Search

The production of mineral fertilisers relies heavily on mineral deposits that are becoming depleted or is based on processes that are highly energy demanding. In this context, and in line with the circular economy and the European Green Deal, the recovery of nitrogen (N), phosphorus (P), and potassium (K) from organic wastes using chemical technologies is an important strategy to produce secondary raw materials for incorporation into mineral fertilisers, partially replacing the traditional sources of N, P, and K. However, there are very few studies on the agronomic and environmental effects of such substitution. The aim of this work was to evaluate plant growth under microcosm conditions and the effect on the soil microbiome of mineral fertilisers in which part of the N, P, or K content comes from bio-based materials (BBMFs), namely ash, struvite, and a patented chemical process. The crop was maize, and a metataxonomic approach was used to assess the effect on the soil microbiome. The BBMF treatments were compared with a control treated with a conventional mineral fertiliser. The conventional fertiliser performed significantly better than the bio-based fertilisers in terms of maize biomass production at the first sampling point 60 days after sowing (DAS), but at the last sampling point, 90 DAS, the BBMFs showed comparable or even better biomass production than the conventional one. This suggests that BBMFs may have a slightly slower nutrient release rate. The use of fertiliser, whether conventional or BBMF, resulted in a significant increase in microbiome biodiversity (Shannon index), while it did not affect species richness. Interestingly, the use of fertilisers modulated the composition of the bacterial community, increasing the abundance of beneficial bacterial taxa considered to be plant-growth-promoting bacteria, without significant differences between the conventional mineral fertilisers and the BBMFs. The predominance of PGPRs in the rhizosphere of crops when BBMFs are used could be part of the reason why BBMFs perform similarly or even better than conventional fertilisers, even if the rate of nutrient release is slower. This hypothesis will be tested in future field trials. Thus, BBMFs are an interesting option to make the food chain more sustainable. [ABSTRACT FROM AUTHOR]

The effects of intensive and reduced tillage, fertilization, and irrigation on soil chemical and microbiological parameters were studied in a long-term field experiment in Hungary. The treatments were plowing tillage, ripper tillage, strip tillage; control (without fertilization), NPK fertilization (N: 160 kg/ha; P: 26 kg/ha; K: 74 kg/ha); and non-irrigation and irrigation. Soil samples were collected through maize monoculture in the fall of 2021 in the 30th year of the experiment. The soil organic carbon, total nitrogen, soil microbial biomass (based on PLFA analysis), and soil enzyme activity were observed to be significantly high in the strip tillage plots, but were lower in the ripper tillage plots, and even lower in the plowing tillage plots. The fungal, arbuscular mycorrhiza fungal, and bacterial biomasses were significantly higher in the strip tillage and ripper tillage plots compared to the plowing tillage plots. The strip tillage treatment was found to be the most favorable cultivation method for improving the microbial biomass and activity of Chernozem soil, followed by the ripper tillage and plowing tillage treatments. The long-term use of chemical fertilizers greatly reduced the soil microbial biomass and negatively impacted the soil microbial community, leading to a decrease in fungi and Gram-negative bacteria. The ratio of cyclopropyl PLFA precursors to cyclopropyl PLFAs, as a "stress factor", indicated the most stressful bacterial environment was that found in the fertilized, non-irrigated plowed soil. [ABSTRACT FROM AUTHOR]

More than 30 years have passed after the collapse of the Soviet Union, and huge areas of soil were left in a fallow state. The study of the microbiological status of fallow soils is an extremely urgent task because fallow soils represent the "hidden" food basket of Eurasia. In this context, we studied the influence of land use type (pasture, vegetable garden, hayfield, or secondary afforestation) on key agrochemical parameters and parameters of soil microbial biodiversity. All anthropogenically transformed soils included in the analysis showed increased humus content and pH shift to a more neutral side compared to the mature soil; the same seemed to be the case for all nutrient elements. It was established that the key factor regulating soil microbiome composition shift was the duration and degree of irreversibility of an agrogenic impact. The key phyla of soil microorganisms were Pseudomonadota, Acidobacteriota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. The proportion of other phyla was quite variative in soils of different land use. At the same time, all the 30-year-old abandoned soils were more similar to each other than to mature reference soil and 130-year-old soils of monoculture vegetable gardens. Thus, the first factor, regulating soil microbiome composition, is a continuation of soil agrogenic transformation. The second factor is the type of land use if the soil age was equal for fallow territory in the case of one initial podzol soil and one type of landscape. Thus, 30-year-old abandoned soils are intermediate in terms of microbial biodiversity between pristine natural podzols and plaggic podzol. It could be suggested that in the case of secondary involvement of soils in agriculture, the composition of the microbiome may turn to mature soil or to plaggic soil under intensive amelioration. [ABSTRACT FROM AUTHOR]

