A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system

Do nanoparticles and colloids replenish soil phosphorus in the rhizosphere of winter wheat?

The rhizosphere is generally depleted in nutrients, but as a hotspot of microbial activity it fosters crop P uptake. We hypothesized that P contents of water extractable nanoparticles (<0.1 μm) and small sized colloids (<0.45 μm) differ between non-rhizosphere and rhizosphere soil. To test this hypothesis, rhizosphere and non-rhizosphere soils (Luvisol and Cambisol) were sampled at harvest period of winter wheat near Selhausen (Germany). Microaggregate and colloidal fractions in the size range of 53-250 μm, 20-53 μm, 0.45-20 μm, and <0.45 μm were separated by wet-sieving and centrifugation. Subsequently, the colloids <0.45 μm were further isolated in 0.66-20 nm, 20-100 nm and 100-450 nm fractions using asymmetric flow field flow fractionation (AF4) and directly analyzed by online coupled organic carbon detector (OCD) and inductively coupled plasma mass spectrometry (ICP-MS) for element composition. No significant differences (p > 0.05) were measured between rhizosphere and non-rhizosphere soil P contents of microaggregate fractions. The rhizosphere soil, however, showed ∼26 % depletion of average P content in the 0.66-20 nm fraction, which went along with an enrichment of P content of the 100-450 nm fraction by a factor of two. Apparently, P uptake by plants results in a redistribution of P in the rhizosphere, with small nanoparticles providing available P to plants while excess residual P is bound to fine colloids.

Spatiotemporal dynamics of reactive oxygen species and its effect on beta-blockers' degradation in aquatic plants' rhizosphere

The pathway for pollutant degradation involving reactive oxygen species (ROS) in the rhizosphere is poorly understood. Herein, a rootchip system was developed to pinpoint the ROS hotspot along the root tip of Iris tectorum. Through mass balance analysis and quenching experiment, we revealed that ROS contributed significantly to rhizodegradation for beta-blockers, ranging from 22.18 % for betaxolol to 83.83 % for atenolol. The identification of degradation products implicated ROS as an important agent to degrade atenolol into less toxic transformation products during phytoremediation. Moreover, an active production of ROS in rhizosphere was identified by mesocosm experiment. Across three root-associated regions aquatic plants inhabiting the rhizosphere accumulated the highest •OH of ∼1200 nM after 3 consecutive days, followed by rhizoplane (∼230 nM) and bulk environment (∼60 nM). ROS production patterns were driven by rhizosphere chemistry (Fe and humic substances) and microbiome variations in different rhizocompartments. These findings not only deepen understanding of ROS production in aquatic plants rhizosphere but also shed light on advancing phytoremediation strategies.

Seasonality and Activity of Arbuscular Mycorrhizal Fungi in the Rhizosphere of Endemic Tree Species

This study analyzed arbuscular mycorrhizal fungi (AMF) activity and soil chemical properties in Aspidosperma pyrifolium, Bauhinia ungulata, Caesalpinia pyramidalis, and Caesalpinia ferrea. AMF spores, root colonization, total glomalin-related soil protein (T-GRSP), easily extracted GRSP (EE-GRSP), and soil chemical properties were measured four times (July 2019, 2020 and December 2019, 2020). Significant differences were observed in AMF spores, root colonization, T-GRSP, and EE-GRSP among the plant species and across seasons. For soil chemical properties, we observed differences among plant species. During the dry season, B. ungulata and C. pyramidalis had the highest AMF spores and root colonization (57.3 ± 0.27 spores 50 g soil-1 and 48.8 ± 1.05, respectively), whereas during the rainy season, C. pyramidalis and C. ferrea showed the highest AMF spores and root colonization (36.6 ± 0.13 spores 50 g soil-1 and 62.2 ± 1.17, respectively). A. pyrifolium showed the highest T-GRSP in both seasons. On the basis of the soil chemical properties, we found that (i) A. pyrifolium, B. ungulata, and C. ferrea showed the highest soil organic carbon (1.32 ± 0.03 g kg-1), phosphorus (7.01 ± 0.26 mg kg-1), and soil pH (5.85 ± 0.23) and (ii) C. pyramidalis showed the highest Ca2+, Mg2+, Na+, H+ + Al3+, K+, and soil total nitrogen (1.36 ± 0.04, 0.73 ± 0.01, 3.72 ± 0.85, 4.56 ± 0.12 cmolc kg-1, 15.43 ± 1.53 mg kg-1, and 0.16 ± 0.01 g kg-1, respectively). Our results highlight the advantage of AMF spores as perennating structures over other AM fungal propagules in seasonal vegetation like Caatinga.

Mitigating sediment cadmium contamination through combining PGPR Enterobacter ludwigii with the submerged macrophyte Vallisneria natans

Sediment cadmium contamination poses risks to aquatic ecosystems. Phytoremediation is an environmentally sustainable method to mitigate cadmium contamination. Submerged macrophytes are affected by cadmium stress, but plant growth-promoting rhizobacteria (PGPR) can restore the health status of submerged macrophytes. Herein, we aimed to reduce sediment cadmium concentration and reveal the mechanism by which the combined application of the PGPR Enterobacter ludwigii and the submerged macrophyte Vallisneria natans mitigates cadmium contamination. Sediment cadmium concentration decreased by 21.59% after submerged macrophytes were planted with PGPR, probably because the PGPR colonized the rhizosphere and roots of the macrophytes. The PGPR induced a 5.09-fold increase in submerged macrophyte biomass and enhanced plant antioxidant response to cadmium stress, as demonstrated by decreases in oxidative product levels (reactive oxygen species and malondialdehyde), which corresponded to shift in rhizosphere metabolism, notably in antioxidant defence systems (i.e., the peroxidation of linoleic acid into 9-hydroperoxy-10E,12Z-octadecadienoic acid) and in some amino acid metabolism pathways (i.e., arginine and proline). Additionally, PGPR mineralized carbon in the sediment to promote submerged macrophyte growth. Overall, PGPR mitigated sediment cadmium accumulation via a synergistic plantmicrobe mechanism. This work revealed the mechanism by which PGPR and submerged macrophytes control cadmium concentration in contaminated sediment.

