Biological Control beneath the Feet: A Review of Crop Protection against Insect Root Herbivores

Phytotoxicity and Phytotoxic Substances in Calamus tenuis Roxb

Calamus tenuis is a shrub species distributed across South Asia. It grows well in diversified habitats and tends to dominate plants in the surrounding environment. The phytotoxicity of C. tenuis and the action of its phytochemicals against other plant species could explain its dominant behavior. Compounds with phytotoxic activity are in high demand as prospective sources of ecofriendly bioherbicides. Therefore, we investigated the phytotoxicity of C. tenuis. Aqueous methanol extracts of this plant species significantly limited the growth of four test plant species, two monocots (barnyard grass and timothy), and two dicots (alfalfa and cress), in a dose- and species-dependent manner. Bio-directed chromatographic isolation of the C. tenuis extracts yielded two major active substances: a novel compound, calamulactone {(S)-methyl 8-(5-oxo-2,5-dihydrofuran-2-yl) octanoate}, and 3-oxo-α-ionone. Both of the identified compounds exerted strong growth inhibitory effects on cress and timothy seedlings. The concentrations of 3-oxo-α-ionone and calamulactone required to limit the growth of the cress seedlings by 50% (I50) were 281.6-199.5 and 141.1-105.5 µM, respectively, indicating that the effect of calamulactone was stronger with lower I50 values. Similarly, the seedlings of timothy also showed a considerably higher sensitivity to calamulactone (I50: 40.5-84.4 µM) than to 3-oxo-α-ionone (I50: 107.8-144.7 µM). The findings indicated that the leaves of C. tenuis have marked growth-inhibitory potential, and could affect surrounding plants to exert dominance over the surrounding plant community. Moreover, the two identified phytotoxic substances might play a key role in the phytotoxicity of C. tenuis, and could be a template for bioherbicide development. This paper was the first to report calamulactone and its phytotoxicity.

Positive Chemotaxis of the Entomopathogenic Nematode Steinernema australe (Panagrolaimorpha: Steinenematidae) towards High-Bush Blueberry (Vaccinium corymbosum) Root Volatiles

The foraging behavior of the infective juveniles (IJs) of entomopathogenic nematodes (EPNs) relies on host-derived compounds, but in a tri-trophic context, herbivore-induced root volatiles act as signals enhancing the biological control of insect pests by recruiting EPNs. In southern Chile, the EPN Steinernema australe exhibits the potential to control the raspberry weevil, Aegorhinus superciliosus, a key pest of blueberry Vaccinium corymbosum. However, there is no information on the quality of the blueberry root volatile plume or the S. australe response to these chemicals as putative attractants. Here, we describe the root volatile profile of blueberries and the chemotaxis behavior of S. australe towards the volatiles identified from Vaccinium corymbosum roots, infested or uninfested with A. superciliosus larvae. Among others, we found linalool, α-terpineol, limonene, eucalyptol, 2-carene, 1-nonine, 10-undecyn-1-ol, and methyl salicylate in root volatiles and, depending on the level of the emissions, they were selected for bioassays. In the dose-response tests, S. australe was attracted to all five tested concentrations of methyl salicylate, 1-nonine, α-terpineol, and 2-carene, as well as to 100 µg mL^-1 of 10-undecyn-1-ol, 0.1 and 100 µg mL^-1 of linalool, and 100 µg mL^-1 of limonene, whereas eucalyptol elicited no attraction or repellency. These results suggest that some volatiles released from damaged roots attract S. australe and may have implications for the biocontrol of subterranean pests.

