Pesticides reduce symbiotic efficiency of nitrogen-fixing rhizobia and host plants

Diffuse soil pollution from agriculture: Impacts and remediation

Agricultural activities are essential for sustaining the global population, yet they exert considerable pressure on the environment. A major challenge we face today is agricultural pollution, much of which is diffuse in nature, lacking a clear point of origin for chemical discharge. Modern agricultural practices, which often depend on substantial applications of fertilizers, pesticides, and irrigation water, are key contributors to this form of pollution. These activities lead to downstream contamination through mechanisms such as surface runoff, leaching, soil erosion, wind dispersal, and sedimentation. The environmental and human health consequences of diffuse pollution are profound and cannot be ignored. Accurate assessment of the risks posed by agricultural pollutants is crucial for ensuring the production of safe, high-quality food while safeguarding the environment. This requires systematic monitoring and evaluation of agricultural practices, including soil testing and nutrient management. Furthermore, the development and implementation of best management practices (BMPs) are critical in reducing the levels of agricultural pollution. Such measures are essential for mitigating the negative impacts on ecosystems and public health. Therefore, the adoption of preventive strategies aimed at minimizing pollution and its associated risks is highly recommended to ensure long-term environmental sustainability and human well-being.

Effects of biological agents on rhizosphere microecological environment and nutrient availability for rice

As the world's population grows, pursuing sustainable agricultural production techniques to increase crop yields is critical to ensuring global food security. The development and application of biological agents is of great significance in promoting the sustainable development of agriculture. This study aimed to investigate the role of JZ (compound microbial agent) and MZ (biological agent made from plant materials) in improving the rhizosphere microecological environment and nutrient availability for rice. This study found that JZ enriched Cyanobacteria with biological nitrogen fixation functions; spraying MZ can enrich some beneficial microbiota, such as Bradyrhizobium, playing a role in symbiotic nitrogen fixation. Meanwhile, JZ and MZ were found to affect rhizosphere soil metabolism and improve potassium and nitrogen availability. JZ may promote the degradation of fungicides in the rhizosphere soil environment. Overall, applying biological agents through optimizing rice growing environment to improve yield showed great potential.

Impact of irrigation, fertilizer, and pesticide management practices on groundwater and soil health in the rice-wheat cropping system-a comparison of conventional, resource conservation technologies and conservation agriculture

Agricultural intensification in the Northwestern Indo-Gangetic Plain (NWIGP), a critical food bowl supporting millions of people, is leading to groundwater depletion and soil health degradation. This is primarily driven by conventional cultivation practices in the rice-wheat (RW) cropping system, which dominates over 85% of the IGP. Therefore, this study presents a systematic literature review of input management in the RW system, analyzes district-wise trends, outlines the current status, identifies problems, and proposes sustainable management options to achieve development goals. Our district-wise analysis estimates potential water savings from 20 to 60% by transitioning from flood to drip, sprinkler, laser land leveling, or conservation agriculture (CA). Alongside integrating water-saving technologies with CA, crop switching and recharge infrastructure enhancements are needed for groundwater sustainability. Furthermore, non-adherence with recommended fertilizer and pesticide practices, coupled with residue burning, adversely affects soil health and water quality. CA practices have demonstrated substantial benefits, including increased soil permeability (up to 51%), improved organic carbon content (up to 38%), higher nitrifying bacteria populations (up to 73%), enhanced dehydrogenase activities (up to 70%), and increased arbuscular mycorrhizal fungi populations (up to 56%). The detection of multiple fertilizers and pesticides in groundwater underscores the need for legislative measures and the promotion of sustainable farming practices similar to European Union strategies. Lastly, emphasis should be placed on fostering shifts in farmers' perceptions toward optimizing input utilization. The policy implications of this study extend beyond the NWIGP region to the entire country, stressing the critical importance of proactive measures to increase environmental sustainability.

Fungal endophytes modulate the negative effects induced by Persistent Organic Pollutants in the antarctic plant Colobanthus quitensis

Antarctica has one of the most sensitive ecosystems to the negative effects of Persistent Organic Pollutants (POPs) on its biodiversity. This is because of the lower temperatures and the persistence of POPs that promote their accumulation or even biomagnification. However, the impact of POPs on vascular plants is unknown. Moreover, fungal symbionts could modulate the effects on host plants to cope with this stress factor. This study investigates the molecular and ecophysiological responses of the Sub-Antarctic and Antarctic plant Colobanthus quitensis to POPs in different populations along a latitudinal gradient (53°- 67° S), emphasizing the role of endophytic fungi. The results show that exposure of POPs in C. quitensis generates oxidative stress and alters its ecophysiological performance. Nevertheless, C. quitensis in association with fungal endophytes and POPs exposure, shows lower lipid peroxidation, higher proline content and higher photosynthetic capacity, as well as higher biomass and survival percentage, compared to plants in the absence of fungal endophytes. On the other hand, the antarctic plant population (67°S) with endophytic fungi presents better stress modulating upon POPs exposure. Endophytic fungi would be more necessary for plant performance towards higher latitudes with extreme conditions, contributing significantly to their general functional adaptation. We develop a transcriptomics analyses n the C. quitensis-fungal endophytes association from the Peninsula population. We observed that fungal endophytes promote tolerance to POPs stress through upregulated genes for the redox regulation based on ascorbate and scavenging mechanisms (peroxidases, MDAR, VTC4, CCS), transformation (monooxygenases) and conjugation of compounds or metabolites (glutathione transferases, glycosyltransferases, S-transferases), and the storage or elimination of conjugates (ABC transporters, C and G family) that contribute to detoxification cell. This work highlights the contribution of endophytic fungi to plant resistance in situations of environmental stress, especially in extreme conditions such as in antarctica exposed to anthropogenic impact. The implications of these findings are relevant for the biosecurity of one of the last pristine bastions worldwide.

Sublethal pesticide exposure in non-target terrestrial ecosystems: From known effects on individuals to potential consequences on trophic interactions and network functioning

Over the last decades, the intensification of agriculture has resulted in an increasing use of pesticides, which has led to widespread contamination of non-target ecosystems in agricultural landscapes. Plants and arthropods inhabiting these systems are therefore chronically exposed to, at least, low levels of pesticides through direct pesticide drift, but also through the contamination of their nutrient sources (e.g. soil water or host/prey tissues). Pesticides (herbicides, acaricides/insecticides and fungicides) are chemical substances used to control pests, such as weeds, phytophagous arthropods and pathogenic microorganisms. These molecules are designed to disturb specific physiological mechanisms and induce mortality in targeted organisms. However, under sublethal exposure, pesticides also affect biological processes including metabolism, development, reproduction or inter-specific interactions even in organisms that do not possess the molecular target of the pesticide. Despite the broad current knowledge on sublethal effects of pesticides on organisms, their adverse effects on trophic interactions are less investigated, especially within terrestrial trophic networks. In this review, we provide an overview of the effects, both target and non-target, of sublethal exposures to pesticides on traits involved in trophic interactions between plants, phytophagous insects and their natural enemies. We also discuss how these effects may impact ecosystem functioning by analyzing studies investigating the responses of Plant-Phytophage-Natural enemy trophic networks to pesticides. Finally, we highlight the current challenges and research prospects in the understanding of the effects of pesticides on trophic interactions and networks in non-target terrestrial ecosystems.