Combined effects of cadmium and simulated acid rain on soil microbial communities in the early cultivation of Populus beijingensis seedlings

The combined cadmium (Cd) and acid rain pollution poses a significant threat to the global ecological environment. Previous studies on the combined adverse effects have predominantly focused on the aboveground plant physiological responses, with limited reports on the microbial response in the rhizosphere soil. This study employed Populus beijingensis seedlings and potting experiments to simulate the impacts of combined mild acid rain (pH=4.5, MA) or highly strong acid rain (pH=3.0, HA), and soil Cd pollution on the composition and diversity of microbial communities, as well as the physiochemical properties in the rhizosphere soil. The results showed that Cd decreased the content of inorganic nitrogen, resulting in an overall decrease of 49.10 % and 46.67 % in ammonium nitrogen and nitrate nitrogen, respectively. Conversely, acid rain was found to elevate the content of total potassium and soil organic carbon by 4.68 %-6.18 % and 8.64-19.16 %, respectively. Additionally, simulated acid rain was observed to decrease the pH level by 0.29-0.35, while Cd increased the pH level by 0.11. Moreover, Cd alone reduced the rhizosphere bacterial diversity, however, when combined with acid rain, regardless of its intensity, Cd was observed to increase the diversity. Fungal diversity was not influenced by the acid rain, but Cd increased fungal diversity to some extend under HA as observed in bacterial diversity. In addition, composition of the rhizosphere bacterial community was primarily influenced by the inorganic nitrogen components, while the fungal community was driven mainly by soil pH. Furthermore, "Metabolism" was emerged as the most significant bacterial function, which was markedly affected by the combined pollution, while Cd pollution led to a shift from symbiotroph to other trophic types for fungi. These findings suggest that simulated acid rain has a mitigating effect on the diversity of rhizosphere bacteria affected by Cd pollution, and also alters the trophic type of these microorganisms. This can be attributed to the acid rain-induced direct acidic environment, as well as the indirect changes in the availability or sources of carbon, nitrogen, or potassium.

Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization

Fixation of atmospheric N2 by free-living diazotrophs accounts for an important proportion of nitrogen naturally introduced to temperate grasslands. The effect of plants or fertilization on the general microbial community has been extensively studied, yet an understanding of the potential combinatorial effects on the community structure and activity of free-living diazotrophs is lacking. In this study we provide a multilevel assessment of the single and interactive effects of different long-term fertilization treatments, plant species and vicinity to roots on the free-living diazotroph community in relation to the general microbial community in grassland soils. We sequenced the dinitrogenase reductase (nifH) and the 16S rRNA genes of bulk soil and root-associated compartments (rhizosphere soil, rhizoplane and root) of two grass species (Arrhenatherum elatius and Anthoxanthum odoratum) and two herb species (Galium album and Plantago lanceolata) growing in Austrian grassland soils treated with different fertilizers (N, P, NPK) since 1960. Overall, fertilization has the strongest effect on the diazotroph and general microbial community structure, however with vicinity to the root, the plant effect increases. Despite the long-term fertilization, plants strongly influence the diazotroph communities emphasizing the complexity of soil microbial communities' responses to changing nutrient conditions in temperate grasslands.

Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham

Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

Bacterially enhanced plant-growing media for controlled environment agriculture

Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.

Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities

Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.

Effects of the application of microbiologically activated bio-based fertilizers derived from manures on tomato plants and their rhizospheric communities

Bio-based fertilizers (BBFs) recovered from animal manure are promising products to optimise resources recovery and generate high agricultural yields. However, their fertilization value may be limited and it is necessary to enrich BBFs with microbial consortia to enhance their fertilization value. Three specific microbial consortia were developed according to the characteristics of three different BBFs produced from manure (bio-dried solid fraction, solid fraction of digestate and biochar) to enhance plant growth and product quality. A greenhouse pot experiment was carried out with tomato plants grown with microbiologically activated BBFs applied either as N-organic fertilizers or as an organic amendment. A next generation sequencing analysis was used to characterise the development of each rhizospheric community. All the activated BBFs gave enhanced tomato yields (fresh and dry weight) compared with the non-activated treatments and similar to, or higher than, chemical fertilization. Concerning the tomato fruits' organoleptic quality, lycopene and carotenoids concentrations were improved by biological activation. Metagenomic analysis points at Trichoderma as the main driver of the positive effects, with the effects of added bacteria being negligible or limited at the early stages after fertilization. In the context of the circular economy, the activated BBFs could be used to replace synthetic fertilisers, reducing costs and environmental burdens and increasing production.

Evaluating pesticide degradation in artificial wetlands with compound-specific isotope analysis: A case study with the fungicide dimethomorph

Pesticide degradation in wetland systems intercepting agricultural runoff is often overlooked and mixed with other dissipation processes when assessing pesticide concentrations alone. This study focused on the potential of compound-specific isotope analysis (CSIA) to estimate pesticide degradation in a stormwater wetland receiving pesticide runoff from a vineyard catchment. The fungicide dimethomorph (DIM), with diastereoisomers E and Z, was the prevalent pesticide in the runoff entering the wetland from June to September 2020. DIM Z, the most commonly detected isomer, exhibited a significant change (Δ(13C) > 3 ‰) in its carbon isotopic composition in the wetland water compared to the runoff and commercial formulation, which indicated degradation. Laboratory DIM degradation assays, including photodegradation and biodegradation in oxic wetland water with and without aquatic plants and in anoxic sediments, indicated that DIM degradation mainly occurred in the wetland sediments. The rapid degradation of both DIM isomers (E:t1/2 = 1.2 ± 0.6, Z: t1/2 = 1.5 ± 0.8 days) in the wetland sediment led to significant carbon isotopic fractionation (εDIM-E = -3.0 ± 0.6 ‰, εDIM-Z = -2.0 ± 0.2 ‰). In contrast, no significant isotope fractionation occurred during DIM photodegradation, despite the rapid isomerization of the E isomer to the Z isomer and a half-life of 15.3 ± 2.2 days for both isomers. DIM degradation was slow (E: t1/2 = 56-62 days, Z: t1/2 = 82-103 days) in oxic water with plants, while DIM persisted (120 days) in water without plants. DIM CSIA was thus used to evaluate the in situ biodegradation of DIM Z in the wetland. The DIM Z degradation estimates based on a classical concentration mass balance (86-94 %) were slightly higher than estimates based on the isotopic mass balance (61-68 %). Altogether, this study shows the potential of CSIA to conservatively evaluate pesticide degradation in wetland systems, offering a reliable alternative to classical labor-intensive mass balance approaches.).

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production

Introduction

Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types.

Methods

Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline.

Results

Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms.

Discussion

Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

Draft genome sequence of the highly copper-tolerant Methylobacterium radiotolerans MLP1 isolated from the rhizosphere of grasses adjacent to mine tailings

We present the genome of a highly copper-tolerant pink-pigmented facultative methylotroph isolated from the rhizosphere of grasses growing close to mine tailings. Based on whole-genome taxonomic analyses, this isolate was named Methylobacterium radiotolerans MLP1. Studies are in progress to infer its genome-based copper resistome.

