Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a ...collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from
Rhizoctonia solani
AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of
Arabidopsis
. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.
The Aznalcóllar accident, which occurred in 1998, spilled 36 × 105 m3 of pyritic sludge and 9 × 105 m3 of acidic water around an area of 43 km2 in the south of Spain. This spill is considered one of ...the most important metal-mining associated accidents worldwide. In this study, two soil remediation techniques were evaluated: the addition of marble sludge (liming treatment, LS) and the mixing of recovered soils (RC) with contaminated soils (CT) (biopile treatment, BS). Both LS and BS significantly reduce the solubility of Cu, Zn, As, and Pb mainly due to the increase in pH and organic matter content, respectively. Soil basal respiration rate and the seed germination and root elongation bioassay with Lactuca sativa were used to evaluate the toxicity of the potential pollution in the sampled soils. Both bioassays showed that the CT soils exhibited the highest toxicity with a significant reduction in the toxicity of the amended soils (LS and BS). The abundance and structure of microbial communities in the soils were determined by qPCR and Illumina 16S rRNA sequencing, respectively. The absolute abundances of total bacterial and archaeal populations, ammonium oxidising bacteria, and denitrifiers in the CT soils were statistically lower than these found in the other three soils. Similarly, the structure of the bacterial community was highly different in the CT soils. Our results underline the persistence of the detrimental effect of pollutants in CT soils compared to the recuperated (RC) and amended soils (LS and BS). We also highlight the uses of liming or biopile as remediation techniques as satisfactory tools to reduce the impact of heavy metals in the contaminated Aznalcóllar soils.
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•The use of liming and biopile showed good performance as remediation techniques.•Soil amendments applied significantly reduced toxicity and heavy metals solubility.•The treatments restored the microbial quality of the soil.•Bacterial community structure at the phylum level is recovered after 20 years.
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•BSR enhanced the OLR of KW HSAD by alleviating fatty acids accumulation.•BSR enhanced the thermodynamic degradation of VFAs at an equivalent OLR.•BSR promoted the SAO-HM pathway by ...enhancing SAOB enrichment.•BSR promoted the enrichment of genes related to essential methanogenesis at high OLR.
The inhibition of fatty acids metabolism is a key limiting factor for organic loading rate (OLR) enhancement during the high-solid anaerobic digestion (HSAD) of kitchen waste (KW). Biogas slurry reflux (BSR) has been demonstrated to enhance system stability and biogas production. However, the mechanism through which BSR modulates fatty acids metabolism, thereby increasing OLR, remains unclear. Therefore, by conducting thermodynamic evaluation and multi-omics analyses, this study explored the feasibility of BSR for enhancing OLR in HSAD and its regulatory role in fatty acids metabolism throughout a semi-continuous long-term (363-day) pilot experiment. In the first OLR increase stage, the system operated stably when the OLR was below 6.0 g·VS/L·d, and the average daily methane yield exceeded 400 mL/g VS. Moreover, functional genes related to fatty acids degradation were enriched. However, fatty acids metabolism was inhibited at an OLR of 6.0 g·VS/L·d, resulting in a noticeable accumulation of fatty acids, leading the system to the brink of collapse. Notably, the implementation of BSR promoted an OLR increase, reaching levels of 7.5 g·VS/L·d. Thermodynamic analyses demonstrated that BSR promoted the thermodynamic degradation of propionate and butyrate under equivalent OLR conditions. Particularly, BSR enhanced the enrichment of Syntrophaceticus and Syntrophomonas, thereby promoting syntrophic acetate oxidizing-hydrogenotrophic methanogenesis. Metagenome and metabolome analyses suggested that BSR promoted medium and long-chain fatty acids degradation and methanogenesis under high OLR (OLR exceeding 6.0 g·VS/L·d). These findings provide systematic insights into the regulation of fatty acids biochemical metabolism through BSR, thus promoting an increase in OLR within plug-flow HSAD.
Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and ...soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.
