Frankia and Alnus rubra Canopy Roots: An Assessment of Genetic Diversity, Propagule Availability, and Effects on Soil Nitrogen

The ecological importance of microbial symbioses in terrestrial soils is widely recognized, but their role in soils that accumulate in forest canopies is almost entirely unknown. To address this gap, this study investigated the Frankia–Alnus rubra symbiosis in canopy and forest floor roots at Olympic National Park, WA, USA. Sixteen mature A. rubra trees were surveyed and Frankia genetic diversity in canopy and forest floor nodules was assessed with sequence-based nifH analyses. A seedling bioassay experiment was conducted to determine Frankia propagule availability in canopy and forest floor soils. Total soil nitrogen from both environments was also quantified. Nodules were present in the canopies of nine of the 16 trees sampled. Across the study area, Frankia canopy and forest floor assemblages were similar, with both habitats containing the same two genotypes. The composition of forest floor and canopy genotypes on the same tree was not always identical, however, suggesting that dispersal was not a strictly local phenomenon. Frankia seedling colonization was similar in canopy soils regardless of the presence of nodules as well as in forest floor soils, indicating that dispersal was not likely to be a major limiting factor. The total soil nitrogen of canopy soils was higher than that of forest floor soils, but the presence of Frankia nodules in canopy soils did not significantly alter soil nitrogen levels. Overall, this study indicates that the Frankia–A. rubra symbiosis is similar in canopy and forest floor environments. Because canopy roots are exposed to different environmental conditions within very small spatial areas and because those areas can be easily manipulated (e.g., fertilizer or watering treatments), they present microbial ecologists with a unique arena to examine root–microbe interactions.     

Frankia inoculation,soil biota,and host tissue amendment influence Casuarina nodulation capacity of a tropical soil

The effects of soil biota, Frankia inoculation and tissue amendment on nodulation capacity of a soil was investigated in a factorial study using bulked soil from beneath a Casuarina cunninghamiana tree and bioassays with C. cunninghamiana seedlings as capture plants. Nodulation capacities were determined from soils incubated in sterile jars at 21 °C for 1, 7, and 28 days, after receiving all combinations of the following treatments: ± steam pasteurization, ± inoculation with Frankia isolate CjI82001, and ± amendment with different concentrations of Casuarina cladode extracts. Soil respiration within sealed containers was determined periodically during the incubation period as a measure of overall microbial activity. Soil respiration, and thus overall microbial activity, was positively correlated with increasing concentrations of Casuarina cladode extracts. The nodulation capacity of soils inoculated with Frankia strain Cj82001 decreased over time, while those of unpasteurized soils without inoculation either increased or remained unaffected. The mean nodulation capacity of unpasteurized soil inoculated with Frankia CjI82001 was two to three times greater than the sum of values for unpasteurized and inoculated pasteurized soils. Our results suggest a positive synergism between soil biota as a whole and Frankia inoculum with respect to host infection.     

The capacity of Jamaican mine spoils, agricultural and forest soils to nodulate Myrica cerifera, Leucaena leucocephala and Casuarina cunninghamiana