Deltamethrin's Effect on Nitrogen-Fixing Nodules in Medicago truncatula

Deltamethrin is used against plant pests (e.g., mites and ants) and, in farm animals, against biting insects because of its acaricidal and repellent effects against ticks, thus protecting the sheep and cattle from the transmission of pathogens. However, its impact on the environment still needs to be fully evaluated. This study evaluates the impact of this pyrethroid on the nitrogen-fixing nodules in Medicago truncatula, a model legume. This research compares nodular biomass and root weight between a deltamethrin-treated section and an untreated control section of this legume. Our results indicate a significant reduction in the biomass of nitrogen-fixing nodules in the treated grove, suggesting that deltamethrin negatively affects the symbiotic relationship between M. truncatula and nitrogen-fixing bacteria. This reduction in nodule formation can impair soil fertility and plant growth, highlighting an ecological risk associated with pyrethroid's use in livestock farming. These findings underscore the need for a shift towards Green Veterinary Pharmacology (GVP), which promotes environmentally sustainable practices in managing livestock health. By minimizing our reliance on harmful chemical treatments, GVP offers viable solutions to protect and enhance ecosystem services such as biological nitrogen fixation that are essential for maintaining soil health and agricultural productivity.

Physiological and biochemical characteristics and microbial responses of Medicago sativa (Fabales: Fabaceae) varieties with different resistance to atrazine stress

Atrazine, a commonly employed herbicide for corn production, can leave residues in soil, resulting in photosynthetic toxicity and impeding growth in subsequent alfalfa (Medicago sativa L.) crops within alfalfa-corn rotation systems. The molecular regulatory mechanisms by which atrazine affects alfalfa growth and development, particularly its impact on the microbial communities of the alfalfa rhizosphere, are not well understood. This study carried out field experiments to explore the influence of atrazine stress on the biomass, chlorophyll content, antioxidant system, and rhizosphere microbial communities of the atrazine-sensitive alfalfa variety WL-363 and the atrazine-resistant variety JN5010. The results revealed that atrazine significantly reduced WL-363 growth, decreasing plant height by 8.58 cm and root length by 5.42 cm (p < 0.05). Conversely, JN5010 showed minimal reductions, with decreases of 1.96 cm in height and 1.26 cm in root length. Chlorophyll content in WL-363 decreased by 35% under atrazine stress, while in JN5010, it was reduced by only 10%. Reactive oxygen species (ROS) accumulation increased by 60% in WL-363, compared to a 20% increase in JN5010 (p < 0.05 for both). Antioxidant enzyme activities, such as superoxide dismutase (SOD) and catalase (CAT), were significantly elevated in JN5010 (p < 0.05), suggesting a more robust defense mechanism. Although the predominant bacterial and fungal abundances in rhizosphere soils remained generally unchanged under atrazine stress, specific microbial groups exhibited variable responses. Notably, Promicromonospora abundance declined in WL-363 but increased in JN5010. FAPROTAX functional predictions indicated shifts in the abundance of microorganisms associated with pesticide degradation, resistance, and microbial structure reconstruction under atrazine stress, displaying different patterns between the two varieties. This study provides insights into how atrazine residues affect alfalfa rhizosphere microorganisms and identifies differential microbial responses to atrazine stress, offering valuable reference data for screening and identifying atrazine-degrading bacteria.

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops

Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices.

Symbiont plasticity as a driver of plant success

We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.

Effects of mixtures of herbicides on nutrient cycling and plant support considering current agriculture practices

The use of mixtures of pesticides and consecutive pesticide applications challenge current regulations aimed at protecting ecosystem health due to unpredictable effects of complex and dynamic mixtures. In this study, we tested the ecotoxicological effects of mixtures of herbicides, applied following a real application scheme of soybean production on soil health in a mesocosm experiment. The experiment included two sequential applications; first, glyphosate + dicamba + clethodim, and 30 days later, flumioxazin + metolachlor. Commercial products were used at the recommended doses and at two other concentrations: half and double the recommended dose. Soybean plants were exposed to the herbicide-contaminated soil from the time of sowing to the beginning of pod formation. Half of the plants were harvested at the vegetative stage and the remaining plants at the reproductive stage to evaluate endpoints related to plant support and nutrient cycling. Plant biomass was significantly affected during the vegetative stage at the recommended and double the recommended dose, with the effects being mixture-dose dependent. Lower total and arbuscular colonization of mycorrhizas were also observed in double the recommended dose, and intermediate results were observed for the recommended dose. Nodule mass and phosphorous concentration in plants decreased with increasing herbicide doses. By the end of the experiment, nodule mass and total mycorrhizal colonization were low in the plants treated with double the recommended dose of herbicides. However, both endpoints reached similar values to the control at lower herbicide doses. Plant height and phenology were only lower at double the recommended dose during the experiment. The use of non-standard endpoints evidenced that important soil functions were transiently or permanently affected, while the realistic application scheme accounted for the impact of the management practice currently used. Pesticide risk assessment should therefore, incorporate both issues to effectively protect the ecosystems.

Probing the potential of salinity-tolerant endophytic bacteria to improve the growth of mungbean [Vigna radiata (L.) Wilczek]

Soil salinity is one of the major limiting factors in plant growth regulation. Salinity-tolerant endophytic bacteria (STEB) can be used to alleviate the negative effects of salinity and promote plant growth. In this study, thirteen endophytic bacteria were isolated from mungbean roots and tested for NaCl salt-tolerance up to 4%. Six bacterial isolates, TMB2, TMB3, TMB5, TMB6, TMB7 and TMB9, demonstrated the ability to tolerate salt. Plant growth-promoting properties such as phosphate solubilization, indole-3-acetic acid (IAA) production, nitrogen fixation, zinc solubilization, biofilm formation and hydrolytic enzyme production were tested in vitro under saline conditions. Eight bacterial isolates indicated phosphate solubilization potential ranging from 5.8-17.7 μg mL-1, wherein TMB6 was found most efficient. Ten bacterial isolates exhibited IAA production ranging from 0.3-2.1 μg mL-1, where TMB7 indicated the highest potential. All the bacterial isolates except TMB13 exhibited nitrogenase activity. Three isolates, TMB6, TMB7 and TMB9, were able to solubilize zinc on tris-minimal media. All isolates were capable of forming biofilm except TMB12 and TMB13. Only TMB2, TMB6 and TMB7 exhibited cellulase activity, while TMB2 and TMB7 exhibited pectinase production. Based on in vitro testing, six efficient STEB were selected and subjected to the further studies. 16S rRNA gene sequencing of efficient STEB revealed the maximum similarity between TMB2 and Rhizobium pusense, TMB3 and Agrobacterium leguminum, TMB5 and Achromobacter denitrificans, TMB6 and Pseudomonas extremorientalis, TMB7 and Bradyrhizobium japonicum and TMB9 and Serratia quinivorans. This is the first international report on the existence of A. leguminum, A. denitrificans, P. extremorientalis and S. quinivorans inside the roots of mungbean. Under controlled-conditions, inoculation of P. extremorientalis TMB6, B. japonicum TMB7 and S. quinivorans TMB9 exhibited maximum potential to increase plant growth parameters; specifically plant dry weight was increased by up to 52%, 61% and 45%, respectively. Inoculation of B. japonicum TMB7 displayed the highest potential to increase plant proline, glycine betaine and total soluble proteins contents by 77%, 78% and 64%, respectively, compared to control under saline conditions. It is suggested that the efficient STEB could be used as biofertilizers for mungbean crop productivity under saline conditions after field-testing.

