesis and functions in nitrogen-fixing rhizobia such as Sinorhizobium meliloti have not been extensively investigated. Thin layer chromatographic and mass spectrometric analyses showed that S. meliloti Rm8530 produces the PAs, putrescine (Put), spermidine (Spd) and homospermidine (HSpd), in their free forms and norspermidine (NSpd) in a form bound to macromolecules. The S. meliloti genome encodes two putative ornithine decarboxylases (ODC) for Put synthesis. Activity assays with the purified enzymes showed that ODC2 (SMc02983) decarboxylates both ornithine and lysine. ODC1 (SMa0680) decarboxylates only ornithine. An odc1 mutant was similar to the wild-type in ODC activity, PA production and growth. In comparison to the wild-type, an odc2 mutant had 45 % as much ODC activity and its growth rates were reduced by 42, 14 and 44 % under non-stress, salt stress or acid stress conditions, respectively. The odc2 mutant produced only trace levels of Put, Spd and HSpd. Wild-type phenotypes were restored when the mutant was grown in cultures supplemented with 1 mM Put or Spd or when the odc2 gene was introduced in trans. odc2 gene expression was increased under acid stress and reduced under salt stress and with exogenous Put or Spd. An odc1 odc2 double mutant had phenotypes similar to the odc2 mutant. These results indicate that ODC2 is the major enzyme for Put synthesis in S. meliloti and that PAs are required for normal growth in vitro.
-
-
-
Ultrastructural and microbial analyses of cellulose degradation in leaf-cutter ant colonies
More LessLeaf-cutter ants (Atta and Acromyrmex) use fresh leaves to cultivate a mutualistic fungus (Leucoagaricus gongylophorus) for food in underground gardens. A new ant queen propagates the cultivar by taking a small fragment of fungus from her parent colony on her nuptial flight and uses it to begin her own colony. Recent research has shown that the ants’ fungus gardens are colonized by symbiotic bacteria that perform important functions related to nitrogen fixation and have been implicated in contributing to plant biomass degradation. Here, we combine bacterial culturing in several media for counts and identification using the 16S rRNA gene with electron microscopy to investigate the process of cellulose degradation in the fungus garden and refuse dumps, and to assess the potential role of symbiotic bacteria. We show through electron microscopy that plant cell walls are visibly degraded in the bottom section of fungus gardens and refuse dumps, and that bacteria are more abundant in these sections. We also consistently isolated cellulolytic bacteria from all sections of fungus gardens. Finally, we show by culture-dependent and electron microscopy analysis that the fungus garden pellets carried by recently mated queens are colonized by fungus garden-associated bacteria. Taken together, our results indicate that cellulose is degraded in fungus gardens, and that fungus garden bacteria that may contribute to this deconstruction are vertically transmitted by new queens.
-
-
-
Physical contact and carbon transfer between a lichen-forming Trebouxia alga and a novel Alphaproteobacterium
More LessRecent progress in molecular techniques has begun to alter traditional recognition of lichens as symbiotic organisms comprised of a fungus and photosynthetic partners (green algae and/or cyanobacteria). Diverse organisms, especially various non-photosynthetic bacteria, are now indicated to be integral components of lichen symbiosis. Although lichen-associated bacteria are inferred to have functions that could support the symbiosis, little is known about their physical and nutritional interaction with fungi and algae. In the present study, we identified specific interaction between a lichen-forming alga and a novel bacterium. Trebouxia alga was isolated from a lichen, Usnea hakonensis, and kept as a strain for 8 years. Although no visible bacterial colonies were observed in this culture, high-throughput sequencing of DNA isolated from the culture revealed that the strain is composed of a Trebouxia alga and an Alphaproteobacterium species. In situ hybridization showed that bacterial cells were localized on the surface of the algal cells. Physiological assays revealed that the bacterium was able to use ribitol, glucose and mannitol, all of which are known to exist abundantly in lichens. It was resistant to three antibiotics. Bacteria closely related to this species were also identified in lichen specimens, indicating that U. hakonensis may commonly associate with this group of bacteria. These features of the novel bacterium suggest that it may be involved in carbon cycling of U. hakonensis as a member of lichen symbiosis and less likely to have become associated with the alga after isolation from a lichen.
-
-
-
DNA double-strand break repair is involved in desiccation resistance of Sinorhizobium meliloti, but is not essential for its symbiotic interaction with Medicago truncatula
More LessThe soil bacterium Sinorhizobium meliloti, a nitrogen-fixing symbiont of legume plants, is exposed to numerous stress conditions in nature, some of which cause the formation of harmful DNA double-strand breaks (DSBs). In particular, the reactive oxygen species (ROS) and the reactive nitrogen species (RNS) produced during symbiosis, and the desiccation occurring in dry soils, are conditions which induce DSBs. Two major systems of DSB repair are known in S. meliloti: homologous recombination (HR) and non-homologous end-joining (NHEJ). However, their role in the resistance to ROS, RNS and desiccation has never been examined in this bacterial species, and the importance of DSB repair in the symbiotic interaction has not been properly evaluated. Here, we constructed S. meliloti strains deficient in HR (by deleting the recA gene) or in NHEJ (by deleting the four ku genes) or both. Interestingly, we observed that ku and/or recA genes are involved in S. meliloti resistance to ROS and RNS. Nevertheless, an S. meliloti strain deficient in both HR and NHEJ was not altered in its ability to establish and maintain an efficient nitrogen-fixing symbiosis with Medicago truncatula, showing that rhizobial DSB repair is not essential for this process. This result suggests either that DSB formation in S. meliloti is efficiently prevented during symbiosis or that DSBs are not detrimental for symbiosis efficiency. In contrast, we found for the first time that both recA and ku genes are involved in S. meliloti resistance to desiccation, suggesting that DSB repair could be important for rhizobium persistence in the soil.
-
-
-
Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021
l-Ornithine production in the alfalfa microsymbiont Sinorhizobium meliloti occurs as an intermediate step in arginine biosynthesis. Ornithine is required for effective symbiosis but its synthesis in S. meliloti has been little studied. Unlike most bacteria, S. meliloti 1021 is annotated as encoding two enzymes producing ornithine: N-acetylornithine (NAO) deacetylase (ArgE) hydrolyses NAO to acetate and ornithine, and glutamate N-acetyltransferase (ArgJ) transacetylates l-glutamate with the acetyl group from NAO, forming ornithine and N-acetylglutamate (NAG). NAG is the substrate for the second step of arginine biosynthesis catalysed by NAG kinase (ArgB). Inactivation of argB in strain 1021 resulted in arginine auxotrophy. The activity of purified ArgB was significantly inhibited by arginine but not by ornithine. The purified ArgJ was highly active in NAO deacetylation/glutamate transacetylation and was significantly inhibited by ornithine but not by arginine. The purified ArgE protein (with a 6His-Sumo affinity tag) was also active in deacetylating NAO. argE and argJ single mutants, and an argEJ double mutant, are arginine prototrophs. Extracts of the double mutant contained aminoacylase (Ama) activity that deacetylated NAO to form ornithine. The purified products of three candidate ama genes (smc00682 (hipO1), smc02256 (hipO2) and smb21279) all possessed NAO deacetylase activity. hipO1 and hipO2, but not smb21279, expressed in trans functionally complemented an Escherichia coli ΔargE : : Km mutant. We conclude that Ama activity accounts for the arginine prototrophy of the argEJ mutant. Transcriptional assays of argB, argE and argJ, fused to a promoterless gusA gene, showed that their expression was not significantly affected by exogenous arginine or ornithine.
