Soil Microbiota Research Articles

Melatonin production by rhizobacteria native strains: Towards sustainable plant growth promotion strategies

In the current context of climate change and water deficit, the selection of native beneficial microorganisms, such as plant growth-promoting rhizobacteria (PGPR), has become a trend for sustainable agriculture due to their ability to improve plant-bacteria interaction with a minimal adverse effect on the soil microbiota compared to commercial PGPR. Until now, the production of phytohormones like melatonin (MT) by native PGPR and their effect on endogenous MT levels in plants have been poorly studied. MT is a ubiquitous phytohormone that protects plants against biotic and abiotic stress by improving the tolerance of stressed plants. In this work, the production of MT by two native PGPR, Enterobacter 64S1 and Pseudomonas 42P4, was evaluated and both PGPR were applied in Arabidopsis thaliana plants grown under drought conditions to assess the inoculation effects. Parameters such as plant growth, leaf cellular membrane damage, leaf protective compounds, and endogenous MT levels under drought and irrigation conditions were evaluated. The results demonstrated that the native strains Pseudomonas 42P4 and Enterobacter 64S1 produce MT and increase the content of endogenous MT in A. thaliana plants under drought. These native strains improved the tolerance of arabidopsis plants to drought by preventing oxidative and membrane damages and improving plant growth. To the best of our knowledge, this is the first report on MT production by native PGPR and their effects on endogenous MT levels in arabidopsis plants, setting the bases to elucidate the role of native PGPR on water deficit conditions.

16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L.

Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop.

Plant species, nitrogen status and endophytes are drivers of soil microbial communities in grasslands

Context There is concern that the introduction of ‘novel’ plant germplasm/traits could outpace our capacity to measure and so assess their impacts on soil microbial communities and function. Aim This study aimed to investigate the effects of plant species/functional traits, nitrogen (N) fertilisation and endophyte infection on grassland soil microbial communities within a short time span of 2 years. Methods Two field experiments with monoculture plots were conducted in a common soil. Experiment 1 compared grasses and legumes, using two cultivars of perennial ryegrass (Lolium perenne) that varied in fructan content, along with the legumes white clover (Trifolium repens) and bird’s-foot trefoil (Lotus pedunculatus) that varied in tannin content. Grass treatments received high and low N application levels. Experiment 2 compared the presence/absence of Epichloë strains in ryegrass, tall fescue (Schedonorus phoenix) and meadow fescue (Schedonorus pratensis). Soil microbial communities were analysed by using high-throughput sequencing of DNA isolated from bulk soil cores. Key results Higher abundance of ligninolytic fungi was found in grass soils and pectinolytic fungi in legume soils. Levels of N fertilisation and fructan in ryegrass had only minor effects on soil fungal communities. By contrast, N fertilisation or fixation had a strong effect on bacterial communities, with higher abundance of nitrifiers and denitrifiers in high-N grass soils and in legume soils than in low-N grass soils. Epichloë affected soil microbiota by reducing the abundance of certain fungal phytopathogens, increasing mycorrhizal fungi and reducing N-fixing bacteria. Conclusions Chemical composition of plant cell walls, which differs between grasses and legumes, and presence of Epichloë in grasses were the main drivers of shifts in soil microbial communities. Implications Impacts of farming practices such as mono- or poly-culture, N fertilisation and presence of Epichloë in grasses on soil microbial communities should be considered in pasture management.

Beneficial soil microbiota as drivers of sustainable crop production

Beneficial soil microbiota as drivers of sustainable crop production

Comparative Analysis of the Impact of Crude Oil and Kerosene on Soil Microbiota and the Bio-utilization Potentials of the Indigenous Microorganisms