Influence of CuO Nanoparticle Aspect Ratio and Surface Charge on Disease Suppression in Tomato (Solanum lycopersicum)

Nanoparticles (NPs) have been shown to deliver micronutrients to plants to improve health, increase biomass, and suppress disease. Nanoscale properties such as morphology, size, composition, and surface chemistry have all been shown to impact nanomaterial interactions with plant systems. An organic-ligand-free synthesis method was used to prepare positively charged copper oxide (CuO) nanospikes, negatively charged CuO nanospikes, and negatively charged CuO nanosheets with exposed (001) crystal faces. X-ray photoelectron spectroscopy measurements show that the negative charge correlates to increased surface concentration of O on the NP surface, whereas relatively higher Cu concentrations are observed on the positively charged surfaces. The NPs were then used to treat tomato (Solanum lycopersicum) grown in soil infested with Fusarium oxysporum f. sp. lycopersici under greenhouse conditions. The negatively charged CuO significantly reduced disease progression and increased biomass, while the positively charged NPs and a CuSO4 salt control had little impact on the plants. Self-assembled monolayers were used to mimic the leaf surface to understand the intermolecular interactions between the NPs and the plant leaf; the data demonstrate that NP electrostatics and hydrogen-bonding interactions play an important role in adsorption onto leaf surfaces. These findings have important implications for the tunable design of materials as a strategy for the use of nano-enabled agriculture to increase food production.

A comprehensive review of chlorophenols: Fate, toxicology and its treatment

Chlorophenols represent one of the most abundant families of toxic pollutants emerging from various industrial manufacturing units. The toxicity of these chloroderivatives is proportional to the number and position of chlorine atoms on the benzene ring. In the aquatic environment, these pollutants accumulate in the tissues of living organisms, primarily in fishes, inducing mortality at an early embryonic stage. Contemplating the behaviour of such xenobiotics and their prevalence in different environmental components, it is crucial to understand the methods used to remove/degrade the chlorophenol from contaminated environment. The current review describes the different treatment methods and their mechanism towards the degradation of these pollutants. Both abiotic and biotic methods are investigated for the removal of chlorophenols. Chlorophenols are either degraded through photochemical reactions in the natural environment, or microbes, the most diverse communities on earth, perform various metabolic functions to detoxify the environment. Biological treatment is a slow process because of the more complex and stable structure of pollutants. Advanced Oxidation Processes are effective in degrading such organics with enhanced rate and efficiency. Based on their ability to generate hydroxyl radicals, source of energy, catalyst type, etc., different processes such as sonication, ozonation, photocatalysis, and Fenton's process are discussed for the treatment or remediation efficiency towards the degradation of chlorophenols. The review entails both advantages and limitations of treatment methods. The study also focuses on reclamation of chlorophenol-contaminated sites. Different remediation methods are discussed to restore the degraded ecosystem back in its natural condition.

Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans

Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.

Promotion of the growth and yield of Zea mays by synthetic microbial communities from Jala maize

Plant growth-promoting bacteria (PGPB) are a source of nutrient supply, stimulate plant growth, and even act in the biocontrol of phytopathogens. However, these phenotypic traits have rarely been explored in culturable bacteria from native maize landraces. In this study, synthetic microbial communities (SynCom) were assembled with a set of PGPB isolated from the Jala maize landrace, some of them with additional abilities for the biocontrol of phytopathogenic fungi and the stimulation of plant-induced systemic resistance (ISR). Three SynCom were designed considering the phenotypic traits of bacterial strains, including Achromobacter xylosoxidans Z2K8, Burkholderia sp. Z1AL11, Klebsiella variicola R3J3HD7, Kosakonia pseudosacchari Z2WD1, Pantoea ananatis E2HD8, Pantoea sp. E2AD2, Phytobacter diazotrophicus Z2WL1, Pseudomonas protegens E1BL2, and P. protegens E2HL9. Plant growth promotion in gnotobiotic and greenhouse seedlings assays was performed with Conejo landrace; meanwhile, open field tests were carried out on hybrid CPL9105W maize. In all experimental models, a significant promotion of plant growth was observed. In gnotobiotic assays, the roots and shoot length of the maize seedlings increased 4.2 and 3.0 times, respectively, compared to the untreated control. Similarly, the sizes and weights of the roots and shoots of the plants increased significantly in the greenhouse assays. In the open field assay performed with hybrid CPL9105W maize, the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated with SynCom 3. In addition, the incidence of rust fungal infections decreased significantly from 12.5% in the control to 8% in the treatment with SynCom 3. All SynCom designs promoted the growth of maize in all assays. However, SynCom 3 formulated with A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola R3J3HD7, P. ananatis E2HD8, P. diazotrophicus Z2WL1, and P. protegens E1BL2 displayed the best results for promoting plant growth, their yield, and the inhibition of fungal rust. This study demonstrated the biotechnological eco-friendly plant growth-promoting potential of SynCom assemblies with culturable bacteria from native maize landraces for more sustainable and economic agriculture.