-
-
-
The Sinorhizobium meliloti sensor histidine kinase CbrA contributes to free-living cell cycle regulation
More LessSinorhizobium meliloti is alternately capable of colonizing the soil as a free-living bacterium or establishing a chronic intracellular infection with its legume host for the purpose of nitrogen fixation. We previously identified the S. meliloti two-component sensor histidine kinase CbrA as playing an important role in regulating exopolysaccharide production, flagellar motility and symbiosis. Phylogenetic analysis of CbrA has highlighted its evolutionary relatedness to the Caulobacter crescentus sensor histidine kinases PleC and DivJ, which are involved in CtrA-dependent cell cycle regulation through the shared response regulator DivK. We therefore became interested in testing whether CbrA plays a role in regulating S. meliloti cell cycle processes. We find the loss of cbrA results in filamentous cell growth accompanied by cells that contain an aberrant genome complement, indicating CbrA plays a role in regulating cell division and possibly DNA segregation. S. meliloti DivK localizes to the old cell pole during distinct phases of the cell cycle in a phosphorylation-dependent manner. Loss of cbrA results in a significantly decreased rate of DivK polar localization when compared with the wild-type, suggesting CbrA helps regulate cell cycle processes by modulating DivK phosphorylation status as a kinase. Consistent with a presumptive decrease in DivK phosphorylation and activity, we also find the steady-state level of CtrA increased in cbrA mutants. Our data therefore demonstrate that CbrA contributes to free-living cell cycle regulation, which in light of its requirement for symbiosis, points to the potential importance of cell cycle regulation for establishing an effective host interaction.
-
-
-
Phylogenetic clustering of Bradyrhizobium symbionts on legumes indigenous to North America
More LessTo analyse determinants of biogeographic structure in members of the genus Bradyrhizobium, isolates were obtained from 41 legume genera, originating from North American sites spanning 48.5 ° of latitude (Alaska to Panama). Sequencing of portions of six gene loci (3674 bp) in 203 isolates showed that there was only a weak trend towards higher nucleotide diversity in tropical regions. Phylogenetic relationships for nifD, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted substantially with a tree inferred for five housekeeping gene loci. For both nifD and housekeeping gene trees, bacteria from each region were significantly more similar, on average, than would be expected if the source location was permuted at random on the tree. Within-region permutation tests also showed that bacteria clustered significantly on particular host plant clades at all levels in the phylogeny of legumes (from genus up to subfamily). Nevertheless, some bacterial groups were dispersed across multiple regions and were associated with diverse legume host lineages. These results indicate that migration, horizontal gene transfer and host interactions have all influenced the geographical divergence of Bradyrhizobium populations on a continental scale.
-
-
-
Biosynthesis of branched-chain amino acids is essential for effective symbioses between betarhizobia and Mimosa pudica
More LessBurkholderia phymatum STM815 and Cupriavidus taiwanensis LMG19424 are betaproteobacterial strains that can effectively nodulate several species of the large legume genus Mimosa. A Tn5 mutant, derived from B. phymatum STM815 (KM60), and another derived from C. taiwanensis LMG19424 (KM184-55) induced Fix− nodules on Mimosa pudica. The Tn5-interrupted genes of the mutants showed strong homologies to ilvE, which encodes a branched-chain amino acid aminotransferase, and leuC, which encodes the large subunit of isopropylmalate isomerase. Both enzymes are known to be involved in the biosynthetic pathways for branched-chain amino acids (BCAAs) (leucine, valine and isoleucine). The B. phymatum ilvE mutant, KM60, was not auxotrophic for BCAAs and could grow well on minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source. However, it grew less efficiently than the wild-type (WT) strain when ammonia was substituted with valine or isoleucine as a nitrogen source. The BCAA aminotransferase activity of KM60 was significantly reduced relative to the WT strain, especially with isoleucine and valine as amino group donors. The C. taiwanensis leuC mutant, KM184-55, could not grow on a minimal medium with pyruvate as a carbon source and ammonia as a nitrogen source, but its growth was restored when leucine was added to the medium. The isopropylmalate isomerase activity of KM184-55 was completely lost compared with the WT strain. Both mutants recovered their respective enzyme activities after complementation with the WT ilvE or leuC genes and were subsequently able to grow as well as their parental strains on minimal medium. They were also able to form nitrogen-fixing nodules on M. pudica. We conclude that the biosynthesis of BCAAs is essential for the free-living growth of betarhizobia, as well as for their ability to form effective symbioses with their host plant.
-
-
-
Glycerol utilization by Rhizobium leguminosarum requires an ABC transporter and affects competition for nodulation
More LessPlasmid curing has shown that the ability to use glycerol as a carbon source is plasmid-encoded in Rhizobium leguminosarum. We isolated the locus responsible for glycerol utilization from plasmid pRleVF39c in R. leguminosarum bv. viciae VF39. This region was analyzed by DNA sequencing and mutagenesis. The locus encompasses a gene encoding GlpR (a DeoR regulator), genes encoding an ABC transporter, and genes glpK and glpD, encoding a kinase and dehydrogenase, respectively. All the genes except the regulatory gene glpR were organized into a single operon, and were required for growth on glycerol. The glp operon was strongly induced by both glycerol and glycerol 3-phosphate, as well as by pea seed exudate. GlpR repressed the operon in the absence of inducer. Mutation of genes encoding the ABC transporter abolished all transport of glycerol in transport assays using radiolabelled glycerol. This confirms that, unlike in other organisms such as Escherichia coli and Pseudomonas aeruginosa, which use facilitated diffusion, glycerol uptake occurs by an active process in R. leguminosarum. Since the glp locus is highly conserved in all sequenced R. leguminosarum and Rhizobium etli strains, as well as in Sinorhizobium spp. and Agrobacterium spp. and other alphaproteobacteria, this process for glycerol uptake is probably widespread. Mutants unable to use glycerol were deficient in competitiveness for nodulation of peas compared with the wild-type, suggesting that glycerol catabolism confers an advantage upon the bacterium in the rhizosphere or in the infection thread.
-
-
-
Characterization of a porin channel in the endosymbiont of the trypanosomatid protozoan Crithidia deanei
Crithidia deanei is a trypanosomatid protozoan that harbours a symbiotic bacterium. The partners maintain a mutualistic relationship, thus constituting an excellent model for studying metabolic exchanges between the host and the symbiont, the origin of organelles and cellular evolution. According to molecular analysis, symbionts of different trypanosomatid species share high identity and descend from a common ancestor, a β-proteobacterium of the genus Bordetella. The endosymbiont is surrounded by two membranes, like Gram-negative bacteria, but its envelope presents special features, since phosphatidylcholine is a major membrane component and the peptidoglycan layer is highly reduced, as described in other obligate intracellular bacteria. Like the process that generated mitochondria and plastids, the endosymbiosis in trypanosomatids depends on pathways that facilitate the intensive metabolic exchanges between the bacterium and the host protozoan. A search of the annotated symbiont genome database identified one sequence with identity to porin-encoding genes of the genus Bordetella. Considering that the symbiont outer membrane has a great accessibility to cytoplasm host factors, it was important to characterize this single porin-like protein using biochemical, molecular, computational and ultrastructural approaches. Antiserum against the recombinant porin-like molecule revealed that it is mainly located in the symbiont envelope. Secondary structure analysis and comparative modelling predicted the protein 3D structure as an 18-domain β-barrel, which is consistent with porin channels. Electrophysiological measurements showed that the porin displays a slight preference for cations over anions. Taken together, the data presented herein suggest that the C. deanei endosymbiont porin is phylogenetically and structurally similar to those described in Gram-negative bacteria, representing a diffusion channel that might contribute to the exchange of nutrients and metabolic precursors between the symbiont and its host cell.
