Biology of Frankia strains, actinomycete symbionts of actinorhizal plants

Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska

In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

Root nodules of red alder (Alnus rubra) and sitka alder (Alnus viridis ssp. sinuata) are inhabited by taxonomically diverse cultivable microbial endophytes

The root nodules of actinorhizal plants are home to nitrogen-fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non-Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non-Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co-occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co-inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.

Responses of attached bacterial communities to blooms of the swimming shelled pteropod Creseis acicula in Daya Bay, southern China

The shelled pteropod Creseis acicula is a marine pelagic shellfish widely distributed from temperate to tropical seas around the world. From June to July 2020, a C. acicula bloom first happened in the Daya Bay, southern China, and its density reached the highest value (5600 ind. m-3) ever recorded around the world. However, few studies have investigated the responses of bacterial communities to the C. acicula bloom. In the present study, we examined the community profiles of three communities of bacteria including the free-living and particle-attached bacteria in the blooming and reference waters, and bacteria attached to the whole body and shell of C. acicula using a high-throughput sequencing method. The results indicated that the C. acicula bloom had a greater impact on particle-attached bacteria than free-living bacteria. Among the bloom-sensitive particle-attached bacteria, the predominant bacterial phyla were Pseudomonadota, Bacteroidota and Verrucomicrobiota in the blooming areas, whereas they were Actinomycetota and Planctomycetota in the reference areas. Specifically, fecal bacteria Haloferula and Halioglobus spp. were significantly enriched in the blooming waters and accumulated on C. acicula shells. Conversely, the significantly lower relative abundance of Nocardioides sp. in the blooming area and accumulated on the whole body of C. acicula indicated their attachment to particles consumed by C. acicula. Overall, our results suggested that the C. acicula bloom influenced marine bacteria, particularly particle-attached bacteria, by increasing (e.g. providing shells and feces) or decreasing (e.g. filter-feeding the suspended particles) the abundance of available substances.

Systematic tracking of nitrogen sources in complex river catchments: Machine learning approach based on microbial metagenomics

Tracking nitrogen pollution sources is crucial for the effective management of water quality; however, it is a challenging task due to the complex contaminative scenarios in the freshwater systems. The contaminative pattern variations can induce quick responses of aquatic microorganisms, making them sensitive indicators of pollution origins. In this study, the soil and water assessment tool, accompanied by a detailed pollution source database, was used to detect the main nitrogen pollution sources in each sub-basin of the Liuyang River watershed. Thus, each sub-basin was assigned to a known class according to SWAT outputs, including point source pollution-dominated area, crop cultivation pollution-dominated area, and the septic tank pollution-dominated area. Based on these outputs, the random forest (RF) model was developed to predict the main pollution sources from different river ecosystems using a series of input variable groups (e.g., natural macroscopic characteristics, river physicochemical properties, 16S rRNA microbial taxonomic composition, microbial metagenomic data containing taxonomic and functional information, and their combination). The accuracy and the Kappa coefficient were used as the performance metrics for the RF model. Compared with the prediction performance among all the input variable groups, the prediction performance of the RF model was significantly improved using metagenomic indices as inputs. Among the metagenomic data-based models, the combination of the taxonomic information with functional information of all the species achieved the highest accuracy (0.84) and increased median Kappa coefficient (0.70). Feature importance analysis was used to identify key features that could serve as indicators for sudden pollution accidents and contribute to the overall function of the river system. The bacteria Rhabdochromatium marinum, Frankia, Actinomycetia, and Competibacteraceae were the most important species, whose mean decrease Gini indices were 0.0023, 0.0021, 0.0019, and 0.0018, respectively, although their relative abundances ranged only from 0.0004 to 0.1 %. Among the top 30 important variables, functional variables constituted more than half, demonstrating the remarkable variation in the microbial functions among sites with distinct pollution sources and the key role of functionality in predicting pollution sources. Many functional indicators related to the metabolism of Mycobacterium tuberculosis, such as K24693, K25621, K16048, and K14952, emerged as significant important factors in distinguishing nitrogen pollution origins. With the shortage of pollution source data in developing regions, this suggested approach offers an economical, quick, and accurate solution to locate the origins of water nitrogen pollution using the metagenomic data of microbial communities.

Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience

Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.