Reduction in the Use of Some Herbicides Favors Nitrogen Fixation Efficiency in Phaseolus vulgaris and Medicago sativa

In recent decades, the quality of agricultural soils has been seriously affected by the excessive application of pesticides, with herbicides being one of the most abundant. Continuous use of herbicides alters the soil microbial community and beneficial interactions between plants and bacteria such as legume-rhizobia spp. symbiosis, causing a decrease in the biological nitrogen fixation, which is essential for soil fertility. Therefore, the aim of this work was to study the effect of two commonly used herbicides (pendimethalin and clethodim) on the legume-rhizobia spp. symbiosis to improve the effectiveness of this process. Phaseolus vulgaris plants grown in pots with a mixture of soil:perlite (3:1 v/v), showed a 44% inhibition of nitrogen fixation rate with pendimethalin. However, clethodim, specifically used against monocots, did not induce significant differences. Additionally, we analyzed the effect of herbicides on root exudate composition, detecting alterations that might be interfering with the symbiosis establishment. In order to assess the effect of the herbicides at the early nodulation steps, nodulation kinetics in Medicago sativa plants inoculated with Sinorhizobium meliloti were performed. Clethodim caused a 30% reduction in nodulation while pendimethalin totally inhibited nodulation, producing a reduction in bacterial growth and motility as well. In conclusion, pendimethalin and clethodim application reduced the capacity of Phaseolus vulgaris and Medicago sativa to fix nitrogen by inhibiting root growth and modifying root exudate composition as well as bacterial fitness. Thus, a reduction in the use of these herbicides in these crops should be addressed to favor a state of natural fertilization of the soil through greater efficiency of leguminous crops.

Phytoremediation of isoproturon-contaminated sites by transgenic soybean

The widespread application of isoproturon (IPU) can cause serious pollution to the environment and threaten ecological functions. In this study, the IPU bacterial N-demethylase gene pdmAB was transferred and expressed in the chloroplast of soybean (Glycine max L. 'Zhonghuang13'). The transgenic soybeans exhibited significant tolerance to IPU and demethylated IPU to a less phytotoxic metabolite 3-(4-isopropylphenyl)-1-methylurea (MDIPU) in vivo. The transgenic soybeans removed 98% and 84% IPU from water and soil within 5 and 14 days, respectively, while accumulating less IPU in plant tissues compared with the wild-type (WT). Under IPU stress, transgenic soybeans showed a higher symbiotic nitrogen fixation performance (with higher total nodule biomass and nitrogenase activity) and a more stable rhizosphere bacterial community than the WT. This study developed a transgenic (TS) soybean capable of efficiently removing IPU from its growing environment and recovering a high-symbiotic nitrogen fixation capacity under IPU stress, and provides new insights into the interactions between rhizosphere microorganisms and TS legumes under herbicide stress.

Leveraging microbiome rediversification for the ecological rescue of soil function

BACKGROUND

Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS

Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS

In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Human body burden of bisphenol A: a case study of lactating mothers in Florianopolis, Brazil

Exclusive breast milk is the diet recommended by the World Health Organization (WHO) until 6 months of age. However, breastfeeding has the potential of transferring certain toxic chemicals from the mother to the infant. Bisphenol A (BPA) is a synthetic chemical used as a monomer in polycarbonate plastics and epoxy resins. Information on BPA concentration in the breast milk of lactating mothers is very limited; thus, this study aimed to determine the concentration of BPA in the colostrum of 64 post-partum women at a university-affiliated tertiary hospital in South Brazil. The results showed that all the breast milk samples contained a high concentration of BPA with a median value of 34.18 ng/mL. Furthermore, the concentration of BPA in mothers was influenced by the consumption of foods packaged in plastic packaging, especially when the plastic is heated (p = 0.0182). The total daily intake of BPA in breastfed infants was 19.5 µg/kg/day and 28.5 µg/kg/day was recorded at the 95th percentile of body weight per day, which is higher than the maximum daily intake estimated by the European Authority of Food Safety. These data showed a high concentration of BPA in the breastmilk of the lactating mothers which might be through the use of plastic containers as food/drink packages. This is of public health importance as the high concentration of BPA in their breast milk can be an indicator of potentially serious health problems in these mothers and much more in the babies breastfed with BPA-contaminated breast milk.

Pesticide contamination in agro-ecosystems: toxicity, impacts, and bio-based management strategies

Continuous rise in application of pesticides in the agro-ecosystems in order to ensure food supply to the ever-growing population is of greater concern to the human health and the environment. Once entered into the agro-ecosystem, the fate and transport of pesticides is determined largely by the nature of pesticides and the soil attributes, in addition to the soil-inhabiting microbes, fauna, and flora. Changes in the soil microbiological actions, soil properties, and enzymatic activities resulting from pesticide applications are the important factors substantially affecting the soil productivity. Disturbances in the microbial community composition may lead to the considerable perturbations in cycling of major nutrients, metals, and subsequent uptake by plants. Indiscriminate applications are linked with the accumulation of pesticides in plant-based foods, feeds, and animal products. Furthermore, rapid increase in the application of pesticides having long half-life has also been reported to contaminate the nearby aquatic environments and accumulation in the plants, animals, and microbes surviving there. To circumvent the negative consequences of pesticide application, multitude of techniques falling in physical, chemical, and biological categories are presented by different investigators. In the present study, important findings pertaining to the pesticide contamination in cultivated agricultural soils; toxicity on soil microbes, plants, invertebrates, and vertebrates; effects on soil characteristics; and alleviation of toxicity by bio-based management approaches have been thoroughly reviewed. With the help of bibliometric analysis, thematic evolution and research trends on the bioremediation of pesticides in the agro-ecosystems have also been highlighted.

Rhizobium leguminosarum bv. viciae-Mediated Silver Nanoparticles for Controlling Bean Yellow Mosaic Virus (BYMV) Infection in Faba Bean Plants

The faba bean plant (Vicia faba L.) is one of the world's most important legume crops and can be infected with various viral diseases that affect its production. One of the more significant viruses in terms of economic impact is bean yellow mosaic virus (BYMV). The current study used the molecularly identified Rhizobium leguminosarum bv. viciae strain 33504-Borg1, a nitrogen-fixing bacteria, to biosynthesize silver nanoparticles (AgNPs) to control BYMV disease in faba bean plants. Scanning electron microscopy (SEM), a particle size analyzer (PSA) with dynamic light scattering (DLS), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), and Fourier transform infrared spectroscopy (FTIR) were used to characterize the prepared AgNPs. The DLS, SEM, and TEM analyses revealed that the AgNPs were spherical and rough, with sizes ranging from 13.7 to 40 nm. The FTIR analysis recognized various functional groups related to AgNP capping and stability. Under greenhouse conditions, spraying faba bean leaves with the AgNPs (100 µg/mL) 24 h before BYMV inoculation induced plant resistance and reduced plant disease severity and virus concentration levels. Contrarily, the AgNP treatment enhanced plant health by raising photosynthetic rates, increasing the fresh and dry weight of the faba bean plants, and increasing other measured metrics to levels comparable to healthy controls. Antioxidant enzymes (peroxidase and polyphenol oxidase) inhibited the development of BYMV in the faba bean plants treated with the AgNPs. The AgNPs decreased oxidative stress markers (H₂O₂ and MDA) in the faba bean plants. The plants treated with the AgNPs showed higher expression levels of PR-1 and HQT than the control plants. The study findings could be used to develop a simple, low-cost, and environmentally friendly method of protecting the faba bean plant from BYMV.