The production of mineral fertilisers relies heavily on mineral deposits that are becoming depleted or is based on processes that are highly energy demanding. In this context, and in line with the circular economy and the European Green Deal, the recovery of nitrogen (N), phosphorus (P), and potassium (K) from organic wastes using chemical technologies is an important strategy to produce secondary raw materials for incorporation into mineral fertilisers, partially replacing the traditional sources of N, P, and K. However, there are very few studies on the agronomic and environmental effects of such substitution. The aim of this work was to evaluate plant growth under microcosm conditions and the effect on the soil microbiome of mineral fertilisers in which part of the N, P, or K content comes from bio-based materials (BBMFs), namely ash, struvite, and a patented chemical process. The crop was maize, and a metataxonomic approach was used to assess the effect on the soil microbiome. The BBMF treatments were compared with a control treated with a conventional mineral fertiliser. The conventional fertiliser performed significantly better than the bio-based fertilisers in terms of maize biomass production at the first sampling point 60 days after sowing (DAS), but at the last sampling point, 90 DAS, the BBMFs showed comparable or even better biomass production than the conventional one. This suggests that BBMFs may have a slightly slower nutrient release rate. The use of fertiliser, whether conventional or BBMF, resulted in a significant increase in microbiome biodiversity (Shannon index), while it did not affect species richness. Interestingly, the use of fertilisers modulated the composition of the bacterial community, increasing the abundance of beneficial bacterial taxa considered to be plant-growth-promoting bacteria, without significant differences between the conventional mineral fertilisers and the BBMFs. The predominance of PGPRs in the rhizosphere of crops when BBMFs are used could be part of the reason why BBMFs perform similarly or even better than conventional fertilisers, even if the rate of nutrient release is slower. This hypothesis will be tested in future field trials. Thus, BBMFs are an interesting option to make the food chain more sustainable.

The effects of intensive and reduced tillage, fertilization, and irrigation on soil chemical and microbiological parameters were studied in a long-term field experiment in Hungary. The treatments were plowing tillage, ripper tillage, strip tillage; control (without fertilization), NPK fertilization (N: 160 kg/ha; P: 26 kg/ha; K: 74 kg/ha); and non-irrigation and irrigation. Soil samples were collected through maize monoculture in the fall of 2021 in the 30th year of the experiment. The soil organic carbon, total nitrogen, soil microbial biomass (based on PLFA analysis), and soil enzyme activity were observed to be significantly high in the strip tillage plots, but were lower in the ripper tillage plots, and even lower in the plowing tillage plots. The fungal, arbuscular mycorrhiza fungal, and bacterial biomasses were significantly higher in the strip tillage and ripper tillage plots compared to the plowing tillage plots. The strip tillage treatment was found to be the most favorable cultivation method for improving the microbial biomass and activity of Chernozem soil, followed by the ripper tillage and plowing tillage treatments. The long-term use of chemical fertilizers greatly reduced the soil microbial biomass and negatively impacted the soil microbial community, leading to a decrease in fungi and Gram-negative bacteria. The ratio of cyclopropyl PLFA precursors to cyclopropyl PLFAs, as a “stress factor”, indicated the most stressful bacterial environment was that found in the fertilized, non-irrigated plowed soil.