This research is focused on evaluating the impact of crude oil and kerosene on soil microbiota. The enumeration of total heterotrophic bacterial count revealed that the soil impacted with crude oil and kerosene yielded low microbial counts ranged from 3.2 × 106 CFU/g, 3.2 × 105 to 2.6 × 103 CFU/g while that of total coliform count obtained from the samples ranges from 2.6 × 105CFU/g to 2.2 × 103 CFU/g. and total fungal count ranged from 2.0 x 102 CFU/g to 1.4 × 102 CFU/g. The genera of bacteria isolated from soils impacted with crude oil and kerosene belong to the genera: Pseudomonas spp., Bacillus spp., Staphylococcus spp., Streptococcus spp., Escherichia coli, Micrococcus spp., Klebsiella spp., Corynebacterium and Salmonella species while Aspergillus spp., Alternaria spp., Candidia spp., Fusarium spp., Trichoderma spp., Mucor spp., Penicillium spp., Cephalosporium spp., Rhizopus spp. are the isolated fungi. The percentage occurrence revealed that Pseudomonas spp. and Escherichia coli had the highest prevalence of 23.1%, followed by Staphylococcus spp. (7.7%), Salmonella spp. (7.7%), Bacillus spp. (7.7%), Micrococcus spp. (7.7%) etc. While the fungal isolates had the following prevalence; Aspergillus spp. (12.5%), Penicillium spp. (12.5%), Candida spp. (12.5%), Mucor spp. (12.5%), etc. The results obtained indicates that crude oil and kerosene have a negative impact on the microbiota of the soil. The combined effect of the compounds is more harmful than their individual effects. This result implies that farmlands impacted with these products would not be suitable for agricultural purposes since the nitrogen fixing bacteria and other soil enriching microorganisms must have been either killed or inactivated by the toxicity of compounds.

Field demonstration of biostimulation with wine pomace extract at a chloroethene contaminated site

Chloroethenes, which are widely used in industrial cleaning solutions and degreasing agents, are carcinogenic and their improper disposal has resulted in the contamination of soil and groundwater. A pilot study was conducted in a field contaminated with trichloroethene to evaluate the effectiveness of wine pomace extract (WPE) as a hydrogen donor in the anaerobic bioremediation of chloroethenes. WPE was prepared by extracting organic acids and other substances from grape pomace generated during winemaking. When WPE was injected into the soil, a reducing environment was created, the concentration of chloroethenes was decreased, and the number of Dehalococcoides spp. was increased. Additionally, before the injection of WPE, microbiota in groundwater and soil was dominated by dechlorinating bacteria, but after the injection, the number of co-metabolizing microorganisms was increased. We found that WPE activates various bacteria involved in the degradation of chloroethenes and can be used in actual contaminated sites.

New genetic markers for <i>Burkholderia pseudomallei</i> strains typing

Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease in humans and animals that may be asymptomatic long-term and quickly develop to pneumonia and septicemia in immunocompromised state and due to predisposing factors. Melioidosis is endemic in countries with tropical and subtropical climates, where B. pseudomallei is a part of the soil and water microbiota of stagnant water bodies, as well as the plant rhizosphere. The recording of imported melioidosis cases in countries with temperate climate zone, along with the continued threat of using this pathogen as a bioterrorism agent, indicate the relevance of research aimed at developing modern methods for its diagnosing and typing. Current research in the intraspecific differentiation of pathogenic strains of infectious diseases tends to use two or more types of molecular markers. A promising direction for the B. pseudomallei strains genotyping is based on using a combination of VNTR loci, which provides a high discriminating ability of the method of multi-locus variable tandem repeat number analysis (MLVA), and slowly evolving single nucleotide polymorphisms (SNPs). The aim of this work was to identify new VNTR and SNP loci suitable for use as genetic markers in molecular typing of the melioidosis causative agent. 20 strains of B. pseudomallei from the collection of the Volgograd Plague Control Research Institute and whole genome sequences of 85 B. pseudomallei strains from the GenBank NCBI database were analyzed. While typing melioidosis causative agent strains from the GenBank NCBI database for 4 VNTR loci, 74 genotypes were identified, of which 64 were unique (HunterGaston index 0.997). It was found that the high allelic polymorphism of VNTR loci limited a potential to determine the geographical and phylogenetic relationships of B. pseudomallei isolates by using the MLVA-4 scheme, and the identified null alleles increased the risk of homoplasia. In this regard, the MLVA-4 scheme was supplemented with a VNTR marker in the BPSS1974 locus encoding a collagen-like protein as well as with SNP markers in the genes of lipid A biosynthesis lauroyl acyltransferase, RNA polymerase sigma factor RpoH, and glutamine amidotransferase. For amplification of the select loci, primers and probes were designed as part of the developed scheme, which were tested in the typing of B. pseudomallei collection strains. According to the results of a cluster analysis for 105 strains of the melioidosis causative agent, an integrated approach turned out to be optimal, allowing differentiation of strains within SNP groups based on VNTR profiles. The methodological approach developed for B. pseudomallei genetic typing, based on a comprehensive analysis of 4 SNP- and 5 MLVA-markers in our modification, allowed to differentiate strains according to the geographical regions of their origin and establish the clonal origin of isolates upon revealing cases of melioidosis.