Enhancing plant defense using rhizobacteria in processing tomatoes: a bioprospecting approach to overcoming Early Blight and Alternaria toxins

Plant growth-promoting rhizobacteria (PGPR) with antagonistic activity toward plant pathogenic fungi are valuable candidates for the development of novel plant protection products based on biocontrol activity. The very first step in the formulation of such products is to screen the potential effectiveness of the selected microorganism(s). In this study, non-pathogenic rhizobacteria were isolated from the rhizosphere of tomato plants and evaluated for their biocontrol activity against three species of mycotoxin-producing Alternaria. The assessment of their biocontrol potential involved investigating both fungal biomass and Alternaria toxin reduction. A ranking system developed allowed for the identification of the 12 best-performing strains among the initial 85 isolates. Several rhizobacteria showed a significant reduction in fungal biomass (up to 76%) and/or mycotoxin production (up to 99.7%). Moreover, the same isolates also demonstrated plant growth-promoting (PGP) traits such as siderophore or IAA production, inorganic phosphate solubilization, and nitrogen fixation, confirming the multifaceted properties of PGPRs. Bacillus species, particularly B. amyloliquefaciens and two strains of B. subtilis, showed the highest efficacy in reducing fungal biomass and were also effective in lowering mycotoxin production. Isolates such as Enterobacter ludwigii, Enterobacter asburiae, Serratia nematodiphila, Pantoea agglomerans, and Kosakonia cowanii showed moderate efficacy. Results suggest that by leveraging the diverse capabilities of different microbial strains, a consortium-based approach would provide a broader spectrum of effectiveness, thereby signaling a more encouraging resolution for sustainable agriculture and addressing the multifaceted nature of crop-related biotic challenges.

Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem

Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.

Bacterial Communities Associated with the Roots of Typha spp. and Its Relationship in Phytoremediation Processes

Heavy metal pollution is a severe concern worldwide, owing to its harmful effects on ecosystems. Phytoremediation has been applied to remove heavy metals from water, soils, and sediments by using plants and associated microorganisms to restore contaminated sites. The Typha genus is one of the most important genera used in phytoremediation strategies because of its rapid growth rate, high biomass production, and the accumulation of heavy metals in its roots. Plant growth-promoting rhizobacteria have attracted much attention because they exert biochemical activities that improve plant growth, tolerance, and the accumulation of heavy metals in plant tissues. Because of their beneficial effects on plants, some studies have identified bacterial communities associated with the roots of Typha species growing in the presence of heavy metals. This review describes in detail the phytoremediation process and highlights the application of Typha species. Then, it describes bacterial communities associated with roots of Typha growing in natural ecosystems and wetlands contaminated with heavy metals. Data indicated that bacteria from the phylum Proteobacteria are the primary colonizers of the rhizosphere and root-endosphere of Typha species growing in contaminated and non-contaminated environments. Proteobacteria include bacteria that can grow in different environments due to their ability to use various carbon sources. Some bacterial species exert biochemical activities that contribute to plant growth and tolerance to heavy metals and enhance phytoremediation.

The microbiome of cereal plants: The current state of knowledge and the potential for future applications

The plant microbiota fulfils various crucial functions related to host health, fitness, and productivity. Over the past years, the number of plant microbiome studies continued to steadily increase. Technological advancements not only allow us to produce constantly increasing datasets, but also to extract more information from them in order to advance our understanding of plant-microbe interactions. The growing knowledge base has an enormous potential to improve microbiome-based, sustainable agricultural practices, which are currently poorly understood and have yet to be further developed. Cereal plants are staple foods for a large proportion of the world's population and are therefore often implemented in microbiome studies. In the present review, we conducted extensive literature research to reflect the current state of knowledge in terms of the microbiome of the four most commonly cultivated cereal plants. We found that currently the majority of available studies are targeting the wheat microbiome, which is closely followed by studies on maize and rice. There is a substantial gap, in terms of published studies, addressing the barley microbiome. Overall, the focus of most microbiome studies on cereal plants is on the below-ground microbial communities, and there is more research on bacteria than on fungi and archaea. A meta-analysis conducted in the frame of this review highlights microbiome similarities across different cereal plants. Our review also provides an outlook on how the plant microbiota could be harnessed to improve sustainability of cereal crop production.

Uptake of the Plant Agriculture-Used Antibiotics Oxytetracycline and Streptomycin by Cherry Radish─Effect on Plant Microbiome and the Potential Health Risk

Antibiotics are used to control certain bacterial diseases in plant agriculture. Understanding antibiotic uptake by edible vegetables after application and associated risks on plant microbiome and human health is critical. In this study, oxytetracycline and streptomycin, the two most commonly used antibiotics in plant agriculture, were applied to cherry radish via continuous soil drenching to study their translocations into plant tissues, influence on radish microbiome, and the potential health risk to mice. The results demonstrated that oxytetracycline induced hormesis in radish plants and both antibiotics were translocated into the leaves, fruits, and roots of radishes from the soil, with significantly higher plant uptake of streptomycin than oxytetracycline. Interestingly, the proportion of culturable oxytetracycline or streptomycin-resistant bacteria in the antibiotic-accumulated radish tissues was significantly higher than that in the antibiotic-free radish tissues, although both bacterial and fungal communities in different radish tissues were not affected by the accumulated antibiotics, demonstrating that antibiotic application could enrich antibiotic resistance in the plant microbiome. Feeding mice with antibiotics-accumulated radish tissues did not show significant effects on the weight and blood glucose levels of mice. Overall, this study provides important insights into the risk of using antibiotics in plant agriculture.

Characterization of the microbial community associated with the roots of joyapa (Macleania rupestris) and the effect of fungal isolates on seedling development

Macleania rupestris is a native Ericaceae with high potential benefits for health and the environment. Characterizing the interactions between M. rupestris and associated fungi is vital to supporting the plant's conservation and future domestication. However, little is known about the relationship between plant growth-promoting endophytes and M. rupestris. To learn more about the soil-associated microbiota of M. rupestris, we analyzed endophyte communities associated with the plant's rhizosphere and surrounding soil using nanopore sequencing. Additionally, fungal endophyte cultivable strains were isolated from the roots of M. rupestris to evaluate their growth-promoting activity on seedlings by applying a strain inoculation bioassay. Over 1000 genera were identified using nanopore sequencing, Bradyrhizobium and Mesorhizobium the most abundant in all samples analyzed. Similarly, six cultivable fungi were characterized by the molecular markers ITS (internal transcribed spacer) and LSU (large subunit). Amongst all isolates, Clonostachys rosea and Trichoderma paravidescens positively impacted seedlings' development. This study shows the potential of fungal strains as inoculants for the potential domestication of Macleania rupestris. Keywords: Endophyte, growth promoter, Macleania rupestris, microbial communities

Pristine and sulfidized zinc oxide nanoparticles alter bacterial communities and metabolite profiles in soybean rhizocompartments