The amount of nanoparticles that enters the environment has increased substantially in the last years. How they might affect plant characteristics and the bacterial community structure when they enter the soil, however, is still debated, as there is a continuous interaction between them. In this study, we determined the effect of silver (Ag-NPs) and hematite (α-Fe2O3-NPs) nanoparticles (0.15 g kg−1) on the characteristics of common bean (Phaseolus vulgaris L.) and the rhizosphere, non-rhizosphere and uncultivated soil bacterial community. The application of Ag-NPs or α-Fe2O3-NPs did not affect plant growth, but changed the amount of some heavy metals in the roots and aerial parts. The application of nanoparticles had a limited effect on the diversity, structure and functional profile of the soil and rhizosphere bacterial communities, but they were altered by cultivation of the bean plants and changed over time. It was found that application of Ag-NPs or α-Fe2O3-NPs had no effect on bean plant growth and only a small effect on the bacterial community structure and its putative metabolic functions. These findings show that in a complex system, such as a soil, different factors might affect the bacterial community structure and alter the possible effect of nanoparticles on it. [ABSTRACT FROM AUTHOR]

Fertile Chernozems of Southern Russia are of great value, so it is important to study the impact of agricultural activities on the soil quality. Changes in taxonomic composition and α-diversity of microbial communities of agricultural soils occupied by pea (Pisum sativum L.) and chickpea (Cicer arietinum L.) in response of cropland management were studied. A field experiment was conducted under four different conditions: (1) control, (2) mineral fertilizers (NPK) application alone, (3) pesticides application alone, and (4) fertilization combined with pesticides. The taxonomic composition of the soil bacterial community was studied by amplification and sequencing of the 16S rRNA gene. The predominance of Actinobacteria (17.7–32.3%), Proteobacteria (17.7–28.2%), Planctomycetes (10.1–21.3%), Acidobacteria (5.3–11.1%), Chloroflexi (1.0–7.1%), Gemmatimonadetes (2.5–8.0%), Bacteroidetes (3.6–11.3%), and Verrucomicrobia (3.9–9.2%) was noted. Introduction of pesticides led to an increase in the relative abundance of Chlorobi and Gemmatimonadetes. The time of sampling was the main significant factor determining the differences in the structure of soil microbial communities. All treatments did not have a significant effect on the α-diversity of the studied soils. Thus, treatment with mineral fertilizers and pesticides does not have a significant negative effect on the bacterial community of cultivated soils. [ABSTRACT FROM AUTHOR]

The introduction of numerous exotic dung beetles across southern Australia in regions where native dung beetles are not generally efficient in processing livestock dung has resulted in significant reductions in the quantity of such dung on the soil surface in recent years. However, the direct impacts of such ecosystem services on pasture quality and soil nutrient mobility have not yet been investigated in the Riverina region of New South Wales (NSW), an area recognised for prime cattle and sheep production in Australia. Utilising 48 soil columns for lysimetry, we quantified the impact of a common introduced dung beetle (Bubas bison) in this region on water quality after permeation through four different soil types sown to winter annual pastures. Dung beetle treatments included dung plus dung beetles, dung alone and no dung beetles, and no dung and no beetles as a control. Dung beetles and soil type impacted on the performance of improved overseeded annual pastures as measured by biomass accumulation over a four-month growing season. The four soil types, namely, Chromosol, Kandosol, Rudosol, and Vertosol, differed considerably with respect to their water-holding capacity and nutrient profiles, as assessed by initial soil testing and soil leachate evaluation following rainfall plus simulated rainfall events. The concentration of Escherichia coli resulting from cattle dung, cattle dung plus beetles, and the control soils without dung or beetles was assessed in collected leachates over a three-month period. E. coli numbers were significantly increased following B. bison activity, when compared to the dung-only and control treatments. Evaluation of the soil microbiome, by assessing genomic DNA in soils sampled 10 cm below the soil surface where dung beetles remained active following tunnelling, revealed significant differences among soil types with respect to bacterial and fungal communities. Within each soil type, dung beetle activity impacted the fungal community structure, but not the bacterial community. Pasture performance as assessed by biomass accumulation was significantly improved following dung beetle activity in later stages of pasture growth, while E. coli numbers and total coliforms appeared unaffected by beetle presence. [ABSTRACT FROM AUTHOR]

