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.
The alternation of drying and rewetting events could dramatically affect the biological and structural properties of soil and consequently influence nutrient transformation. To examine whether ...organic amendments could improve the resistance and resilience of microbial function (extracellular enzyme activities), community composition (phospholipid fatty acids), and soil structure to drying-rewetting alternation, cropland soils with or without wheat-straw amendment were allowed to desiccate in a microcosm for two months, followed by moist incubation for five weeks, and continuously moist treatments were maintained at 50% water holding capacity during the entire period, as a control treatment. Straw amendment increased microbial biomass, extracellular enzyme activities, the relative abundance of fungal groups, dissolved organic carbon, and proportion of large macroaggregates (>2000μm), but decreased mineral nitrogen and available phosphorus. The drying-rewetting treatment increased microbial biomass carbon and β-glucosidase activities by 10% and 13% in straw-amended soils, respectively, but not in unamended soils, and decreased the urease and alkaline phosphomonoesterase activities by >15% in unamended soils, but not in amended soils. The contents of fungi, actinomycetes, Pseudomonas spp., and Bacillus spp. decreased with drying, and more so with the subsequent rewetting, but recovered by the end of the experiment. The drying-rewetting treatment caused a decrease in the nitrate content in both soils (>10%) and an increase in the macroaggregates of straw-amended soils (~8%). These results indicated that improved soil aggregation, as a result of straw amendment, protected microbial communities from drought stress and that nutrient acquisition promoted the post-rewetting colonization of heterotrophic communities characterized by hydrolase production, which consequently facilitated aggregate re-formation. Thus, straw amendment positively contributed to aggregate turnover and to both microbial and enzymatic responses to drying-rewetting events, which suggests that straw amendment is favorable to maintain soil function under conditions of increasing rainfall variability.
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•We tested the effects of straw addition and DRW on microbial community and aggregation.•Straw improved soil aggregation and microbial community resistance to drought.•Straw addition increased hydrolase activities and their resilience after rewetting.•Post-rewetting nutrient acquisition drove colonization of heterotrophic communities.•Straw amendment favored soil functional stability during drying and rewetting.
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.
Highlights • Conditionally rare taxa (CRTs) contribute to microbial community changes but their ecological roles are largely unknown. • CRTs are difficult to observe due to their inherent rarity, ...technological limitations with sequencing, and modest time series data. • Conceptualizing microbial taxa as dynamic components along species occurrence and species abundance distributions will improve understanding of CRTs and their transitions into and out of the rare biosphere. • As CRTs are better documented, we can better pose and test hypotheses about their contributions to community resilience after perturbation and ecoevolutionary dynamics.
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.
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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