Soils from seven sites on the island of Jamaica were assayed for the symbiotic diazotrophs Frankia and Rhizobium using serial dilutions. Most probable number and least squares regression methods were used to estimate each soil's capacity to nodulate native Myrica cerifera, exotic Leucaena leucocephala and exotic Casuarina cunninghamiana. The sample sites included a montane forest, a slash-and-burn agricultural site, reclaimed bauxite mining areas, abandoned sugar cane fields, and a garden plot. None of the host plants used in the bioassay were present on the sites sampled except for scattered L. leucocephala on one site. Frankia capable of nodulating M. cerifera, which is native to Jamaican highlands, occurred at all sites sampled. No C. cunninghamiana-infective Frankia was detected in soils sampled. Only soils from one site on the tropical coastal plain harbored rhizobia able to nodulate L. leucocephala (37 nodulation units cm^?3 of soil). A subset of nodulated M. cerifera and L. leucocephala reduced acetylene to ethylene indicating nitrogenase activity. The slash-and-burn agricultural site, which was situated at an elevation of 200 m and possessed both high natural fertility and high soil moisture-supplying capacity, had significantly greater Myrica infectious capacity (1 000 nodulation units cm^?3 of soil) than the other sites (7?207 nodulation units cm^?3 of soil). A planned, paired comparison revealed that a recently cultivated sugar cane field and a recently reclaimed bauxite mining site together had significantly less Myrica-infective Frankia (4 nodulation units cm^?3 of soil) than a corresponding pair of sites consisting of a sugar cane field abandoned for 25 years and a bauxite mining site reclaimed 20 years before sampling (118 nodulation units cm^?3 of soil). Results indicate that Myrica-infective Frankia is widespread in Jamaica, that the number of Myrica-infective Frankia units vary from site to site in accordance with soil type and soil history, that Jamaican sites sampled lack soil Frankia populations capable of nodulating a casuarina host, that rhizobial symbionts capable of nodulating L. leucocephala may be geographically restricted to lowlands in Jamaica, and that the occurrence of Frankia in these soils is independent of host plant presence.     

Glasshouse evaluation of the growth ofAlnus rubra andAlnus glutinosa on peat and acid brown earth soils when inoculated with four sources ofFrankia

The effects of soil type (an acid peat and 2 acid brown earths) andFrankia source (3 spore-positive crushed nodule inocula and spore-negative crushed nodules containing the singleFrankia ArI5) on nodulation, N content and growth ofAlnus glutinosa andA. rubra were determined in a glasshouse pot experiment of two years duration. Plants on all soils required additional P for growth. Growth of both species was very poor on peat withA. glutinosa superior toA. rubra. The former species was also superior toA. rubra on an acid brown earth with low pH and low P content. Some plant-inoculum combinations were of notable effectivity on particular soils but soil type was the major source of variation in plant weight. Inoculation with crushed nodules containingFrankia ArI5 only gave poor infection of the host plant, suggesting that inoculation with locally-collected crushed nodules can be a preferred alternative to inoculation withFrankia isolates of untested effectivity. Evidence of adaptation ofFrankia to particular soils was obtained. Thus, while the growth of all strains was stimulated by mineral soil extracts, inhibitory effects of peat extracts were more apparent with isolates from nodules from mineral soils than from peat, suggesting that survival ofFrankia on peat may be improved by strain selection.     

Effects of soil acidity on nodulation ofAlnus glutinosa and viability ofFrankia

Summary Black alder seedlings were grown from seed for 7 weeks in six soils limed to various pH levels and inoculated withFrankia in two inoculation-seeding time combinations (inoculated and seeded concurrently; inoculated then seeded 5 weeks after inoculation). Three mine soils and three non-mine soils were used. Soil pHs in the study ranged from 3.6 to 7.6. In the second inoculation-seeding time combination, a series of soil samples at each of the pH levels below 7.0 were relimed to pH 7.0 immediately prior to seeding. The purpose of the study was to examine the effects of soil acidity on the nodulation of black alder byFrankia and the viability ofFrankia in acid soils. Based on the average number of nodules established per seedling, soil pH was determined to be a significant factor affecting nodulation in the mine soils. The highest levels of nodulation occurred between soil pH 5.5 and 7.2. Below pH 5.5, nodulation was reduced. There was also evidence of decreased viability of the endophyte below pH 4.5.     

Survival ofFrankia strains introduced into soil

Factors affecting the establishment of Alnus/Frankia symbioses were studied partly by following the survival ofFrankia strains exposed to different soil conditions, and partly by investigating the effect of pH on nodulation. TwoFrankia strains were used, both of the Sp⁻ type (sporangia not formed in nodules). One of the strains sporulated heavily, while the other formed mainly hyphae. The strains originated fromAlnus incana root nodules growing in soils of pH 3.5 and 5.0. The optimum pH for their growth in pure culture was found to be 6.7 and 6.2, respectively. The strains were introduced into twoFrankia-free soils, peat and fine sand. Their survival, measured as the persistance of nodulation capacity using the plant infection technique, was followed for 14 months. The survival curves of the strains were similar despite the morphological differences between the strains in pure culture. The nodulation capacities declined over time both at 14 and 22°C. Survival was better in soils limed to a pH above 6 than in soils at their original pH (peat 2.9, fine sand 4.2). The effect of pH on nodule formation in Alnus seedlings by theFrankia strains was studied in liquid culture. The number of nodules increased linearly within the pH range studied (3.5–5.8). No nodules were formed at pH 3.5.     