Stress tolerance in entomopathogenic nematodes: Engineering superior nematodes for precision agriculture

Entomopathogenic nematodes (EPNs) are soil-dwelling parasitic roundworms commonly used as biocontrol agents of insect pests in agriculture. EPN dauer juveniles locate and infect a host in which they will grow and multiply until resource depletion. During their free-living stage, EPNs face a series of internal and environmental stresses. Their ability to overcome these challenges is crucial to determine their infection success and survival. In this review, we provide a comprehensive overview of EPN response to stresses associated with starvation, low/elevated temperatures, desiccation, osmotic stress, hypoxia, and ultra-violet light. We further report EPN defense strategies to cope with biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing the genetic and biochemical basis of these strategies to the nematode model Caenorhabditis elegans, we provide new avenues and targets to select and engineer precision nematodes adapted to specific field conditions.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Effectiveness of the Entomopathogenic Fungal Species Metarhizium anisopliae Strain NCAIM 362 Treatments against Soil Inhabiting Melolontha melolontha Larvae in Sweet Potato (Ipomoea batatas L.)

The effect of fungal entomopathogen M. anisopliae strain NCAIM 362 against M. melolontha larvae in sweet potato was tested under open field conditions when crop management included compost supply and soil cover (agro-foil or agro-textile). Additionally, the effect of M. anisopliae same strain against M. melolontha was compared with the effect of α-cypermethrin under greenhouse conditions. Soil microbial community using Illumina sequencing and soil biological activity were tested as possible parameter influencing M. anisopliae effect. According to the results, compost supply and textile cover may enhance the effectiveness of M. anisopliae under open field conditions, while no effect of fungal treatment was detected under greenhouse conditions. Even if soil parameters (chemical composition, bacterial, and biological activity) were identical, the effect of α-cypermethrin against M. melolontha larvae was significant: lower ratio of larval survival and less damaged tubers were detected after the chemical treatment. Our results suggest that M. anisopliae strain NCAIM 362 is not effective to control M. melolontha larvae, further pieces of research are needed to test other species of the Metarhizium genus to find an effective agent for sustainable pest control in sweet potato.

Preventative Approach to Microbial Control of Capnodis tenebrionis by Soil Application of Metarhizium brunneum and Beauveria bassiana

Management of the Mediterranean flat-headed root-borer, Capnodis tenebrionis, is critical due to the larvae’s root localization. Neonate larvae can be exposed to natural enemies before penetrating the roots. Application of Metarhizium brunneum strain Mb7 and Beauveria bassiana strain GHA formulations on rice granules was investigated for their efficacy against C. tenebrionis larvae. Mb7 application, evaluated on apricot twigs, significantly and dose-dependently reduced colonization rates of neonates, with highest mortality at 10⁸ conidia/g soil. Neonate susceptibility to Mb7 and GHA was evaluated on potted rootstocks (GF677 almond × peach, 2729 plum) planted in entomopathogenic fungi (EPF)-premixed soil (1.3–1.6 × 10⁵ conidia/cm³ soil) or in EPF-free soil surface-treated with 5 g Mb7 fungal granules (1.25 × 10⁹ conidia). Larval colonization rates were reduced 7.4-fold in 2729 by both fungi; only Mb7 completely prevented colonization of GF677 by larvae. Larvae inside plant galleries exhibited mycosis with EPF-treated soils and both fungi proliferated on larval frass. Mb7 conidia germinated in the rhizosphere of GF677, and conidia of both fungi remained viable throughout the trial. Galleria baiting technique was used on EPF-treated soil to evaluate EPF infectivity over time; Mb7 and GHA persisted 180 and 90 days post inoculation, respectively. The formulation (fungus-covered rice grains), delivery method (mixing with soil) and persistence (3–6 months) of Mb7 and GHA are feasible for potential field application to control C. tenebrionis.

Biotechnological Potential of Bdellovibrio and Like Organisms and Their Secreted Enzymes

Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria that selectively prey on a broad range of Gram-negative bacteria, including multidrug-resistant human pathogens. Due to their unique lifestyle, they have been long recognized as a potential therapeutic and biocontrol agent. Research on BALOs has rapidly grown over the recent decade, resulting in many publications concerning molecular details of bacterial predation as well as applications thereof in medicine and biotechnology. This review summarizes the current knowledge on biotechnological potential of obligate predatory bacteria and their secreted enzymes.

