Progress in environmental monitoring and mitigation strategies for herbicides and insecticides: A comprehensive review

Herbicides and insecticides are pervasively applied in agricultural sector to increase the yield by controlling or eliminating bug vermin and weeds. Although, resistance development occurs, direct and indirect impact on human health and ecosystem is clearly visible. Normally, herbicides and pesticides are water soluble in nature; accordingly, it is hard to decrease their deadliness and to dis-appear them from the environment. They are profoundly specific, and considered as poisonous to various peoples in agricultural and industrial work places. In order to substantially reduce the harmful impacts, it is crucial to thoroughly examine the detection and mitigation measures for these compounds. The primary objective of this paper is to provide an overview of various herbicide and pesticide detection techniques and associated remedial techniques. A short summary on occurrence and harmful effects of herbicides/insecticides on ecosystem has been included to the study. The conventional and advanced, rapid techniques for the detection of insecticides and herbicides were described in detail. A detailed overview on several mitigation strategies including advanced oxidation, adsorption, electrochemical process, and bioremediation as well as the mechanism behind the strategic approaches to reduce the effects of growing pesticide pollution has been emphasized. Regardless of the detection techniques and mitigation strategies, the recent advances employed, obstacles, and perspectives have been discussed in detail.

Domestication shapes the endophytic microbiome and metabolome of Salicornia europaea

AIMS

We aim at understanding the effect of domestication on the endophytic microbiome and metabolome of Salicornia europaea and collecting evidence on the potential role of microbial populations and metabolites in the adaptation of plants to different ecological contexts (wild vs crops).

METHODS AND RESULTS

Samples were collected from a natural salt marsh (wild) and an intensive crop field (crop). High-throughput sequencing of the 16S rRNA gene, gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) were used to analyze the endophytic bacterial communities and the metabolite profiles of S. europaea roots, respectively. The elemental analysis of the plant shoots was performed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS).Overall, significant differences were found between the microbiome of wild and cultivated plants. The later showed a higher relative abundance of the genera Erythrobacter, Rhodomicrobium, and Ilumatobacter than wild plants. The microbiome of wild plants was enriched in Marinobacter, Marixanthomonas, and Thalassospira. The metabolite profile of crop plants revealed higher amounts of saturated and non-saturated fatty acids and acylglycerols. In contrast, wild plants contained comparatively more carbohydrates and most macroelements (i.e. Na, K, Mg, and Ca).

CONCLUSIONS

There is a strong correlation between plant metabolites and the endosphere microbiome of S. europaea. In wild populations, plants were enriched in carbohydrates and the associated bacterial community was enriched in genes related to primary metabolic pathways such as nitrogen metabolism and carbon fixation. The endosphere microbiome of crop plants was predicted to have higher gene counts related to pathogenesis. Crop plants also exhibited higher amounts of azelaic acid, an indicator of exposure to phytopathogens.

Crop rotations increased soil ecosystem multifunctionality by improving keystone taxa and soil properties in potatoes

Continuous cropping of the same crop leads to soil degradation and a decline in crop production, and these impacts could be mitigated through rotation cropping. Although crop rotation enhances soil fertility, microbial community diversity, and potato yield, its effects on the soil ecosystem multifunctionality (EMF) remain unclear. In the present research, we comparatively examined the effects of potato continuous cropping (PP) and rotation cropping [potato-oat rotation (PO) and potato-forage maize rotation (PFM)] on the soil EMF as well as the roles of keystone taxa, microbes abundance, and chemical properties in EMF improvement. It was demonstrated that soil EMF is increased in rotation cropping (PO and PFM) than PP. Soil pH was higher in rotation cropping (PO and PFM) than in PP, while total phosphorus (TP) and available phosphorus (AP) were significantly decreased than that in PP. Rotation cropping (PO and PFM) markedly changed the bacterial and fungal community compositions, and improved the potential plant-beneficial fungi, e.g., Schizothecium and Chaetomium, while reducing the abundances of the potentially phytopathogenic fungi, e.g., Alternaria, Fusarium, Verticillium dahiae, Gibberella, Plectosphaerella, Colletotrichum, Phoma, and Lectera in comparison with PP. Also, co-occurrence patterns for bacteria and fungi were impacted by crop rotation, and keystone taxa, e.g., Nitrospira.1, Lysinibacillus, Microlunatus.1, Sphingomonas.3, Bryobacter.1, Micromonospora, and Schizothecium, were enriched in PO and PFM than PP. The structural equation model (SEM) further demonstrated that cropping systems increased soil ecosystem multifunctionality through regulating SOM and keystone taxa (Schizothecium1), and keystone taxa were mediated by soil pH. This study suggested that rotation cropping might contribute to the improvement of soil ecosystem multifunctionality as well as the development of disease-suppressive soils in comparison with potato continuous cropping.