-
-
-
Identification and localization of the multiple bacterial symbionts of the termite gut flagellate Joenia annectens
More LessThe hindgut of wood-feeding lower termites is densely colonized by a multitude of symbiotic micro-organisms. While it is well established that the eukaryotic flagellates play a major role in the degradation of lignocellulose, much less is known about the identity and function of the prokaryotic symbionts associated with the flagellates. Our ultrastructural investigations of the gut flagellate Joenia annectens (from the termite Kalotermes flavicollis) revealed a dense colonization of this flagellate by diverse ecto- and endosymbiotic bacteria. Phylogenetic analysis of the small-subunit rRNA gene sequences combined with fluorescence in situ hybridization allowed us to identify and localize the different morphotypes. Furthermore, we could show that K. flavicollis harbours two phylotypes of J. annectens that could be distinguished not only by their small-subunit rRNA gene sequences, but also by differences in their assemblages of bacterial symbionts. Each of the flagellate populations hosted phylogenetically distinct ectosymbionts from the phylum Bacteroidetes, one of them closely related to the ectosymbionts of other termite gut flagellates. A single phylotype of ‘Endomicrobia’ was consistently associated with only one of the host phylotypes, although not all individuals were colonized, corroborating that ‘Endomicrobia’ symbionts do not always cospeciate with their host lineages. Flagellates from both populations were loosely associated with a single phylotype of Spirochaetales attached to their cell surface in varying abundance. Current evidence for the involvement of Bacteroidales and ‘Endomicrobia’ symbionts in the nitrogen metabolism of the host flagellate is discussed.
-
-
-
Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade
In this paper, we describe the regulatory roles of VisN, VisR and Rem in the expression of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum biovar viciae strains VF39SM and 3841. Individual mutations in the genes encoding these proteins resulted in a loss of motility and an absence of flagella, indicating that these regulatory genes are essential for flagellar synthesis and function. Transcriptional experiments involving gusA–gene fusions in wild-type and mutant backgrounds were performed to identify the genes under VisN/R and Rem regulation. Results showed that the chemotaxis and motility genes of R. leguminosarum could be separated into two groups: one group under VisN/R-Rem regulation and another group that is independent of this regulation. VisN and VisR regulate the expression of rem, while Rem positively regulates the expression of flaA, flaB, flaC, flaD, motA, motB, che1 and mcpD. All of these genes except mcpD are located within the main motility and chemotaxis gene cluster of R. leguminosarum. Other chemotaxis and motility genes, which are found outside of the main motility gene cluster (che2 operon, flaH for VF39SM, and flaG) or are plasmid-borne (flaE and mcpC), are not part of the VisN/R-Rem regulatory cascade. In addition, all genes exhibited the same regulation pattern in 3841 and in VF39SM, except flaE and flaH. flaE is not regulated by VisN/R-Rem in 3841 but it is repressed by Rem in VF39SM. flaH is under VisN/R-Rem regulation in 3841, but not in VF39SM. A kinetics experiment demonstrated that a subset of the flagellar genes is continuously expressed in all growth phases, indicating the importance of continuous motility for R. leguminosarum under free-living conditions. On the other hand, motility is repressed under symbiotic conditions. Nodulation experiments showed that the transcriptional activators VisN and Rem are dramatically downregulated in the nodules, suggesting that the symbiotic downregulation of motility-related genes could be mediated by repressing the expression of VisN/R and Rem.
-
-
-
Extensive genomic diversity of closely related Wolbachia strains
Using microarray-based comparative genome hybridization (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the closely related Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. simulans (wAu, wRi, wSim). A large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. Each strain caused an average of ∼60 genes to be removed from the core genome. As such, these organisms do not appear to have the streamlined genomes expected of obligate intracellular bacteria. Prophage, hypothetical and ankyrin repeat genes are over-represented in the absent/divergent genes, with 21–87 % of absent/divergent genes coming from prophage regions. The only wMel region absent/divergent in all five query strains is that containing WD_0509 to WD_0511, including a DNA mismatch repair protein MutL-2, a degenerate RNase, and a conserved hypothetical protein. A region flanked by the two portions of the WO-B prophage in wMel is found in four of the five Wolbachia strains as well as on a plasmid of a rickettsial endosymbiont of Ixodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.
-
-
-
The Sinorhizobium meliloti MsbA2 protein is essential for the legume symbiosis
Sinorhizobium meliloti is a beneficial legume symbiont, closely related to Brucella species, which are chronic mammalian pathogens. We discovered that the S. meliloti MsbA2 protein is essential to ensure the symbiotic interaction with the host plant, alfalfa. S. meliloti invades plant cells via plant-derived structures known as infection threads. However, in the absence of MsbA2, S. meliloti remains trapped within abnormally thickened infection threads and induces a heightened plant defence response, characterized by a substantial thickening of the nodule endodermis layer and the accumulation of polyphenolic compounds. The S. meliloti MsbA2 protein is homologous to the Escherichia coli lipopolysaccharide/phospholipid trafficking protein MsbA. However, MsbA2 was not essential for the membrane transport of either lipopolysaccharide or phospholipids in S. meliloti. We determined that the msbA2 gene is transcribed in free-living S. meliloti and that in the absence of MsbA2 the polysaccharide content of S. meliloti is altered. Consequently, we propose a model whereby the altered polysaccharide content of the S. meliloti msbA2 mutant could be responsible for its symbiotic defect by inducing an inappropriate host response.
-
-
-
A Mesorhizobium loti mutant with reduced glucan content shows defective invasion of its host plant Lotus japonicus
More LessRandom transposon mutagenesis led to the isolation of a novel Mesorhizobium loti mutant that is defective in nitrogen fixation during symbiosis with Lotus japonicus. The mutated locus, designated cep, encodes a putative cell-envelope protein displaying no significant sequence similarity to proteins with known functions. This mutant elicits the formation of nodule-like bumps and root-hair curling, but not the elongation of infection threads, on L. japonicus roots. This is reminiscent of the phenotypes of rhizobial mutants impaired in cyclic β-glucan biosynthesis. The cep mutant exhibits partially reduced content of cell-associated glucans and intermediate deficiency of motility under hypo-osmotic conditions as compared to a glucan-deficient mutant. Second-site pseudorevertants of the cep mutant were isolated by selecting for restoration of symbiotic nitrogen fixation. A subset of pseudorevertants restored both symbiotic capability and glucan content to levels comparable to that of the wild-type. These results suggest that the Cep product acts on a successful symbiosis by affecting cell-associated glucan content.