Insights into the functional role of Actinomycetia in promoting plant growth and biocontrol in tea (Camellia sinensis) plants

Tea, a highly aromatic and globally consumed beverage, is derived from the aqueous infusion of dried leaves of Camellia sinensis (L.) O. Kuntze. Northeast India, encompassing an expansive geographical area between 24° and 27° N latitude and 88° and 95° E longitude, is a significant tea-producing region covering approximately 312,210 hectares. Despite its prominence, this region faces persistent challenges owing to a conducive climate that harbors the prevalence of pests, fungal pathogens, and weeds, necessitating agrochemicals. Helopeltis theivora, Oligonychus coffeae, and Biston suppressaria are prominent among the tea pests in this region. Concurrently, tea plants encounter fungal infections such as blister blight, brown root rot, and Fusarium dieback. The growing demand for safer tea production and the need to reduce pesticide and fertilizer usage has spurred interest in exploring biological control methods. This review focuses on Actinomycetia, which potentially safeguards plants from diseases and pest infestations by producing many bioactive substances. Actinomycetia, which resides in the tea rhizosphere and internal plant tissues, can produce antagonistic secondary metabolites and extracellular enzymes while promoting plant growth. Harnessing the biocontrol potential of Actinomycetia offers a promising solution to enhance tea production, while minimizing reliance on harmful agrochemicals, contributing to a more environmentally conscious and economically viable tea cultivation system.

Bacterial community and culturable actinomycetes of Phyllostachys viridiglaucescens rhizosphere

During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds.

Comparative analysis of nitrogen content and its influence on actinorhizal nodule and rhizospheric microorganism diversity in three Alnus species

Alnus spp. (alder) are typical nonleguminous nitrogen-fixing trees that have a symbiotic relationship with Frankia. To explore the differences in nitrogen-fixing microorganisms between three alders (A. cremastogyne, A. glutinosa, and A. formosana) with different chromosome ploidies, the community structure and compositional diversity of potential nitrogen-fixing microorganism in root nodules and rhizosphere soil were comparatively analyzed using 16S rRNA and nitrogenase (nifH) gene sequencing. The nitrogen contents in the root nodules and rhizosphere soil were also determined. The results showed that the contents of total nitrogen and nitrate nitrogen in the root nodules of the three alders are significantly higher than those in the rhizosphere soils, while the ammonium nitrogen content show the opposite trend. The family, genus, and species levels showed obviously differences between root nodules and rhizosphere soils, while there were no significant differences at the classification level between the three alders. At the phylum level, the dominant phyla from 16S rRNA and nifH gene data in the root nodules and rhizosphere soil of the three alders are phylum Actinomycetota and phylum Pseudomonadota, respectively. The LEfSe results showed that there are significant differences in the dominant groups in the root nodules and rhizosphere oil of the three alders. The relative abundances of dominant groups also showed obvious differences between the root nodules and rhizosphere soils of three alders. The relative abundances of Frankia and unclassified_Frankia in root nodules are obviously higher than those in rhizosphere soils, and their relative abundances in A. glutinosa root nodules are significantly higher than those in A. cremastogyne and A. formosana at the genus and species levels. The diversity of potential nitrogen-fixing microorganism from 16S rRNA and nifH gene data in the A. glutinosa root nodules and rhizosphere soils are all higher than those in A. cremastogyne and A. formosana. The results of functional prediction also showed that the OTUs for nitrogen fixation, nitrate respiration, and ureolysis in A. glutinosa root nodules are higher than those in the other two alders. Redundancy analysis revealed that the total nitrogen content mostly affects the Frankia community. Overall, there are significant differences in the community composition and structure of potential nitrogen-fixing microorganism in the root nodules and rhizosphere soils between the three alders. A. glutinosa showed a relatively stronger nitrogen fixation capacity than A. formosana and A. cremastogyne. The results help elucidates how the community structure and nitrogen-fixing ability of potential nitrogen-fixing microorganism differ between alder species and serve as a reference for applying Frankia to alder plantations.

Frankia nepalensis sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Coriaria nepalensis Wall

Strains CN4T, CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus. The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N2-fixing vesicles and do not fix nitrogen in vitro. The peptidoglycan of strain CN4T contains meso-diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H4) and MK-9(H6) are the predominant menaquinones (>15 %), and iso-C16 : 0 and C17 : 1ω8c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4T is most closely related to Frankia saprophytica CN 3T. An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3T , Frankia asymbiotica M16386T and Frankia inefficax EuI1cT with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4T, CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4T has a 10.76 Mb genome. CN4T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4T (=DSM 114740T = LMG 32595T) to a novel species, with CN4T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.

Effects of different remediation methods on phosphorus transformation and availability

The effects of different heavy metal pollution remediation methods on soil nutrient transformation and soil health remain unclear. In this study, the effects of phytoextraction (PE) and passivation remediation (PR) on Cd-polluted soil phosphorus transformation and availability were compared by pot experiment. The results showed that PE significantly reduced the concentrations of total and available Cd (both H2O-Cd and DTPA-Cd) in soil, PR also decreased available Cd content but had no significant effect on total Cd content. PE slightly increased soil pH and NH4+-N content, while PR significantly increased soil pH, NO3--N and AK content. PE promoted the conversion of stable P (including HCl-Pi and residual-Pt), and increased the content of labile P (including H2O-Pi, NaHCO3-Pi and NaHCO3-Po) and the proportion of moderately labile P (including NaOH-Pi and NaOH-Po), while PR showed the opposite trend. PE showed a higher soil phoC gene abundance and acid phosphatase (ACP) activity, while PR showed a higher phoD gene copies and alkaline phosphatase (ALP) activity. Soil bacteria and phoD-harboring bacteria community was significantly affected by remediation methods and soil types. Compared with PR, PE reduced phoD-harboring bacterial diversity but significantly increased the abundance of genera associated with P dissolution (Streptomyces) and P conversion (Bradyrhizobium and Frankia), both of which were significantly positively correlated with labile P or moderately labile P. In general, compared with PR, PE can effectively remove soil Cd pollution, while maintaining a higher content of labile P and a higher proportion of moderately labile P, which can be considered as a green and sustainable remediation strategy conducive to soil quality.