Are Northwestern Patagonian “mallín” wetland meadows reservoirs of <Emphasis Type="BoldItalic">Ochetophila trinervis</Emphasis> infective <Emphasis Type="BoldItalic">Frankia?</Emphasis>

“Mallín” (plural mallines) is a particular kind of wetland occurring in Patagonian steppe and forests. In Northwest Patagonia, mallines are humid meadows with high net primary production. It was previously found that a mallín soil in the steppe devoid of actinorhizal plants had a higher Frankia nodulation capacity in Ochetophila trinervis (sin. Discaria trinervis) than other soils in the region. Under the hypothesis that mallín wetland meadows are reservoir of infective Frankia, we studied the Frankia nodulation capacity in O. trinervis of 12 mallín and their neighbouring steppe soils, by using plant bioassays. A qualitative plant bioassay showed that infective Frankia was present in most soils. The number of nodules per plant in seedlings inoculated with mallín soils was negatively correlated with soil water content while the opposite was true for plants inoculated with soils from neighbouring steppe. A quantitative bioassay was performed with eight representative soils, selected according to the number of nodules per plant produced in the qualitative assay and to the presence or not of different actinorhizal plants at the sites. Frankia nodulation units per cm³ of soil (NU) in mallín soils were higher than those in steppe. Water and organic matter content of soils were correlated with the higher nodulation capacity of mallines, which may account for the saprotrophic growth of Frankia in soils. The symbiosis was effective in plants inoculated with all soil samples. These results suggest that Northwestern Patagonian mallín wetland meadows are reservoirs of infective and effective Frankia propagules in O. trinervis.     

Extraction of ribosomal RNA from soil for detection of Frankia with oligonucleotide probes

Sequences of 16S rRNA of the nitrogen-fixing Frankia strain Ag45/Mut15 and the ineffective Frankia strain AgB1.9 were used to design a genus-specific oligonucleotide probe. Hybridization experiments of this Frankia probe and a second probe, specific for Nif⁺-Frankia strains only, were used to detect Frankia specific target sequences in RNA isolations from soil. A method is described for direct isolation of RNA from a loamy soil and a peat. Yields of about 10 ng RNA/g wet soil are obtained without detectable contamination with humic acids. Isolation of RNA after initial extraction of bacteria from soil resulted in significantly lower RNA yields, compared to the direct isolation procedure. Hybridization with both probes against rRNA isolations from Frankia-containing soil could detect target sequences within RNA isolations from 1 g wet soil with an estimated detection limit of 10⁴ cells.     

Effects of Zn<Superscript>2+</Superscript> on nodulation and growth of a South American actinorhizal plant, <Emphasis Type="Italic">Discaria americana</Emphasis> (Rhamnaceae)

Discaria americana is a xerophytic shrub which lives in symbiosis with an actinomycete of the genus Frankia. The objective of this paper was to investigate the effects of high soil Zn²⁺ concentrations on growth and nodulation on the association Discaria americana–Frankia with the aim of determining if this association is suitable for improving contaminated soils. Two experiments were performed in 1 dm³ pots containing soil and different Zn additions, from 0 to 2,000 mg Zn²⁺ kg⁻¹ dry soil, with or without N fertilization. Zn additions strongly delayed shoot and root growth, but once growth was initiated, the biomass production of the plants supplied with moderate Zn amounts did not differ from the control plants. Zn reduced the final nodule number, but not the total nodule biomass. At the end of the experiment only the highest Zn treatments showed a lower nodule weight than the control plants, while N addition completely inhibited nodulation. It is concluded than Zn reduces the number of Frankia infections, but once the actinomycete is inside the roots, nodules can continue growing according to plant demand for N, compensating the reduced nodule number with more biomass. On the other hand, there is a toxic effect of Zn itself on plants when present in very high concentrations.     