Effect of PVC microplastics on soil microbial community and nitrogen availability under laboratory-controlled and field-relevant temperatures

Microplastics have been reported to affect soil microbiota and nitrogen cycling under controlled temperature conditions, but their impact under field temperature regimes remains unclear. In this study, we compared the impacts of plasticized polyvinyl chloride (PVC) microplastics in an acidic agricultural soil at laboratory-controlled (25 °C) and field-relevant (outdoor ambient, 2–26 °C) temperature conditions. The results showed that changes in soil indicators were roughly the same under the two temperature conditions after 30 d, with increased NH4+-N content and urease activity, decreased NO3−-N content, potential nitrification rate and ammonia-oxidizing archaea abundance, unaltered bacterial abundance, and significant shifts in bacterial community composition. Probably because microbial activity differed at different temperatures, clear discrepancies were also observed: 1) the lowest observed effect concentration was 0.1 % w/w at 25 °C while it was 0.05 % w/w at ambient temperature; 2) a clear dose-effect relationship was observed at 25 °C but not at ambient temperature; and 3) in addition to a range of bacterial taxa that were commonly influenced by microplastics (e.g., Bradyrhizobium, Burkholderia-Caballeronia-Paraburkholderia, Sinomonas, and Sphingomonas), Amycolatopsis, Nocardia and unclassified Saccharimonadales were more responsive at 25 °C while Bacillus and Mycobacterium for ambient temperature. The findings provide insights into the interaction of microplastics with soil microbes under different temperatures and help to understand the threshold values of plasticized PVC microplastics in soil ecosystems.

Citizen Contribution for Searching for Alternative Antimicrobial Activity Substances in Soil.

Antimicrobial resistance (AMR) is problematic worldwide, and due to the loss of efficiency of many antibiotics, the pressure to discover alternative antimicrobial molecules has increased. Soil harbors a great biodiversity and biomass of microorganisms, and many antibiotics are produced by soil microbiota. Therefore, soil is a promising reservoir to find new antimicrobial agents. In this respect, novel pedagogical strategies regarding the AMR global crisis have recently been developed in different countries worldwide. Highlighted is the service-learning project "MicroMundo" integrated in a global Citizen Science project called "Tiny Earth". Hence, the present work aimed at determining the antimicrobial activity of soil bacteria, the biodiversity of the selected isolates as putative antimicrobial producers, and their antibiotic resistance profile. Moreover, through the MicroMundo project, we tried to illustrate the relevant link between science and education and the benefits of implementing service-learning methodologies to raise awareness of the AMR problem and to contribute to the search for new alternatives. A total of 16 teachers, 25 university students and 300 secondary school students participated in the search for antimicrobial activity on a collection of 2600 isolates obtained from a total of 130 soil samples analysed. In total, 132 isolates (5% of total tested) were selected as potential antimicrobial producers when two indicator bacteria were used (Escherichia coli and Staphylococcus epidermidis); the most frequent genus among these isolates was Bacillus, followed by Pseudomonas, Paenibacillus and Serratia. The antimicrobial activity (AA) of the 132 potential antimicrobial producers was studied in a second step against 15 indicator bacteria (of six genera and thirteen species, including relevant pathogens). Of the 132 potentially producing bacteria, 32 were selected for further characterization. In this respect, 18 isolates showed low AA, 12 isolates were considered as medium producers, and 2 highly antimicrobial-producing isolates were found (Brevibacillus laterosporus X7262 and Staphylococcus hominis X7276) showing AA against 80% of the 15 indicators tested. Moreover, 48% of the antimicrobial-producing bacteria were susceptible to all antibiotics tested. Due to citizen science, antimicrobial-producing bacteria of great interest have been isolated, managing to raise awareness about the problem of AMR.