A Review on Traditional Ecological Knowledge and Its Role in Natural Resources Management: North East India, a Cultural Paradise

Sustainable management of natural resources plays a critical role in poverty alleviation and overall socio-economic development. North East (NE) India is blessed as a biodiversity hotspot, being also home to around 150 ethnic tribes with diverse ethical, cultural and traditional beliefs, endorsing the region as a cultural paradise rich in natural resources and traditional ecological knowledge (TEK). Conversely, the severely constrained nature of TEK, has juxtaposed TEK practices and sustainable natural resources management (NRM) in this review. Deliberating on the broader perspectives of TEK and ensuing practices, we have identified twelve sustainable development goals (SDGs) which are directly correlated to the TEK and practices of NE region. This review has meticulously detailed TEK and practices that can help in achieving various sustainable development targets of different SDGs in a more comprehensive and eco-friendly manner. Houde's manifestation to differentiate each element of TEK and practices present in the NE region of the country, such as traditional farming and irrigation systems, sacred groves, and cultural belief systems of different tribes, have been systematically analyzed and documented for each of the eight states of this region. The benefits accrued modern practices related to NRM are correlated with TEK, or adaptive empirical knowledge system. Indigenous agricultural systems, watershed management, biodiversity conservation, and ethnomedicinal therapeutic systems in NE India formed a vital part of the review. However, rapid urbanization, industrialization, and deforestation warrant an urgent need to systematically collate, document, analyze, and conserve the TEK of the indigenous communities of NE India.

Diversity and regulation of symbiotic nitrogen fixation in plants

Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.

Neighbours in nodules: the interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes of alder

In the present study, we report the in vitro interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes (NFNE) isolated from alder. The supernatant of NFNE grown in nitrogen-replete medium had neutral or negative effects on Frankia growth; none had a stimulatory effect. Inhibitory effects were observed for supernatants of some NFNE, notably Micromonospora, Pseudomonas, Serratia and Stenotrophomonas isolates. However, some NFNE-Frankia coculture supernatants could stimulate Frankia growth when used as a culture medium supplement. This was observed for supernatants of Frankia cocultured with Microvirga and Streptomyces isolates. In nitrogen-limited conditions, cocultures of Frankia with some NFNE, including some rhizobia and Cytobacillus, resulted in higher total biomass than Frankia-only cultures, suggesting cooperation, while other NFNE were strongly antagonistic. Microscopic observation of cocultures also revealed compromised Frankia membrane integrity, and some differentiation into stress resistance-associated morphotypes such as sporangia and reproductive torulose hyphae (RTH). Furthermore, the coculture of Frankia with Serratia sp. isolates resulted in higher concentrations of the auxinic plant hormone indole-3-acetic acid and related indolic compounds in the culture supernatant. This study sheds new light on the breadth of microbial interactions that occur amongst bacteria that inhabit the understudied ecological niche of the alder nodule.

Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization

Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.

Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa

The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C_16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4^T and Agncl-10, and Agncl-8^T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4^T (=DSM 107976^T = CECT 9711^T) and Agncl-8^T (=DSM 107980^T = CECT 9715^T) as the respective type strains.

Potential Roles of Soil Microorganisms in Regulating the Effect of Soil Nutrient Heterogeneity on Plant Performance

The spatially heterogeneous distribution of soil nutrients is ubiquitous in terrestrial ecosystems and has been shown to promote the performance of plant communities, influence species coexistence, and alter ecosystem nutrient dynamics. Plants interact with diverse soil microbial communities that lead to an interdependent relationship (e.g., symbioses), driving plant community productivity, belowground biodiversity, and soil functioning. However, the potential role of the soil microbial communities in regulating the effect of soil nutrient heterogeneity on plant growth has been little studied. Here, we highlight the ecological importance of soil nutrient heterogeneity and microorganisms and discuss plant nutrient acquisition mechanisms in heterogeneous soil. We also examine the evolutionary advantages of nutrient acquisition via the soil microorganisms in a heterogeneous environment. Lastly, we highlight a three-way interaction among the plants, soil nutrient heterogeneity, and soil microorganisms and propose areas for future research priorities. By clarifying the role of soil microorganisms in shaping the effect of soil nutrient heterogeneity on plant performance, the present study enhances the current understanding of ecosystem nutrient dynamics in the context of patchily distributed soil nutrients.

