Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization

Biopreparations for the decomposition of crop residues

Recently, there has been growing interest in biopreparations that intensify the decomposition of crop residues. These preparations can promote nutrient cycling and soil fertility, ultimately supporting healthy plant growth and increasing agricultural productivity. However, the development and commercialization of biopreparations poses unique challenges. Producers of biopreparations struggle to develop highly effective preparations, which then face regulatory hurdles and must win market acceptance. This literature review provides up-to-date data on microbial preparations available commercially on the European market, along with information on current relevant regulations. Challenges for the development and commercialization of new biopreparations are also discussed. The development and commercialization of biopreparations require a comprehensive approach that addresses the complex interplay of microbial and environmental factors. The need for more specific regulations on biopreparations for decomposing crop residues, clearer instructions on their use, and further research on the overall impact of biopreparations on the soil metabolome and optimal conditions for their application were indicated. Moreover, manufacturers should prioritize the development of high-quality products that meet the needs of farmers and address concerns about environmental impact and public acceptance.

Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water

The quantity and quality of DNA isolated from environmental samples are crucial for getting robust high-throughput sequencing data commonly used for microbial community analysis. The differences in the nature and physicochemical properties of environmental samples impact DNA yields, and therefore, an optimisation of the protocols is always recommended. For instance, samples collected from corroded areas contain high concentrations of metals, salts, and hydrocarbons that can interfere with several steps of the DNA extraction protocols, thereby reducing yield and quality. In this study, we compared the efficiency of commercially available DNA extraction kits and laboratory-adopted methods for microbial community analysis of iron incrustations and oilfield-produced water samples. Modifications to the kits manufacturers' protocols were included to maximise the yield and quality. For iron incrustations, the modified protocol for FastDNA Spin Kit for Soil yielded higher DNA and resulted in higher diversity, including the recovery of low-abundant and rare taxa in the samples, compared to DNeasy PowerSoil Pro Kit. The DNA extracted with modified phenol-chloroform methods yielded higher DNA but failed to pass quality control PCR for 16S sequencing with and without purification. The protocols mentioned here can be used to maximise DNA recovery from iron incrustations and oilfield-produced water samples.

Recycling eutrophic lake sediments into grass production: A four-year field experiment on agronomical and environmental implications

Inefficient use of phosphorus (P) fertilizers leads to the transfer of P into water bodies, causing their eutrophication. Sediment removal is a promising lake restoration strategy that removes nutrients including P accumulated in lake sediments, and opens the opportunity to use removed nutrients in agriculture. In the present study, we investigated the effects of using a thick layer of sediment from the eutrophic Lake Mustijärv on plant growth, and estimated the environmental impacts of different sediment application methods by analyzing greenhouse gas emissions, N and P leaching, aggregate stability, and soil biota. The field experiment (2017-2020) was established on the lake shore with the following treatments: the agricultural control soil (Soil) surrounding the lake, pure sediment (Sed), biochar-treated sediment (SB), and biochar and soil mixed with sediment (SSB). The sediment-based treatments resulted in a similar grass growth performance to the Soil. The availability of most macro- and micronutrients including P (75 vs. 21 g m^-3) were far greater in the Sed compared to the Soil. The sediment-based growing media emitted more CO₂ than the Soil (579 vs. 400 mg CO₂ - C m^-2 h^-1) presumably due to the high rate of organic matter decomposition. The bacterial and fungal community structures of the Sed were strongly differentiated from those of Soil. Also, Sed had lower bacterial diversity and a higher abundance of the bacterial phyla associated with solubilizing P including Proteobacteria and Chloroflexi. Sediment-based growing media increased more than seven times the risk of mineral N and P leaching, and the biochar treatment only had a short-lived beneficial effect on reduction of the sediment's leached P concentration. The sediment application rate should be adjusted to match the crop requirements to minimize greenhouse gas emissions and nutrient leaching when upscaling the case study to larger lakes with similar sediment properties.