-
-
-
Phylogenetic diversity of ‘Endomicrobia’ and their specific affiliation with termite gut flagellates
More Less‘Endomicrobia’, a distinct and diverse group of uncultivated bacteria in the candidate phylum Termite Group I (TG-1), have been found exclusively in the gut of lower termites and wood-feeding cockroaches. In a previous study, we had demonstrated that the ‘Endomicrobia’ clones retrieved from Reticulitermes santonensis represent intracellular symbionts of the two major gut flagellates of this termite. Here, we document that ‘Endomicrobia’ are present also in many other gut flagellates of lower termites. Phylogeny and host specificity of ‘Endomicrobia’ were investigated by cloning and sequencing of the small subunit rRNA genes of the flagellate and the symbionts, which originated from suspensions of individual flagellates isolated by micropipette. Each flagellate harboured a distinct phylogenetic lineage of ‘Endomicrobia’. The results of fluorescent in situ hybridization with ‘Endomicrobia’-specific oligonucleotide probes corroborated that ‘Endomicrobia’ are intracellular symbionts specifically affiliated with their flagellate hosts. Interestingly, the ‘Endomicrobia’ sequences obtained from flagellates belonging to the genus Trichonympha formed a monophyletic group, suggesting co-speciation between symbiont and host.
-
-
-
Host-specific regulation of symbiotic nitrogen fixation in Rhizobium leguminosarum biovar trifolii
More LessStrains of Rhizobium leguminosarum bv. trifolii (Rlt) able to form effective nodules on Trifolium ambiguum (Caucasian clover, CC) form ineffective nodules on Trifolium repens (white clover, WC), whereas strains that form effective nodules on WC usually do not nodulate CC. Here, we investigate the genetic basis of the host-specific nitrogen-fixation phenotype of CC rhizobia. A cosmid library of the symbiotic plasmid from the WC rhizobium strain Rlt NZP514 was introduced into the CC rhizobium strain Rlt ICC105. An 18 kb Asp718 fragment containing the nifABHDKEN and fixABCX genes of NZP514 that imparted the Fix+ phenotype was identified. Tn5 mutagenesis of this region revealed that the nifHDKEN, fixABC and nifB genes were required for the Fix+ phenotype, but that the nifA gene was not. Introduction of several plasmids containing NZP514 nif/fix genes into an ICC105 nifA mutant strain demonstrated that the NifA protein of ICC105 was able to activate expression of the NZP514 nif/fix genes but not the ICC105 nif/fix genes in WC nodules. Reporter gene fusion studies showed that the host-specific regulation of the nif/fix genes depended on the DNA region between the promoters of the divergently transcribed nifH and fixA genes. We hypothesize that a protein acting either in response to a host-specific signal or in the absence of such a signal is able to bind upstream of the NifA-binding sites and interact with NifA to prevent it activating nif/fix gene expression.
-
-
-
Quorum-sensing-regulated transcriptional initiation of plasmid transfer and replication genes in Rhizobium leguminosarum biovar viciae
More LessTransfer of the Rhizobium leguminosarum biovar viciae symbiosis plasmid pRL1JI is regulated by a cascade of gene induction involving three LuxR-type quorum-sensing regulators, TraR, BisR and CinR. TraR induces the plasmid transfer traI-trb operon in a population-density-dependent manner in response to N-acylhomoserine lactones (AHLs) made by TraI. Expression of the traR gene is primarily induced by BisR in response to AHLs made by CinI, and expression of cinI is induced by CinR and repressed by BisR. Analysis of transcription initiation of cinI, traR and traI identified potential regulatory domains recognized by the CinR, BisR and TraR regulators. Deletion and mutation of the cinI promoter identified potential recognition motifs for activation by CinR and repression by BisR. Analysis of the DNA sequence upstream of traI and expression of transcriptional gene fusions revealed a predicted TraR-binding (tra-box) domain. Two transcript initiation sites were identified upstream of the plasmid replication gene repA, which is divergently transcribed from traI; one of these repA transcripts requires the quorum-sensing cascade mediated via BisR and TraR, showing that the pRL1JI plasmid replication genes are co-regulated with the plasmid transfer genes.
-
-
-
Sinorhizobium meliloti pSymB carries genes necessary for arabinose transport and catabolism
More LessArabinose is a known component of plant cell walls and is found in the rhizosphere. In this work, a previously undeleted region of the megaplasmid pSymB was identified as encoding genes necessary for arabinose catabolism, by Tn5-B20 random mutagenesis and subsequent complementation. Transcription of this region was measured by β-galactosidase assays of Tn5-B20 fusions, and shown to be strongly inducible by arabinose, and moderately so by galactose and seed exudate. Accumulation of [3H]arabinose in mutants and wild-type was measured, and the results suggested that this operon is necessary for arabinose transport. Although catabolite repression of the arabinose genes by succinate or glucose was not detected at the level of transcription, both glucose and galactose were found to inhibit accumulation of arabinose when present in excess. To determine if glucose was also taken up by the arabinose transport proteins, [14C]glucose uptake rates were measured in wild-type and arabinose mutant strains. No differences in glucose uptake rates were detected between wild-type and arabinose catabolism mutant strains, indicating that excess glucose did not compete with arabinose for transport by the same system. Arabinose mutants were tested for the ability to form nitrogen-fixing nodules on alfalfa, and to compete with the wild-type for nodule occupancy. Strains unable to utilize arabinose did not display any symbiotic defects, and were not found to be less competitive than wild-type for nodule occupancy in co-inoculation experiments. Moreover, the results suggest that other loci are required for arabinose catabolism, including a gene encoding arabinose dehydrogenase.
-
-
-
Multiple gene genealogical analyses reveal both common and distinct population genetic patterns among replicons in the nitrogen-fixing bacterium Sinorhizobium meliloti
Sheng Sun, Hong Guo and Jianping XuSinorhizobium meliloti is a Gram-negative alpha-proteobacterium that can form symbiotic relationships with alfalfa and fix atmospheric nitrogen. The complete genome of a laboratory strain, Rm1021, was published in 2001, and the genome of this strain is arranged in three replicons: a chromosome of 3.65 million base pairs (Mb), and two megaplasmids, pSymA (1.35 Mb) and pSymB (1.68 Mb). However, the potential difference in genetic variation among the three replicons in natural strains remains poorly understood. In this study, a total of 16 gene fragments were sequenced, four from pSymA and six each from the chromosome and pSymB, for 49 natural S. meliloti strains. The analyses identified significant differences in divergence among genes, with the mean Hasegawa–Kishino–Yano–1985 (HKY85) distance ranging from 0.00157 to 0.04109 between pairs of strains. Overall, genes on pSymA showed the highest mean HKY85 distance, followed by those on pSymB and the chromosome. Although evidence for recombination was found, the authors' population genetic analyses revealed overall significant linkage disequilibria among genes within both pSymA and the chromosome. However, genes on pSymB were in overall linkage equilibrium, consistent with frequent recombination among genes on this replicon. Furthermore, the genealogical comparisons among the three replicons identified significant incongruence, indicating reassortment among the three replicons in natural populations. The results suggest both shared and distinct patterns of molecular evolution among the three replicons in the genomes of natural strains of S. meliloti.
-
-
-
Rhizobia and plant-pathogenic bacteria: common infection weapons
More LessPlant-interacting micro-organisms can establish either mutualistic or pathogenic associations. Although the outcome is completely different, common molecular mechanisms that mediate communication between the interacting partners seem to be involved. Specifically, nitrogen-fixing bacterial symbionts of legume plants, collectively termed rhizobia, and phytopathogenic bacteria have adopted similar strategies and genetic traits to colonize, invade and establish a chronic infection in the plant host. Quorum-sensing signals and identical two-component regulatory systems are used by these bacteria to coordinate, in a cell density-dependent manner or in response to changing environmental conditions, the expression of important factors for host colonization and infection. The success of invasion and survival within the host also requires that rhizobia and pathogens suppress and/or overcome plant defence responses triggered after microbial recognition, a process in which surface polysaccharides, antioxidant systems, ethylene biosynthesis inhibitors and virulence genes are involved.