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae

The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.

Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance

As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.

Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions

The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species. Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.

Hydroxypyridinones in nitrogen-fixing bacterial cultures: A metal buffer for molybdenum and simulation of natural conditions

Organic matter regulates the availability of important trace elements in aquatic and terrestrial ecosystems by acting as a source and container for microbes. To overcome the limitation of trace elements, nitrogen-fixing bacteria, for example, release low-molecular-weight chelators (metallophores), which scavenge the essential cofactors of the nitrogenase, iron and molybdenum, via complexation and subsequent uptake. The formation of metallophores is triggered by limiting conditions, which must be replicated in the laboratory in order to study metallophores as a mediator in metal cycling. While EDTA-based buffer systems for metal cations are well established, there is limited knowledge regarding the buffering of oxoanions such as molybdate in a bacterial growth medium. To mimic the availability of molybdenum in nature under laboratory conditions, this study created a Mo-buffer system for bacterial growth media of the model organisms Azotobacter vinelandii and Frankia sp. CH37. We investigated selected hydroxypyridinones (HPs) as potential molybdenum-chelating agents, determining the amount required for efficient molybdenum complexation by calculating speciation plots of the various candidate complexes in artificial growth media at various pH values. The Mo-maltol system was identified as an ideal, non-toxic molybdenum-buffer system. In the presence of the Mo-maltol system, the growth of Frankia sp. was limited under diazotrophic conditions, whereas A. vinelandii could acquire molybdenum through the release of protochelin and subsequent molybdenum uptake. The study paves the way for unravelling molybdenum recruitment and homeostasis under limiting conditions in bacteria.

Seasonal Variation of the Atmospheric Bacterial Community in the Greenlandic High Arctic Is Influenced by Weather Events and Local and Distant Sources

The Arctic is a hot spot for climate change with potentially large consequences on a global scale. Aerosols, including bioaerosols, are important players in regulating the heat balance through direct interaction with sunlight and indirectly, through inducing cloud formation. Airborne bacteria are the major bioaerosols with some species producing the most potent ice nucleating compounds known, which are implicated in the formation of ice in clouds. Little is known about the numbers and dynamics of airborne bacteria in the Arctic and even less about their seasonal variability. We collected aerosol samples and wet deposition samples in spring 2015 and summer 2016, at the Villum Research Station in Northeast Greenland. We used amplicon sequencing and qPCR targeting the 16S rRNA genes to assess the quantities and composition of the DNA and cDNA-level bacterial community. We found a clear seasonal variation in the atmospheric bacterial community, which is likely due to variable sources and meteorology. In early spring, the atmospheric bacterial community was dominated by taxa originating from temperate and Subarctic regions and arriving at the sampling site through long-range transport. We observed an efficient washout of the aerosolized bacterial cells during a snowstorm, which was followed by very low concentrations of bacteria in the atmosphere during the consecutive 4 weeks. We suggest that this is because in late spring, the long-range transport ceased, and the local sources which comprised only of ice and snow surfaces were weak resulting in low bacterial concentrations. This was supported by observed changes in the chemical composition of aerosols. In summer, the air bacterial community was confined to local sources such as soil, plant material and melting sea-ice. Aerosolized and deposited Cyanobacteria in spring had a high activity potential, implying their activity in the atmosphere or in surface snow. Overall, we show how the composition of bacterial aerosols in the high Arctic varies on a seasonal scale, identify their potential sources, demonstrate how their community sizes varies in time, investigate their diversity and determine their activity potential during and post Arctic haze.

Pseudogenization of the rhizobium-responsive EXOPOLYSACCHARIDE RECEPTOR in Parasponia is a rare event in nodulating plants

BACKGROUND

Nodule symbiosis with diazotrophic Frankia or rhizobium occurs in plant species belonging to ten taxonomic lineages within the related orders Fabales, Fagales, Cucurbitales, and Rosales. Phylogenomic studies indicate that this nitrogen-fixing nodulation trait has a single evolutionary origin. In legume model plants, the molecular interaction between plant and rhizobium microsymbiont is mapped to a significant degree. A specific LysM-type receptor kinase, LjEPR3 in Lotus japonicus and MtLYK10 in Medicago truncatula, was found to act in a secondary identity-based mechanism, controlling intracellular rhizobium infection. Furthermore, LjEPR3 showed to bind surface exopolysaccharides of Mesorhizobium loti, the diazotrophic microsymbiont of L. japonicus. EPR3 orthologous genes are not unique to legumes. Surprisingly, however, its ortholog EXOPOLYSACCHARIDE RECEPTOR (EPR) is pseudogenized in Parasponia, the only lineage of non-legume plants that nodulate also with rhizobium.