Deciphering roles of microbiota in arsenic biotransformation from the earthworm gut and skin

Biotransformation mediated by microbes can affect the biogeochemical cycle of arsenic. However, arsenic biotransformation mediated by earthworm-related microorganisms has not been well explored, especially the role played by earthworm skin microbiota. Herein, we reveal the profiles of arsenic biotransformation genes (ABGs) and elucidate the microbial communities of the earthworm gut, skin, and surrounding soil from five different soil environments in China. The relative abundance of ABGs in the earthworm skin microbiota, which were dominated by genes associated with arsenate reduction and transport, was approximately three times higher than that in the surrounding soil and earthworm gut microbiota. The composition and diversity of earthworm skin microbiota differed significantly from those of the soil and earthworm gut, comprising a core bacterial community with a relative abundance of 96% Firmicutes and a fungal community with relative abundances of 50% Ascomycota and 13% Mucoromycota. In addition, stochastic processes mainly contributed to the microbial community assembly across all samples. Moreover, fungal genera such as Vishniacozyma and Oomyces were important mediators of ABGs involved in the biogeochemical cycle of arsenic. This is the first study to investigate earthworm skin as a reservoir of microbial diversity in arsenic biotransformation. Our findings broaden the current scientific knowledge of the involvement of earthworms in the arsenic biogeochemical cycle.

Cell-free microbial culture filtrates as candidate biostimulants to enhance plant growth and yield and activate soil- and plant-associated beneficial microbiota.

In this work we compiled information on current and emerging microbial-based fertilization practices, especially the use of cell-free microbial culture filtrates (CFs), to promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identified limitations to bring microbial CFs to the market as biostimulants. In nature, plants act as metaorganisms, hosting microorganisms that communicate with the plants by exchanging semiochemicals through the phytosphere. Such symbiotic interactions are of high importance not only for plant yield and quality, but also for functioning of the soil microbiota. One environmentally sustainable practice to increasing crop productivity and/or protecting plants from (a)biotic stresses while reducing the excessive and inappropriate application of agrochemicals is based on the use of inoculants of beneficial microorganisms. However, this technology has a number of limitations, including inconsistencies in the field, specific growth requirements and host compatibility. Beneficial microorganisms release diffusible substances that promote plant growth and enhance yield and stress tolerance. Recently, evidence has been provided that this capacity also extends to phytopathogens. Consistently, soil application of microbial cell-free culture filtrates (CFs) has been found to promote growth and enhance the yield of horticultural crops. Recent studies have shown that the response of plants to soil application of microbial CFs is associated with strong proliferation of the resident beneficial soil microbiota. Therefore, the use of microbial CFs to enhance both crop yield and stress tolerance, and to activate beneficial soil microbiota could be a safe, efficient and environmentally friendly approach to minimize shortfalls related to the technology of microbial inoculation. In this review, we compile information on microbial CFs and the main constituents (especially volatile compounds) that promote plant growth, yield and stress tolerance, and their effects on plant-associated beneficial microbiota. In addition, we identify challenges and limitations for their use as biostimulants to bring them to the market and we propose remedial actions and give suggestions for future work.

Application of malrstone-based conditioner and plantation of Jerusalem artichoke improved properties of saline-alkaline soil in Inner Mongolia

Soil salinization is a critical environmental issue restricting agricultural production. Inner Mongolia is one of the areas with severe land salinization in China. This study aimed to investigate the effects of conditioning agent (containing marlstone and a range of enzymes) and cultivating Jerusalem artichoke on saline soils in Inner Mongolia. The effects of conditioner (0, 0.06 and 0.18 kg/m2) on soil physical, chemical and biological properties, including soil carbon fractions and microbiota in saline soils planted with Jerusalem artichoke, were characterized. The results showed that soil salinity was reduced significantly after cultivating Jerusalem artichoke and declined also after the conditioner addition. The application of conditioner increased the content of DOC (dissolved organic carbon), HFOC (heavy fraction organic carbon) and the content of aggregates >0.25 mm compared to the soil planted with Jerusalem artichoke alone. The relative abundance of halophilic bacteria such as Thioalkalivibrio and Thiohalobacter was greater in the CK (non-treated control). By contrast, the relative abundance of microorganisms with the carbon assimilation and nitrogen fixation capacities, such as Cyanobacteria and Rhodovulum, was greater in the conditioner-treated and Jerusalem artichoke-planted treatments. The planting of Jerusalem artichoke reduced soil salinity, increased soil organic carbon fractions, improved soil structure, and altered the soil microbial community, with the application of the conditioning agent enhancing these positive changes. The co-occurrence network structure of “Jerusalem artichoke-conditioner-saline soil-soil microorganism” was established, which provided scientific basis for Jerusalem artichoke-conditioner to improve saline soil.