A better understanding of bacterial communities and metabolomic responses to pristine zinc oxide manufacture nanoparticles (ZnO MNPs) and its sulfidized product (s-ZnO MNPs), as well as their corresponding Zn ions in rhizocompartments, critical in the plant-microbe interactions, could contribute to the sustainable development of nano-enabled agriculture. In this study, soybean (Glycine max) were cultivated in soils amended with three Zn forms, namely ZnSO₄·7H₂O, ZnO MNPs and s-ZnO MNPs at 0, 100 and 500 mg·kg^-1 for 70 days. Three Zn forms exposures profoundly decreased the bacterial alpha diversity in roots and nodules. High dose (500 mg·kg^-1) groups had a stronger impact on the bacterial beta diversity than low dose (100 mg·kg^-1) groups. In the rhizosphere soil and roots, 500 mg·kg^-1 of ZnSO₄ and s-ZnO MNPs treatments showed the largest shifts in bacterial community structure, respectively. In addition, several significant changed bacterial taxa and metabolites were found at the high dose groups, which were associated with carbon and nitrogen metabolism. PLS-DA plot showed good discrimination in metabolomic profiles of rhizosphere soil and roots between three Zn forms treatments and control. Most metabolic pathways perturbed were closely linked to oxidative stress. Overall, our study indicates either dissolved or nano-particulate Zn exposure at high dose can drastically affected bacterial communities and metabolite profiles in soybean rhizocompartments.

The Impacts of Phosphorus-Containing Compounds on Soil Microorganisms of Rice Rhizosphere Contaminated by Lead

The cost effectiveness of using exogenous phosphorus to remediate heavy metals in soil, which would alter the structure of the soil microbial community, had been widely acknowledged. In the present study, phospholipid fatty acid (PLFA) technology was taken as the breakthrough point, and rhizosphere soil microorganisms in different growth stages (jointing stage and maturity stage) of Minghui 86 (MH) and Yangdao No.6 (YD) rice were taken as the research objects. As revealed by the results, the rhizosphere soil microorganisms of MH and YD had distinct sensitivities to exogenous phosphorus and had a certain inhibitory effect on MH and YD enhancement. The sensitivity of rice root soil microorganisms to exogenous phosphorus also varied in different growth stages of rice. Bacteria were the dominant microorganism in the soil microbial community of rice roots, and the gain of exogenous phosphorus had a certain impact on the structure of the two soil microbial communities. Through analysis of the microbial community characteristics of MH rice and YD soil after adding exogenous phosphorus, further understanding was attained with respect to the effect of exogenous phosphorus on the microbial community characteristics of rice rhizosphere soil and the impact thereof on ecological functions.

Range grasses to improve soil properties, carbon sustainability, and fodder security in degraded lands of semi-arid regions

Tropical grasses are the primary source of forage for livestock and a valuable resource for improving soil health and environmental sustainability in semi-arid regions. A study was carried out in a semi-arid region of central India to determine the short-term (6-year) impact of nine range grasses on soil physio-chemical and biological properties, carbon stock, and forage security. The experiment was carried out in a randomized block design with three replications. Results show that the majority of the grass roots were distributed in the upper soil layer (0-10 cm, 63.5-76.5 %), and then in the middle (10-20 cm, 21.3-25 %) and lower (20-30 cm, 2.2-11.5 %) layers. Perennial tussock grass (Heteropogon contortus (L.) P. Beauv. ex Roem. & Schult) had a higher root volume (2219 mm³), followed by Guinea grass [Megathyrsus maximus (Jacq.) B.K. Simon & S.W.L. Jacobs] (1860 mm³). A lower soil bulk density (BD, 1.11-1.23 g cm^-3), higher gravimetric water content (GMW, 14.0-17.8 %), and soil organic carbon (0.38-0.73 %) were recorded for grass-cultivated plots compared to the barren land (1.38 g cm^-3, 13.0 %, and 0.28 %, respectively). The perennial tussock grass and Guinea grass resulted in the highest soil microbial biomass carbon (SMBC, 70.1 mg kg^-1 soil) and enzyme activities (dehydrogenase, 17.09 μg TPF g^-1 day^-1 and fluorescein diacetate activity 4.94 μg fluorescein g^-1 h^-1). The considerable improvement in soil properties with minimal inputs resulted in a higher sustainable yield index and carbon sustainability index in plots planted with Guinea grass (0.9 and 89.29) and perennial tussock grass (0.89 and 71.61). Therefore, the cultivation of either Guinea grass or perennial tussock grass as an intercrop or sole crop in the semi-arid environment can be an ecologically sound strategy to improve soil health, C sequestration, and fodder supply.

Simple extraction methods for pesticide compound-specific isotope analysis from environmental samples

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Extractions from soil, plants, and water were tested for pesticide C and N CSIA.

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Pesticide recoveries strongly varied among compounds and matrices properties.

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Tested extraction methods caused no effect on δ¹³C and δ¹⁵N of pesticides.

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C and N pesticide CSIA can be applied in situ to agricultural water samples.

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Pesticide CSIA for soil and sediment samples are limited to source areas.

Compound-specific isotope analysis (CSIA) is a powerful approach to evaluate the transformation of organic pollutants in the environment. However, the application of CSIA to micropollutants, such as pesticides, remains limited because appropriate extraction methods are currently lacking. Such methods should address a wide range of pesticides and environmental matrices, while recovering sufficient mass for reliable CSIA without inducing stable isotope fractionation. Here, we present simple extraction methods for carbon and nitrogen CSIA for different environmental matrices and six commonly used herbicides, i.e., atrazine, terbutryn, acetochlor, alachlor, butachlor, and S-metolachlor, and three fungicides, i.e., dimethomorph, tebuconazole, and metalaxyl. We examined the potential of several extraction methods for four types of soils or sediments, three types of environmental waters and aerial and root plant samples for multielement (ME)-CSIA.•

Pesticide extraction recoveries varied depending on the physical characteristics of the pesticides and matrix properties for environmental water (77 to 87%), soil and sediment (35 to 82%), and plant (40 to 59%) extraction.

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The tested extraction methods did not significantly affect the carbon and nitrogen stable isotope signatures of pesticides (Δ(¹³C) <0.9‰ for Δ(¹⁵N) <1.0‰).

Amendment with Burkina Faso phosphate rock-enriched composts alters soil chemical properties and microbial structure, and enhances sorghum agronomic performance

Low soil available phosphorus (P) severely limits crop production in sub-Saharan Africa. The present study evaluated phosphate rock-enriched composts as locally available low-cost fertilizers for sorghum production. The treatments consisted of sorghum straw, compost (COMP), phosphate rock (BPR), BPR-enriched compost (P-COMP), BPR-rhizosphere soil-enriched compost (P-COMP-SOIL), nitrogen-phosphorus-potassium treatment (NPK, 60–39–25), and control (NK, 60–25). Sorghum straw and compost were applied at 1.34 tons ha⁻¹. N, P, and K in all treatments, excluding the control, were adjusted to 60, 39, and 25 kg ha⁻¹, with urea, BPR, and KCl, respectively. Sorghum vr. kapelga was cultivated and soil samples were collected at the S5, S8, and S9 growth stages. P-COMP-SOIL and NPK yielded better sorghum yields than the other treatments. The rhizosphere soil of P-COMP-SOIL had high abundance of soil bacteria and AMF, and genes involved in P solubilization, such as: acid phosphatase (aphA), phosphonatase (phnX), glucose dehydrogenase (gcd), pyrroloquinoline quinone (pqqE), phosphate-specific transporter (pstS). The superior performance of the P-COMP-SOIL was associated with its higher available P content and microbial abundance. Multivariate analysis also revealed vital contributions of N, carbon, and exchangeable cations to sorghum growth. Soils could be amended with phosphate rock-rhizosphere soil-enriched composts, as an alternative to chemical fertilizers.