-
-
-
FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti
More LessThe FixLJ two-component system of Sinorhizobium meliloti is a global regulator, turning on nitrogen-fixation genes in microaerobiosis. Up to now, nifA and fixK were the only genes known to be directly regulated by FixJ. We used a genomic SELEX approach in order to isolate new FixJ targets in the genome. This led to the identification of 22 FixJ binding sites, including the known sites in the fixK1 and fixK2 promoters. FixJ binding sites are unevenly distributed among the three replicons constituting the S. meliloti genome: a majority are carried either by pSymA or by a short chromosomal region of non-chromosomal origin. Thus FixJ binding sites appear to be preferentially associated with the pSymA replicon, which carries the fixJ gene. Functional analysis of FixJ targets led to the discovery of two new FixJ-regulated genes, smc03253 and proB2. This FixJ-dependent regulation appears to be mediated by a duplication of the whole fixK promoter region, including the beginning of the fixK gene. Similar duplications were previously reported for the nifH promoter. By systematic comparison of all promoter regions we found 17 such duplications throughout the genome, indicating that promoter duplication is a common mechanism for the evolution of regulatory pathways in S. meliloti.
-
-
-
Symbionts of the gut flagellate Staurojoenina sp. from Neotermes cubanus represent a novel, termite-associated lineage of Bacteroidales: description of ‘Candidatus Vestibaculum illigatum’
More LessThe symbioses between cellulose-degrading flagellates and bacteria are one of the most fascinating phenomena in the complex micro-ecosystem found in the hindgut of lower termites. However, little is known about the identity of the symbionts. One example is the epibiotic bacteria colonizing the surface of hypermastigote protists of the genus Staurojoenina. By using scanning electron microscopy, it was shown that the whole surface of Staurojoenina sp. from the termite Neotermes cubanus is densely covered with long rod-shaped bacteria of uniform size and morphology. PCR amplification of 16S rRNA genes from isolated protozoa and subsequent cloning yielded a uniform collection of clones with virtually identical sequences. Phylogenetic analysis placed them as a new lineage among the Bacteroidales, only distantly related to other uncultivated bacteria in the hindgut of other termites, including an epibiont of the flagellate Mixotricha paradoxa. The closest cultivated relative was Tannerella forsythensis (<85 % sequence identity). Fluorescence in situ hybridization with a newly designed clone-specific oligonucleotide probe confirmed that these sequences belong to the rod-shaped epibionts of Staurojoenina sp. Transmission electron microscopy confirmed the presence of a Gram-negative cell wall and revealed special attachment sites for the symbionts on the cell envelope of the flagellate host. Based on the isolated phylogenetic position and the specific association with the surface of Staurojoenina sp., we propose to classify this new taxon of Bacteroidales under the provisional name ‘Candidatus Vestibaculum illigatum’.
-
-
-
Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
More LessWigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.
-
-
-
Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum
More LessRhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R. leguminosarum fur partially corrected an Escherichia coli fur mutant and R. leguminosarum Fur protein bound to canonical fur boxes. The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake. Neither Irr nor Fur is needed for symbiotic N2 fixation on peas. As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX. R. leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B. japonicum Irr. The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed.
-
-
-
Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle a
More LessaThe GenBank accession number for the sequence reported in this paper is AF495758.
Blochmannia (Candidatus Blochmannia gen. nov.) is the primary bacterial endosymbiont of the ant genus Camponotus. Like other obligate endosymbionts of insects, Blochmannia occurs exclusively within eukaryotic cells and has experienced long-term vertical transmission through host lineages. In this study, PFGE was used to estimate the genome size of Blochmannia as approximately 800 kb, which is significantly smaller than its free-living relatives in the enterobacteria. This small genome implies that Blochmannia has deleted most of the genetic machinery of related free-living bacteria. Due to restricted gene exchange in obligate endosymbionts, the substantial gene loss in Blochmannia and other insect mutualists may reflect irreversible specialization to a host cellular environment.
-
-
-
Reassessment of major products of N2 fixation by bacteroids from soybean root nodules
More LessNH3/ was the principal product from soybean bacteroids, prepared by various procedures, when assayed in solution in a flow chamber under N2 fixation conditions. In addition, small quantities of alanine were produced (reaching 20% of NH3/ under some conditions). Some 15N was assimilated by bacteroids purified from soybean root nodules on Percoll density gradients and shaken with 15N2 and 0·008 atm O2. Under these conditions, accounted for 93% of the 15N fixed into the soluble fraction. This fraction contained no measurable [15N]alanine. Neither these bacteroids nor those prepared by the previously used differential centrifugation method, when incubated with exogenous alanine under non-N2-fixing conditions, gave rise to NH3 from alanine. Therefore, contamination of bacteroid preparations with enzymes of plant cytosolic origin and capable of producing NH3 from alanine cannot explain the failure to detect [15N]alanine [as reported elsewhere: Waters, J. K., Hughes, B. L., II, Purcell, L. C., Gerhardt, K. O., Mawhinney, T. P. & Emerich, D. W. (1998). Proc Natl Acad Sci USA 95, 12038–12042]. Cell-free extracts of the bacteroids as used in the 15N experiments contained alanine dehydrogenase and were able to produce alanine from pyruvate and . Other experiments with alanine dehydrogenase in extracts of cultured rhizobia and bacteroids are reported and discussed in relation to the 15N experiments. Possible reasons for the differences between laboratories regarding the role of alanine are discussed. It is concluded that NH3 is the principal soluble product of N2 fixation by suspensions of soybean bacteroids ex planta and that should continue to be considered the principal product of N2 fixation which is assimilated in vivo in soybean nodules.
-
-
-
Establishment of a functional symbiosis between the cyanobacterium Nostoc punctiforme and the bryophyte Anthoceros punctatus requires genes involved in nitrogen control and initiation of heterocyst differentiation
More LessThe GenBank accession numbers for the coding regions of ntcA, hetR and hetF are AY038370, AF318069 and AF288130, respectively.
Three mutant strains (ntcA, hetR, hetF) of the cyanobacterium Nostoc punctiforme unable to differentiate heterocysts were characterized and examined for their ability to form a symbiotic association with the bryophyte Anthoceros punctatus. Previously unknown characteristics of the N. punctiforme hetR mutant include differentiation of chilling-resistant akinetes, while vegetative cells of the ntcA mutant randomly lysed, yielding short filaments, following ammonium deprivation. Strains with mutations in hetF and hetR infected A. punctatus with similar frequency to that of wild-type N. punctiforme but did not support growth of the plant partner. These results confirm that the infection of A. punctatus by hormogonia leading to the establishment of an association is physiologically uncoupled from the development of a functional diazotrophic association. They also indicate that heterocyst regulatory elements downstream from HetR and HetF are required in both free-living and symbiotic heterocyst differentiation and nitrogenase expression. A strain with a mutation in the global nitrogen regulator ntcA did not infect A. punctatus despite its ability to differentiate hormogonia at a low frequency. When complemented with one or more copies of ntcA, the mutant strain infected A. punctatus at a similar frequency as the wild-type and supported growth of the plant partner in the absence of combined nitrogen. These results established a connection between the presence of a functional copy of ntcA and the magnitude of hormogonium differentiation, and the behaviour of the formed hormogonia.
-
-
-
Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts
More LessThe GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.
The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaseolus vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.
