Igneous phosphate rock solubilization by biofilm-forming mycorrhizobacteria and hyphobacteria associated with Rhizoglomus irregulare DAOM 197198

Mixed Consortium of Salt-Tolerant Phosphate Solubilizing Bacteria Improves Maize (Zea mays) Plant Growth and Soil Health Under Saline Conditions

The rhizobacterial isolate SP-167 exhibited considerable phosphate solubilization, IAA production, exo-polysaccharides, proline, APX, and CAT at a concentration of 6% NaCl (w/v). 16S rDNA sequencing and BLAST analysis showed that isolate SP-167 was Klebsiella sp. In this study, T2 and T8 consortium was developed on the basis of the compatibility of isolate SP-167 with Kluyvera sp. and Enterobacter sp. At 6% NaCl (w/v) concentration, T2 and T8 showed increased PGP properties such as phosphate solubilization, IAA, Proline activity, CAT, POD, and EPS than isolate SP-167. The maximum increase in shoot length was recorded in T2-treated maize plants as compared to the control after 60 days in 1% NaCl stress. The N, P, and K content of leaves were significantly increased in maize plants with the inoculation of both the T2 and T8 consortium. The electrical conductivity of soil was decreased significantly in the T2 inoculated 1% NaCl (w/v) treated pot after 30, 60, and 90 days. In this study, soil enzymes DHA and PPO were significantly increased in both T2 and T8 treated combinations. The Na concentration in root and shoot were significantly decreased in T8 inoculated plant than in T2, as confirmed by the translocation factor study.

Exopolysaccharides from agriculturally important microorganisms: Conferring soil nutrient status and plant health

A wide variety of microorganisms secretes extracellular polymeric substances or commonly known as exopolysaccharides (EPS), which have been studied to influence plant growth via various mechanisms. EPS-producing microorganisms have been found to have positive effects on plant health such as by facilitating nutrient entrapment in the soil, or by improving soil quality, especially by helping in mitigating various abiotic stress conditions. The various types of microbial polysaccharides allow for the compartmentalization of the microbial community enabling them to endure undressing stress conditions. With the growing population, there is a constant need for developing sustainable agriculture where we could use various PGPR to help the plant cope with various stress conditions and simultaneously enhance the crop yield. These polysaccharides have also found application in various sectors, especially in the biomedical fields, manifesting their potential to act as antitumor drugs, play a significant role in immune evasion, and reveal various therapeutic potentials. These constitute high levels of bioactive polysaccharides which possess a wide range of implementation starting from industrial applications to novel food applications. In this current review, we aim at presenting a comprehensive study of how these microbial extracellular polymeric substances influence agricultural productivity along with their other commercial applications.

Cultural techniques capture diverse phosphate-solubilizing bacteria in rock phosphate-enriched habitats

Phosphorus (P) deficiency is a common problem in croplands where phosphate-based fertilizers are regularly used to maintain bioavailable P for plants. However, due to their limited mobility in the soil, there has been an increased interest in microorganisms that can convert insoluble P into a bioavailable form, and their use to develop phosphate-solubilizing bioinoculants as an alternative to the conventional use of P fertilizers. In this study, we proposed two independent experiments and explored two entirely different habitats to trap phosphate-solubilizing bacteria (PSBs). In the first experiment, PSBs were isolated from the rhizoplane of native plant species grown in a rock-phosphate (RP) mining area. A subset of 24 bacterial isolates from 210 rhizoplane morphotypes was selected for the inorganic phosphate solubilizing activities using tricalcium phosphate (TCP) as the sole P source. In the second experiment, we proposed an innovative experimental setup to select mycohyphospheric bacteria associated to arbuscular mycorrhizal fungal hyphae, indigenous of soils where agronomic plant have been grown and trapped in membrane bag filled with RP. A subset of 25 bacterial isolates from 44 mycohyphospheric morphotypes was tested for P solubilizing activities. These two bacterial subsets were then screened for additional plant growth-promoting (PGP) traits, and 16S rDNA sequencing was performed for their identification. Overall, the two isolation experiments resulted in diverse phylogenetic affiliations of the PSB collection, showing only 4 genera (24%) and 5 species (17%) shared between the two communities, thus underlining the value of the two protocols, including the innovative mycohyphospheric isolate selection method, for selecting a greater biodiversity of cultivable PSB. All the rhizoplane and mycohyphospheric PSB were positive for ammonia production. Indol-3-acetic acid (IAA) production was observed for 13 and 20 isolates, respectively among rhizoplane and mycohyphospheric PSB, ranging, respectively, from 32.52 to 330.27 μg mL-1 and from 41.4 to 963.9 μg mL-1. Only five rhizoplane and 12 mycohyphospheric isolates were positively screened for N2 fixation. Four rhizoplane PSB were identified as siderophore producers, while none of the mycohyphospheric isolates were. The phenotype of one PSB rhizoplane isolate, assigned to Pseudomonas, showed four additive PGP activities. Some bacterial strains belonging to the dominant genera Bacillus and Pseudomonas could be considered potential candidates for further formulation of biofertilizer in order to develop bioinoculant consortia that promote plant P nutrition and growth in RP-enriched soils.

Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress

Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.

Disentangling arbuscular mycorrhizal fungi and bacteria at the soil-root interface

Arbuscular mycorrhizal fungi (AMF) are essential components of the plant root mycobiome and are found in approximately 80% of land plants. As obligate plant symbionts, AMF harbor their own microbiota, both inside and outside the plant root system. AMF-associated bacteria (AAB) possess various functional traits, including nitrogen fixation, organic and inorganic phosphate mobilization, growth hormone production, biofilm production, enzymatic capabilities, and biocontrol against pathogen attacks, which not only contribute to the health of the arbuscular mycorrhizal symbiosis but also promote plant growth. Because of this, there is increasing interest in the diversity, functioning, and mechanisms that underlie the complex interactions between AMF, AAB, and plant hosts. This review critically examines AMF-associated bacteria, focusing on AAB diversity, the factors driving richness and community composition of these bacteria across various ecosystems, along with the physical, chemical, and biological connections that enable AMF to select and recruit beneficial bacterial symbionts on and within their structures and hyphospheres. Additionally, potential applications of these bacteria in agriculture are discussed, emphasizing the potential importance of AMF fungal highways in engineering plant rhizosphere and endophyte bacteria communities, and the importance of a functional core of AAB taxa as a promising tool to improve plant and soil productivity. Thus, AMF and their highly diverse bacterial taxa represent important tools that could be efficiently explored in sustainable agriculture, carbon sequestration, and reduction of greenhouse gas emissions related to nitrogen fertilizer applications. Nevertheless, future studies adopting integrated multidisciplinary approaches are crucial to better understand AAB functional diversity and the mechanisms that govern these tripartite relationships.

Plant Growth-Promoting Bacteria (PGPB) with Biofilm-Forming Ability: A Multifaceted Agent for Sustainable Agriculture

Plant growth-promoting bacteria (PGPB) enhance plant growth, as well as protect plants from several biotic and abiotic stresses through a variety of mechanisms. Therefore, the exploitation of PGPB in agriculture is feasible as it offers sustainable and eco-friendly approaches to maintaining soil health while increasing crop productivity. The vital key of PGPB application in agriculture is its effectiveness in colonizing plant roots and the phyllosphere, and in developing a protective umbrella through the formation of microcolonies and biofilms. Biofilms offer several benefits to PGPB, such as enhancing resistance to adverse environmental conditions, protecting against pathogens, improving the acquisition of nutrients released in the plant environment, and facilitating beneficial bacteria–plant interactions. Therefore, bacterial biofilms can successfully compete with other microorganisms found on plant surfaces. In addition, plant-associated PGPB biofilms are capable of protecting colonization sites, cycling nutrients, enhancing pathogen defenses, and increasing tolerance to abiotic stresses, thereby increasing agricultural productivity and crop yields. This review highlights the role of biofilms in bacterial colonization of plant surfaces and the strategies used by biofilm-forming PGPB. Moreover, the factors influencing PGPB biofilm formation at plant root and shoot interfaces are critically discussed. This will pave the role of PGPB biofilms in developing bacterial formulations and addressing the challenges related to their efficacy and competence in agriculture for sustainability.