More than 30 years have passed after the collapse of the Soviet Union, and huge areas of soil were left in a fallow state. The study of the microbiological status of fallow soils is an extremely urgent task because fallow soils represent the “hidden” food basket of Eurasia. In this context, we studied the influence of land use type (pasture, vegetable garden, hayfield, or secondary afforestation) on key agrochemical parameters and parameters of soil microbial biodiversity. All anthropogenically transformed soils included in the analysis showed increased humus content and pH shift to a more neutral side compared to the mature soil; the same seemed to be the case for all nutrient elements. It was established that the key factor regulating soil microbiome composition shift was the duration and degree of irreversibility of an agrogenic impact. The key phyla of soil microorganisms were Pseudomonadota, Acidobacteriota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. The proportion of other phyla was quite variative in soils of different land use. At the same time, all the 30-year-old abandoned soils were more similar to each other than to mature reference soil and 130-year-old soils of monoculture vegetable gardens. Thus, the first factor, regulating soil microbiome composition, is a continuation of soil agrogenic transformation. The second factor is the type of land use if the soil age was equal for fallow territory in the case of one initial podzol soil and one type of landscape. Thus, 30-year-old abandoned soils are intermediate in terms of microbial biodiversity between pristine natural podzols and plaggic podzol. It could be suggested that in the case of secondary involvement of soils in agriculture, the composition of the microbiome may turn to mature soil or to plaggic soil under intensive amelioration.

Doped compost consists of compost inoculated with Bacillus siamensis SCFB3-1 that is formulated in biochar and then mixed with the compost. The study objective was to analyze, at field scale, the effect of doped compost on the melon and pepper yield and on the soil microbiome, hypothesizing that the synergy between the components of doped compost confers additional benefits to the crop. Two doses of compost (2 and 5 t/ha) and two doses of the inoculant (biochar+SCFB3-1) with respect to the compost (3% and 6% w:w) were tested. The highest yield was observed for a reduced dose of mineral fertilization (NPK -20%) with a compost dose of 2 t/ha with 6% of the inoculant. Specifically, the yield increase compared with the control, which only received NPK, was a 47% increase in melon and 28% in pepper. The microbiome of the bulk soil was not modified by the doped compost, but the composition of the rhizosphere microbiome changed, increasing in the abundance of Bacillus (the inoculated strain), but also changing the relative abundance of other genera in the bacterial community. Future works will be focused on unravelling the possible effects of phytohormones on the observed results. [ABSTRACT FROM AUTHOR]

The amount of nanoparticles that enters the environment has increased substantially in the last years. How they might affect plant characteristics and the bacterial community structure when they enter the soil, however, is still debated, as there is a continuous interaction between them. In this study, we determined the effect of silver (Ag-NPs) and hematite (α-Fe2O3-NPs) nanoparticles (0.15 g kg−1) on the characteristics of common bean (Phaseolus vulgaris L.) and the rhizosphere, non-rhizosphere and uncultivated soil bacterial community. The application of Ag-NPs or α-Fe2O3-NPs did not affect plant growth, but changed the amount of some heavy metals in the roots and aerial parts. The application of nanoparticles had a limited effect on the diversity, structure and functional profile of the soil and rhizosphere bacterial communities, but they were altered by cultivation of the bean plants and changed over time. It was found that application of Ag-NPs or α-Fe2O3-NPs had no effect on bean plant growth and only a small effect on the bacterial community structure and its putative metabolic functions. These findings show that in a complex system, such as a soil, different factors might affect the bacterial community structure and alter the possible effect of nanoparticles on it.

Fertile Chernozems of Southern Russia are of great value, so it is important to study the impact of agricultural activities on the soil quality. Changes in taxonomic composition and α-diversity of microbial communities of agricultural soils occupied by pea (Pisum sativum L.) and chickpea (Cicer arietinum L.) in response of cropland management were studied. A field experiment was conducted under four different conditions: (1) control, (2) mineral fertilizers (NPK) application alone, (3) pesticides application alone, and (4) fertilization combined with pesticides. The taxonomic composition of the soil bacterial community was studied by amplification and sequencing of the 16S rRNA gene. The predominance of Actinobacteria (17.7–32.3%), Proteobacteria (17.7–28.2%), Planctomycetes (10.1–21.3%), Acidobacteria (5.3–11.1%), Chloroflexi (1.0–7.1%), Gemmatimonadetes (2.5–8.0%), Bacteroidetes (3.6–11.3%), and Verrucomicrobia (3.9–9.2%) was noted. Introduction of pesticides led to an increase in the relative abundance of Chlorobi and Gemmatimonadetes. The time of sampling was the main significant factor determining the differences in the structure of soil microbial communities. All treatments did not have a significant effect on the α-diversity of the studied soils. Thus, treatment with mineral fertilizers and pesticides does not have a significant negative effect on the bacterial community of cultivated soils.