Microbiome profile of soil and rhizosphere plants growing in traditional oil mining land in Wonocolo, Bojonegoro, Indonesia

Traditional oil mining poses negative effects on the environment through pollution with crude oil. One of the traditional mining sites in Wonocolo, Bojonegoro, Indonesia was reported to contaminate the surrounding area with a high level of crude oil. Therefore, this study aims to examine the microbiome profiles of contaminated soil and the rhizosphere of naturalized plants growing at the sites. It was conducted in Wonocolo, Bojonegoro to obtain an insight into the possible remediation efforts of using indigenous hydrocarbon-degrading bacteria and naturalized plants as in situ remediation agents. The results showed that the soil located close to the oil well-contained a high level of crude oil at 24.8%, and exhibited a distinct microbiome profile compared to those located further which had lower crude oil contamination of 14.15, 10.89, and 4.9%. Soil with the highest level of crude oil contamination had a comparatively higher relative abundance of assA, an anaerobic alkene-degrading gene. Meanwhile, the rhizosphere of the two naturalized plants, Muntingia calabura, and Pennisetum purpureum, exhibited indifferent microbiome profiles compared to the soil. They were found to contain less abundant hydrocarbon-degrading genes, such as C230, PAH-RHD-GP, nahAc, assA, and alkB suggesting that these naturalized plants might not be a suitable tool for in-situ remediation.

Exploiting the Potential of Bioreactors for Creating Spatial Organization in the Soil Microbiome: A Strategy for Increasing Sustainable Agricultural Practices

Industrial production of synthetic nitrogen fertilizers and their crop application have caused considerable environmental impacts. Some eco-friendly alternatives try to solve them but raise some restrictions. We tested a novel method to produce a nitrogen bioinoculant by enriching a soil microbial community in bioreactors supplying N2 by air pumping. The biomass enriched with diazotrophic bacteria was diluted and applied to N-depleted and sterilized soil of tomato plants. We estimated microbial composition and diversity by 16S rRNA metabarcoding from soil and bioreactors at different run times and during plant uprooting. Bioreactors promoted the N-fixing microbial community and revealed a hided diversity. One hundred twenty-four (124) operational taxonomic units (OTUs) were assigned to bacteria with a greater Shannon diversity during the reactor’s steady state. A total of 753 OTUs were found in the rhizospheres with higher biodiversity when the lowest concentration of bacteria was applied. The apparent bacterial abundance in the batch and continuous bioreactors suggested a more specific functional ecological organization. We demonstrate the usefulness of bioreactors to evidence hidden diversity in the soil when it passes through bioreactors. By obtaining the same growth of inoculated plants and the control with chemical synthesis fertilizers, we evidence the potential of the methodology that we have called directed bioprospecting to grow a complex nitrogen-fixing microbial community. The simplicity of the reactor’s operation makes its application promising for developing countries with low technological progress.

Pseudomonas aeruginosa isolate PM1 effectively controls virus infection and promotes growth in plants

A bacterial isolate PM1 obtained from the rhizosphere of healthy plants was identified as Pseudomonas aeruginosa by biochemical characteristics and 16S rRNA gene sequence (GenBank ID OL321133.1). It induced resistance in Nicotiana tabacum cv. Xanthi-nc and Cyamopsis tetragonoloba, against Tobacco mosaic virus (TMV) and Sunn-hemp rosette virus (SRV), respectively. Foliar treatment with isolate PM1 curbed TMV accumulation in susceptible N. tabacum cv. White Burley. PM1 was more effective as a foliar than a root/soil drench treatment, evident through a comparative decrease in ELISA values, and reduced viral RNA accumulation. Foliar and soil drench treatment with PM1 resulted in a disease index of 48 and 86 per cent, and a control rate of 48.9 and 8.5 per cent, respectively. PM1 exhibited phosphate solubilization, produced siderophores, auxins, HCN, and ammonia, all important plant growth-promoting traits. Foliar treatment with PM1 enhanced growth in tobacco, while its volatiles significantly promoted seedling growth in C. tetragonoloba. Of the several metabolites produced by the isolate, many are known contributors to induction of systemic resistance, antibiosis, and growth promotion in plants. Soluble metabolites of PM1 were less effective in inducing antiviral resistance in N. tabacum cv. Xanthi-nc in comparison with its broth culture. PM1 and its metabolites were antagonistic to Gram-positive Bacillus spizizenii and Staphylococcus aureus, and fungi Fusarium oxysporum, Aspergillus niger, and Rhizopus stolonifer. Its volatiles were inhibitory to F. oxysporum and R. stolonifer. Thus, PM1 exhibited considerable potential for further evaluation in plant virus control and production of diverse metabolites of use in agriculture and medicine.

Maize (Zea mays L.) genotypes induce the changes of rhizosphere microbial communities

Plant-microbe interactions affect ecosystem function, and plant species influence relevant microorganisms. However, the different genotypes of maize that shape the structure and function of the rhizosphere microbial community remain poorly investigated. During this study, the structures of the rhizosphere microbial community among three genotypes of maize were analyzed at the seedling and maturity stages using high-throughput sequencing and bioinformatics analysis. The results demonstrated that Tiannuozao 60 (N) showed higher bacterial and fungal diversity in both periods, while Junlong1217 (QZ) and Fujitai519 (ZL) had lower diversity. The bacterial community structure among the three varieties was significantly different; however, fewer differences were found in the fungal community. The bacterial community composition of N and QZ was similar yet different from ZL at the seedling stage. The bacterial networks of the three cultivars were more complex than the fungal networks, and the networks of the mature stages were more complex than those of the seedling stages, while the opposite was true for the fungi. FAPROTAX functional and FUNGuild functional predictions revealed that different varieties of maize were different in functional abundance at the genus level, and these differences were related to breeding characteristics. This study suggested that different maize genotypes regulated the rhizosphere bacterial and fungal communities, which would help guide practices.