Ecotoxicological implications of residual pesticides to beneficial soil bacteria: A review

Optimization of crop production in recent times has become essential to fulfil food demands of constantly increasing human populations worldwide. To address this formidable challenge, application of agro-chemicals including synthetic pesticides in intensive farm practices has increased alarmingly. The excessive and indiscriminate application of pesticides to foster food production however, leads to its exorbitant deposition in soils. After accumulation in soils beyond threshold limits, pesticides harmfully affect the abundance, diversity and composition and functions of rhizosphere microbiome. Also, the cost of pesticides and emergence of resistance among insect-pests against pesticides are other reasons that require attention. Due to this, loss in soil nutrient pool cause a substantive reduction in agricultural production which warrant the search for newer environmentally friendly technology for sustainable crop production. Rhizosphere microbes, in this context, play vital roles in detoxifying the polluted environment making soil amenable for cultivation through detoxification of pollutants, rhizoremediation, bioremediation, pesticide degradation, and stress alleviation, leading to yield optimization. The response of soil microorganisms to range of chemical pesticides is variable ranging from unfavourable to the death of beneficial microbes. At cellular and biochemical levels, pesticides destruct the morphology, ultrastructure, viability/cellular permeability, and many biochemical reactions including protein profiles of soil bacteria. Several classes of pesticides also disturb the molecular interaction between crops and their symbionts impeding the overall useful biological processes. The harmful impact of pesticides on soil microbes, however, is poorly researched. In this review, the recent findings related with potential effects of synthetic pesticides on a range of soil microbiota is highlighted. Emphasis is given to find and suggest strategies to minimize the chemical pesticides usage in the real field conditions to preserve the viability of soil beneficial bacteria and soil quality for safe and sustainable crop production even in pesticide contaminated soils.

Unraveling the potential of pesticide-tolerant Pseudomonas sp. augmenting biological and physiological attributes of Vigna radiata (L.) under pesticide stress

In the agricultural domain, chemical pesticides are repetitively and harshly used to kill harmful pests, but they often pose a serious threat to microbial diversity, soil fertility and agricultural output. To deal with these problems, pesticide-tolerant plant growth promoting (PGP) rhizobacterial strains are often used to combat pesticidal toxicity. Here, Pseudomonas sp. PGR-11 (accession no. OM348534), recovered from a Vigna radiata (L.) rhizosphere, produced various growth regulating (GR) substances, including indole-3-acetic acid (IAA; 82.5 ± 9.2 μg mL^-1), enzyme 1-aminocyclopropane 1-carboxylate (ACC) deaminase (μM α-ketobutyrate mg^-1 protein h^-1), siderophores and ammonia. Strain PGR-11 grew well when cultured in growth medium with added metalaxyl (MTXL; 1200 μg mL^-1), carbendazim (CBZM; 800 μg mL^-1) and tebuconazole (TBZL; 1600 μg mL^-1). Pseudomonas sp. synthesized PGP substances even in the presence of increasing doses of pesticides. The phytotoxicity of the tested pesticides was assessed both in vitro and under pot-house conditions using a Vigna radiata (L.) crop. Increasing concentrations of chemical pesticides negatively impacted the growth, physiological and biochemical features. However, pesticide-tolerant Pseudomonas sp. relieved the toxicity and improved the biological attributes of the plant. Bio-inoculated plants showed significant enhancement in germination attributes, dry biomass, symbiotic features and yield features when compared to un-inoculated ones. Furthermore, with 100 μg metalaxyl kg^-1 soil, strain PGR-11 increased the chl-a, chl-b, total chlorophyll, carotenoids, SPAD index, photosystem efficiency (Fv/Fm), PSII quantum yield (FPSII), photochemical quenching (qP) and non-photochemical quenching (NpQ) content by 12, 19, 16, 27, 34, 41, 26, 29 and 33%, respectively, over un-inoculated but pesticide-treated plants. Additionally, inoculation of Pseudomonas sp. with 100 μg tebuconazole kg^-1 soil caused a significant (p ≤ 0.05) enhancement in transpiration rate (E), stomatal conductance (g _s), photosynthetic rate (P _N), vapor pressure deficit (kPa) and internal CO₂ concentration (C _i) of 19, 26, 23, 28 and 34%, respectively. Conclusively, the power to tolerate abnormally high pesticide concentration, the capacity to produce/secrete PGP substances even in a pesticide-stressed medium and the potential for improving/increasing the growth and physiology of plants by pesticide detoxification makes Pseudomonas sp. PGR-11 a fascinating choice for augmenting the productivity of V. radiata (L.) even in pesticide-stressed soils. The current findings will be helpful for exploring pesticide-tolerant ACC-deaminase-positive microbial strains as gifted entities for the environmental bioremediation of pesticides.

Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa

Grain legumes play a significant role in smallholder farming systems in Africa because of their contribution to nutrition and income security and their role in fixing nitrogen. Biological Nitrogen Fixation (BNF) serves a critical role in improving soil fertility for legumes. Although much research has been conducted on rhizobia in nitrogen fixation and their contribution to soil fertility, much less is known about the distribution and diversity of the bacteria strains in different areas of the world and which of the strains achieve optimal benefits for the host plants under specific soil and environmental conditions. This paper reviews the distribution, characterization, and commercialization of elite rhizobia strains in Africa.

Soil salinization accelerates microbiome stabilization in iterative selections for plant performance

Climate change-related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt-amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high-biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add-back control (re-adding initial frozen soil microbiome) as a within-generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add-back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.

Farm-scale differentiation of active microbial colonizers

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Recent advances in nanoremediation: Carving sustainable solution to clean-up polluted agriculture soils

Agriculture is one of the foremost significant human activities, which symbolizes the key source for food, fuel and fibers. This activity results in a lot of ecological harms particularly with the excessive usage of chemical fertilizers and pesticides. Different agricultural practices have remained industrialized to advance food production, due to the growth in the world population and to meet the food demand through the routine use of more effective fertilizers and pesticides. Soil is intensely embellished by environmental contamination and it can be stated as "universal incline." Soil pollution usually occurs from sewage wastes, accidental discharges or as byproducts of chemical residues of unrestrained production of numerous materials. Soil pollution with hazardous materials alters the physical, chemical, and biological properties, causing undesirable changes in soil fertility and ecosystem. Engineered nanomaterials offer various solutions for remediation of contaminated soils. Engineered nanomaterial-enable technologies are able to prevent the uncontrolled release of harmful materials into the environment along with capabilities to combat soil and groundwater borne pollutants. Currently, nanobiotechnology signifies a hopeful attitude to advance agronomic production and remediate polluted soils. Studies have outlined the way of nanomaterial applications to restore the eminence of the environment and assist the detection of polluted sites, along with potential remedies. This review focuses on the latest developments in agricultural nanobiotechnology and the tools developed to combat soil or land and or terrestrial pollution, as well as the benefits of using these tools to increase soil fertility and reduce potential toxicity.