Doped compost consists of compost inoculated with Bacillus siamensis SCFB3-1 that is formulated in biochar and then mixed with the compost. The study objective was to analyze, at field scale, the effect of doped compost on the melon and pepper yield and on the soil microbiome, hypothesizing that the synergy between the components of doped compost confers additional benefits to the crop. Two doses of compost (2 and 5 t/ha) and two doses of the inoculant (biochar+SCFB3-1) with respect to the compost (3% and 6% w:w) were tested. The highest yield was observed for a reduced dose of mineral fertilization (NPK -20%) with a compost dose of 2 t/ha with 6% of the inoculant. Specifically, the yield increase compared with the control, which only received NPK, was a 47% increase in melon and 28% in pepper. The microbiome of the bulk soil was not modified by the doped compost, but the composition of the rhizosphere microbiome changed, increasing in the abundance of Bacillus (the inoculated strain), but also changing the relative abundance of other genera in the bacterial community. Future works will be focused on unravelling the possible effects of phytohormones on the observed results.

Nowadays, the most significant consequence of climate change is drought stress. Drought is one of the important, alarming, and hazardous abiotic stresses responsible for the alterations in soil environment affecting soil organisms, including microorganisms and plants. It alters the activity and functional composition of soil microorganisms that are responsible for crucial ecosystem functions and services. These stress conditions decrease microbial abundance, disturb microbial structure, decline microbial activity, including enzyme production (e.g., such as oxidoreductases, hydrolases, dehydrogenase, catalase, urease, phosphatases, β-glucosidase) and nutrient cycling, leading to a decrease in soil fertility followed by lower plant productivity and loss in economy. Interestingly, the negative effects of drought on soil can be minimized by adding organic substances such as compost, sewage slugs, or municipal solid waste that increases the activity of soil enzymes. Drought directly affects plant morphology, anatomy, physiology, and biochemistry. Its effect on plants can also be observed by changes at the transcriptomic and metabolomic levels. However, in plants, it can be mitigated by rhizosphere microbial communities, especially by plant growth-promoting bacteria (PGPB) and fungi (PGPF) that adapt their structural and functional compositions to water scarcity. This review was undertaken to discuss the impacts of drought stress on soil microbial community abundance, structure and activity, and plant growth and development, including the role of soil microorganisms in this process. Microbial activity in the soil environment was considered in terms of soil enzyme activities, pools, fluxes, and processes of terrestrial carbon (C) and nitrogen (N) cycles. A deep understanding of many aspects is necessary to explore the impacts of these extreme climate change events. We also focus on addressing the possible ways such as genome editing, molecular analysis (metagenomics, transcriptomics, and metabolomics) towards finding better solutions for mitigating drought effects and managing agricultural practices under harsh condition in a profitable manner.

The present study investigated the potential changes in the structure of bacterial communities and their functional profiles in the rhizospheres of Panax notoginseng cultivated under field (CK) and pine forest conditions (T). The rhizospheres of two-year-old P. notoginseng plants were used to extract DNA for metagenomic sequencing and metabolites for metabolomic profiling. The results revealed a higher root weight (p < 0.05) in plants grown under the forest than CK. The rhizospheric bacterial community comprised mainly three dominant phyla including Acidobacteria, Proteobacteria, and Candidatus rokubacteria which accounted for 75% of the total microbial population. Among them, Acidobacteria was the most abundant bacterial taxa, accounting for 42.4% and 40.4% of the total populations in CK and T, respectively. Relative abundances of bacterial genera revealed that Bradyrhizobium, Candidatus koribacter and Edaphobacter, were the dominant genera in both groups. Comparatively, a higher Proteobacteria to Acidobacteria ratio was observed in forest rhizospheres than in field conditions. Candidatus Rokubacteria and Candidatus nitrostelea were identified as biomarker taxa in forest rhizospheres, while the same could be said for taxa belonging to betaproteobacteria and gammaproteobacteria, Burkholderiales and Verrucomicrobia for field rhizospheres. No differential metabolite contents were observed between the two rhizosphere groups, indicating no adverse effects of P. notoginseng cultivation on the soil quality under forest plantation.

Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community.