Nitrogen-fixing, phosphate-potassium-mobilizing ability of Rahnella bacteria isolated from wheat roots

As the number of people on earth increases, so does the need for food. Providing the population with environmentally friendly agricultural food is one of the urgent problems of our time. Currently, the main direction of modern organic farming is the use of biofertilizers. Bacterial preparations are capable of influencing the physiological processes of plants in small quantities, leading to increase in plant productivity. The objective of this work was to study rhizobacteria associated with wheat roots. For this purpose, we took more than 100 isolates of rhizobacteria from the rhizosphere and root surface of wheat plants grown in irrigated fields of Tashkent, Syrdarya, Andijan, Kashkadarya regions. Rhizobacteria were grown on nutrient media of Döbereiner, Ashby, Pikovsky, and Zack, and 25 isolates of associative rhizobacteria were selected based on the characteristics of absorption of molecular nitrogen, mobilization of phosphorus and potassium. They actively dissolved Сa3(PO4)2 and KAlSiO4 for 3 days. They were found to produce organic acids. In organic farming, nitrogen-fixing, phosphorus- and potassium-mobilizing rhizobacteria are of great practical importance, while our experiments on obtaining biological products are considered as an environmentally friendly and cost-effective way to increase crop yields. From the surface of wheat roots grown in different zones of Uzbekistan, when screening for nitrogen fixation, we selected 3 isolates with acetylene reductase activity of 79–91 nmol C2H4/flacon/24h. We determined that bacteria completely mobilized phosphate, forming 100% acid when grown in a medium containing Ca3(PO4)2 for 5 days. The ability of the bacteria to mobilize potassium was studied on a nutrient KAlSiO4-containing medium. The bacteria were observed to mobilize potassium, forming 90–100% acid within 15 days. Based on the study of the 16S rRNA gene of bacteria, we identified rhizobacteria UT3, UT4, and UT9 as Rahnella aquatilis.

Mycorrhizae Helper Bacteria: Unlocking Their Potential as Bioenhancers of Plant-Arbuscular Mycorrhizal Fungal Associations

The dynamic interactions of plants and arbuscular mycorrhizal fungi (AMF) that facilitate the efficient uptake of minerals from soil and provide protection from various environmental stresses (biotic and abiotic) are now also attributed to a third component of the symbiosis. These are the less investigated mycorrhizae helper bacteria (MHB), which constitute a dense, active bacterial community, tightly associated with AMF, and involved in the development and functioning of AMF. Although AMF spores are known to host several bacteria in their spore walls and cytoplasm, their role in promoting the ecological fitness and establishment of AMF symbiosis by influencing spore germination, mycelial growth, root colonization, metabolic diversity, and biocontrol of soil borne diseases is now being deciphered. MHB also promote the functioning of arbuscular mycorrhizal symbiosis by triggering various plant growth factors, leading to better availability of nutrients in the soil and uptake by plants. In order to develop strategies to promote mycorrhization by AMF, and particularly to stimulate the ability to utilize phosphorus from the soil, there is a need to decipher crucial metabolic signalling pathways of MHB and elucidate their functional significance as mycorrhiza helper bacteria. MHB, also referred to as AMF bioenhancers, also improve agronomic efficiency and formulations using AMF along with enriched population of MHB are a promising option. This review covers the aspects related to the specificity and mechanisms of action of MHB, which positively impact the formation and functioning of AMF in mycorrhizal symbiosis, and the need to advocate MHB as AMF bioenhancers towards their inclusion in integrated nutrient management practices in sustainable agriculture.

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.

Long-Term Persistence of Arbuscular Mycorrhizal Fungi in the Rhizosphere and Bulk Soils of Non-host Brassica napus and Their Networks of Co-occurring Microbes