Ecosystem consequences of introducing plant growth promoting rhizobacteria to managed systems and potential legacy effects

The rapidly growing industry of crop biostimulants leverages the application of plant growth promoting rhizobacteria (PGPR) to promote plant growth and health. However, introducing nonnative rhizobacteria may impact other aspects of ecosystem functioning and have legacy effects; these potential consequences are largely unexplored. Nontarget consequences of PGPR may include changes in resident microbiomes, nutrient cycling, pollinator services, functioning of other herbivores, disease suppression, and organic matter persistence. Importantly, we lack knowledge of whether these ecosystem effects may manifest in adjacent ecosystems. The introduced PGPR can leave a functional legacy whether they persist in the community or not. Legacy effects include shifts in resident microbiomes and their temporal dynamics, horizontal transfer of genes from the PGPR to resident taxa, and changes in resident functional groups and interaction networks. Ecosystem functions may be affected by legacies PGPR leave following niche construction, such as when PGPR alter soil pH that in turn alters biogeochemical cycling rates. Here, we highlight new research directions to elucidate how introduced PGPR impact resident microbiomes and ecosystem functions and their capacity for legacy effects.

Climate-Resilient Microbial Biotechnology: A Perspective on Sustainable Agriculture

We designed this review to describe a compilation of studies to enlighten the concepts of plant–microbe interactions, adopted protocols in smart crop farming, and biodiversity to reaffirm sustainable agriculture. The ever-increasing use of agrochemicals to boost crop production has created health hazards to humans and the environment. Microbes can bring up the hidden strength of plants, augmenting disease resistance and yield, hereafter, crops could be grown without chemicals by harnessing microbes that live in/on plants and soil. This review summarizes an understanding of the functions and importance of indigenous microbial communities; host–microbial and microbial–microbial interactions; simplified experimentally controlled synthetic flora used to perform targeted operations; maintaining the molecular mechanisms; and microbial agent application technology. It also analyzes existing problems and forecasts prospects. The real advancement of microbiome engineering requires a large number of cycles to obtain the necessary ecological principles, precise manipulation of the microbiome, and predictable results. To advance this approach, interdisciplinary collaboration in the areas of experimentation, computation, automation, and applications is required. The road to microbiome engineering seems to be long; however, research and biotechnology provide a promising approach for proceeding with microbial engineering and address persistent social and environmental issues.

Benefits of applying organic amendments from recycled wastes for fungal community growth in restored soils of a limestone quarry in a semiarid environment

Applying organic amendments to recover physical, chemical, and biological qualities of soil may enable recovery of soils degraded by mining in semiarid climates. This study's aim was to investigate the development and changes in the composition of fungal communities in restored soils with five different types of organic amendments (two types of vegetable compost and sewage sludge compost, and a mixture of both) compared with unamended soils and surrounding natural soils and to examine the relationships between the fungal taxa, the new physico-chemical and biological soil properties of technosoils after 18 months of restoration, and natural soils. Restoration improved soil quality and fungal diversity, placing these soils in an intermediate position between unrestored soils (with no fungi present) and undisturbed reference soils, which were the most fungal diverse. Sewage-treated soils and their mixtures showed high nitrogen and carbohydrate content as well as high basal respiration and fatty acid content, suggesting that they provided readily biodegradable organic matter. In contrast, greenhouse compost-treated soils showed high total organic carbon and polyphenol content, whereas garden compost-treated soils showed intermediate values. The biological soil properties of both composts showed were similar to those of the reference soils, suggesting that composts contained more resilient organic matter. Organic amendments of dissimilar origin caused significantly different fungal soil communities at the genus level among the restored soils. Results indicated that soil pH, electrical conductivity, total nitrogen content, soil basal respiration, fungi/bacteria-PLFA ratio, and dehydrogenase and β-glucosidase activities, together with Pearson's correlations, revealed that these properties and nutrient content (total organic carbon, C/N ratio, carbohydrates, and polyphenols) influenced 40 soil fungal taxa. Therefore, the organic amendments led to changes in soil properties that favoured plant cover by promoting the soil fungal community growth beneficial to the carbon cycle and symbiotic with plants.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects

Agriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested.

Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience

Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.