Distribution ofFrankia in soils from forest and afforestation sites in northern Sweden

Summary The presence in soil ofFrankia, capable of forming nitrogen-fixing root nodules onAlnus incana (L.) Moench, was investigated. Intact soil cores from forested as well as disturbed sites were sampled and both alder-rich and alder-free sites were included in the study. Surface-sterilized alder seeds were sown in the soil cores which were kept in sterile culture tubes in a growth chamber. Root nodules with nitrogenase activity developed in soil cores from all sites studied. Thus, infective and effectiveFrankia was present in all of the soils sampled, even from sites free from actinorhizal plants and irrespective of pH and nitrogen content of the soils.     

Morphological and molecular characterization of Frankia sp. isolates from nodules of Alnus nepalensis Don

Nodules collected from Alnus nepalensis growing in mixed forest stands at three different sites around Shillong, were crushed in various culture media to obtain isolates of Frankia. The isolates were found to have typical Frankia morphology as revealed by the scanning electron microscope. Seedlings inoculated with isolates or crushed nodules formed nitrogen fixing nodules. Frankia specific DNA probes amplified the DNA of the tested isolate AnpUS4. Partial nucleotide sequence of the 16S rRNA gene indicated that AnpUS4 was phylogenetically distinct from all other Frankia strains characterized so far.     

The production and utilisation of monoclonal antibodies for identification of a Frankia strain utilised as inoculum for Casuarina equisetifolia

Monoclonal antibodies were raised against Frankia 0RS020607, a strain isolated originally by H.G. Diem from nodules of Casuarina equisetifolia from Senegal. One of these antibodies, mAb8C5, was shown by ELISA to have high, but not absolute specificity for 0RS020607. This antibody was employed to investigate the mobility and persistence of 0RS020607 in plantations of C. equisetifolia. Seedlings were inoculated in pots of sand in a forest nursery with 0RS020607, with local crushed nodule suspensions or were left uninoculated. They were planted out after 5 months in experimental plots on a moderately fertile black soil site and on a low organic, oxidised red soil site. Compared with crushed nodule inoculated seedlings or uninoculated controls, growth of seedlings at transplant was improved by inoculation with Frankia 0RS020607. However, 4 years after transplant to experimental plots, the growth of trees receiving different treatments was similar. The possibility that movement of ORS 020607 between treatment plots contributed to new nodulation and enhanced growth of uninoculated trees was tested using mAb8C5 in ELISA of Frankia mycelium, extracted from the nodules of trees of the three treatments. No significant differences in reactivity were detected between nodules from uninoculated and 0RS020607 inoculated trees at either the black or the red soil sites, showing that 0RS020607 moved between treatment plots at both sites. However, at both sites, nodules from plots of trees that were inoculated originally with local crushed nodules gave reactions in ELISA that were significantly lower than values for 0RS020607 inoculated trees, possibly due to the competitive effects for new nodulation of enhancement of the indigenous population of Frankia. Serological techniques using antibodies of high specificity against Frankia strains have value for rapid screening of field samples as a preliminary for further analysis by more discriminatory techniques based on assays of genetic polymorphisms.     

Presence of sporangia of Frankia in the rhizosphere of Discaria (Rhamnaceae)

Discaria trinervis and Discaria americana are native actinorhizal plants in Argentina. Discaria seedlings growing in N-free liquid culture, inoculated with dry soils, developed Frankia colonies in the rhizosphere. The occurrence of hyphae, vesicles and sporangia characteristic of Frankia are described in these colonies. The presence of sporangia of Frankia has previously neither been reported in the genus Discaria, nor in the other genera of the tribe Colletieae inside root nodules or outside roots. The infective capacity of the colonies has been demonstrated.     