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (Brassica napus), an important crop in the Canadian Prairies that is known to not form this association. From 2008 to 2018, an experiment was replicated at three locations of the Canadian Prairies and it was used to assess the impact of canola on the community of AMF naturally occurring in three cropping systems, canola monoculture, or canola in two different rotation systems (2-years, canola-wheat and 3-years, barley-pea-canola). We sampled canola rhizosphere and bulk soils to: (i) determine diversity and community structure of AMF, we expected that canola will negatively impact AMF communities in function of its frequency in crop rotations and (ii) wanted to assess how these AMF communities interact with other fungi and bacteria. We detected 49 AMF amplicon sequence variants (ASVs) in canola rhizosphere and bulk soils, confirming the persistence of a diversified AMF community in canola-planted soil, even after 10 years of canola monoculture, which was unexpected considering that canola is among non-mycorrhizal plants. Network analysis revealed a broad range of potential interactions between canola-associated AMF and some fungal and bacterial taxa. We report for the first time that two AMF, Funneliformis mosseae and Rhizophagus iranicus, shared their bacterial cohort almost entirely in bulk soil. Our results suggest the existence of non-species-specific AMF-bacteria or AMF-fungi relationships that could benefit AMF in absence of host plants. The persistence of an AMF community in canola rhizosphere and bulk soils brings a new light on AMF ecology and leads to new perspectives for further studies about AMF and soil microbes interactions and AMF subsistence without mycotrophic host plants.

Interaction Between Halotolerant Phosphate-Solubilizing Bacteria (Providencia rettgeri Strain TPM23) and Rock Phosphate Improves Soil Biochemical Properties and Peanut Growth in Saline Soil

Soil salinity has adverse effects on soil microbial activity and nutrient cycles and therefore limits crop growth and yield. Amendments with halotolerant phosphate-solubilizing bacteria (PSB) and rock phosphate (RP) may improve properties of saline soil. In this study, we investigated the effects of RP either alone or in combination with PSB (Providencia rettgeri strain TPM23) on peanut growth and soil quality in a saline soil. With the combined application of RP and PSB, plant length and biomass (roots and shoots) and uptake of phosphorus (P), nitrogen (N), and potassium (K) increased significantly. Soil Na+ and Cl- contents decreased in the PR alone or PR combined with PSB treatment groups. There were strongly synergistic effects of RP and PSB on soil quality, including a decrease in pH. The soil available N, P, and K contents were significantly affected by the PSB treatments. In addition, the alkaline phosphomonoesterases, urease, and dehydrogenase activities increased significantly compared with the untreated group; highest alkaline phosphomonoesterases activity was observed in the RP and PSB treatment groups. The composition of rhizosphere soil bacterial communities was determined using 454-pyrosequencing of the 16S rRNA gene. In the PR alone or PR combined with PSB treatment groups, the structure of the soil bacterial community improved with increasing richness and diversity. With PSB inoculation, the relative abundance of Acidobacteria, Chloroflexi, and Planctomycetes increased. The three phyla were also positively correlated with soil available N and root dry weight. These results suggested microbiological mechanisms by which the combined use of RP and PSB improved saline soil and promoted plant growth. Overall, the study indicates the combined use of RP and PSB can be an economical and sustainable strategy to increase plant growth in P-deficient and salt-affected soils.

Diversity and Functionalities of Unknown Mycorrhizal Fungal Microbiota

Beneficial ecosystem services provided by arbuscular mycorrhizal fungi (AMF) are the outcome of their synergistic actions with diverse bacterial communities (AMF-associated bacteria; AAB) living in strict association with AMF hyphae and spores. Herein, bacterial diversity associated with 6 AMF species from 33 different co-cultures belonging to order Glomerales and Diversisporales were identified, using a combination of culture-dependent functional analyses and amplicon sequencing. Overall, 231 bacterial strains were isolated from the AMF spores and hyphae which covered 30 bacterial genera and 52 species. Hierarchical clustering based on plant growth promoting traits identified 9 clades comprising diverse bacterial genera with clades 7, 8 and 9 representing the most functionally rich AAB. High-throughput amplicon sequencing across a small subset of 8 AMF co-cultures spread across 3 AMF genera identified Operational Taxonomic Units belonging to 118 bacterial genera. The study revealed a greater diversity of AAB from spores of in vitro transformed AMF root co-cultures rather than in situ, pot AMF cultures. Functionally active, culturable AABs with multiple plant growth promoting traits such as phosphate solubilisation, nitrogen fixation, biofilm formation, enzyme and plant growth regulator production along with biocontrol activity were identified. These properties could be utilized individually and/or as consortia with AMF, as biological growth enhancers.

It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator

Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.