Ecological performance of multifunctional pesticide tolerant strains of Mesorhizobium sp. in chickpea with recommended pendimethalin, ready-mix of pendimethalin and imazethpyr, carbendazim and chlorpyrifos application

The present study was designed to screen the Mesorhizobium strains (50) for tolerance with four recommended pesticides in chickpea. In-vitro, robust pesticide tolerant strains were developed in pesticides amended media over several generations. Further, verification of the multifunctional traits of pesticide tolerant mesorhizobia under pesticide stress was conducted in-vitro. Among different pesticides, significantly high tolerance in Mesorhizobium strains was observed with recommended doses of pendimethalin (37%) and ready-mix (36%) followed by chlorpyrifos (31%) and carbendazim (30%), on an overall basis. Based on multifunctional traits, Mesorhizobium strains viz. MR2, MR17 and recommended MR33 were the most promising. Ecological performance of the potential Mesorhizobium strains alone and in dual-inoculation with recommended PGP rhizobacterium strain RB-1 (Pseudomonas argenttinensis JX239745.1) was subsequently analyzed in field following standard pesticide application in PBG-7 and GPF-2 chickpea varieties for two consecutive rabi seasons (2015 and 2016). Dual-inoculant treatments; recommended RB-1 + MR33 (4.1%) and RB-1 + MR2 (3.8%) significantly increased the grain yield over Mesorhizobium alone treatments viz MR33 and MR2, respectively. Grain yield in PBG7 variety was significantly affected (7.3%) by the microbial inoculant treatments over GPF2 variety. Therefore, the potential pesticide tolerant strains MR2 and MR33 can be further explored as compatible dual-inoculants with recommended RB-1 for chickpea under environmentally stressed conditions (pesticide application) at multiple locations. Our approach using robust multifunctional pesticide tolerant Mesorhizobium for bio-augmentation of chickpea might be helpful in the formulation of effective bio-inoculants consortia in establishing successful chickpea-Mesorhizobium symbiosis.

Molecular identification and biological control of Ralstonia solanacearum from wilt of papaya by natural compounds and Bacillus subtilis: An integrated experimental and computational study

Ralstonia solanacearum is a harmful pathogen that causes severe wilt disease in several vegetables. In the present study, we identified R. solanacearum from wilt of papaya by 16S rRNA PCR amplification. Virulence ability of R. solanacearum was determined by amplification of approximately 1500 bp clear band of hrpB gene. Further, in-vitro seed germination assay showed that R. solanacearum reduced the germination rate up to 26.21%, 34% and 33.63% of cucumber, bottle guard and pumpkin seeds, respectively whereas shoot and root growth were also significantly decreased. Moreover, growth inhibition of R. solanacearum was recorded using antibacterial compound from medicinal plant and antagonistic B. subtilis. Petroleum ether root extract of Rauvolfia serpentina showed highest 22 ± 0.04 mm diameter of zone of inhibition where methanolic extract of Cymbopogon citratus and ethanolic extract of Lantana camara exhibited 20 ± 0.06 mm and 20 ± 0.01 mm zone of inhibition against R. solanacearum, respectively. In addition, bioactive compounds of B. subtilis inhibited R. solanacearum growth by generating 17 ± 0.09 mm zone of inhibition. To unveil the inhibition mechanism, we adopted chemical-protein interaction network and molecular docking approaches where we found that, rutin from C. citratus interacts with citrate (Si)-synthase and dihydrolipoyl dehydrogenase of R. solanacearum with binding affinity of -9.7 kcal/mol and -9.5 kcal/mol while quercetin from B. subtillis interacts with the essential protein F0F1 ATP synthase subunit alpha of the R. solancearum with binding affinity of -6.9 kcal/mol and inhibit the growth of R. solanacearum. Our study will give shed light on the development of eco-friendly biological control of wilt disease of papaya.

Symbiosis and the Anthropocene

Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and "farmed" organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.

The effect of organic farming on water reusability, sustainable ecosystem, and food toxicity

Water is a fundamental necessity for people's well-being and the ecosystem's sustainability; however, its toxicity due to agrochemicals usage for food production leads to the deterioration of water quality. The poor water quality diminishes its reusability, thus limiting efficient water usage. Organic farming is one of the best ways that does not only reduce the deterioration of water quality but also decrease food toxicity. In organic farming, the crop is grown with no/less chemical usage. Besides, organic farming maintains biodiversity and reduces the anthropogenic footprint on soil, air, water, wildlife, and especially on the farming communities. Fields that are organically managed continuously for years have fewer pest populations and were attributed to increased biodiversity and abundance of multi-trophic interactions as well as to changes in plant metabolites. Fewer insect pests (pathogen vectors), in turn, would result in fewer crop diseases and increase crop production. This review highlights that organic farming may play a critical role in the reduction of pests and pathogens, which eventually would reduce the need for chemical reagents to protect crops, improving yield quality and water reusability.

Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.

Can dispersal be leveraged to improve microbial inoculant success?

Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.

The Challenge of Combining High Yields with Environmentally Friendly Bioproducts: A Review on the Compatibility of Pesticides with Microbial Inoculants

Inoculants or biofertilizers aiming to partially or fully replace chemical fertilizers are becoming increasingly important in agriculture, as there is a global perception of the need to increase sustainability. In this review, we discuss some important results of inoculation of a variety of crops with rhizobia and other plant growth-promoting bacteria (PGPB). Important improvements in the quality of the inoculants and on the release of new strains and formulations have been achieved. However, agriculture will continue to demand chemical pesticides, and their low compatibility with inoculants, especially when applied to seeds, represents a major limitation to the success of inoculation. The differences in the compatibility between pesticides and inoculants depend on their active principle, formulation, time of application, and period of contact with living microorganisms; however, in general they have a high impact on cell survival and metabolism, affecting the microbial contribution to plant growth. New strategies to solve the incompatibility between pesticides and inoculants are needed, as those that have been proposed to date are still very modest in terms of demand.

Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil

A Gram-negative, facultative anaerobic, non-lagellated and rod-shaped bacterium FML-4^T was isolated from a chlorothalonil-contaminated soil in Nanjing, China. Phylogenetic analyses of 16S rRNA genes revealed that the strain FML-4^T shared the highest sequence similarity of 97.1% with Ciceribacter thiooxidans KCTC 52231^T, followed by Rhizobium rosettiformans CCM 7583^T (97.0%) and R. daejeonense KCTC 12121^T (96.8%). Although the sequence similarities of the housekeeping genes thrC, rceA, glnII, and atpD between strain FML-4^T and C. thiooxidans KCTC 52231^T were 83.8%, 88.7%, 86.2%, and 92.0%, respectively, strain FML-4^T formed a monophyletic clade in the cluster of Rhizobium species. Importantly, the feature gene of the genus Rhizobium, nifH gene (encoding the dinitrogenase reductase), was detected in strain FML-4^T but not in C. thiooxidans KCTC 52231^T. In addition, strain FML-4^T contained the summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), C_19:0 cyclo ω8c and C_16:0 as the major fatty acids. Genome sequencing of strain FML-4^T revealed a genome size of 7.3 Mbp and a G+C content of 63.0 mol%. Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization, average nucleotide identity (ANI, similarity 77.3-75.4%), and digital DNA-DNA hybridization (dDDH, similarity 24.5-22.3%), it was concluded that strain FML-4^T represented a novel species of the genus Rhizobium, for which the name Rhizobium flavescens sp. nov. was proposed (type strain FML-4^T = CCTCC AB 2019354^T = KCTC 62839^T).