-
-
-
Distribution of repC plasmid-replication sequences among plasmids and isolates of Rhizobium leguminosarum bv. viciae from field populations
More LessThe distribution of four classes of related plasmid replication genes (repC) within three field populations of Rhizobium leguminosarum in France, Germany and the UK was investigated using RFLP, PCR-RFLP and plasmid profile analysis. The results suggest that the four repC classes are compatible: when two or more different repC sequences are present in a strain they are usually associated with different plasmids. Furthermore, classical incompatibility studies in which a Tn5-labelled plasmid with a group IV repC sequence was transferred into field isolates by conjugation demonstrated that group IV sequences are incompatible with each other, but compatible with the other repC groups. This supports the idea that the different repC groups represent different incompatibility groups. The same field isolates were also screened for chromosomal (plac12) and symbiotic gene (nodD-F region) variation. Comparison of these and the plasmid data suggest that plasmid transfer does occur within field populations of R. leguminosarum but that certain plasmid-chromosome combinations are favoured.
-
-
-
Transcriptional activity of the symbiotic plasmid of Rhizobium etli is affected by different environmental conditions
More LessGlobal patterns of transcriptional activity of the symbiotic plasmid (pSym) of Rhizobium etli were studied under a variety of environmental conditions, including some relevant to the symbiotic process. 32P-labelled single-stranded complementary DNAs synthesized from total RNA were used as hybridization probes against an ordered collection of cosmid clones that covered the whole pSym. Our results showed that, under aerobic conditions, discrete regions of the pSym are differentially transcribed depending on the carbon and nitrogen sources employed. In general, poor carbon or nitrogen sources allowed greater expression than rich ones. Time-course experiments with the nod gene inducer genistein led us to the identification of new regions responsive to this flavonoid. Widespread transcription was observed during microaerobiosis, but not under aerobic conditions, indicating that oxygen concentration is a major effector of transcriptional activity in the pSym. This response was reduced, but not suppressed, in a nifA mutant, indicating the location of regions whose transcription may depend on other oxygen-sensitive regulators. During symbiosis, almost the entire pSym was actively transcribed and the transcription pattern was similar to that observed during microaerobiosis. The experimental approach described allowed the identification and localization of specific regions in the pSym whose expression depends on defined environmental stimuli.
-
-
-
Nitrogen limitation of chemostat-grown Rhizobium etli elicits higher infection-thread formation in Phaseolus vulgaris
More LessThe symbiotic association between rhizobia and legume roots is a complex process involving many steps. An infection thread is a tubular structure of host origin formed during the infection of legume roots by rhizobia. Previous studies with batch cultures have reported that optimal attachment of rhizobia to root hairs coincides with nutrient limitation. In this study, the ability of chemostat-grown, nutrient-limited Rhizobium etli cells to form infection threads with its symbiotic partner Phaseolus vulgaris was investigated. Rhizobia were grown in a chemostat in synthetic media under C- or N-limiting conditions. Infection-thread formation was examined after inoculation of seedlings with a rhizobial cell suspension from each treatment. The number of infection threads was estimated by light microscopy after staining root sections with o-toluidine. Exopolysaccharide (EPS) production was also measured, and the cellular content and electrophoretic pattern of lipopolysaccharide (LPS) determined semiquantitatively. N-limited cells showed a markedly higher infectivity (measured as infection-thread formation) than C-limited cells. With one of the two bean cultivars used, the number of infection threads produced by N-limited cells was higher than that produced by exponentially growing cells in batch cultures. The higher infectivity of N-limited cells was correlated with higher EPS production. Electrophoretic analysis of LPS showed that C- and N-limited cells shared a common profile but the relative concentration of short LPS forms differed.
-
-
-
A metabolic study of Buchnera, the intracellular bacterial symbionts of the pea aphid Acyrthosiphon pisum
More LessCells of the bacterium Buchnera were isolated from embryos of the pea aphid Acyrthosiphon pisum, with an intact perisymbiont membrane (the insect membrane which surrounds each bacterial cell inside the aphid). The bacterial preparations respired aerobically, consuming oxygen at an average rate of 24 nmol (mg protein)−1 min−1. The bacteria took up a range of carboxylic acids and the amino acids glutamate and aspartate from an external concentration of 0·5 mm at rates of 1–10 nmol (mg protein)−1 h−1; glucose was taken up at 0·17 nmol (mg protein)−1 h−1. Glutamate uptake was proportional to its external concentration, at all concentrations tested between 15 μm and 10 mm. Saturable systems for the uptake of succinate and aspartate were identified. The kinetic constants were: K m 0·79 mm, V max 12·6 nmol (mg protein)−1 min−1 for succinate; and K m 0·22 mm, V max 3·3 nmol (mg protein)−1 min−1 for aspartate. Succinate uptake was not inhibited by the uncoupler CCCP and was markedly stimulated by ATP, suggesting that its transport is not linked to a proton-motive force but is dependent on an energized membrane and possibly mediated by a co-transport system involving another ion.
-
-
-
Phage Induction of Lysogenic Rhizobium leguminosarum biovar trifolii in both the Free-living and the Symbiotic Form
More LessA lysogenic strain, Rhizobium leguminosarum biovar trifolii UK-1: φU, was isolated from a wild white clover nodule. It was symbiotically effective on white clover. A lysogenic phage (U-mole) was induced from this strain by treatment with either UV irradiation or mitomycin C. Phage U-mole had an icosahedral head (40 nm wide), a short tail (9 nm long) and tail fibres (15 nm long). Phage U-mole was induced with mitomycin C both from bacterial cells in infection threads and from bacteroids in nodules. Southern hybridization using EcoRI fragments of phage U-mole as probe indicated that phage U-mole DNA was integrated into the chromosome of strain UK-1: øU at a site involving the 60 kb EcoRI fragment of phage U-mole. Phage U-mole also lysogenized the wild-type strain R. leguminosarum biovar trifolii 4S. The resulting lysogenized strain, 4S:øU, had lost its 315 kb Sym plasmid and its nodulation ability.
-
-
-
Symbiotic Plasmid Rearrangement in a Hyper-recombinant Mutant of Rhizobium leguminosarum biovar phaseoli
More LessThe symbiotic plasmid of Rhizobium leguminosarum biovar phaseoli strain CFN23 has been previously shown to undergo a series of genetic rearrangements that modify the bacterial symbiotic phenotype. A hyper-recombinant derivative of strain CFN23 was isolated. This derivative (strain CFN2300) has a similar phenotype to that reported for Escherichia coli mutants defective in DNA metabolism. The frequency of CFN23 symbiotic plasmid deletion is increased in the CFN2300 background, suggesting that homologous genetic recombination is involved in the generation of this genetic rearrangement.
-
-
-
Chemotaxis of Rhizobium leguminosarum biovar phaseoli towards Flavonoid Inducers of the Symbiotic Nodulation Genes
Chemotaxis of Rhizobium leguminosarum biovar phaseoli RP8002 towards a range of carbohydrates, phenolic compounds and flavonoids was assayed. Xylose (peak response 10−4 M), sucrose (peak response 10−6 M) and raffinose (peak response 10−5 M) were strong chemoattractants amongst the carbohydrates, whilst glucose, fructose, galactose and maltose produced little or no detectable response. Of the monocyclic phenolic compounds, vanillyl alcohol, p-hydroxybenzoic acid (both peak responses 10−6 M) and 3,4-dihydroxybenzoic acid (peak response 10−4 M) all evoked strong chemotactic responses. Amongst the nod-inducing flavonoids, apigenin and luteolin were both strong chemoattractants (peaks at 10−5 M) while naringenin produced a very low response. Competition experiments suggest that apigenin and luteolin are recognized by a common receptor, but that there exists a separate receptor for luteolin alone. The inhibitors of nod-induction, umbelliferone and acetosyringone, both produced strong chemotactic responses, with peaks at 10−3 M and 10−2 M respectively. This evidence is indicative of a role for chemotaxis towards nod-inducing flavonoids in the initiation of root nodule formation by rhizobia, and also suggests that chemotaxis may influence the host range of the interaction.