Arbuscular mycorrhizal colonization alters biochemical, molecular defense responses and root exudate composition against Phytophthora capsici infection in black pepper

Mycorrhizal symbiosis benefits the host plants in several aspects. Among the soil microbiota, AM fungi have established a substantial potential to decrease crop damage from plant pathogens in several crops, yet the mechanism of its action in black pepper has not yet been studied. In this study, we investigated the effect of mycorrhizal colonization on biochemical, molecular defense responses, and root exudates composition in the Phytophthora capsici -black pepper host-pathosystem. Four biochemical parameters such as total phenols, orthodihydroxy (OD) phenols, peroxidase activity, and lignin were studied to delineate the effect of mycorrhizal colonization upon pathogen inoculation. Total phenol, OD phenol, and lignin content increased consistently upon challenge inoculation with P. capsici as well as in AM alone inoculated plants in both leaves as well as roots. Similar peroxidase activity was noticed in AM alone and challenged inoculated plants. The quantitative polymerase chain reaction analysis showed that AM pre-inoculation led to up regulation of pathogenesis related genes viz., cAPX, Osmotin and β-1,3-glucanase, phenylalanine ammonia-lyase and NPR 1 in black pepper leaves and roots upon of P. capsici inoculation. Sole inoculation of P. capsici also positively influenced the copies of most genes studied. Root exudates of AM colonized plants showed higher fatty acid/fatty acyl compounds viz., tetradecanoic acid, n-hexadecanoic acid, octadecanoic acid, and nonacos-1-ene compared to P. capsici inoculated plants. On the other hand, most of the alkane hydrocarbons such as (z)-3-tetradecene, octylcyclohexane, 4-cyclohexylundecane, and decylcyclohexane were observed majorly in the root exudates of P. capsici inoculated plants. Multivariate analysis of the root exudate data revealed that AM colonization in black pepper roots normalized the content of root exudates during Phytophthora infection comparable to control plants. Our findings indicates that the AM colonization enhances the resistance of P. capsici in black pepper plants by alterations in defense enzymes and gene expression and root exudates composition.

Increasing Wood δ15N in Response to Pig Manure Application

Intensive livestock management impacts forest and trees in different ways. Pig manure is a major source of nitrogen (N) pollution of surface and ground waters in some European regions such as north-eastern Spain, but it is understudied how manure application impacts agroforestry systems. How pig manure affects tree radial growth and the N cycle was assessed by measuring N concentrations in soil, leaves and wood and δ15N in tree-ring wood in two tree species widely planted for agricultural (Prunus dulcis) and reforestation (Pinus halepensis) purposes in the study area. Soil physicochemical characteristics and the biomass and structure of major soil microbial groups were also measured. Trees irrigated with pig effluent (manure application) and control trees not subjected to manure application were compared. Soil N, phosphorus (P) and potassium (K) concentrations of fertilized trees increased, but soil microbiota biomass decreased. Similar growth between fertilized and non-fertilized pine trees was found, but lower growth in fertilized almond trees was observed. Leaf N concentrations decreased but δ15N wood increased in trees subjected to pig manure application. Pig manure application alters the N cycling in the soil and within trees.

Divergent taxonomic responses of below-ground microbial communities to silicate fertilizer and biofertilizer amendments in two rice ecotypes

Using silicate fertilizer and bacterial inoculum as biofertilizer is significant for increasing soil silicon (Si) availability and rice agronomic performance. To use microbial technology for sustainable agriculture, it is crucial to have a deeper knowledge of how microbial populations shift among the plant hosts and related compartments, as well as how they respond to various fertilization models. In this study, the effects of silicate fertilizer, a single bacterial strain Bacillus mucilagniosis as biofertilizer, and their integrated application on soil physiochemical properties and soil microbiota structure, composition, and diversity in two eco-geographically diverse races (Indica and Japonica rice) were evaluated. Plant compartment, cultivar type, and fertilizer treatments contributed to microbiome variation. Indica and Japonica harbor different root microbiota; notably, taxa enriched in the rhizosphere soil were more diverse than in the root. Bacterial genera Leptonema, Azospira, Aquabacterium, Fluviicola, Aquabacterium, Leptonema, and fungal genera Metarhizium, Malassezia, and Cladosporium all were found in the rice core microbiome. Both silicate and biofertilizer applications increase the relative abundance of Betaproteobacteria, Deltaproteobacteria, and Actinobacteria, while suppressing fungal pathogens Alternaria and Fusarium. Silicate and bacterial inoculum applications increased the soil pH, available silicon content (ASi), available phosphorous (AP), available potassium (AK), and organic carbon (OC), while reduced the total nitrogen (N). These changes were also associated with major bacterial phyla Spirochaetes, Bacteroidetes, Actinobacteria, and Proteobacteria, except for Acidobacteria, and fungal phyla Ascomycota, Mortierellomycota and unassigned fungi. Several treatment-specific biomarkers were revealed through Linear discriminant analysis effect size (LEfSe) analysis. In conclusion, the change in the structure of root-associated communities driven by plant compartment and genetics suggests dynamic interactions in the host plant microbiome. Short-term silicate and biofertilizer amendments improved soil physiochemical status and altered bacterial and saprotrophic fungal communities, which have important implications for sustainable rice production.