Microbes drive biogeochemical cycles of nutrients controlling water quality in freshwater ecosystems, yet little is known regarding how spatiotemporal variation in the microbial community affects ...this ecosystem-level functional processes to resist perturbations. Here we examined spatiotemporal dynamics of microbial communities in paired stratified water columns and sediments collected from the Xiaowan Reservoir of Lancang-Mekong River over a year long period. Results highlighted distinctive spatiotemporal patterns of microbial communities in water columns mainly driven by sulfate, dissolved oxygen, nitrate and temperature, whilst sediment communities only showed a seasonal variation pattern governed by pH, reduced inorganic sulfur, sulfate, organic matter and total nitrogen. Microbial co-occurrence networks revealed the succession of keystone taxa in both water columns and sediments, reflecting core ecological functions in response to altered environmental conditions. Specifically, in shallow water, keystone nitrogen fixers and denitrifiers were responsible for providing nitrogen nutrients in summer, while recalcitrant substance degraders likely supplied microbially available organic matters to maintain ecosystem stability in winter. But in deep water, methane oxidation was the critical process linked to microbial-mediated cycle of carbon, nitrogen and sulfur. In addition, carbon metabolism and mercury methylation mediated by sulfate reducers, denitrifiers and nitrogen fixers were core functioning features of sediments in summer and winter, respectively. This work expands our knowledge of the importance of keystone taxa in maintaining stability of reservoir ecosystems under changing environments, providing new perspectives for water resource conservation and management.
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•Spatiotemporal dynamics in water microbiota correlated primarily with sulfate.•Keystone species in shallow water mainly mediated carbon and nitrogen cycles.•Methane oxidation was inferred as the key process in deep reservoir water.•Changes in the sediment community were temporal.
Increased phosphorus (P) uptake during intercropping has been demonstrated previously between specific crop species, e.g. cereal–legumes, in P deficient alkaline or neutral soils. The evidence is ...less strong in P deficient acidic soils. To assess the interspecific effects of acidic soils on P uptake, and to determine the biochemical mechanisms involved, a field experiment with maize-based (Zea mays) intercropping was conducted with the legumes chickpea (Cicer arietinum) and soybean (Glycine max), as well as the cereal wheat (Triticum aestivum), respectively, in subtropical acidic soils of Southern China. The land equivalent ratio (LER) values (on an average of 1.20 and 1.07 for maize–chickpea and maize–soybean, respectively; and from 0.85 to 1.08 on average for maize–wheat after P fertilization) indicated that the interspecific stimulation of P uptake may be a general phenomenon i.e. controlled by soil P availability rather than crop species or soil type. Rhizosphere soil pH increased compared to that of non-rhizosphere even following the addition of the acidic calcium superphosphate (on an average of 0.16–0.56 pH units), suggesting rhizosphere acidification due to intercropping could not be the cause of increased P uptake in acid soils, unlike in alkaline or calcareous soils. The microbial phospholipids fatty acid (PLFA) profiles varied with both intercropping species and soil P status, indicating a selective enrichment of competent species (arbuscular mycorrhizal fungi, gram-negative bacteria, actinomycetes, and probably P solubilizing microorganisms) that may be responsible for increased P uptake during intercropping. The results suggest that root contact modified the microbial communities and the dominant microbial species in the intercropped rhizosphere, thereby contributing to increased P uptake during intercropping in acidic soils.
► A field experiment with maize-based intercropping in acidic soils was conducted. ► Interspecific stimulation of P uptake was generally controlled by soil P status. ► Rhizosphere acidification was not the cause for increased P uptake in acid soils. ► Root contact modified the microbial community and dominant microbial species. ► Microbial interaction may contribute to increased P uptake during intercropping.
Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil ...microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3−-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.
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•Rhizosphere soil bacterial and fungal alpha-diversity and community structure varied along altitudes.•Rhizosphere soil microbial alpha-diversity was related closely with soil properties.•Rhizosphere soil microbial community variations were mainly affected by soil properties and root traits of host plant.•The responses to altitude of soil microbes varied with microbial taxa.
The microbial community composition and chemical characteristics of a Brazilian milk kefir sample produced during its manufacturing and refrigerated storage were investigated by culture-dependent and ...-independent methods and HPLC. Lactococcus lactis ssp. cremoris and ssp. lactis, Leuconostoc mesenteroides, Acetobacter lovaniensis, and Saccharomyces cerevisiae were isolated, whereas the detected bands on denaturing gel gradient electrophoresis corresponded to Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus parakefiri, and S. cerevisiae. After fermentation, lactic acid bacteria were present at levels of 10 log units, whereas acetic acid bacteria and yeast were present at levels of 7.8 and 6 log units, respectively. The lactic acid bacteria and yeast counts remained constant, whereas acetic acid bacteria counts decreased to 7.2 log units during storage. From fermentation to final storage, the pH, lactose content and citric acid of the kefir beverage decreased, followed by an increase in the concentrations of glucose, galactose, ethanol, and lactic, acetic, butyric, and propionic acids. These microbiological and chemical characteristics contribute to the unique taste and aroma of kefir. This research may serve as a basis for the future industrial production of this beverage in Brazil.