-
-
-
Symbiotic Phenotypes of Auxotrophic Mutants of Rhizobium meliloti104A14
More LessAuxotrophic mutants of Rhizobium meliloti 104A14 were isolated using nitrous acid mutagenesis followed by penicillin enrichment. Mutants in ornithine transcarbamylase, argininosuccinate synthetase or serine-glycine biosynthesis formed nitrogen-fixing (Fix+) nodules on the roots of alfalfa (Medicago sativa). Mutants with defects in ornithine, pyrimidine, purine, asparagine, leucine, methionine or tyrosine biosynthesis, in one-carbon metabolism or in carbamoylphosphate synthetase formed nodules but these nodules were unable to fix nitrogen. Prototrophic revertants were always Fix+. Plasmids that would complement many of these auxotrophs were isolated by transduction with a P2 cosmid gene bank of R. meliloti 104A14. These plasmids were then introduced into mutants of the same and different classes and the growth and symbiotic phenotypes of the new strains were determined. In all cases, complementation of the nutritional defect restored symbiotic nitrogen fixation.
-
-
-
Plasmids and Symbiotic Effectiveness of Representative Phage Types from Two Indigenous Populations of Rhizobium meliloti
More LessSUMMARY: Phage types representative of the population of indigenous Rhizobium meliloti at each of two sites were evaluated for plasmid content by agarose gel electrophoresis and for symbiotic effectiveness with Medicago sativa cv. Saranac. Relative to four strains used commercially, 55 and 65 phage types representing these populations showed a high average level of symbiotic effectiveness; only a single type from one site was relatively ineffective in symbiosis. On the basis of plasmid number and molecular mass, 160 isolates comprising 45 and 48 types from both sites were placed in 22 different groups with 17 and 13 groups from the respective sites. The number of plasmids varied between one and five per isolate with molecular masses ranging from 5 MDa to considerably greater than 267 MDa. Only five isolates lacked a plasmid with mobility in agarose gels corresponding to that of a reference megaplasmid but instead showed a band of lesser mobility and therefore greater molecular mass. Phage types, which were divided into plasmid groups solely on the basis of differences between isolates from each site, may reflect adaptation of R. meliloti to their respective sites. Differences between isolates within certain phage types due to the presence or absence of a single plasmid may have resulted from genetic interchange between indigenous R. meliloti. There was no significant correlation between plasmid number or mass and symbiotic effectiveness or phage sensitivity of the phage types from either site.
-
-
-
Ammonia Transport in Free-living and Symbiotic Rhizobium sp. ANU289
More LessSummary: [14C]Methylamine uptake by free-living Rhizobium sp. ANU289 had Michaelis–Menten kinetics (apparent K m 6.6 μm). Uptake was competitively inhibited by ammonia (K i 0.4 μm) and was dependent on an energized membrane. Uptake by bacteria had an optimum at pH 7.0. Methylamine uptake by bacteroids from siratro root nodules was much slower than that by free-living bacteria at pH 7.0 but increased exponentially with the pH of the medium. Uptake by bacteroids did not show saturation kinetics and was insensitive to the presence of ammonia or uncouplers. These results suggest that free-living bacteria (grown under conditions where ammonia is limiting) have an active transport mechanism for the uptake of ammonium ions; this carrier is not operative in the symbiotic state, where passive diffusion of ammonia occurs. In the free-living state, the ammonium carrier is under genetic control, being repressed by growth on high concentrations of ammonia. Derepression occurs under conditions of nitrogen starvation.
-
-
-
Effect of Transfer of Symbiotic Plasmids and of Hydrogenase Genes (hup) on Symbiotic Efficiency of Rhizobium leguminosarum Strains
More LessSummary: Plasmid-encoded symbiotic determinants from the Rhizobium leguminosarum strain MA1 (817) with uptake hydrogenase activity (Hup+) and from the Hup− strain MC1 (18a) were mobilized by recombination with the self-transmissible plasmid pVW5JI. The symbiotic determinants were transferred by conjugation from strain MA1 to strain MC1 and to a derivative of MC1 without the symbiotic plasmid, and vice versa, thus constructing four types of transconjugants. The determinants for a total recycling hydrogenase in strain MA1 were found to be encoded on the symbiotic plasmid.
Strain MC1 fixed 60% more N2 in pea root nodules, determined as mg nitrogen per plant, than strain MA1. This difference was not increased in the MC1 derivative that obtained hydrogenase activity. Plants inoculated with a derivative of strain MA1, however, where the symbiotic plasmid was replaced by that of strain MC1 had a high percentage nitrogen content. It was concluded that the symbiotic plasmid and the genetic background were more important for plant nitrogen accumulation than uptake hydrogenase.
-
-
-
Sugar Metabolism and the Symbiotic Properties of Carbohydrate Mutants of Rhizobium leguminosarum
More LessRhizobium leguminosarum metabolizes sugars via the Entner-Doudoroff and pentose phosphate pathways but does not have a functional Embden-Meyerhof pathway. Although some sugar catabolizing enzymes are constitutive, activities of the ‘Entner-Doudoroff’ enzymes vary with the carbon source. Bacteroids have complete pathways for sugar catabolism even though the specific activities of some enzymes, e.g., glucokinase, are lower than in free-living cells. Tn5-induced mutants lacking glucokinase, fructokinase and pyruvate dehydrogenase have been isolated. Although these mutants are unable to utilize sugars, they all nodulate peas and fix N2. The capacity to utilize particular C6 and C12 sugars is apparently not essential for bacteroid development or the establishment of effective N2 fixation.
-
-
-
Contribution of the Symbiotic Plasmid to the Competitiveness of Rhizobium leguminosarum
More LessFour different symbiotic plasmids from Rhizobium leguminosarum were introduced into three different recipient strains that lacked plasmid-linked symbiotic determinants. The twelve synthetic strains so constructed were each tested for competitiveness against a standard reference strain. The recipient strain and the introduced symbiotic plasmid contributed about equally to competitiveness in forming root nodules on pea plants: there was also significant interaction between strain and plasmid, although this was much less important than the main effects. Competitiveness for growth on the legume root surface (the rhizosphere) was attributable entirely to the recipient strain; the introduced plasmid had no significant effect.
-
-
-
Antibiotic Activity of Xenorhabdus spp., Bacteria Symbiotically Associated with Insect Pathogenic Nematodes of the Families Heterorhabditidae and Steinernematidae
More LessA wide range of micro-organisms, including yeasts, was found to be inhibited by the primary form of Xenorhabdus spp., but not by the secondary form. Only one Xenorhabdus strain, the symbiont of Neoaplectana glaseri, did not inhibit any of the micro-organisms tested; it is suggested that this strain may not have been isolated in the primary form. Gram-positive bacteria were sensitive to all active isolates of Xenorhabdus; each of the yeasts and almost all of the Gram-negative bacteria were sensitive to some but not all Xenorhabdus isolates. Each Xenorhabdus isolate was sensitive to some other Xenorhabdus isolates. The antibiotic activity of X. nematophilus was unaffected by autoclaving but was lost after dialysis. Anaerobically incubated Xenorhabdus spp. did not exhibit antibiotic activity.