Exploring plant growth-promoting rhizobacteria as stress alleviators: a methodological insight

Rhizospheric and root-endophyte bacteria can stimulate plant growth through diverse biochemical mechanisms and pathways, particularly under biotic and abiotic stresses. For this reason, biotechnological trends on plant growth-promoting rhizobacteria (PGPR) application as biofertilizers, bioremediators, and stress alleviators are gaining increasing interest as ecofriendly strategies for sustainable agriculture management and soil restoration. The first steps needed to implement these technologies are isolation, screening, and characterization of PGPR that can be potentially applied as bioinoculants to alleviate biotic and/or abiotic stresses. Therefore, a complete and accurate methodological study and laboratory techniques are required to warrant the correct achievement of these steps. This review compiles and details the fundamentals, methods, and procedures of key protocols used in isolation and characterization of PGPR for plant stress alleviation.

Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting

Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.

Effects of Plant Fine Root Functional Traits and Soil Nutrients on the Diversity of Rhizosphere Microbial Communities in Tropical Cloud Forests in a Dry Season

The composition and diversity of rhizosphere microbial communities may be due to root–soil–microbial interactions. The fine root functional traits and rhizosphere soil environmental factors of 13 representative plants in the Bawangling tropical cloud forest of Hainan Island were measured, to assess the key factors driving plant rhizosphere microbial communities. Illumina MiSeq sequencing technology was used to sequence the v3-V4 region of the 16SrDNA gene of 13 plant rhizosphere soil bacteria and the ITS1 region of the fungal ITSrDNA gene. Results showed that there were 355 families, 638 genera, and 719 species of rhizosphere soil bacteria as well as 29 families, 31 genera, and 31 species of rhizosphere soil fungi in the tropical cloud forests. The fine root traits, such as root phosphorus content, the specific root length and specific root area, were significantly negatively correlated with the Faith-pd indices of the bacterial community but were not correlated with the diversity of fungi communities. The soil pH was significantly and positively correlated with the Chao1 index, OTUs, Faith-pd and Simpson indices of the bacteria and fungi communities. The soil available phosphorus content was significantly and negatively correlated with the bacteria Simpson and the fungus Faith-pd indices. ABT analysis showed that soil pH and soil available phosphorus were the most important environmental conditions contributing to the rhizosphere bacterial and fungi communities, respectively. Our findings demonstrate that the soil environments had more influence on rhizosphere soil microbial diversity than the fine root functional traits.

Diversity of Sclerotium rolfsii antagonist fungi isolated from soils of the rhizosphere of tomato crops and identification of some antifungal compounds

Sclerotium rolfsii Sacc. the causative agent of white rot is one of the destructive pathogens of nightshade crops. In Côte d'Ivoire, this fungal pathogen constitutes a major constraint for the cultivation of tomato (Solanum lycopersicum) with 41.01% crop losses in humid forest areas. Controlling this fungus with synthetic chemicals can be effective, but harmful to human health and the environment. The use of biological control agents could be an alternative approach to control S. rolfsii. In this perspective, the objective of this work was to select fungi from the rhizosphere of tomato crops capable of inhibiting the growth of S. rolfsii. To do this, 153 fungi were isolated from the rhizosphere and from direct confrontation tests 10 fungi whose antagonistic power of S. rolfsii varied between 27 and 60% were selected. Molecular identification (ITS) of these antagonist fungi revealed that the isolates belonged to the genera Talaromyces sp. (n = 4), Trichoderma sp. (n = 3), Penicillium sp. (n = 2) and Clonostachys sp. (n = 1). Among these fungi, Talaromyces purpureogenus and Talaromyces assiutensis were able to diffuse compounds in agar capable of inhibiting the growth of S. rolfsii. The chemical study of these 2 fungi made it possible to identify mitorubrin and mitorubrinol produced by T. purpureogenus and spiculisporic acid produced by T. assiutensis. Mitorubrin and mitorubrinol had inhibitory activities of 100 and 70% at 10 mg/mL, respectively, whereas spiculisporic acid showed moderate inhibition of 38 at 20 mg/mL of the growth of S. rolfsii; however, its abundant production by the fungus could be an advantage in the control of this phytopathogen. Isolated from the same biotope as S. rolfsii, T. purpureogenus and T. assiutensis represent favorable candidates for the biological control against S. rolfsii.

Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere

The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.

Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.

Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA gene barcoding to compare bacterial species composition at seedling, vegetative, early- and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on nonserpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

ACC deaminase positive Enterobacter-mediated mitigation of salinity stress, and plant growth promotion of Cajanus cajan: a lab to field study

Salinity is a major abiotic stress that negatively impacts plant health and soil microbiota. ACC (1-aminocyclopropane carboxylic acid) deaminase producing microorganisms act as natural stress busters that protect plants from different kinds of stresses. The study focused on the isolation of potent, indigenous, multi-trait ACC deaminase producers. The shortlisted ACC deaminase producers were checked for their ability to promote growth of Cajanus cajan, and mitigate stress under laboratory conditions followed by validation of their potency in naturally saline field conditions. Physiological stress markers were assessed to evaluate the impact of salinity in plants treated with ACC deaminase producer, compared to controls. Further, the contribution of ACC deaminase in stress mitigation was demonstrated by using a chemical inhibitor for ethylene biosynthesis. This study presents a polyphasic approach, transitioning from the rhizospheric soil to the laboratory to validation in the field, and puts forth a promising eco-friendly alternative for sustainable agriculture.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01031-0.

Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer

Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO₃⁻/NH₄⁺ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.

Appraising the potential of EPS-producing rhizobacteria with ACC-deaminase activity to improve growth and physiology of maize under drought stress

Rhizobacteria containing 1-aminocyclopropane-1-carboxylic acid-deaminase (ACC-deaminase) and exopolysaccharides (EPS) activity are important to induce stress tolerance in plants. The present study was conducted to screen and characterize plant growth-promoting rhizobacteria (PGPR) with ACC-deaminase and EPS-producing activity for improving maize growth under drought stress. Eighty-five rhizobacterial strains were isolated from the rain-fed areas, among those 69 isolates were able to utilize ACC and 31 strains were found positive for EPS production. These strains containing ACC-deaminase and/or EPS-producing activity were subjected to drought tolerance assay by inducing water stress in media using polyethylene glycol 6000. Based on results of the drought tolerance bioassay, 12 most prominent strains were selected to evaluate their growth-promoting abilities in maize under water-stressed conditions by conducting jar trial. The impact of strains on maize growth parameters was variable. Strains with co-existence of ACC-deaminase and EPS-producing activity showed comparatively better results than those with either ACC-deaminase or EPS-producing activity only. These strains were also significantly better in improving the plant physiological parameters including photosynthesis rate, stomatal conductance, vapor pressure, water-use efficiency and transpiration rate. The strain D₃ with co-existence of ACC-deaminase and EPS-producing activity was significantly better in colonizing maize roots, improving plant growth and physiological parameters. The strain was named as Bacillus velezensis strain D₃ (accession number MT367633) as confirmed through results of 16S rRNA partial gene sequencing. It is concluded that the strains with co-existence of ACC-deaminase and EPS-producing activity could be better suited for improving crop growth and physiology under drought stress.