Endocrine Disruptor Exposure Causes Infochemical Dysregulation and an Ecological Cascade from Zooplankton to Algae

Endocrine disruption is intimately linked to controlling the population of pollutant-exposed organisms through reproduction and development dysregulation. This study investigated how endocrine disruption in a predator organism could affect prey species biology through infochemical communication. Daphnia magna and Chlorella vulgaris were chosen as model prey and predator planktons, respectively, and fenoxycarb was used for disrupting the endocrine system of D. magna. Hormones as well as endo- and exometabolomes were extracted from daphnids and algal cells and their culture media and analyzed using liquid chromatography with tandem mass spectrometry. Biomolecular perturbations of D. magna under impaired offspring production and hormone dysregulation were observed. Differential biomolecular responses of the prey C. vulgaris, indicating changes in methylation and infochemical communication, were subsequently observed under the exposure to predator culture media, containing infochemicals released from the reproducibly normal and abnormal D. magna, as results of fenoxycarb exposure. The observed cross-species transfer of the endocrine disruption consequences, initiated from D. magna, and mediated through infochemical communication, demonstrates a novel discovery and emphasizes the broader ecological risk of endocrine disruptors beyond reproduction disruption in target organisms.

Neonicotinoid Seed Treatments Have Significant Non-target Effects on Phyllosphere and Soil Bacterial Communities

The phyllosphere and soil are dynamic habitats for microbial communities. Non-pathogenic microbiota, including leaf and soil beneficial bacteria, plays a crucial role in plant growth and health, as well as in soil fertility and organic matter production. In sustainable agriculture, it is important to understand the composition of these bacterial communities, their changes in response to disturbances, and their resilience to agricultural practices. Widespread pesticide application may have had non-target impacts on these beneficial microorganisms. Neonicotinoids are a family of systemic insecticides being vastly used to control soil and foliar pests in recent decades. A few studies have demonstrated the long-term and non-target effects of neonicotinoids on agroecosystem microbiota, but the generality of these findings remains unclear. In this study, we used 16S rRNA gene amplicon sequencing to characterize the effects of neonicotinoid seed treatment on soil and phyllosphere bacterial community diversity, composition and temporal dynamics in a 3-year soybean/corn rotation in Quebec, Canada. We found that habitat, host species and time are stronger drivers of variation in bacterial composition than neonicotinoid application. They, respectively, explained 37.3, 3.2, and 2.9% of the community variation. However, neonicotinoids did have an impact on bacterial community structure, especially on the taxonomic composition of soil communities (2.6%) and over time (2.4%). They also caused a decrease in soil alpha diversity in the middle of the growing season. While the neonicotinoid treatment favored some bacterial genera known as neonicotinoid biodegraders, there was a decline in the relative abundance of some potentially beneficial soil bacteria in response to the pesticide application. Some of these bacteria, such as the plant growth-promoting rhizobacteria and the bacteria involved in the nitrogen cycle, are vital for plant growth and improve soil fertility. Overall, our results indicate that neonicotinoids have non-target effects on phyllosphere and soil bacterial communities in a soybean-corn agroecosystem. Exploring the interactions among bacteria and other organisms, as well as the bacterial functional responses to the pesticide treatment, may enhance our understanding of these non-target effects and help us adapt agricultural practices to control these impacts.

Molecular Biology in the Improvement of Biological Nitrogen Fixation by Rhizobia and Extending the Scope to Cereals

The contribution of biological nitrogen fixation to the total N requirement of food and feed crops diminished in importance with the advent of synthetic N fertilizers, which fueled the “green revolution”. Despite being environmentally unfriendly, the synthetic versions gained prominence primarily due to their low cost, and the fact that most important staple crops never evolved symbiotic associations with bacteria. In the recent past, advances in our knowledge of symbiosis and nitrogen fixation and the development and application of recombinant DNA technology have created opportunities that could help increase the share of symbiotically-driven nitrogen in global consumption. With the availability of molecular biology tools, rapid improvements in symbiotic characteristics of rhizobial strains became possible. Further, the technology allowed probing the possibility of establishing a symbiotic dialogue between rhizobia and cereals. Because the evolutionary process did not forge a symbiotic relationship with the latter, the potential of molecular manipulations has been tested to incorporate a functional mechanism of nitrogen reduction independent of microbes. In this review, we discuss various strategies applied to improve rhizobial strains for higher nitrogen fixation efficiency, more competitiveness and enhanced fitness under unfavorable environments. The challenges and progress made towards nitrogen self-sufficiency of cereals are also reviewed. An approach to integrate the genetically modified elite rhizobia strains in crop production systems is highlighted.

Ecological impact of organochlorine pesticides consortium on autochthonous microbial community in agricultural soil

Organochlorine pesticides (OCPs) used in agricultural practices are of global concern due to their toxicological hazards on biomes of the impacted soil. Geochemistry and microbiome of OCPs-impacted (OW) soil was determined and compared with those of pristine (L1) soils. Microbiome of OW was based on sequencing total 16S rRNA genes of prokaryotes and Internal Transcribed Spacer (ITS2) regions between 5.8S and 28S rRNA genes of eukaryotes using Illumina MiSeq platform for bacterial and fungal communities, respectively. Geochemical properties of OW were assessed for ecological risks of OCPs on biota via risk quotient (RQ) and maximum cumulative ratio (MCR). It was established OW was polluted with 15 OCPs, along with consequential nitrate and phosphorous deficiencies. Ten of the 15 OCPs exerted severe ecological risk (RQ > 1: 4-992), of which endosulfan contributed 76% of the ecotoxicity (MCR = 1.3) on OW. The key players in OW were observed to be Enterobacteriaceae and Mortierellaceae represented by Escherichia and Mortierella taxa, respectively. Low abundance of Nitrospirae species and extinction of Glomeromycota in OW connoted serious toxicological consequences of the OCPs. Taxon XOR (Taxon Exclusive Or) analysis revealed 38,212 and 63,474 counts of bacterial and fungal species, respectively, were exclusively found in the impacted OW and possibly contributed to natural attenuation of the OCPs in the impacted agricultural soil. Conversely, 61,005 (bacteria) and 33,397 (fungi) species counts that were missing in OCPs-impacted OW, but present in pristine L1, opined the species as bio-indicators of OCPs ecotoxicity in agricultural soils. While the species tagged as bio-indicators would be valuable in monitoring OCPs pollution, those suggested to be players in self-recovery process will be invaluable to designing bioremediation strategies for OCPs-impacted agricultural soil.