The application of organic materials that promote beneficial microbial activity is vital to maintaining soil health and crop productivity. We investigated the effect on the soil microbiome of applying biochar (BC), poultry litter (PL), and a combination of biochar and poultry litter (BC/PL) in soybean cultivation at the Red River Research Station (Bossier City, LA, USA). We characterized the microbial profiles, community structure, and co-occurrence network from sequencing data to infer microbial interactions in the soil samples collected in the first and second years of each soil treatment (2016 and 2017, respectively). Our results showed that soil treatments with BC, PL, and a combination of both moderately changed the microbial community composition and structure. In particular, genera significantly affected by the different soil treatments were identified via differential abundance analysis. In addition, canonical correspondence analysis revealed that soil chemical properties, total N in the first year, and total C and pH in the second year influenced the community variability. The differentially enriched bacterial ASVs and co-occurring taxa were linked to nutrient cycling. This study provides insights into the impact of soil carbon amendment on the soil microbiome, a process which favors beneficial bacteria and promotes soybean growth.

The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.

Loss of organic matter content of cultivated soils is observed in many regions of Europe. The possibility of using organic waste as a soil additive that enriches the soil with organic matter and essential components is important in soil quality protection and waste management. This research concerned the influence of six organic wastes—two industrial composts, three digestates and meat bone meal—on soil microbial properties. The study of functional microbial diversity concerns the determination of the catabolic capacity of bacterial, fungal and anaerobic communities in relation to carbon substrates in metabolic profiling plates (Biolog® ECO, FF, AN (Biolog Inc., Hayward, CA, USA)). The assessment of genetic diversity was made on the basis of analysis of the restriction profile of ammonia-oxidizing archaea. Additionally, soil dehydrogenases activity was determined. The research showed that the type of organic waste used had an influence on the microbiological parameters. The application of exogenous organic matter caused increases in functional and genetic microbial diversity. The nature of the noted changes was short term and periodic. The values of the microbiological parameters in soils with organic waste were similar to those of the control samples. This indicates an improved microbiological balance and stability of the soil environment after the application of exogenous organic matter.

Previous studies conducted on a unique field site comprising three contrasting soils (diluvial sand DS, alluvial loam AL, loess loam LL) under identical cropping history, demonstrated soil type-dependent differences in biocontrol efficiency against Rhizoctonia solani-induced bottom rot disease in lettuce by two bacterial inoculants (Pseudomonas jessenii RU47 and Serratia plymuthica 3Re-4-18). Disease severity declined in the order DS > AL > LL. These differences were confirmed under controlled conditions, using the same soils in minirhizotron experiments. Gas chromatography-mass spectrometry (GC-MS) profiling of rhizosphere soil solutions revealed benzoic and lauric acids as antifungal compounds; previously identified in root exudates of lettuce. Pathogen inoculation and pre-inoculation with bacterial inoculants significantly increased the release of antifungal root exudates in a soil type-specific manner; with the highest absolute levels detected on the least-affected LL soil. Soil type-dependent differences were also recorded for the biocontrol effects of the two bacterial inoculants; showing the highest efficiency after double-inoculation on the AL soil. However, this was associated with a reduction of shoot growth and root hair development and a limited micronutrient status of the host plants. Obviously, disease severity and the expression of biocontrol effects are influenced by soil properties with potential impact on reproducibility of practical applications.

Nowadays, the most significant consequence of climate change is drought stress. Drought is one of the important, alarming, and hazardous abiotic stresses responsible for the alterations in soil environment affecting soil organisms, including microorganisms and plants. It alters the activity and functional composition of soil microorganisms that are responsible for crucial ecosystem functions and services. These stress conditions decrease microbial abundance, disturb microbial structure, decline microbial activity, including enzyme production (e.g., such as oxidoreductases, hydrolases, dehydrogenase, catalase, urease, phosphatases, β-glucosidase) and nutrient cycling, leading to a decrease in soil fertility followed by lower plant productivity and loss in economy. Interestingly, the negative effects of drought on soil can be minimized by adding organic substances such as compost, sewage slugs, or municipal solid waste that increases the activity of soil enzymes. Drought directly affects plant morphology, anatomy, physiology, and biochemistry. Its effect on plants can also be observed by changes at the transcriptomic and metabolomic levels. However, in plants, it can be mitigated by rhizosphere microbial communities, especially by plant growth-promoting bacteria (PGPB) and fungi (PGPF) that adapt their structural and functional compositions to water scarcity. This review was undertaken to discuss the impacts of drought stress on soil microbial community abundance, structure and activity, and plant growth and development, including the role of soil microorganisms in this process. Microbial activity in the soil environment was considered in terms of soil enzyme activities, pools, fluxes, and processes of terrestrial carbon (C) and nitrogen (N) cycles. A deep understanding of many aspects is necessary to explore the impacts of these extreme climate change events. We also focus on addressing the possible ways such as genome editing, molecular analysis (metagenomics, transcriptomics, and metabolomics) towards finding better solutions for mitigating drought effects and managing agricultural practices under harsh condition in a profitable manner. [ABSTRACT FROM AUTHOR]