A phytoremediation coupled with agro-production mode suppresses Fusarium wilt disease and alleviates cadmium phytotoxicity of cucumber (Cucumis sativus L.) in continuous cropping greenhouse soil

Cadmium (Cd) contamination and continuous cropping obstacle often coexist in greenhouse soil and seriously restrict cucumber production. In this study, hyperaccumulator Sedum alfredii Hance was intercropped with spring cucumber (Cucumis sativus L.), then rotated with low accumulator water spinach and autumn cucumber under rational water regime, composited amendment was applied to soil before transplanting autumn cucumber. The results showed that, compared with conventional crop rotation system (Chinese cabbage and cucumber rotation), superposition management practice suppressed Fusarium wilt disease by 28.4 and 57.4% and increased yield by 35.2 and 383% for spring and autumn cucumbers, respectively. Meanwhile, photosynthetic characteristics, antioxidant system and fruit quality were significantly improved. Furthermore, this mode modified soil microbial community structure, enhanced soil enzyme activities, and simultaneously reduced soil total and phytoavailable Cd by 30.3 and 47.7%, respectively. These results demonstrated a feasible technical system to achieve phytoremediation coupled with argo-production in Cd contaminated greenhouse soil with continuous cropping obstacle and provided useful information for further revelation of interaction mechanisms between multicropping and comprehensive biofortification measurements.

Bioaugmented Phytoremediation of Metal-Contaminated Soils and Sediments by Hemp and Giant Reed

We assessed the effects of EDTA and selected plant growth-promoting rhizobacteria (PGPR) on the phytoremediation of soils and sediments historically contaminated by Cr, Ni, and Cu. A total of 42 bacterial strains resistant to these heavy metals (HMs) were isolated and screened for PGP traits and metal bioaccumulation, and two Enterobacter spp. strains were finally selected. Phytoremediation pot experiments of 2 months duration were carried out with hemp (Cannabis sativa L.) and giant reed (Arundo donax L.) grown on soils and sediments respectively, comparing in both cases the effects of bioaugmentation with a single PGPR and EDTA addition on plant and root growth, plant HM uptake, HM leaching, as well as the changes that occurred in soil microbial communities (structure, biomass, and activity). Good removal percentages on a dry mass basis of Cr (0.4%), Ni (0.6%), and Cu (0.9%) were observed in giant reed while negligible values (<100‰) in hemp. In giant reed, HMs accumulated differentially in plant (rhizomes > > roots > leaves > stems) with largest quantities in rhizomes (Cr 0.6, Ni 3.7, and Cu 2.2 g plant^–1). EDTA increased Ni and Cu translocation to aerial parts in both crops, despite that in sediments high HM concentrations in leachates were measured. PGPR did not impact fine root diameter distribution of both crops compared with control while EDTA negatively affected root diameter class length (DCL) distribution. Under HM contamination, giant reed roots become shorter (from 5.2 to 2.3 mm cm^–3) while hemp roots become shorter and thickened from 0.13 to 0.26 mm. A consistent indirect effect of HM levels on the soil microbiome (diversity and activity) mediated by plant response (root DCL distribution) was observed. Multivariate analysis of bacterial diversity and activity revealed not only significant effects of plant and soil type (rhizosphere vs. bulk) but also a clear and similar differentiation of communities between control, EDTA, and PGPR treatments. We propose root DCL distribution as a key plant trait to understand detrimental effect of HMs on microbial communities. Positive evidence of the soil-microbe-plant interactions occurring when bioaugmentation with PGPR is associated with deep-rooting perennial crops makes this combination preferable over the one with chelating agents. Such knowledge might help to yield better bioaugmented bioremediation results in contaminated sites.

Rhizosphere effect on removal and bioavailability of PAHs in contaminated agricultural soil

The rhizosphere effect of ryegrass (Lolium perenne L.) on polycyclic aromatic hydrocarbons (PAHs) dissipation, bioavailability and the structure change of microbial community was investigated using a compartmented device-rhizobox. The PAHs removal efficiency, bioavailability and the change in structure of the microbial community were ascertained using HPLC, Tenax-TA extraction and PCR-DGGE, respectively. The results showed that in the root area (R1) and bulk soil (CK), the removal of 3-ring PAHs were 97.72 ± 0.34% and 95.51 ± 0.75%, 4-ring PAHs were 89.01 ± 1.61% and 78.65 ± 0.47%, 5-ring PAHs were 77.64 ± 4.05% and 48.63 ± 3.19%, 6-ring PAHs were 68.69 ± 3.68% and 36.09 ± 1.78%, respectively. The average removal efficiency of the total PAHs after 80 days followed the order: R1M (91.1%) > CKM (84.9%) > CK (77.6%), indicating that planted soil with inoculation of Mycobacterium sp. as well as non-planted soil inoculated with Mycobacterium sp. could both significantly accelerate the removal of PAHs compared to control soil. The bioavailability ratio of PAHs with 3 and 4 rings tended to decrease (from 59.9% to 14.8% for 3-ring and 7.61% to 5.08% for 4-ring, respectively in R1) while those with 5 rings increased significantly (from 2.41% to 33.78% in R1) during the last 40 days, indicating that bioavailability alteration varies with the number of rings in the PAHs. In addition, PAH bioavailability generally did not show a significant difference between treated soil and control soil. These results suggest that ryegrass rhizosphere effect as well as inoculation of Mycobacterium sp. can accelerate PAH removal in polluted soil. The bacteria community structure demonstrated a complex interplay of soil, bacteria and ryegrass root, and potential PAH degraders were present in abundance. This study provides the exploring data of rhizosphere and bioaugmentation effect on PAH dissipation in agricultural soil, as well as the change of bioavailability and microbial composition thereof.

The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria

Root−associated microbial communities play important roles in the process of adaptation of plant hosts to environment stressors, and in this perspective, the microbiome of halophytes represents a valuable model for understanding the contribution of microorganisms to plant tolerance to salt. Although considered as the most promising halophyte candidate to crop cultivation, Salicornia ramosissima is one of the least-studied species in terms of microbiome composition and the effect of sediment properties on the diversity of plant-growth promoting bacteria associated with the roots. In this work, we aimed at isolating and characterizing halotolerant bacteria associated with the rhizosphere and root tissues of S. ramosissima, envisaging their application in saline agriculture. Endophytic and rhizosphere bacteria were isolated from wild and crop cultivated plants, growing in different estuarine conditions. Isolates were identified based on 16S rRNA sequences and screened for plant-growth promotion traits. The subsets of isolates from different sampling sites were very different in terms of composition but consistent in terms of the plant-growth promoting traits represented. Bacillus was the most represented genus and expressed the wider range of extracellular enzymatic activities. Halotolerant strains of Salinicola, Pseudomonas, Oceanobacillus, Halomonas, Providencia, Bacillus, Psychrobacter and Brevibacterium also exhibited several plant-growth promotion traits (e.g., 3-indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophores, phosphate solubilization). Considering the taxonomic diversity and the plant-growth promotion potential of the isolates, the collection represents a valuable resource that can be used to optimize the crop cultivation of Salicornia under different environmental conditions and for the attenuation of salt stress in non-halophytes, considering the global threat of arable soil salinization.