Order of microbial succession affects rhizobia-mediated biocontrol efforts against Phytophthora root rot

The management of soilborne root diseases in pulse crops is challenged by a limited range of resistance sources and often a complete absence of in-crop management options. Therefore, alternative management strategies need to be developed. We evaluated disease limiting interactions between the rhizobia species Mesorhizobium ciceri, and the oomycete pathogen Phytophthora medicaginis, which causes Phytophthora root rot (PRR) of chickpea (Cicer arietinum). For the PRR susceptible var. Sonali plants, post-pathogen M. ciceri inoculation significantly improved probability of plant survival when compared to P. medicaginis infected plants only pre-inoculated with M. ciceri (75 % versus 35 %, respectively). Potential mechanisms for these effects were investigated: rhizobia inoculation benefits to plant nodulation were not demonstrated, but the highest nodule N-fixation activity of P. medicaginis inoculated plants occurred for the post-pathogen M. ciceri treatment; rhizobia inoculation treatment did not reduce lesion development but certain combinations of microbial inoculation led to significant reduction in root growth. Microcosm studies, however, showed that the presence of M. ciceri reduced growth of P. medicaginis isolates. Putative chickpea disease resistance gene expression was evaluated using qPCR in var. Sonali roots. When var. Sonali plants were treated with M. ciceri post-P. medicaginis inoculation, the gene regulation in the plant host became more similar to PRR moderately resistant var. PBA HatTrick. These results suggest that M. ciceri application post P. medicaginis inoculation may improve plant survival by inducing defense responses similar to a PRR moderately resistant chickpea variety. Altogether, these results indicate that order of microbial succession can significantly affect PRR plant survial in susceptible chickpea under controlled conditions and improved plant survival effects are due to a number of different mechanisms including improved host nutrition, through direct inhibiton of pathogen growth, as well as host defense priming.

Chlorpyrifos inhibits nitrogen fixation in rice-vegetated soil containing Pseudomonas stutzeri A1501

Chlorpyrifos, a common organophosphorus pesticide, is widely used for agricultural pest control and can inhibit nitrogen-fixing bacteria biomass in paddy. In this study, the additions of chlorpyrifos (1 and 8 mg kg^-1) to soil, with or without Pseudomonas stutzeri A1501, resulted in a significant decrease in nitrogen fixation, despite insignificant effects on the abundances of P. stutzeri A1501 and bacteria in soil. Toxic effect of chlorpyrifos on P. stutzeri A1501 nitrogenase activity in medium was also observed, accompanied by a significant reduction in the expression of nitrogen-fixing related genes (nifA and nifH). Furthermore, rhizosphere colonization and biofilm formation by P. stutzeri A1501 were repressed by chlorpyrifos, leading to decreased nitrogenase activity in the rhizosphere. Biofilm formation in medium was inhibited by bacterial hyperkinesis and reduction of extracellular polymeric substance, including exopolysaccharides and proteins. Together, these findings showed that chlorpyrifos-induced production of reactive oxygen species (ROS) which was directly responsible for reduced nitrogenase activity in the medium, soil, and rhizosphere by inhibiting the expressions of nitrogen-fixing related genes. Furthermore, the inhibition of biofilm formation by chlorpyrifos or ROS likely aggravated the reduction in rhizospherere nitrogenase activity. These findings provide potentially valuable insights into the toxicity of chlorpyrifos on nitrogen-fixing bacteria and its mechanisms. Furthermore, for sustainable rice production, it is necessary to evaluate whether other pesticides affect nitrogen fixation and select pesticides that do not inhibit nitrogen fixation.

The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes

Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.

Synthetic Symbiosis under Environmental Disturbances

The power of synthetic biology is immense. Will it, however, be able to withstand the environmental pressures once released in the wild. As new technologies aim to do precisely the same, we use a much simpler model to test mathematically the effect of a changing environment on a synthetic biological system. We assume that the system is successful if it maintains proportions close to what we observe in the laboratory. Extreme deviations from the expected equilibrium are possible as the environment changes. Our study provides the conditions and the designer specifications which may need to be incorporated in the synthetic systems if we want such “ecoblocs” to survive in the wild.

By virtue of complex ecologies, the behavior of mutualisms is challenging to study and nearly impossible to predict. However, laboratory engineered mutualistic systems facilitate a better understanding of their bare essentials. On the basis of an abstract theoretical model and a modifiable experimental yeast system, we explore the environmental limits of self-organized cooperation based on the production and use of specific metabolites. We develop and test the assumptions and stability of the theoretical model by leveraging the simplicity of an artificial yeast system as a simple model of mutualism. We examine how one-off, recurring, and permanent changes to an ecological niche affect a cooperative interaction and change the population composition of an engineered mutualistic system. Moreover, we explore how the cellular burden of cooperating influences the stability of mutualism and how environmental changes shape this stability. Our results highlight the fragility of mutualisms and suggest interventions, including those that rely on the use of synthetic biology.

IMPORTANCE The power of synthetic biology is immense. Will it, however, be able to withstand the environmental pressures once released in the wild. As new technologies aim to do precisely the same, we use a much simpler model to test mathematically the effect of a changing environment on a synthetic biological system. We assume that the system is successful if it maintains proportions close to what we observe in the laboratory. Extreme deviations from the expected equilibrium are possible as the environment changes. Our study provides the conditions and the designer specifications which may need to be incorporated in the synthetic systems if we want such “ecoblocs” to survive in the wild.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Modelling and control of a banana soilborne pest in a multi-seasonal framework

We study the infestation dynamics of banana or plantain plants by Radopholus similis, a plant-parasitic nematode that causes severe damages. Two control strategies are implemented in our model: pesticides, which are widely used, and fallows, which are more environmentally friendly. To represent the host-parasite dynamics, two semi-discrete models are proposed. During each cropping season, free nematodes enter the plant roots, on which they feed and reproduce. At the end of the cropping season, fruits are harvested. In the first model, the parent plant is cut down to be replaced by one of its suckers and pesticides are applied. In the second model, the parent plant is uprooted and a fallow period is introduced, inducing the decay of the free pest populations; at the beginning of the next cropping season, a pest-free vitroplant is planted. For both models, the effective reproduction number of pests is computed, assuming that the infestation dynamics are fast compared to the other processes, which leads to the model order reduction. Conditions on the pesticide load or the fallow duration are then derived to ensure the stability of the periodic pest free solution. Finally, numerical simulations illustrate these theoretical results.