The present study investigated the potential changes in the structure of bacterial communities and their functional profiles in the rhizospheres of Panax notoginseng cultivated under field (CK) and pine forest conditions (T). The rhizospheres of two-year-old P. notoginseng plants were used to extract DNA for metagenomic sequencing and metabolites for metabolomic profiling. The results revealed a higher root weight (p < 0.05) in plants grown under the forest than CK. The rhizospheric bacterial community comprised mainly three dominant phyla including Acidobacteria, Proteobacteria, and Candidatus rokubacteria which accounted for 75% of the total microbial population. Among them, Acidobacteria was the most abundant bacterial taxa, accounting for 42.4% and 40.4% of the total populations in CK and T, respectively. Relative abundances of bacterial genera revealed that Bradyrhizobium, Candidatus koribacter and Edaphobacter, were the dominant genera in both groups. Comparatively, a higher Proteobacteria to Acidobacteria ratio was observed in forest rhizospheres than in field conditions. Candidatus Rokubacteria and Candidatus nitrostelea were identified as biomarker taxa in forest rhizospheres, while the same could be said for taxa belonging to betaproteobacteria and gammaproteobacteria, Burkholderiales and Verrucomicrobia for field rhizospheres. No differential metabolite contents were observed between the two rhizosphere groups, indicating no adverse effects of P. notoginseng cultivation on the soil quality under forest plantation. [ABSTRACT FROM AUTHOR]

Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community. [ABSTRACT FROM AUTHOR]

The application of organic materials that promote beneficial microbial activity is vital to maintaining soil health and crop productivity. We investigated the effect on the soil microbiome of applying biochar (BC), poultry litter (PL), and a combination of biochar and poultry litter (BC/PL) in soybean cultivation at the Red River Research Station (Bossier City, LA, USA). We characterized the microbial profiles, community structure, and co-occurrence network from sequencing data to infer microbial interactions in the soil samples collected in the first and second years of each soil treatment (2016 and 2017, respectively). Our results showed that soil treatments with BC, PL, and a combination of both moderately changed the microbial community composition and structure. In particular, genera significantly affected by the different soil treatments were identified via differential abundance analysis. In addition, canonical correspondence analysis revealed that soil chemical properties, total N in the first year, and total C and pH in the second year influenced the community variability. The differentially enriched bacterial ASVs and co-occurring taxa were linked to nutrient cycling. This study provides insights into the impact of soil carbon amendment on the soil microbiome, a process which favors beneficial bacteria and promotes soybean growth. [ABSTRACT FROM AUTHOR]

The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization. [ABSTRACT FROM AUTHOR]

Loss of organic matter content of cultivated soils is observed in many regions of Europe. The possibility of using organic waste as a soil additive that enriches the soil with organic matter and essential components is important in soil quality protection and waste management. This research concerned the influence of six organic wastes—two industrial composts, three digestates and meat bone meal—on soil microbial properties. The study of functional microbial diversity concerns the determination of the catabolic capacity of bacterial, fungal and anaerobic communities in relation to carbon substrates in metabolic profiling plates (Biolog® ECO, FF, AN (Biolog Inc., Hayward, CA, USA)). The assessment of genetic diversity was made on the basis of analysis of the restriction profile of ammonia-oxidizing archaea. Additionally, soil dehydrogenases activity was determined. The research showed that the type of organic waste used had an influence on the microbiological parameters. The application of exogenous organic matter caused increases in functional and genetic microbial diversity. The nature of the noted changes was short term and periodic. The values of the microbiological parameters in soils with organic waste were similar to those of the control samples. This indicates an improved microbiological balance and stability of the soil environment after the application of exogenous organic matter. [ABSTRACT FROM AUTHOR]