Production of Organic Acids by Arbuscular Mycorrhizal Fungi and Their Contribution in the Mobilization of Phosphorus Bound to Iron Oxides

Most plants living in tropical acid soils depend on the arbuscular mycorrhizal (AM) symbiosis for mobilizing low-accessible phosphorus (P), due to its strong bonding by iron (Fe) oxides. The roots release low-molecular-weight organic acids (LMWOAs) as a mechanism to increase soil P availability by ligand exchange or dissolution. However, little is known on the LMWOA production by AM fungi (AMF), since most studies conducted on AM plants do not discriminate on the LMWOA origin. This study aimed to determine whether AMF release significant amounts of LMWOAs to liberate P bound to Fe oxides, which is otherwise unavailable for the plant. Solanum lycopersicum L. plants mycorrhized with Rhizophagus irregularis were placed in a bicompartmental mesocosm, with P sources only accessible by AMF. Fingerprinting of LMWOAs in compartments containing free and goethite-bound orthophosphate (OP or GOE-OP) and phytic acid (PA or GOE-PA) was done. To assess P mobilization via AM symbiosis, P content, photosynthesis, and the degree of mycorrhization were determined in the plant; whereas, AM hyphae abundance was determined using lipid biomarkers. The results showing a higher shoot P content, along with a lower N:P ratio and a higher photosynthetic capacity, may be indicative of a higher photosynthetic P-use efficiency, when AM plants mobilized P from less-accessible sources. The presence of mono-, di-, and tricarboxylic LMWOAs in compartments containing OP or GOE-OP and phytic acid (PA or GOE-PA) points toward the occurrence of reductive dissolution and ligand exchange/dissolution reactions. Furthermore, hyphae grown in goethite loaded with OP and PA exhibited an increased content of unsaturated lipids, pointing to an increased membrane fluidity in order to maintain optimal hyphal functionality and facilitate the incorporation of P. Our results underpin the centrality of AM symbiosis in soil biogeochemical processes, by highlighting the ability of the AMF and accompanying microbiota in releasing significant amounts of LMWOAs to mobilize P bound to Fe oxides.

Plant-associated fungal biofilms-knowns and unknowns

Nearly all microbes, including fungi, grow firmly attached to surfaces as a biofilm. Yet, attention toward fungal interactions with plants and the environment is dedicated to free-floating (planktonic) cells. Fungal biofilms are generally thought to configure interactions across and among plant populations. Despite this, plant fungal biofilm research lags far behind the research on biofilms of medically important fungi. The deficit in noticing and exploring this research avenue could limit disease management and plant improvement programs. Here, we provide the current state of knowledge of fungal biofilms and the different pivotal ecological roles they impart in the context of disease, through leveraging evidence across medically important fungi, secondary metabolite production, plant beneficial functions and climate change. We also provide views on several important information gaps potentially hampering plant fungal biofilm research, and propose a way forward to address these gaps.

Short Rotation Intensive Culture of Willow, Spent Mushroom Substrate and Ramial Chipped Wood for Bioremediation of a Contaminated Site Used for Land Farming Activities of a Former Petrochemical Plant

The aim of this study was to investigate the bioremediation impacts of willows grown in short rotation intensive culture (SRIC) and supplemented or not with spent mushroom substrate (SMS) and ramial chipped wood (RCW). Results did not show that SMS significantly improved either biomass production or phytoremediation efficiency. After the three growing seasons, RCW-amended S. miyabeana accumulated significantly more Zn in the shoots, and greater increases of some PAHs were found in the soil of RCW-amended plots than in the soil of the two other ground cover treatments' plots. Significantly higher Cd concentrations were found in the shoots of cultivar 'SX61'. The results suggest that 'SX61' have reduced the natural attenuation of C10-C50 that occurred in the unvegetated control plots. The presence of willows also tended to increase the total soil concentrations of PCBs. Furthermore, we found that many contaminant concentrations were subject to seasonal oscillations, showing average increases throughout the whole experimental site after a growing period, while showing significantly different variations, such as lesser increases or even decreases, after a dormant period. These observations suggest that contaminants may have leached or degraded faster in untreated conditions, and conversely to have mobilized towards trees through water flow driven by plant transpiration during growing seasons.

Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies

Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.

Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome

Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.

Microbial biofilms in nature: unlocking their potential for agricultural applications

Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.

Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions

The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.

Arbuscular Mycorrhizal Fungal Communities of Native Plant Species under High Petroleum Hydrocarbon Contamination Highlights Rhizophagus as a Key Tolerant Genus

Arbuscular mycorrhizal fungi (AMF) have been shown to play an important role in increasing plant fitness in harsh conditions. Therefore, AMF are currently considered to be effective partners in phytoremediation. However, AMF communities in high levels of petroleum pollution are still poorly studied. We investigated the community structures of AMF in roots and rhizospheric soils of two plant species, Eleocharis elliptica and Populus tremuloides, growing spontaneously in high petroleum-contaminated sedimentation basins of a former petrochemical plant (91,000 μg/Kg of C10–C50 was recorded in a basin which is 26-fold higher than the threshold of polluted soil in Quebec, Canada). We used a PCR cloning, and sequencing approach, targeting the 18S rRNA gene to identify AMF taxa. The high concentration of petroleum-contamination largely influenced the AMF diversity, which resulted in less than five AMF operational taxonomical units (OTUs) per individual plant at all sites. The OTUs detected belong mainly to the Glomerales, with some from the Diversisporales and Paraglomerales, which were previously reported in high concentrations of metal contamination. Interestingly, we found a strong phylogenetic signal in OTU associations with host plant species identity, biotopes (roots or soils), and contamination concentrations (lowest, intermediate and highest). The genus Rhizophagus was the most dominant taxon representing 74.4% of all sequences analyzed in this study and showed clear association with the highest contamination level. The clear association of Rhizophagus with high contamination levels suggests the importance of the genus for the use of AMF in bioremediation, as well as for the survey of key AMF genes related to petroleum hydrocarbon resistance. By favoring plant fitness and mediating its soil microbial interactions, Rhizophagus spp. could enhance petroleum hydrocarbon pollutant degradation by both plants and their microbiota in contaminated sites.

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments

Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

Growth-promoting bacteria and arbuscular mycorrhizal fungi differentially benefit tomato and corn depending upon the supplied form of phosphorus

The ability of plants to take up phosphorus (P) from soil depends on root morphology and root exudates release and can be modulated by beneficial soil microbes. These microbes can solubilize P, affect root elongation and branching, and lead to a higher uptake of P and other nutrients. However, coordination of these mechanisms is unclear, especially the mechanism for changing the available form of P. We aimed to dissect the effects of two different beneficial microbial taxa (plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF)) on root morphological traits, plant nutrient content, and growth in tomato and corn fertilized with either Gafsa rock phosphate (RP) or triple superphosphate (TSP), which have contrasting solubility levels. Tomato and corn were grown in pots and inoculated with one of three PGPB species or a mix of two AMF species or were not inoculated. Root traits, botanical fractions, and the contents of various mineral nutrients were measured. TSP stimulated tomato biomass accumulation compared to RP but did not stimulate corn biomass accumulation. PGPB improved the growth of both plant species under RP, with limited differences among the strains, whereas AMF only improved tomato growth under TSP. These differences between microbial systems were explained by a bacterial effect on the total root length but not on the mean root diameter and by the ability of AMF to improve the mineral nutrient content. The effects of PGPB were less dependent on the plant species and on P form than the effects of AMF.These results have implications for the improvement of the early plant growth through the management of beneficial microbes.

Soil Microbial Resources for Improving Fertilizers Efficiency in an Integrated Plant Nutrient Management System