Assessing the impact of seasonal freezing and thawing on the soil microbial quality in arid northwest China

In drylands, soil microorganisms play a vital role in restoring degraded soils, and soil microbiota is significantly affected by human activities and climate events, such as seasonal freezing and thawing. However, the response of soil microbes to freezing and thawing, as well as their properties in drylands agroecosystems, remains unknown. This study investigated the effects of seasonal freezing and thawing on soil fungal and bacterial communities, multifunctionality, and soil microbial quality in a dryland agroecosystem. It has been observed that seasonal freezing and thawing promoted nutrient releases such as total carbon and available phosphorus. After thawing, soil catalase and cellulase activities increased while acid phosphatase and urease activities and total nitrogen content at topsoil decreased. Soil microbial biomass carbon content at 0–40 cm depth was significantly reduced by 94.77 %. Importantly, freezing and thawing considerably shifted the composition of fungal groups, while the soil bacterial community exhibited more stress tolerance to freezing-thawing. Compared to pre-freezing, the relative abundance of dominant fungal phyla such as Basidiomycota and Mortierellomycota decreased. At the same time, Ascomycota increased after thawing, and the relative abundance of pathogenic fungus also increased. For dominant bacteria phylum, freezing and thawing increased the relative abundance of Proteobacteria and Gemmatimonadetes while Micrococcaceae declined. Freezing and thawing significantly increased bacterial diversity and evenness by 4.94 % and 4.19 %, respectively, but decreased fungal richness and diversity by 23.49 % and 14.91 %, respectively. The minimum and total data sets were used to evaluate soil quality and we found that freezing and thawing significantly negatively impacted soil multifunctionality and microbial quality. In summary, this study demonstrates that the seasonal freezing-thawing has a significant negative impact on soil microbial quality and multifunctionality, and accelerates soil degeneration in dryland agroecosystem.

Elevated ozone enhances the network stability of rhizospheric bacteria rather than fungi

The detrimental effects of elevated ozone (O3) on plants vary by species, and are closely related to soil microbial communities. Soil microbial communities vary in composition depending on the plant species. However, little is known about the effects of O3 on the soil microbiota associated with different plant genotypes in forests. Herein, we applied low O3 (24.7 ppb, charcoal-filtered air (CF-O3)), ambient O3 (58.3 ppb, A-O3), and elevated O3 (99.7 ppb, E-O3) to O3-tolerant and O3-sensitive poplar plants. We found that the compositions of rhizospheric bacterial communities were governed by O3 and poplar genotypes (Adonis, P < 0.05), while the compositions of fungal communities were driven by poplar genotype alone (R2 = 0.117, P < 0.05). Further analyses showed that O3 and poplar genotype had direct effects on both bacterial and fungal communities, and indirect effects on bacteria, via changing soil ammonia and nitrate nitrogen concentrations. Under E-O3 stress, the O3-tolerant poplar had more stable bacterial molecular ecological networks than the O3-sensitive poplar, while fungal communities were unaffected in both poplar genotypes. Our research combines the ecological stability of the soil microbiota with a deeper understanding of intraspecific O3-sensitive characteristics of poplars, thereby enhancing our knowledge regarding the global threat posed by elevated O3 to agroforestry-based climate change policy.