Photorhabdus: a tale of contrasting interactions

Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus Photorhabdus comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore Photorhabdus has three distinct and obligate roles to play during this life-cycle: (1) Photorhabdus must kill the insect host; (2) Photorhabdus must be capable of supporting nematode growth and development; and (3) Photorhabdus must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between Photorhabdus and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.

Current Knowledge of the Entomopathogenic Fungal Species Metarhizium flavoviride Sensu Lato and Its Potential in Sustainable Pest Control

Fungal entomopathogens are gaining increasing attention as alternatives to chemical control of arthropod pests, and the literature on their use under different conditions and against different species keeps expanding. Our review compiles information regarding the entomopathogenic fungal species Metarhizium flavoviride (Gams and Rozsypal 1956) (Hypocreales: Clavicipitaceae) and gives account of the natural occurrences and target arthropods that can be controlled using M. flavoviride. Taxonomic problems around M. flavoviride species sensu lato are explained. Bioassays, laboratory and field studies examining the effect of fermentation, culture regimes and formulation are compiled along with studies on the effect of the fungus on target and non-target organisms and presenting the effect of management practices on the use of the fungus. Altogether, we provide information to help conducting basic studies, and by pointing out relatively uncharted territories, help to set new research areas.

Contribution of different predator guilds to tritrophic interactions along ecological clines

The strengths of interactions between plants, herbivores, and predators are predicted to relax with elevation. Despite the fundamental role predators play in tritrophic interactions, high-resolution experimental evidence describing predation across habitat gradients is still scarce in the literature and varies by predator. With this opinion paper, we look at how tritrophic strength of systems including different vertebrate and invertebrate predator guilds changes with elevation. Specifically, we focus on how birds, ants, parasitoids, and nematodes exert top-down pressure as predators and propose ways, in which each group could be better understood through elevational gradient studies. We hope to enrich future perspectives for disentangling the different biotic and abiotic factors underlying predator-mediated trophic interactions in a diversity of habitats.

Modulating CRISPR gene drive activity through nucleocytoplasmic localization of Cas9 in S. cerevisiae

Background

The bacterial CRISPR/Cas genome editing system has provided a major breakthrough in molecular biology. One use of this technology is within a nuclease-based gene drive. This type of system can install a genetic element within a population at unnatural rates. Combatting of vector-borne diseases carried by metazoans could benefit from a delivery system that bypasses traditional Mendelian laws of segregation. Recently, laboratory studies in fungi, insects, and even mice, have demonstrated successful propagation of CRISPR gene drives and the potential utility of this type of mechanism. However, current gene drives still face challenges including evolved resistance, containment, and the consequences of application in wild populations. Additional research into molecular mechanisms that would allow for control, titration, and inhibition of drive systems is needed.

Results

In this study, we use artificial gene drives in budding yeast to explore mechanisms to modulate nuclease activity of Cas9 through its nucleocytoplasmic localization. We examine non-native nuclear localization sequences (both NLS and NES) on Cas9 fusion proteins in vivo through fluorescence microscopy and genomic editing. Our results demonstrate that mutational substitutions to nuclear signals and combinatorial fusions can both modulate the level of gene drive activity within a population of cells.

Conclusions

These findings have implications for control of traditional nuclease-dependent editing and use of gene drive systems within other organisms. For instance, initiation of a nuclear export mechanism to Cas9 could serve as a molecular safeguard within an active gene drive to reduce or eliminate editing.

Improving the annotation of the Heterorhabditis bacteriophora genome

Background

Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes.

Findings

We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant.

Conclusions

Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species’ genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.

