Green alder ( Alnus viridis ) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently

Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites

Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.

Nitrogen translocation by Highland cattle grazing in Alnus viridis-encroached pastures

During the last decades, Alnus viridis has expanded over former montane pastures and meadows, due to land use and abandonment. This nitrogen-fixing woody species has triggered negative agro-environmental impacts, such as nitrogen (N) leaching, soil acidification and a reduced biodiversity. The aim of this study was to estimate the N translocation from A. viridis-encroached areas to adjacent open pastures by Highland cattle. In 2019 and 2020, Highland cattle herds equipped with GPS collars were placed in four A. viridis-encroached paddocks across Italy and Switzerland. The N content was measured in A. viridis leaves, herbaceous vegetation, and cattle dung pats, which were collected throughout the grazing season. Using GPS locations and collar activity sensors, livestock activity phases were discriminated. The N ingested by cattle was estimated through the N content of herbaceous vegetation and A. viridis leaves of vegetation patches visited by cattle during 24 h before dung sampling (N_24H). The N content of herbaceous vegetation significantly increased with increasing A. viridis cover. The average N content in dung pats (31.2 ± 3.4 g.kg^-1 DM) was higher than average values from literature on grazing cattle. Moreover, it was positively related to the N_24H. Most of this N (29.5 ± 10.3 kg ha^-1 yr^-1) was translocated towards resting areas, which generally occurred on flat open pastures. Our results highlight the potential of Highland cattle to effectively translocate part of the ingested N from A. viridis-encroached towards targeted open areas, thus bringing new perspective for forage yield and quality improvement in the long-term.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10705-023-10282-0.

Proposal of 'Candidatus Frankia alpina', the uncultured symbiont of Alnus alnobetula and A. incana that forms spore-containing nitrogen-fixing root nodules

The members of the genus Frankia are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on Alnus spp. (Betulaceae), Myrica spp., Morella spp. and Comptonia spp. (Myricaceae) that have global distributions. Some of these strains produce not only hyphae and vesicles, as other cluster 1 strains do, but also numerous sporangia in their host symbiotic tissues, hence their phenotype being described as spore-positive (Sp+). While Sp+ strains have resisted repeated attempts at cultivation, their genomes have recently been characterized and found to be different from those of all described species, being markedly smaller than their phylogenetic neighbours. We thus hereby propose to create a 'Candidatus Frankia alpina' species for some strains present in nodules of Alnus alnobetula and A. incana that grow in alpine environments at high altitudes or in subarctic environments at high latitudes.

Disentangling the effects of driving forces on soil bacterial and fungal communities under shrub encroachment on the Guizhou Plateau of China

Global shrub encroachment (SE) affects the structure and function of grassland ecosystem. The effects of SE on plant and soil abiotic properties have been well studied; however, little is known about the extent to which driving forces structure soil microbes under SE, especially in subalpine regions of the Guizhou Plateau of China, which is undergoing progressive SE. We investigated the plant factors (viz, plant diversity and relative shrub cover), soil physicochemical properties, enzymatic activities, and microbial communities, quantified microbial element limitations under three encroachment stages, and disentangled the effects sizes of the factors that structure the diversity and composition of soil microbial communities. Redundancy analysis showed that soil factors made a greater contribution than plant factors to shaping the diversity and composition of the soil bacterial community, soil chemical factors made a greater contribution than physical factors both to structuring the diversity and composition of the soil bacterial community and to structuring the composition of the soil fungal community; and soil nutrient stoichiometry made a greater contribution than soil nutrient content to shaping soil bacterial community's diversity and fungal community's composition. In contrast, soil nutrient content made a greater contribution than soil nutrient stoichiometry to shaping the soil bacterial community's composition. The decrease in bacterial community's diversity observed under SE was attributable to increases in the carbon and nitrogen limitations consequent to SE, and the nitrogen limitation had a greater contribution to the soil bacterial community's diversity and composition than did the carbon limitation. These findings provide updated knowledge of the driving forces shaping the diversity and composition of soil microbial communities, which could be crucial for improving microbial prediction models and revealing the element cycling that occurs in SE biomes.

Feedback Regulation of N Fixation in Frankia-Alnus Symbiosis Through Amino Acids Profiling in Field and Greenhouse Nodules

Symbiosis established between actinorhizal plants and Frankia spp., which are nitrogen-fixing actinobacteria, promotes nodule organogenesis, the site of metabolic exchange. The present study aimed to identify amino acid markers involved in Frankia-Alnus interactions by comparing nodules and associated roots from field and greenhouse samples. Our results revealed a high level of citrulline in all samples, followed by arginine (Arg), aspartate (Asp), glutamate (Glu), γ-amino-n-butyric acid (GABA), and alanine (Ala). Interestingly, the field metabolome approach highlighted more contrasted amino acid patterns between nodules and roots compared with greenhouse samples. Indeed, 12 amino acids had a mean relative abundance significantly different between field nodule and root samples, against only four amino acids in greenhouse samples, underlining the importance of developing "ecometabolome" approaches. In order to monitor the effects on Frankia cells (respiration and nitrogen fixation activities) of amino acid with an abundance pattern evocative of a role in symbiosis, in-vitro assays were performed by supplementing them in nitrogen-free cultures. Amino acids had three types of effects: i) those used by Frankia as nitrogen source (Glu, Gln, Asp), ii) amino acids stimulating both nitrogen fixation and respiration (e.g., Cit, GABA, Ala, valine, Asn), and iii) amino acids triggering a toxic effect (Arg, histidine). In this paper, a N-metabolic model was proposed to discuss how the host plant and bacteria modulate amino acids contents in nodules, leading to a fine regulation sustaining high bacterial nitrogen fixation.