An optimized biofumigant improves pepper yield without exerting detrimental effects on soil microbial diversity

BackgroundBiofumigation is a non-chemical sustainable approach that reshapes soil microbiota to overcome challenges in way of continuous cultivation. However, the type and quantity of substrate have a significant impact on microbiota shifts and the subsequent success of biofumigation. Moreover, studies on the effects of biofumigant concentration in combination with fumigation duration on soil microbiota dynamics are very rare.Research methodsWe performed microcosm experiments to investigate how a biofumigant (Korean canola cultivar, HanRa) at various concentrations (0.5%, 1%, 2–4% w/w: biofumigant/soil) and fumigation periods (2–4 weeks) affects the soil bacterial and fungal communities. Subsequently, pot experiments employing two Korean canola cultivars (HanRa and YongSan) at 1% (w/w) were carried out.ResultsIllumina MiSeq analysis revealed that 2–4% biofumigant, regardless of incubation period, had a significant negative impact on microbial diversity and network complexity. In contrast, 1% biofumigant transformed the bacterial, fungal, and inter-kingdom networks into a highly connected and complex network without affecting microbial diversity. Bacillus, Clostridium, and Pseudomonas were the most highly stimulated bacterial genera in the biofumigated soils, whereas the abundance of Acidobacteria members was greatly reduced. The 2–4% amendments had substantially and more differentially abundant Fusarium than the 1%. Soil nutrition (e.g., pH, nitrate, ammonium, and exchangeable potassium), fruit yield, and weed suppression were enhanced in subsequent pot experiments. Of the nine soil chemical properties, phosphate and exchangeable potassium were the main factors influencing the microbial community assembly.ConclusionsOptimized biofumigation-mediated increase in nitrate, ammonium, and potassium availability in the soil without causing any negative effects on soil microbial diversity indicates its potential as a preplant to improve crop productivity. This study contributes significantly to our understanding of how an optimal biofumigant can help ameliorate obstacles in continuous cropping.Graphical

Arbuscular Mycorrhiza Symbiosis as a Factor of Asteraceae Species Invasion

Invasive weeds of the Asteraceae family are widespread in the world. Arbuscular mycorrhiza (AM) is one of the main factors contributing to the successful distribution of these species that is most clearly manifested in the subfamily Asteroideae. The benefits of plant-AMF symbiosis are most significant under unfavorable biotic and abiotic conditions. The specificity of the relationship between arbuscular mycorrhizal fungi (AMF) communities and plants and is determined at the presymbiotic stage. The AMF colonization level is higher in invasive species than in native ones, but AMF communities associated with Asteraceae invasive species are less diverse. AMF communities of Asteraceae invaders often include fewer common species (e.g., species belonging to Diversisporales). Invaders also reduce native AMF species richness in new areas. Arbuscular mycorrhizal fungi can form mycorrhizal networks that allow the redistribution of nutrients in plant communities. The most significant influence of AMF associated with invasive Asteraceae plants is seen in the formation of soil and rhizosphere microbiota, including the suppression of beneficial soil bacteria and fungi. This review could be useful in the development of practical recommendations for the use of AMF-based fertilizers.

Allelopathic Effects of Amomum villosum Lour. Volatiles from Different Organs on Selected Plant Species and Soil Microbiota.

Amomum villosum Lour. is a perennial herb of the Zingiberaceae family, which is widely distributed in Xishuangbanna, Yunnan Province in Southwest China. Large amounts of volatile components contained in this plant enter the surrounding atmosphere and soil through volatilization, foliar leaching, root exudation, and residue decomposition. However, the ecological role of these compounds is currently unclear. The aim of this study was to compare the differences in the composition of volatile oils from stems, leaves, and young fruits of A. villosum, identify chemicals that had allelopathic effects, and explore the effects of the oil on the diversity and composition of soil microbiomes. Volatile oils were obtained by steam distillation and characterized by gas chromatography−mass spectrometry, and then were tested for allelopathic activity using seedlings of Lactuca sativa L. and Lolium perenne L. as test species. The results showed that the oils from stems and leaves were rich in monoterpene hydrocarbons, unlike the oxygenated monoterpenes which dominated oils from young fruits. Leaves > stems > young fruits: this was the order of the allelopathic effects of volatile oils from various A. villosum organs. Among the four main chemical components in the oils, only α-pinene, which is abundant in leaves, had a stronger allelopathic action than the crude oils, implying that it might be a potential allelochemical. Experiments on soil microorganisms indicated that 3.0 mg/mL oil had the greatest effect on the structure of the soil fungal community. It can be concluded that A. villosum is capable of releasing allelochemicals which affect the growth of other plant species and the diversity and community structure of soil microorganisms.