Tuning CRISPR-Cas9 Gene Drives in Saccharomyces cerevisiae

Control of biological populations is an ongoing challenge in many fields, including agriculture, biodiversity, ecological preservation, pest control, and the spread of disease. In some cases, such as insects that harbor human pathogens (e.g., malaria), elimination or reduction of a small number of species would have a dramatic impact across the globe. Given the recent discovery and development of the CRISPR-Cas9 gene editing technology, a unique arrangement of this system, a nuclease-based "gene drive," allows for the super-Mendelian spread and forced propagation of a genetic element through a population. Recent studies have demonstrated the ability of a gene drive to rapidly spread within and nearly eliminate insect populations in a laboratory setting. While there are still ongoing technical challenges to design of a more optimal gene drive to be used in wild populations, there are still serious ecological and ethical concerns surrounding the nature of this powerful biological agent. Here, we use budding yeast as a safe and fully contained model system to explore mechanisms that might allow for programmed regulation of gene drive activity. We describe four conserved features of all CRISPR-based drives and demonstrate the ability of each drive component-Cas9 protein level, sgRNA identity, Cas9 nucleocytoplasmic shuttling, and novel Cas9-Cas9 tandem fusions-to modulate drive activity within a population.

The first report of Xenorhabdus indica from Steinernema pakistanense: co-phylogenetic study suggests co-speciation between X. indica and its steinernematid nematodes

During a survey in agricultural fields of the sub-humid region of Meerut district, India, two strains of entomopathogenic nematodes, labelled CS31 and CS32, were isolated using the Galleria baiting technique. Based on morphological and morphometric studies, and molecular data, the nematodes were identified as Steinernema pakistanense, making this finding the first report of this species from India. For the first time, we performed a molecular and biochemical characterization of the bacterial symbiont of S. pakistanense. Furthermore, a co-phylogenetic analysis of the bacteria from the monophyletic clade containing a symbiont of S. pakistanense, together with their nematode hosts, was conducted, to test the degree of nematode–bacteria co-speciation. Both isolates were also tested in a laboratory assay for pathogenicity against two major pests, Helicoverpa armigera and Spodoptera litura. The morphology of the Indian isolates corresponds mainly to the original description, with the only difference being the absence of a mucron in first-generation females and missing epiptygmata in the second generation. The sequences of bacterial recA and gyrB genes have shown that the symbiont of S. pakistanense is closely related to Xenorhabdus indica, which is associated with some other nematodes from the ‘bicornutum’ group. Co-phylogenetic analysis has shown a remarkable congruence between the nematode and bacterial phylogenies, suggesting that, in some lineages within the Steinernema / Xenorhabdus complex, the nematodes and bacteria have undergone co-speciation. In the virulence assay, both strains caused a 100% mortality of both tested insects after 48 h, even at the lowest doses of 25 infective juveniles per insect, suggesting that S. pakistanense could be considered for use in the biocontrol of these organisms in India.

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.

In-Field Habitat Management to Optimize Pest Control of Novel Soil Communities in Agroecosystems

The challenge of managing agroecosystems on a landscape scale and the novel structure of soil communities in agroecosystems both provide reason to focus on in-field management practices, including cover crop adoption, reduced tillage, and judicial pesticide use, to promote soil community diversity. Belowground and epigeal arthropods, especially exotic generalist predators, play a significant role in controlling insect pests, weeds, and pathogens in agroecosystems. However, the preventative pest management tactics that dominate field-crop production in the United States do not promote biological control. In this review, we argue that by reducing disturbance, mitigating the effects of necessary field activities, and controlling pests within an Integrated Pest Management framework, farmers can facilitate the diversity and activity of native and exotic arthropod predators.

Communication in the Phytobiome

The phytobiome is composed of plants, their environment, and diverse interacting microscopic and macroscopic organisms, which together influence plant health and productivity. These organisms form complex networks that are established and regulated through nutrient cycling, competition, antagonism, and chemical communication mediated by a diverse array of signaling molecules. Integration of knowledge of signaling mechanisms with that of phytobiome members and their networks will lead to a new understanding of the fate and significance of these signals at the ecosystem level. Such an understanding could lead to new biological, chemical, and breeding strategies to improve crop health and productivity.