-
-
-
Improvement of Symbiotic Properties in Rhizobium leguminosarum by Plasmid Transfer
More LessTransfer of plasmid pIJ1008, a recombinant of two indigenous Rhizobium leguminosarum plasmids into R. leguminosarum strain 300 produced strain 3960, which reduced significantly more N2 in pea root nodules than did strain 300 itself. Strain 3960 was superior to the field isolate 128C53, from which the symbiotic determinants of pIJ1008 were derived, and transfer of plasmid pIJ1008 into two other genetic backgrounds also improved symbiotic performance compared to the introduction of other nodulation plasmids.
As plasmid pIJ1008 carries genetic determinants for an uptake hydrogenase activity (Hup+) as well as nodulation capability (Nod+) and other determinants for symbiotic nitrogen fixation (Fix+), the increased effectiveness of strains carrying pIJ1008 may result from their capacity to conserve energy by recovering H2 evolved by nitrogenase.
Intact plant studies with 15N showed that the superior N2 fixation capability associated with pIJ1008 was enhanced by 2 mm-NO3 −, a common concentration of soil N. It was also shown that, as plants grew older, the hydrogenase determined by pIJ1008 was not able to recycle all the hydrogen evolved by pea root nodules.
-
-
-
Only One of the Large Plasmids in Rhizobium leguminosarum Strain PRE is Strongly Expressed in the Endosymbiotic State
More LessPlasmid DNA from six strains of Rhizobium leguminosarum was separated by agarose gel electrophoresis and showed a large variation in the number and size of the plasmids. Blotting on to nitrocellulose and hybridization with a probe containing nif (nitrogen fixation) genes from Rhizobium meliloti demonstrated that all strains contain only one plasmid carrying nif genes. The molecular weights of the nif plasmids ranged between approximately 130 × 106 and 550 × 106. Using DNA-DNA hybridization no homologous sequences were detected between the nif plasmid of strain PRE and the other plasmid present in this strain. Hybridizations with RNA from bacteroids showed that only the nif plasmid is strongly expressed in the endosymbiotic state. No selective amplification of plasmid DNA occurs during the transition of free-living bacteria into bacteroids.
-
-
-
Glutamate Synthase Activity in Symbiotic Cyanobacteria
More LessGlutamate synthase (GOGAT) activities of the symbiotic cyanobacteria of the lichens Peltigera canina and Peltigera aphthosa and of the water fern Azolla caroliniana have been determined and, like glutamine synthetase (GS) activity, found to be substantially reduced compared with the activities found in the free-living cyanobacteria. A similar reduction in GOGAT activity was not noted in the symbiotic green alga (Coccomyxa sp.) in P. aphthosa. The selective reduction of GS-GOGAT activity in symbiosis may be related to the production of extracellular nitrogen by the symbiotic cyanobacterium.
-
-
-
Transfer of Symbiotic Genes with Bacteriocinogenic Plasmids in Rhizobium leguminosarum
More LessTransfer of derivatives of the bacteriocinogenic plasmid pRL1JI into eight symbiotically defective strains of R. leguminosarum resulted in suppression of the mutant phenotype in four cases. These included non-infective, ineffective and temperature-sensitive ineffective phenotypes. However, in none of these strains was the defect suppressible after high frequency transfer of derivatives of two other bacteriocinogenic plasmids, pRL3JI or pRL4JI. Nodulation ability was co-transferred at high frequency (> 95 %) with bacteriocin production by the plasmid pRL1JI. The other two plasmids, pRL3JI and pRL4JI, also mediated the transfer of nodulation ability but at much lower frequency (10−3 to 10−4 per plasmid transfer). Sometimes, transconjugants that had acquired nodulation ability after the transfer of derivatives of plasmids pRL3JI or pRL4JI acted subsequently as high frequency donors for nodulation ability in a manner that was apparently similar to strains containing pRL1JI.
-
-
-
Carbohydrate Metabolism in Rhizobium trifolii: Identification and Symbiotic Properties of Mutants
More LessCrude extracts of Rhizobium trifolii strain 7000 contained enzymes of the Entner–Doudoroff and pentose phosphate pathways. No phosphofructokinase (EC 2.7.1.11) activity and only a low activity of fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) were found, suggesting that the Embden–Meyerhof–Parnas pathway was not physiologically important in this strain.
Independent carbohydrate-negative mutants of R. trifolii were isolated and characterized as deficient in glucokinase (glk; EC 2.7.1.2), fructose uptake (fup), the Entner–Doudoroff pathway (edp) and pyruvate carboxylase (pyc; EC 6.4.1.1). Glucokinase was essential for glucose phosphorylation in R. trifolii and was also required for growth on sucrose. The edp mutant was impaired in growth on all hexoses tested except galactose, suggesting that the ED pathway was the major pathway used by R. trifolii for the catabolism of these sugars. Galactose may be catabolized via a different pathway, possibly involving an NADP+-linked galactose dehydrogenase. Pyruvate carboxylase was an important anaplerotic enzyme in R. trifolii required for growth on all carbon sources tested, except succinate.
All the mutants, including a glk fup double mutant, formed an effective symbiosis on red clover, suggesting that neither glucose, fructose nor sucrose are used by the bacteroids to provide ATP and reductant for nitrogen fixation. The bacteroids probably receive a supply of tricarboxylic acid cycle intermediates from the plant cytosol, and these may be their major source of energy.
-
-
-
Genetic Relationships among Bacterial Endosymbionts of Paramecium aurelia
More LessGenetic relationships among bacterial endosymbionts of Paramecium assigned to the genus Caedobacter Preer et al. 1974 were determined using DNA-DNA hybridization techniques. It was shown that mu, nu and pi endosymbionts are closely related to each other, but not to any of the strains of kappa endosymbionts tested, and that kappa consists of at least three distinct and genetically diverse groups. Therefore, it is proposed that Caedobacter be split into two genera, Caedobacter and Pseudocaedobacter, depending upon the ability or lack of ability, respectively, to produce cells containing R bodies. Strains were screened for covalently closed, circular DNA by ethidium bromide/CsCl centrifugation, but only pi and hump-killer kappa particles were found to contain this form of DNA.
-
-
-
The Fine Structure of a Nuclear Envelope Associated Endosymbiont of Paramecium
More LessSummaryParticles of a newly described endosymbiont of Paramecium, here referred to as epsilon, have a fine structure that is essentially identical to that of Gram-negative bacteria. The symbionts occur only within loculi formed by extension of the outer membrane of the nuclear envelopes.
-
-
-
Mutations in Symbiotic Effectiveness in Rhizobium trifolii Caused by Transforming DNA and Other Agents
More LessSUMMARYA strain of Bhizobium trifolii able to fix nitrogen in root nodules of clover plants lost its effectiveness when treated with deoxyribonucleic acid (DNA) from an ineffective strain. Attempts to transform two ineffective strains to effectiveness failed, even when the donor of DNA and the recipient strains were genetically related and apparently differed only in symbiotic property. The efficiency of transformation by DNA to ineffectiveness was compared with mutagenic and selective treatments. The results support the idea that symbiotic effectiveness involves compatability between several plant and bacterial factors, changes in any one of which makes the bacterium ineffective.
-