RESULTS

Analysis of genome sequences showed that EPR3 orthologous genes are highly conserved in nodulating plants. We identified a conserved retrotransposon insertion in the EPR promoter region in three Parasponia species, which associates with defected transcriptional regulation of this gene. Subsequently, we studied the EPR gene of two Trema species as they represent the sister genus of Parasponia for which it is assumed it lost the nitrogen-fixing nodulation trait. Both Trema species possess apparently functional EPR genes that have a nodulation-specific expression profile when introduced into a Parasponia background. This indicates the EPR gene functioned in nodulation in the Parasponia-Trema ancestor.

CONCLUSION

We conclude that nodule-specific expression of EPR3 orthologous genes is shared between the legume and Parasponia-Trema lineage, suggesting an ancestral function in the nitrogen-fixing nodulation trait. Pseudogenization of EPR in Parasponia is an exceptional case in nodulating plants. We speculate that this may have been instrumental to the microsymbiont switch -from Frankia to rhizobium- that has occurred in the Parasponia lineage and the evolution of a novel crack entry infection mechanism.

Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari

Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites, and we determined a mite pathogenic virus (Betabaculovirus) that could be tested for using in biocontrol of agricultural pest mites.

Silver nanomaterials released from commercial textiles have minimal impacts on soil microbial communities at environmentally relevant concentrations

Silver nanomaterials (Ag NMs) have been used in a variety of commercial products to take advantage of their antimicrobial properties. However, there are concerns that these AgNMs can be released during/after use and enter wastewater streams, potentially impacting aquatic systems or accumulating in wastewater biosolids. Biosolids, which are a residual of wastewater treatment processes, have been found to contain AgNMs and are frequently used as agricultural fertilizer. Since the function of soil microbial communities is imperative to nutrient cycling and agricultural productivity, it is important to characterize and assess the effects that silver nanomaterials could have in agricultural soils. In this study agricultural soil was amended with pristine engineered (PVP-coated or uncoated AgNMs), aged silver (sulphidized or released from textiles) nanomaterials, and ionic silver to determine the fate and toxicity over the course of three months. Exposures were carried out at various environmentally relevant concentrations (1 and 10 mg Ag/kg soil) representing between 30 to over 800 years of equivalent biosolid loadings. Over thirteen different methodologies and measures were used throughout this study to assess for potential effects of the silver nanomaterials on soil, including microbial community composition, average well colour development (AWCD) and enzymatic activity. Overall, the AgNM exposures did not exhibit significant toxic effects to the soil microbial communities in terms of density, activity, function and diversity. However, the positive ionic silver treatment (100 mg Ag/kg soil) resulted in suppression to microbial activity while also resulting in significantly higher populations of Frankia alni (nitrogen-fixer) and Arenimonas malthae (phytopathogen) as compared to the negative control (p < 0.05, Tukey HSD) which warrants further investigation.

Optimization of Tissue Culturing and Genetic Transformation Protocol for Casuarina equisetifolia

Casuarina equisetifolia is widely used in agroforestry plantations for soil stabilization, ecosystem rehabilitation, reclamation, and coastal protection. Moreover, C. equisetifolia has remarkable resistance to typhoons, desert, low soil fertility, drought, and salinity, but not cold. Therefore, it is significant to breed high-quality Casuarina varieties to improve the tolerance and adaptability to cold weather by molecular techniques. The establishment of a rapid and efficient callus induction and regeneration system via tissue culture is pre-requisite for the genetic transformation of C. equisetifolia, which is so far lacking. In this study, we reported an efficient and rapid regeneration system using stem segment explants, in which callus induction was found to be optimal in a basal medium supplemented with 0.1 mg⋅L^-1 TDZ and 0.1 mg⋅L^-1 NAA, and proliferation in a basal medium containing 0.1 mg⋅L^-1 TDZ and 0.5 mg⋅L^-1 6-BA. For bud regeneration and rooting, the preferred plant growth regulator (PGR) in basal medium was 0.5 mg⋅L^-1 6-BA, and a combination of 0.02 mg⋅L^-1 IBA and 0.4 mg⋅L^-1 IAA, respectively. We also optimized genetic a transformation protocol using Agrobacterium tumefaciens harboring the binary vector pCAMBIA1301 with β-glucuronidase (GUS) as a reporter gene. Consequently, 5 mg L^-1 hygromycin, 20 mg L^-1 acetosyringone (As), and 2 days of co-cultivation duration were optimized to improve the transformation efficiency. With these optimized parameters, transgenic plants were obtained in about 4 months. Besides that, Agrobacterium rhizogenes-mediated transformation involving adventitious root induction was also optimized. Our findings will not only increase the transformation efficiency but also shorten the time for developing transgenic C. equisetifolia plants. Taken together, this pioneer study on tissue culturing and genetic transformation of C. equisetifolia will pave the way for further genetic manipulation and functional genomics of C. equisetifolia.