A modified sucrose fractionation procedure for the isolation of frankiae from actinorhizal root nodules and soil samples

Summary The isolation and pure culture of the symbiotic nitrogen-fixing frankiae has always been difficult. In the past the isolation of these actinomycetes directly from soil samples has proven impossible and isolations from root nodules of many genera has been only poorly successful. We report here a modified sucrose fractionation procedure which increased the success of isolations from root nodules and which permitted the isolation ofFrankia directly from soil samples. Crushed nodule suspensions or soil suspensions were incubated briefly in 0.7% phenol (carbolic acid) just before application to a sucrose density gradient. This phenol incubation decreased the number of contaminating eubacteria and fungi but more importantly increased the number ofFrankia developing on the isolation plates. If the phenol incubation was used solely without sucrose fractionation noFrankia were isolated, suggesting the death of the organisms due to phenol toxicity. The use of selective nitrogen-deficient media proved important for the isolation of frankiae from soils.     

Landscape‐scale Variation in Pathogen‐suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica

Bacteria in the genus Streptomyces are ubiquitous in soil and are well‐known for their production of diverse secondary metabolites, including antibiotics that can inhibit soil‐borne plant pathogens and suppress disease. Pathogen‐suppressive soil bacteria have the potential to influence plant community composition and diversity, but remain relatively unexplored in tropical forest soils. To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil‐borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde) and quantified antibiotic‐mediated pathogen inhibition against three plant pathogens. The potential for pathogen inhibition and disease suppression by Streptomyces was highly variable across the landscape. Densities of pathogen‐suppressive Streptomyces varied by over ten‐fold and were correlated with soil nutrients across the plots. In particular, Streptomyces communities became more pathogen‐suppressive as labile soil P decreased. Inhibitor densities were significantly higher in Santa Rosa than Palo Verde, which may be related to differences in soil texture and/or plant community composition between the two forests. Our findings suggest potential differences in the degree and specificity of antibiotic‐mediated disease suppression in tropical dry forest soils of Costa Rica, and highlight the need for further studies on the drivers of pathogen‐suppressive phenotypes as well as the consequences of spatially variable pathogen inhibition for plant community composition in tropical forest ecosystems.     

Effects of sodium chloride and melibiose on the in vitro growth and sporulation of Frankia strain HFPCcI3 isolated from Casuarina cunninghamiana

The in vitro growth and sporulation of Frankia isolate HFPCcI3, a nitrogen-fixing symbiont of Casuarina, was inhibited by both the toxic and osmotic effects of sodium chloride. This was demonstrated by comparing HFPCcI3 halotolerance with its tolerance to metabolically neutral melibiose osmoticum at sodium chloride and melibiose concentrations from 0 to 500 mmol L^-1. The osmotolerance of this strain is similar to that of other Frankia strains, whereas the halotolerance of this strain is greater than that reported for Frankia strains isolated from actinorhizal plants from moist, temperate regions lacking sodic soils. This finding suggests that differential strain-specific mechanisms are involved in Frankia's ability to tolerate dry versus sodic soil conditions and has important implications for the microbial ecology of soils supporting Casuarina spp.     

Nodulation potential of soils from red alder stands covering a wide age range

Red alder (Alnus rubra Bong.) stands in the Pacific Northwest are the common first stage in succession following disturbance. These stands are highly productive and contribute a large amount of N to the soils as a result of their N₂-fixing symbiosis with Frankia. As these alder stands age, the soils not only increase in total N, but concentrations of NO^– ₃ increase and pH decreases as a result of nitrification. The objective of this study was to determine how the nodulation capacity of Frankia varies as red alder stands age and if differences in nodulation capacity are related to changes in soil properties. Nodulation capacity was determined by a red alder seedling bioassay for soils from red alder stands in the Oregon coast range covering a wide range of ages. Six chronosequences were sampled, each containing a young, an intermediate, and an older alder stand. Soil total N, total C, NO^– ₃, NH⁺ ₄, and pH were measured on the same soil samples. These factors as well as alder stand characteristics were compared with nodulation capacity in an attempt to identify soil characteristics typical in developing alder stands that most strongly affect nodulation capacity. Soil pH and NO^– ₃ concentration were highly correlated with nodulation capacity and with each other. Cluster analysis of the sites using these two variables identified two groups with distinctly different nodulation capacities. The cluster with the higher nodulation capacity was lower in NO^– ₃ and higher in pH than the other cluster, which included the majority of sites. There was substantial overlap in the age ranges for the two clusters and there was no significant correlation between age and nodulation capacity. Thus nodulation capacity appears to be most closely related to soil properties than to stand age.     