Tomorrow's agriculture, challenged by increasing global demand for food, scarcity of arable lands, and resources alongside multiple environment pressures, needs to be managed smartly through sustainable and eco-efficient approaches. Modern agriculture has to be more productive, sustainable, and environmentally friendly. While macronutrients such as nitrogen (N), phosphorus (P), potassium (K), and sulfur (S) supplied by mineral fertilizers are vital to crop production, agriculturally beneficial microorganisms may also contribute directly (i.e., biological N2 fixation, P solubilization, and phytohormone production, etc.) or indirectly (i.e., antimicrobial compounds biosynthesis and elicitation of induced systemic resistance, etc.) to crop improvement and fertilizers efficiency. Microbial-based bioformulations that increase plant performance are greatly needed, and in particular bioformulations that exhibit complementary and synergistic effects with mineral fertilization. Such an integrated soil fertility management strategy has been demonstrated through several controlled and non-controlled experiments, but more efforts have to be made in order to thoroughly understand the multiple functions of beneficial microorganisms within the soil microbial community itself and in interaction with plants and mineral resources. In fact, the combined usage of microbial [i.e., beneficial microorganisms: N2-fixing (NF), P-solubilizing, and P mobilizing, etc.] and mineral resources is an emerging research area that aims to design and develop efficient microbial formulations which are highly compatible with mineral inputs, with positive impacts on both crops and environment. This novel approach is likely to be of a global interest, especially in most N- and P-deficient agro-ecosystems. In this review, we report on the importance of NF bacteria and P solubilizing/mobilizing microbes as well as their interactions with mineral P fertilization in improving crop productivity and fertilizers efficiency. In addition, we shed light on the interactive and synergistic effects that may occur within multi-trophic interactions involving those two microbial groups and positive consequences on plant mineral uptake, crop productivity, and resiliency to environmental constraints. Improving use of mineral nutrients is a must to securing higher yield and productivity in a sustainable manner, therefore continuously designing, developing and testing innovative integrated plant nutrient management systems based on relevant biological resources (crops and microorganisms) is highly required.

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

BACKGROUND

One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life.

METHODS

Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed.

RESULTS

The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation.

CONCLUSIONS

Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.

Phosphate-Solubilizing Bacteria Nullify the Antagonistic Effect of Soil Calcification on Bioavailability of Phosphorus in Alkaline Soils

Phosphate-solubilizing bacteria (PSB) reduce the negative effects of soil calcification on soil phosphorus (P) nutrition. In this incubation study, we explored the ability of PSB (control and inoculated) to release P from different P sources [single super phosphate (SSP), rock phosphate (RP), poultry manure (PM) and farm yard manure (FYM)] with various soil lime contents (4.78, 10, 15 and 20%) in alkaline soil. PSB inoculation progressively enriched Olsen extractable P from all sources compared to the control over the course of 56 days; however, this increase was greater from organic sources (PM and FYM) than from mineral P sources (SSP and RP). Lime addition to the soil decreased bioavailable P, but this effect was largely neutralized by PSB inoculation. PSB were the most viable in soil inoculated with PSB and amended with organic sources, while lime addition decreased PSB survival. Our findings imply that PSB inoculation can counteract the antagonistic effect of soil calcification on bioavailable P when it is applied using both mineral and organic sources, although organic sources support this process more efficiently than do mineral P sources. Therefore, PSB inoculation combined with organic manure application is one of the best options for improving soil P nutrition.

Plant growth-promoting activities for bacterial and fungal endophytes isolated from medicinal plant of Teucrium polium L

Bacterial and fungal endophytes are widespread inhabitants inside plant tissues and have been shown to assist plant growth and health. However, little is known about plant growth-promoting endophytes (PGPE) of medicinal plants. Therefore, the aims of this study were to identify bacterial and fungal endophytes of Teucrium polium and to characterize plant growth-promoting (PGP) properties of these endophytes. Seven bacterial endophytes were isolated and identified as Bacillus cereus and Bacillus subtilis, where five endophytic fungi were obtained and assigned to Penicillium chrysogenum and Penicillium crustosum. The isolated endophytes differentially produced indole acetic acid (IAA) and ammonia, and in addition to their enzymatic and antimicrobial activities, they exhibited variable capacity for phosphate solubilization. In order to investigate the effect of endophytes on plant growth, four representative endophytes and their consortiums were selected concerning to their potential ability to promote plant growth. The results indicated that microbial endophytes isolated from medicinal plants possessing a vital role to improve plant growth and could be used as inoculants to establish a sustainable crop production system.

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the long-term use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly Massilia and Herbaspirillum) was enriched in the RP-amended soil. Klebsiella was the second most abundant taxon in the RP-treated soil. Burkholderia sp. and Bacillus sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were Scutellospora and Racocetra. These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.