The Microbiome of the Lebanese Wild Apple, Malus trilobata, is a Rich Source of Potential Biocontrol Agents for Fungal Post-harvest Pathogens of Apples

The widespread use of harmful fungicides in the agricultural sector has led to a demand for safer alternatives to protect against crop pathogens. The domestic apple is the second most highly consumed fruit in the world and encounters several pre- and post-harvest fungal and bacterial phytopathogens. The goal of this study was to explore the uncharacterized microbiome of a wild apple, Malus trilobata, as a potential source of novel biocontrol agents for two post-harvest fungi that affect commercial apples: Botrytis cinerea and Penicillium expansum. We sampled microflora associated with the leaves, bulk soil, and roots of Malus trilobata in two regions of Lebanon: Ehden reserve in the north and Dhour EL Choueir near Beirut. The two regions have different soil types Dhour EL Choueir and samples from the two regions showed very different microbial compositions, with greater microbial diversity among those from Ehden reserve. Molecular characterization revealed a wide variety of genera displaying activity against the two fungal pathogens, including several with previously unknown antifungal activity: Bosea, Microlunatus, Microbacterium, Mycetecola, Rhizobium and Paraphoma. In total, 92 strains inhibited Penicillium expansum (39%) and 87 strains inhibited Botrytis cinerea (38%) out of 237 screened. Further chemical and genetic characterization of one or more selected strains could pave the way for future development of new biocontrol agents for post-harvest applications.

Diazotrophic Bacteria Pantoea dispersa and Enterobacter asburiae Promote Sugarcane Growth by Inducing Nitrogen Uptake and Defense-Related Gene Expression

Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane yield is commonplace, but it causes substantial environmental damages, particularly soil, and water pollution. Certain rhizosphere microbes are known to be beneficial for sugarcane production, but much of the sugarcane rhizosphere microflora remains unknown. We have isolated several sugarcane rhizosphere bacteria, and 27 of them were examined for N-fixation, plant growth promotion, and antifungal activity. 16S rRNA gene sequencing was used to identify these strains. Among the isolates, several strains were found to have a relatively high activity of nitrogenase and ACC deaminase, the enzyme that reduces ethylene production in plants. These strains were found to possess nifH and acdS genes associated with N-fixation and ethylene production, respectively. Two of these strains, Pantoea dispersa-AA7 and Enterobacter asburiae-BY4 showed maximum plant growth promotion (PGP) and nitrogenase activity, and thus they were selected for detailed analysis. The results show that they colonize different sugarcane tissues, use various growth substrates (carbon and nitrogen), and tolerate various stress conditions (pH and osmotic stress). The positive effect of AA7 and BY4 strains on nifH and stress-related gene (SuCAT, SuSOD, SuPAL, SuCHI, and SuGLU) expression and the induction of defense-related processes in two sugarcane varieties, GT11 and GXB9, showed their potential for stress amelioration and PGP. Both bacterial strains increased several sugarcane physiological parameters. i.e., plant height, shoot weight, root weight, leaf area, chlorophyll content, and photosynthesis, in plants grown under greenhouse conditions. The ability of rhizobacteria on N-fixing in sugarcane was also confirmed by a ¹⁵N isotope-dilution study, and the estimate indicates a contribution of 21-35% of plant nitrogen by rhizobacterial biological N fixation (BNF). This is the first report of sugarcane growth promotion by N-fixing rhizobacteria P. dispersa and E. asburiae strains. Both strains could be used as biofertilizer for sugarcane to minimize nitrogen fertilizer use and better disease management.

Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbiological references. This study, however, has attempted to access the application of FAPROTAX in soil environments. We hypothesized that FAPROTAX was compatible with terrestrial ecosystems. The potential use of FAPROTAX to assign ecological functions of soil bacteria was investigated using meta-analysis and our newly designed experiments. Soil samples from two major terrestrial ecosystems, including agricultural land and forest, were collected. Bacterial taxonomy was analyzed using Illumina sequencing of the 16S rRNA gene and ecological functions of the soil bacteria were assigned by FAPROTAX. The presence of all functionally assigned OTUs (Operation Taxonomic Units) in soil were manually checked using peer-reviewed articles as well as standard microbiology books. Overall, we showed that sample source was not a predominant factor that limited the application of FAPROTAX, but poor taxonomic identification was. The proportion of assigned taxa between aquatic and non-aquatic ecosystems was not significantly different (p > 0.05). There were strong and significant correlations (σ = 0.90–0.95, p < 0.01) between the number of OTUs assigned to genus or order level and the number of functionally assigned OTUs. After manual verification, we found that more than 97% of the FAPROTAX assigned OTUs have previously been detected and potentially performed functions in agricultural and forest soils. We further provided information regarding taxa capable of N-fixation, P and K solubilization, which are three main important elements in soil systems and can be integrated with FAPROTAX to increase the proportion of functionally assigned OTUs. Consequently, we concluded that FAPROTAX can be used for a fast-functional screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases.

Bacterial seed endophyte shapes disease resistance in rice

Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.

Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms

Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate. Here we report on the microbial diversity within the rhizosphere of Larix decidua, a dominant tree species in the Alps, as compared with the microbiome within the surrounding soil. We describe how increased light intensity influenced the rhizobiome and put emphasize on methane cycling microorganisms. Microbial taxa were classified into 26 bacterial, 4 archaeal and 6 fungal phyla revealing significant differences between bulk and rhizosphere soils. The dominant prokaryotic phyla were Proteobacteria, Acidobacteria, Actinobacteria (both, rhizosphere and bulk soil) and Bacteroidetes (rhizosphere soil only) and dominant fungal phyla in both fractions included Ascomycota and Basidiomycota. The rhizosphere community was indicated by Suillus sp., plant growth-promoting bacteria and Candidatus Saccharibacteria. Predicted genes in membrane transport and carbohydrate metabolism were significantly more abundant in rhizosphere soils while genes connected with energy metabolisms and cell motility increased in bulk soils. Dominant methanotrophic microorganisms were Upland Soil Cluster (USC) α methanotrophs, Methylogaea spp. and Methylosinus spp., while most methanogens belonged to Methanomassiliicoccales. The overall abundance of methanotrophs distinctly increased in the rhizosphere but to a very different species-specific extent. The increased light intensity only led to minor changes in the rhizobiome, nevertheless a couple of indicator species (e.g. Pseudomonas sp.) for intensified light conditions were established.