Worker-dependent gut symbiosis in an ant

The hallmark of eusocial insects, honeybees, ants, and termites, is division of labor between reproductive and non-reproductive worker castes. In addition, environmental adaption and ecological dominance are also underpinned by symbiotic associations with beneficial microorganisms. Microbial symbionts are generally considered to be maintained in an insect colony in two alternative ways: shared among all colony members or inherited only by a specific caste. Especially in ants, the reproductive caste plays a crucial role in transmission of the symbionts shared among colony members over generations. Here, we report an exceptional case, the worker-dependent microbiota in an ant, Diacamma cf. indicum from Japan. By collecting almost all the individuals from 22 colonies in the field, we revealed that microbiota of workers is characterized by a single dominant bacterium localized at the hindgut. The bacterium belonging to an unclassified member within the phylum Firmicutes, which is scarce or mostly absent in the reproductive castes. Furthermore, we show that the gut symbiont is acquired at the adult stage. Collectively, our findings strongly suggest that the specific symbiont is maintained by only workers, demonstrating a novel pattern of ant-associated bacterial symbiosis, and thus further our understanding of host-microbe interactions in the light of sociobiology.

Draft genomes of non-nitrogen-fixing Frankia strains

In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa, genospecies CN and Ag, respectively. Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.

Frankobactin Metallophores Produced by Nitrogen-Fixing Frankia Actinobacteria Function in Toxic Metal Sequestration

A series of new metallophores, referred to as frankobactins, were extracted from cultures of the symbiotic and nitrogen-fixing actinobacterium Frankia sp. CH37. Structure elucidation revealed a 2-hydroxyphenyl-substituted oxazoline core and a chain composed of five proteinogenic and nonproteinogenic amino acids, suggesting nonribosomal peptide synthesis as the biosynthetic origin. By whole-genome sequencing, bioinformatic analysis, and comparison with other Frankia strains, the genetic locus responsible for the biosynthesis was detected. Spectrophotometric titration of frankobactin with Fe(III) and Cu(II) and mass spectrometry established the 1:1 (metal:frankobactin) coordination. Uptake experiments suggested that frankobactin A₁ (1) did not serve to recruit iron, but to detoxify Cu(II). As frankobactin A₁ prevents the cellular entry of Cu(II), it could play a crucial role in the symbiosis of Frankia sp. and its host in the reclamation of copper-contaminated soil.

Genome Sequence of Frankia sp. Strain CH37, a Metallophore-Producing, Nitrogen-Fixing Actinobacterium Isolated from the Sea Buckthorn, Hippophae rhamnoides (Elaeagnaceae)

We report the genome sequence of Frankia sp. strain CH37, a filamentous nitrogen-fixing soil-dwelling Gram-positive bacterium and hyper-producer of metal-complexing organic ligands (metallophores) isolated from the sea buckthorn (Hippophae rhamnoides). The 9.7-Mbp sequence, obtained using PacBio technology, harbors 7,766 predicted coding sequences, including gene clusters for metallophore production.

We report the genome sequence of Frankia sp. strain CH37, a filamentous nitrogen-fixing soil-dwelling Gram-positive bacterium and hyperproducer of metal-complexing organic ligands (metallophores) isolated from the sea buckthorn (Hippophae rhamnoides). The 9.7-Mbp sequence, obtained using PacBio technology, harbors 7,766 predicted coding sequences, including gene clusters for metallophore production.

Draft Genome Sequences for the Frankia sp. strains CgS1, CcI156 and CgMI4, Nitrogen-Fixing Bacteria Isolated from Casuarina sp. in Egypt

Frankia sp. strains CgS1, CcI156 and CgMI4 were isolated from Casuarina glauca and C. cunninghamiana nodules. Here, we report the 5.26-, 5.33- and 5.20-Mbp draft genome sequences of Frankia sp. strains CgS1, CcI156 and CgMI4, respectively. Analysis of the genome revealed the presence of high numbers of secondary metabolic biosynthetic gene clusters.

Genome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest Soil

Frankiaceae are bacterial endosymbionts that are also found free-living in soil. Here, we present the genome sequences of two novel bacterial members of the order Frankiales, class Actinobacteria, isolated from temperate terrestrial forest soils. The genomes for MT45 and GAS493 indicate a genetic capacity for carbohydrate degradation but not nitrogen fixation.

Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China

Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.

Draft Genome Sequences of 10 Bacterial Strains Isolated from Root Nodules of Alnus Trees in New Hampshire

Here, we report the draft genome sequences obtained for 10 bacterial strains isolated from root nodules of Alnus trees. These members of the nodule microbiome were sequenced to determine their potential functional roles in plant health. The selected strains belong to the genera Rhodococcus, Kocuria, Rothia, Herbaspirillum, Streptomyces, and Thiopseudomonas.