THE OCCURRENCE AND DISTRIBUTION OF ACRASIEAE IN FORESTS OF SUBTROPICAL AND TROPICAL AMERICA

Forests of the subtropical and tropical regions of North America harbor cellular slime molds not found in the soils of temperate deciduous forests investigated previously. However, most species found in the temperate forest are common in the tropics. Although the diversity of forms is greater in the soils of tropical forests the numbers of Acrasieae per unit of soil are comparable. Characteristic of tropical and subtropical forest soils are Acrasieae bearing crampon bases, of which four new species of Dictyostelium are presently known. Also present, but less frequently isolated, are two other new species of the genus Dictyostelium and two still undescribed species of the Guttulinaceae. Occasional isolates of D. purpureum and D. discoideum were found that produce macrocysts, which seem, also, to be confined to tropical and subtropical areas. Macro-cysts were previously known only in D. mucoroides and D. minutum isolated from temperate forest soils. The occurrence and distribution of Acrasieae in warm temperate desert and mesquite-scrub, in subtropical hammock, and in tropical thorn, deciduous, seasonal evergreen, rain, and cloud forests were investigated. Acrasieae were well represented in all of these forests except desert. The number of species and the total populations were largest in seasonal evergreen forests. The composition of the cellular slime mold populations and the dominant species within these populations could be related to the soil environment as expressed by the dominant vegetation.     

Phylogeny and assemblage composition of Frankia in Alnus tenuifolia nodules across a primary successional sere in interior Alaska

In nitrogen (N) fixing symbioses, host‐symbiont specificity, genetic variation in bacterial symbionts and environmental variation represent fundamental constraints on the ecology, evolution and practical uses of these interactions, but detailed information is lacking for many naturally occurring N‐fixers. This study examined phylogenetic host specificity of Frankia in field‐collected nodules of two Alnus species (A. tenuifolia and A. viridis) in interior Alaska and, for A. tenuifolia, distribution, diversity, spatial autocorrelation and correlation with specific soil factors of Frankia genotypes in nodules collected from replicated habitats representing endpoints of a primary sere. Frankia genotypes most commonly associated with each host belonged to different clades within the Alnus‐infective Frankia clade, and for A. tenuifolia, were divergent from previously described Frankia. A. tenuifolia nodules from early and late succession habitats harboured distinct Frankia assemblages. In early succession, a single genotype inhabited 71% of nodules with no discernable autocorrelation at any scale, while late succession Frankia were more diverse, differed widely among plants within a site and were significantly autocorrelated within and among plants. Early succession Frankia genotype occurrence was strongly correlated with carbon/nitrogen ratio in the mineral soil fraction, while in late succession, the most common genotypes were correlated with different soil variables. Our results suggest that phylogenetic specificity is a significant factor in the A. tenuifolia‐Frankia interaction and that significant habitat‐based differentiation may exist among A. tenuifolia‐infective genotypes. This is consistent with our hypothesis that A. tenuifolia selects specific Frankia genotypes from early succession soils and that this choice is attenuated in late succession.     

Life in soil by the actinorhizal root nodule endophyte <Emphasis Type="BoldItalic">Frankia</Emphasis>. A review

Frankia is a genus of soil actinomycetes famous for its ability to form N₂-fixing root nodule symbioses with actinorhizal plants. Although Frankia strains display a high diversity in terms of ecological niches in soil, current knowledge about Frankia is dominated by its life as an endophyte in root nodules. Increased use of molecular methods has refined and expanded insights into endophyte-host specificities and Frankia phylogeny. This review has focus on Frankia as a soil organism, including its part of microbial consortia, and how to study Frankia in soil. We highlight the use of nodulation tests and molecular methods to reveal population size and genetic diversity of Frankia in soil and discuss how autoregulation of nodulation and interactions with other soil microorganisms may influence the results. A comprehensive record of published interactions between Frankia and other soil microbes is summarized.