Ameliorating biological attributes of agricultural soils is desirable, and one avenue is introducing beneficial microbes via commercial biostimulant products. Although gaining popularity with ...farmers, scientific evaluation of such products in field-grown crops is often lacking. We tested two microbial products, Soil-Life™ and Nutri-Life Platform®, in a commercial sugarcane crop by profiling bacterial and fungal communities in soil and roots using high throughput phylogenetic marker gene sequencing. The products, one predominantly consisting of
Lactobacillus
and the other of
Trichoderma
, were applied as a mixture as per manufacturers’ instructions. Additives included in the formulations were not listed, and plots that did not receive the product mixture were the controls. The compositions of bacterial communities of soil and sugarcane roots, sampled 2, 5 and 25 weeks after application, were unaffected by the products. Soil fungal communities were also unaffected, but sugarcane roots had a greater relative abundance of three unidentified taxa in genera
Marasmius
,
Fusarium
and
Talaromyces
in the treated plots. Sugarcane yield was similar across all treatments that included a 25% lower nitrogen fertiliser rate. Further research must examine if the altered root fungal community is a consistent feature of the tested products, and if it conveys benefits. We conclude that putative biostimulants can be evaluated by analysing the composition of microbial communities. DNA profiling should be complemented by cost-benefit analysis to build a public information base documenting the effects of microbial biostimulants. Such knowledge will assist manufacturers in product development and farmers in making judicious decisions on product selection, to ensure that the anticipated benefits of microbial biostimulants are realised for broad acre cropping.
Soil microorganisms are known to be sensitive to disturbances in their surroundings, and those microbial shifts can reflect the soil health status. Therefore, these shifts can potentially be used as ...a bio-indicator for soil health. However, measurements taken directly on field samples are often affected by strong spatiotemporal trends that are not related to the soil health status. To address this issue, this study aimed to understand whether the response of the bacterial and fungal soil communities after short-term disturbances in a controlled incubator experiment has the potential to reflect the soil health status. The study was conducted on two arable soils with contrasting health status, which was determined based on extensive background information up to ten years. We studied the response of the soil bacterial and fungal communities after short-term disturbances (drying-rewetting and/or chitin amendment, consecutive disturbances). These disturbances were selected because drying and rewetting alters the moisture dynamics and consequently the dynamics of the bacterial and fungal communities, whereas chitin application releases nitrogen into the soil and boosts the microbial biomass and activity. Three techniques were applied and compared to study the response in the bacterial and fungal communities: metabarcoding (relative changes), PLFA analysis (absolute biomass) and HWC (labile C fraction). Using metabarcoding, the soil microbial communities gave a consistently greater response in the less healthy soil after short-term disturbances. More specifically, shifts upon drying and rewetting were up to two- to three-fold larger in the less healthy soil compared to the healthy soil. Soils that were exposed to drought for a second time were less responsive, even for the less healthy soil, indicating that a legacy effect is present. Whereas we expected that chitin could at least partially reduce the effects of drought, the combination of both disturbances led to more shifts in the microbial community, but mostly in the less healthy soil. Shortly after disturbances, the response of the bacterial and fungal soil communities measured by metabarcoding, in a pot trial, reflected the soil health status. The magnitude of the response for bacteria and fungi were both valuable for the assessment of soil health. Traditional soil health indicators like HWC and PLFA, but also DNA-related indicators such as diversity and taxonomical indicators were less sensitive to measure this response. This leads us to recommend the magnitude of the response of bacteria and fungi analyzed shortly after disturbances and measured with metabarcoding, being a consistent and sensitive bio-indicator for soil health.
The raw demultiplexed sequence data are available in the NCBI Sequence Read Archie under accession number PRJNA735907. Scripts used to run all data analysis can be found at https://gitlab.com/lljoos/soilmicrobiome_droughtrewettingchitin.
•Soil microorganisms are sensitive to short-terms disturbances and can reflect the soil health.•DNA-based indicators most suitable to determine soil health after short-term disturbances.•Bacterial and fungal DNA-based indicators are both sensitive.•The magnitude of the response is more sensitive than specific community changes.
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