Efficient native strains of rhizobia improved nodulation and productivity of French bean (Phaseolus vulgaris L.) under rainfed condition

Biological nitrogen fixation is the most important eco-friendly approach to nitrogenous fertilizer management in the rhizosphere. Rhizobium is considered the most important symbiotic N-fixing microorganism. Native strains of Rhizobium perform better than the non-native strains by getting ambient conditions for growth and proliferation. Native strains enhance the soil fertility and productivity of pulses. The study was carried out in three phases, i.e., pot experiment, field experiment, and farmers' field demonstrations. In a pot experiment, two isolated rhizobia were inoculated to seeds of French bean (Phaseolus vulgaris) and applied with and without lime to evaluate crop growth, photosynthetic activity, and nodule characteristics of the target crop. In the field, strains were inoculated to seeds of French bean, which received different combinations of inputs- inorganic fertilizers, lime, and boron- to study the influence of native stains on crop productivity and agronomic efficiency. In comparison to non-limed packaging, the amounts of chlorophyll a, chlorophyll b, total chlorophyll, and chlorophyll a:b were, respectively, 13% to 30%, 1% to 15%, 10% to 27%, and 1% to 20% greater in limed packages. In limed packages compared to non-limed packages, the root length, biomass, density, and growth rate were increased by 16% to 17%, 36% to 52%, 38% to 49%, and 36% to 52%, respectively. In contrast to non-limed packages, limed packages had nodule attributes like the number of nodules per plant and nodular weight, which were 28% to 41% and 33% to 37% greater, respectively. Inoculation of native rhizobia strains with liming to acid soil increased 46% to 72% of leaf nitrogen content over non-limed rhizobia inoculated packages. In a field experiment, the adoption of soil test-based fertilizer application had an advantage of 25% in pod yield over farmers' practice. Acid soil amelioration with lime improved pod yield from 14% to 39% over non-limed packages. Farmers' field demonstration recorded the highest pod yield in the package where seeds were inoculated with S2 (RBHR-21) strain added with soil test-based fertilizers (STD) followed by STD + S1 (RBHR-15) with 98% and 84% increase over farmers' practice. However, experimental evidence favored using both strains for bio-inoculation of the French bean crop.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

BACKGROUND

Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).

RESULTS

The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.

CONCLUSION

Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.

Soil Sterilization Eliminates Beneficial Microbes That Provide Natural Pest Suppression Ecosystem Services Against Radopholus similis and Fusarium Oxysporum V5w2 in the Endosphere and Rhizosphere of Tissue Culture Banana Plants

Endosphere and rhizosphere microbes offer plant growth promotion and pest suppression ecosystem services in banana-based agroecosystems. Interest has been growing towards the use of such beneficial microbes in protecting vulnerable tissue culture banana plants against pathogens such as Radopholus similis and Fusarium oxysporum. A screenhouse experiment with potted tissue culture banana plants was conducted using sterile and non-sterile soil to investigate the effect of soil biota on R. similis and F. oxysporum strain V5w2. Plants grown in non-sterile soil had lower damage and R. similis density in roots and rhizosphere, while most plant growth-related parameters including root freshweight, shoot freshweight, total freshweight, plant height, and leaf size were larger compared to those from sterile soil. Shoot dryweight and Mg content were higher in plants from sterile soil, while their leaves developed discolored margins. R. similis-inoculated plants in sterile soil were smaller, had more dead roots, higher nematode density, and produced fewer and smaller leaves, than those from non-sterile soil. For all plant growth-related parameters, nematode density and root damage, no differences were recorded between controls and F. oxysporum V5w2-inoculated plants; and no differences between those inoculated with R. similis only and the ones co-inoculated with the nematode and F. oxysporum V5w2. Banana roots inoculated with F. oxysporum V5w2 were lighter in color than those without the fungus. Independent or combined inoculation of banana plants with F. oxysporum V5w2 and R. similis resulted in lower optical density of root extracts. In vitro assays indicated the presence of Fusarium spp. and other root endophytic microbes that interacted antagonistically with the inoculated strain of F. oxysporum V5w2. It is concluded that, soil sterilization eliminates beneficial microbes that provide natural pest suppression ecosystem services against R. similis and F. oxysporum in the endosphere and rhizosphere of tissue culture banana plants. I recommend the integration of microbiome conservation into tissue culture technology through the proposed “Tissue Culture Microbiome Conservation Technology.”