Characterization of Vesicle Differentiation Mutants of Frankia casuarinae

The nitrogen-fixing actinobacterium Frankia develops unique multicellular structures called vesicles, which are the site of nitrogen fixation. These vesicles are surrounded by a thick hopanoid lipid envelope that protects nitrogenase against oxygen inactivation. The phenotypes of five mutants that form smaller numbers of vesicles were investigated. The vesicles of these mutants were smaller than those of the wild type and had a phase dark appearance. They induced the expression of a glutamine synthetase gene in hyphae cells in response to ammonium starvation. These results suggest that genes impaired in the mutants do not function in global nitrogen regulation, but specifically function in vesicle differentiation.

Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus

Most land plants establish mutualistic interactions with arbuscular mycorrhizal (AM) fungi. Intracellular accommodation of AM fungal symbionts remodels important host traits like root morphology and nutrient acquisition. How mycorrhizal colonization impacts plant microbiota is unclear. To understand the impact of AM symbiosis on fungal microbiota, ten Lotus japonicus mutants impaired at different stages of AM formation were grown in non-sterile natural soil and their root-associated fungal communities were studied. Plant mutants lacking the capacity to form mature arbuscules (arb^- ) exhibited limited growth performance associated with altered phosphorus (P) acquisition and reduction-oxidation (redox) processes. Furthermore, arb^- plants assembled moderately but consistently different root-associated fungal microbiota, characterized by the depletion of Glomeromycota and the concomitant enrichment of Ascomycota, including Dactylonectria torresensis. Single and co-inoculation experiments showed a strong reduction of root colonization by D. torresensis in the presence of AM fungus Rhizophagus irregularis, particularly in arbuscule-forming plants. Our results suggest that impairment of central symbiotic functions in AM host plants leads to specific changes in root microbiomes and in tripartite interactions between the host plant, AM and non-AM fungi. This lays the foundation for mechanistic studies on microbe-microbe and microbe-host interactions in AM symbiosis of the model L. japonicus.

A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a

Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.

Actinobacteria from Extreme Niches in Morocco and Their Plant Growth-Promoting Potentials

The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from the desert, and from a marine environment. In total, 23 actinobacteria were isolated, 8 from Merzouga sand soil; 5 from Cannabis sativa rhizospheric soil; 5 from Toubkal mountain; 4 from a Draa sfar mining site; and 1 from marine soil. Based on their genotypic classification using 16S rRNA gene sequences, 19 of all belonged to the genus Streptomyces (82%) while the rest are the members of the genera Nocardioides (4.5%), Saccharomonospora (4.5%), Actinomadura (4.5%), and Prauserella (4.5%). Isolates Streptomyces sp. TNC-1 and Streptomyces sp. MNC-1 showed the highest level of phosphorus solubilization activity with 12.39 and 8.56 mg/mL, respectively. All 23 isolates were able to solubilize potassium, and 91% of them could grow under nitrogen-free conditions. The ability of the isolated actinobacteria to form indole-3-acetic acid (IAA) ranged from 6.70 to 75.54 μg/mL with Streptomyces sp. MNC-1 being the best IAA producer. In addition, all of the actinobacteria could produce siderophores, with Saccharomonospora sp. LNS-1 synthesizing the greatest amount (138.92 μg/mL). Principal coordinate analysis revealed that Streptomyces spp. MNC-1, MNT-1, MNB-2, and KNC-5; Saccharomonospora sp. LNS-1; and Nocardioides sp. KNC-3 each showed a variety of high-level plant growth-promoting activities. The extreme environments in Morocco are rich with bioactive actinobacteria that possess a variety of plant growth-promoting potentials that can further benefit green and sustainable agriculture.

Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.

Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.)

Frankia bacteria are nitrogen fixing species from the Actinobacterium phylum which live on the root nodules of plants. They have been hypothesised to have significant potential for natural product biosynthesis. The cytochrome P450 monooxygenase complement of Frankia sp. EuI1c (Frankia inefficax sp.), which comprises 68 members, was analysed. Several members belonged to previously uncharacterised bacterial P450 families. There was an unusually high number of CYP189 family members (21) suggesting that this family has undergone gene duplication events which are classified as "blooms". The likely electron transfer partners for the P450 enzymes were also identified and analysed. These consisted of predominantly [3Fe-4S] cluster containing ferredoxins (eight), a single [2Fe-2S] ferredoxin and a couple of ferredoxin reductases. Three of these CYP family members were produced and purified, using Escherichia coli as a host, and their substrate range was characterised. CYP1027H1 and CYP150A20 bound a broad range of norisoprenoids and terpenoids. CYP1074A2 was highly specific for certain steroids including testosterone, progesterone, stanolone and 4-androstene-3,17-dione. It is likely that steroids are the physiological substrates of CYP1074A2. These results also give an indication that terpenoids are the likely substrates of CYP1027H1 and CYP150A2. The large number of P450s belonging to distinct families as well as the associated electron transfer partners found in different Frankia strains highlights the importance of this family of enzymes has in the secondary metabolism of these bacteria.

Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for systematics and, due to the boom in complete genome sequencing, their use has become widespread. Yet, in the case of uncultured strains, for which complete genome sequences cannot be easily obtained, sequencing many markers is complicated and time consuming. Taking the advantage of the organization of ribosomal protein coding genes in large gene clusters, we amplified a 32 kb conserved region encompassing the spectinomycin (spc) operon using long range PCR from isolated and from uncultured nodular endophytic Frankia strains. The phylogenetic analysis of the 27 ribosomal protein genes contained in this region provided a robust phylogenetic tree consistent with phylogenies based on larger set of markers, indicating that this subset of ribosomal proteins contains enough phylogenetic signal to address systematic issues. This work shows that using long range PCR could break down the barrier preventing the use of ribosomal proteins as phylogenetic markers when complete genome sequences cannot be easily obtained.

Metagenomic insights into diazotrophic communities across Arctic glacier forefields

Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.

Metallophore profiling of nitrogen-fixingFrankiaspp. to understand metal management in the rhizosphere of actinorhizal plants

Frankiaspp. are widespread nitrogen-fixing and metallophore releasing soil bacteria, which often live in symbiosis with a broad spectrum of hosts.

Retrotransposons in Betula nana, and interspecific relationships in the Betuloideae, based on inter-retrotransposon amplified polymorphism (IRAP) markers

The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical features and nucleotide similarities between left and right LTR sequences. Of the five retroelements, three elements were found to be Ty1/Copia retrotransposons; identity of the other two elements could not be ascertained due to sequence undetermined 'N' bases in the sequence database. Inter-retrotranposon amplified polymorphism (IRAP) analysis, based on the LTR sequences of the mined LTR-retrotransposons, produced 179 discernible IRAP bands among the Alnus and Betula genera. Sequence analysis revealed no size homoplasy among the homologous IRAP bands. Phylogenetic and principle coordinate analysis, based on the band sharing among the taxa, showed the species in two different genera were clearly separated. The subgenera in each genus of Alnus and Betula were also distinguishable from the IRAP profiles. In the genus Betula, the species in subgenus Betula showed mixed clustering between species. This is incongruent with the phylogeographical distribution of the species.

Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes

There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta, and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens.

The PEG-responding desiccome of the alder microsymbiont Frankia alni

Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.

Short-duration hydrothermal fermentation of food waste: preparation of soil conditioner for amending organic-matter-impoverished arable soils

Soil conditioners can be used to compensate for the insufficient soil nutrition and organic matter (OM) of arable soils. However, the traditional preparation method for soil conditioners is lengthy and requires facilities that occupy large tracts of land. In this study, a short-duration hydrothermal fermentation (SHF) method was developed for the preparation of soil conditioners from food waste. The SHF method required only 18 h to produce soil conditioners with physicochemical characteristics that were similar to those of soil conditioners obtained through traditional fermentation (TF), which takes 20 days to complete. Inoculation and dynamic SHF significantly affected the distribution of different molecular weight fractions in the prepared soil conditioners. The results of spectral analysis revealed that a large amount of soluble microbial byproducts and carbohydrate C formed in the SHF soil conditioner. This effect indicated that the SHF soil conditioner supplied not only immediately available nutrients, which can stimulate the growth of soil microbial communities, but also provided sustained-release nutrients for the long-term cultivation of crops on OM-impoverished soils. Cyanobacteria were present in the SHF soil conditioner at a relative abundance of 6.29%, which was 28.6 and 314.5 times those in the raw material and TF soil conditioner, respectively. Amending OM-impoverished soil with the SHF soil conditioner enhanced the carbon pool management index of the resulting SHF soil by 1.50 and 1.12 times those of unfertilized soil and TF soil, respectively. These results indicated that the SHF soil exhibited a high capacity to supply nutrients for crop growth.

Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes

Grain legumes are a cost-effective alternative for the animal protein in improving the diets of the poor in South-East Asia and Africa. Legumes, through symbiotic nitrogen fixation, meet a major part of their own N demand and partially benefit the following crops of the system by enriching soil. In realization of this sustainability advantage and to promote pulse production, United Nations had declared 2016 as the "International Year of pulses". Grain legumes are frequently subjected to both abiotic and biotic stresses resulting in severe yield losses. Global yields of legumes have been stagnant for the past five decades in spite of adopting various conventional and molecular breeding approaches. Furthermore, the increasing costs and negative effects of pesticides and fertilizers for crop production necessitate the use of biological options of crop production and protection. The use of plant growth-promoting (PGP) bacteria for improving soil and plant health has become one of the attractive strategies for developing sustainable agricultural systems due to their eco-friendliness, low production cost and minimizing consumption of non-renewable resources. This review emphasizes on how the PGP actinobacteria and their metabolites can be used effectively in enhancing the yield and controlling the pests and pathogens of grain legumes.

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.