Plant Symbionts Are Engineers of the Plant-Associated Microbiome

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.

Shrub Encroachment Shapes Soil Nutrient Concentration, Stoichiometry and Carbon Storage in an Abandoned Subalpine Grassland

Soil nutrient stoichiometry plays a substantial role in terrestrial carbon and nutrient cycling. However, the changes in soil nutrient stoichiometry with shrub encroachment (SE) remain poorly understood, especially in subalpine areas. We examined the changes in soil nutrient concentration, nutrient stoichiometry, and organic carbon (OC) storage (at a depth of 0–5, 5–10 and 10–20 cm) in three successional shrub encroachment stages (early, mid and late) in an abandoned subalpine Eulalia pallens (Hackel) Kuntze grassland. An ANOVA showed that SE did not produce serious soil acidification, but significantly increased the soil OC and total phosphorous (TP) concentration, and improved the stoichiometry ratio of soil OC to total nitrogen (OC:TN) in all layers. OC storage tended to increase with SE. SE thus did not indicate degradation of the grassland. A redundancy analysis (RDA) and partial RDA revealed that the shrub relative cover and soil water content were the most important factors affecting the soil nutrient concentration, that the soil available phosphorous (AP), nitrogen, potassium, calcium (ACa), and magnesium concentration and shrub relative cover were the most important factors influencing soil nutrient stoichiometry ratios, and that soil OC:TN, TN:TP, OC:TN:TP, and AP:ACa ratios, bulk density, and pH were the most important factors influencing soil OC storage over SE. Our study provides insights into SE in grassland areas, and potentially provides a useful reference for ongoing grassland conservation and restoration in subalpine regions.

In Planta Sporulation of Frankia spp. as a Determinant of Alder-Symbiont Interactions

The Alnus genus forms symbiosis with the actinobacteria Frankia spp. and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta Spore-positive (Sp+) strains are predominant on Alnus incana and Alnus viridis in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, as well as the effect of the sporulation genotype on the ectomycorrhizal (ECM) communities. Trapping experiments were conducted using A. glutinosa, A. incana, and A. viridis plantlets on 6 soils, differing in the alder species and the frequency of Sp+ nodules in the field. Higher diversity of Frankia spp. and variation in Sp+ frequencies were observed in the trapping than in the fields. Both indigenous and trapping species shape Frankia community structure in trapped nodules. Nodulation impediments were observed under several trapping conditions in Sp+ soils, supporting a narrower host range of Sp+ Frankia species. A. incana and A. viridis were able to associate equally with compatible Sp+ and Sp- strains in the greenhouse. Additionally, no host shift was observed for Alnus-specific ECM, and the sporulation genotype of Frankia spp. defined the ECM communities on the host roots. The symbiotic association is likely determined by the host range, the soil history, and the type of in planta Frankia species. These results provide an insight into the biogeographical drivers of alder symbionts in the Holarctic region.IMPORTANCE Most Frankia-actinorhiza plant symbioses are capable of high rates of nitrogen fixation comparable to those found on legumes. Yet, our understanding of the ecology and distribution of Frankia spp. is still very limited. Several studies have focused on the distribution patterns of Frankia spp., demonstrating a combination of host and pedoclimatic parameters in their biogeography. However, very few have considered the in planta sporulation form of the strain, although it is a unique feature among all symbiotic plant-associated microbes. Compared with Sp- Frankia strains, Sp+ strains would be obligate symbionts that are highly dependent on the presence of a compatible host species and with lower efficiency in nitrogen fixation. Understanding the biogeographical drivers of Sp+ Frankia strains might help elucidate the ecological role of in planta sporulation and the extent to which this trait mediates host-partner interactions in the alder-Frankia-ECM fungal symbiosis.

1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species

BACKGROUND

Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding modes of action involve a modulation of plant hormonal balance, such as the deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Despite its ecological importance, our understanding of ACC deamination is impaired by a lack of direct molecular tools. Here, we developed PCR primers to quantify the ACC deaminase gene acdS and its mRNA in soil communities and assessed acdS⁺ microorganisms colonizing maize and other Poaceae species.

RESULTS

Effective acdS primers suitable for soil microbial communities were obtained, enabling recovery of bona fida acdS genes and transcripts of diverse genetic backgrounds. High numbers of acdS genes and transcripts were evidenced in the rhizosphere of Poaceae, and numbers fluctuated according to plant genotype. Illumina sequencing revealed taxonomic specificities of acdS⁺ microorganisms according to plant host. The phylogenetic distance between Poaceae genotypes correlated with acdS transcript numbers, but not with acdS gene numbers or the genetic distance between acdS functional groups.

CONCLUSION

The development of acdS primers enabled the first direct analysis of ACC deaminase functional group in soil and showed that plant ability to interact with soil-inhabiting acdS⁺ microorganisms could also involve particular plant traits unrelated to the evolutionary history of Poaceae species.