Soil Microbes Determine Outcomes of Pathogenic Interactions Between Radopholus similis and Fusarium oxysporum V5w2 in Tissue Culture Banana Rhizospheres Starved of Nitrogen, Phosphorus, and Potassium

The contributions of soil biota toward outcomes of pathogenic interactions between Radopholus similis and Fusarium oxysporum V5w2 in tissue culture banana plants starved of nitrogen (N), phosphorus (P), and potassium (K) were investigated. The study was based on three screenhouse factorial experiments (2 × 2 × 2) comprising of potted banana plants with or without R. similis, with or without F. oxysporum V5w2, and either grown in sterile or non-sterile soil. All plants in each of the three experiments received nutrient solutions that were deficient in N, P, or K, respectively. In all the three nutritional regimes, plants inoculated with R. similis were heavily colonized by the nematode with high percentage dead roots and necrosis, while their root biomasses were low. N-starved plants co-inoculated with R. similis and F. oxysporum V5w2 had lower percentage dead roots and tended to have numerically lower nematode density compared to those treated with R. similis only, especially in non-sterile soil. N-starved plants inoculated with R. similis had higher shoot dry weight, were taller with more leaves that were larger, compared to those not inoculated with the nematode. Plants grown in non-sterile soil had lower percentage dead roots, necrosis and R. similis density than those from sterile soil, regardless of the nutrient regime. N-starved plants from non-sterile soil were shorter with smaller leaves having decreased chlorophyll content and lower biomass, compared to those from sterile soil. By contrast, P and K starved plants from non-sterile soil were taller with larger leaves and more biomass, compared to those from sterile soil. Roots inoculated with R. similis had higher endophytic colonization by Fusarium spp., especially when co-inoculated with F. oxysporum V5w2 and grown in sterile soil among the N and K-starved plants. In conclusion, pathogenic interactions between R. similis and F. oxysporum V5w2 are predominantly suppressed by a complex of soil microbes that exert plant growth promoting effects in tissue culture banana plants through N, P, and K dependent processes. Nitrogen is the most important limiting factor in rhizosphere interactions between banana roots, beneficial microbes and the pathogens. Soil sterilization and the stringent aseptic tissue culture techniques still require the development of alternative innovative ways of conserving microbial services for sustainable agriculture.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.

Recent Advances in the Molecular Effects of Biostimulants in Plants: An Overview

As the world develops and population increases, so too does the demand for higher agricultural output with lower resources. Plant biostimulants appear to be one of the more prominent sustainable solutions, given their natural origin and their potential to substitute conventional methods in agriculture. Classified based on their source rather than constitution, biostimulants such as humic substances (HS), protein hydrolysates (PHs), seaweed extracts (SWE) and microorganisms have a proven potential in improving plant growth, increasing crop production and quality, as well as ameliorating stress effects. However, the multi-molecular nature and varying composition of commercially available biostimulants presents challenges when attempting to elucidate their underlying mechanisms. While most research has focused on the broad effects of biostimulants in crops, recent studies at the molecular level have started to unravel the pathways triggered by certain products at the cellular and gene level. Understanding the molecular influences involved could lead to further refinement of these treatments. This review comprises the most recent findings regarding the use of biostimulants in plants, with particular focus on reports of their molecular influence.

Phytomicrobiome for promoting sustainable agriculture and food security: Opportunities, challenges, and solutions

Ensuring food security in an environmentally sustainable way is a global challenge. To achieve this agriculture productivity requires increasing by 70 % under increasingly harsh climatic conditions without further damaging the environmental quality (e.g. reduced use of agrochemicals). Most governmental and inter-governmental agencies have highlighted the need for alternative approaches that harness natural resource to address this. Use of beneficial phytomicrobiome, (i.e. microbes intimately associated with plant tissues) is considered as one of the viable solutions to meet the twin challenges of food security and environmental sustainability. A diverse number of important microbes are found in various parts of the plant, i.e. root, shoot, leaf, seed, and flower, which play significant roles in plant health, development and productivity, and could contribute directly to improving the quality and quantity of food production. The phytomicrobiome can also increase productivity via increased resource use efficiency and resilience to biotic and abiotic stresses. In this article, we explore the role of phytomicrobiome in plant health and how functional properties of microbiome can be harnessed to increase agricultural productivity in environmental-friendly approaches. However, significant technical and translation challenges remain such as inconsistency in efficacy of microbial products in field conditions and a lack of tools to manipulate microbiome in situ. We propose pathways that require a system-based approach to realize the potential to phytomicrobiome in contributing towards food security. We suggest if these technical and translation constraints could be systematically addressed, phytomicrobiome can significantly contribute towards the sustainable increase in agriculture productivity and food security.