Integrated microbiome and metabolomics analysis reveal the relationship between plant-specialized metabolites and microbial community in Phellodendron amurense.

Phellodendron amurense is the essential source of bisbenzylisoquinoline alkaloids (BIAs), making it a highly valued raw material in traditional Chinese medicine. The plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, the root-associated microbiomes of P. amurense, as well as the potential correlation between its bioactive compounds and these microbiomes, remain poorly understood. Here, the metabolic profiles of root, rhizosphere, and bulk soils of P. amurense revealed the dramatic differences in the relative content of plant-specialized metabolites. A total of 31, 21, and 0 specialized metabolites in P. amurense were identified in the root, rhizosphere soil, and bulk soil, respectively, with higher content of the seven major BIAs observed in the rhizosphere compared with that in the bulk soils. The composition of the bulk and rhizosphere microbiomes was noticeably distinct from that of the endospheric microbiome. The phylum Cyanobacteria accounted for over 60% of the root endosphere communities, and the α-diversity in root was the lowest. Targeted seven BIAs, namely, berberine, palmatine, magnocurarine, phellodendrine, jatrorrhizine, tetrahydropalmatine, and magnoflorine, were significantly positively correlated with Nectriaceae and Sphingobacteriaceae. This study has illuminated the intricate interaction networks between P. amurense root-associated microorganisms and their key chemical compounds, providing the theoretical foundation for discovering biological fertilizers and laying the groundwork for cultivating high-quality medicinal plants.

Combined effects of mulch film-derived microplastics and pesticides on soil microbial communities and element cycling.

Pesticides and microplastics (MPs) derived from mulch film in agricultural soil can independently impact soil ecology, yet the consequences of their combined exposure remain unclear. Therefore, the effects of simultaneous exposure to commonly used pesticides (imidacloprid and flumioxazin) and aged mulch film-derived MPs on soil microorganisms and element cycles in cotton fields were investigated. The combined exposure influenced soil microorganisms, alongside processes related to carbon, nitrogen, and phosphorus cycles, exhibiting effects that were either neutralized or enhanced compared to individual exposures. The impact of pesticides in combined exposure was notably more significant and played a dominant role than that of MPs. Specifically, combined exposure intensified changes in soil bacterial community and symbiotic networks. The combined exposure neutralized NH4+, NO3-, DOC, and A-P contents, shifting from 0.33 % and 40.23 % increase in MPs and pesticides individually to a 40.24 % increase. Moreover, combined exposure resulted in the neutralization or amplification of the nitrogen-fixing gene nifH, nitrifying genes (amoA and amoB), and denitrifying genes (nirS and nirK), the carbon cycle gene cbbLG and the phosphorus cycle gene phoD from 0.48 and 2.57-fold increase to a 2.99-fold increase. The combined exposure also led to the neutralization or enhancement of carbon and nitrogen cycle functional microorganisms, shifting from a 1.53-fold inhibition and 10.52-fold increase to a 6.39-fold increase. These findings provide additional insights into the potential risks associated with combined pesticide exposure and MPs, particularly concerning soil microbial communities and elemental cycling processes.

Exploring the microbiome of coffee plants: Implications for coffee quality and production.

Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as "coffee microorganisms", "microorganisms-coffee interactions", "coffee fermentation", "coffee quality", and 'coffee post-harvest processing". The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.

Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis.

The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.

Characteristics of microbial community structure and influencing factors of Yangcheng Lake and rivers entering Yangcheng Lake during the wet season.

Yangcheng Lake, a typical fishery lake in the middle and lower reaches of the Yangtze River, is threatened by eutrophication. As the main performers of biogeochemical cycles, microorganisms affect the ecological stability of the lake. To study the structural characteristics of the microbial community in Yangcheng Lake and rivers entering Yangcheng Lake and the response relationship with environmental factors, the microbial community was categorized based on the contour of Yangcheng Lake, the major rivers entering Yangcheng Lake, and the pollution sources. The distribution characteristics of seven physicochemical indices were analyzed, including total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), water temperature (WT), pH, dissolved oxygen (DO), and ratio of total nitrogen to total phosphorus (TN/TP). Characterization of microbial community structure based on 16S rRNA high-flux sequencing technology and ANOSIM analysis were used to explore the differences in the relative abundance of microorganisms at each sampling point in the lake and rivers, and redundancy analysis (RDA) was used to analyze the relationship between the microbial community and physicochemical factors. The results showed that the dominant phyla, genera of microorganisms, and the total number of OTUs in the lake and rivers were similar. The dominant phyla included Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia; the dominant genera included the hgcI clade, CL500-29 marine group, Microcystis PCC-7914, Chloroplast_norank, Clade III_norank, and Flavobacterium. ANOSIM analyses revealed that the microbial community of Yangcheng Lake exhibited an association with geographical space, while the microbial community in the rivers that was linked to the type of pollution source. Redundancy analysis (RDA) indicated that dissolved oxygen (DO), total nitrogen (TN), and pH were significantly correlated with the dominant phyla in Yangcheng Lake (p < 0.05), while total nitrogen (TN), water temperature(WT), and the ratio of total nitrogen to total phosphorus (TN/TP) were significantly related with the dominant genera in Yangcheng Lake (p < 0.05). Total nitrogen (TN) was also significantly linked to the dominant phyla and genera of the tributaries (p < 0.05). Despite the structural similarities in microbial communities between Yangcheng Lake and its inflowing rivers, environmental factors demonstrated significant associations with these communities, providing crucial data support for pollution prevention and the ecological restoration of Yangcheng Lake.

Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding.

Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.

Broad environmental adaptation of abundant microbial taxa in Robinia pseudoacacia forests during long-term vegetation restoration.

Vegetation restoration has significant impacts on ecosystems, and a comprehensive understanding of microbial environmental adaptability could facilitate coping with ecological challenges such as environmental change and biodiversity loss. Here, abundant and rare soil bacterial and fungal communities were characterized along a 15-45-year chronosequence of forest vegetation restoration in the Loess Plateau region. Phylogenetic-bin-based null model analysis (iCAMP), niche breadth index, and co-occurrence network analysis were used to assess microbial community assembly and environmental adaptation of a Robinia pseudoacacia plantation under long-term vegetation restoration. The drift process governed community assembly of abundant and rare soil fungi and bacteria. With increasing soil total phosphorus content, the relative importance of drift increased, while dispersal limitation and heterogeneous selection exhibited opposite trends for abundant and rare fungi. Rare soil fungal composition dissimilarities were dominated by species replacement processes. Abundant microbial taxa had higher ecological niche width and contribution to ecosystem multifunctionality than rare taxa. Node property values (e.g., degree and betweenness) of abundant microbial taxa were substantially higher than those of rare microbial taxa, indicating abundant species occupied a central position in the network. This study provides insights into the diversity and stability of microbial communities during vegetation restoration in Loess Plateau. The findings highlight that abundant soil fungi and bacteria have broad environmental adaptation and major implications for soil multifunctionality under long-term vegetation restoration.

Effects of the Supplementation of Essential Oil Mixtures on Growth Performance, Nutrient Digestibility, Immune Status and Microbial Community in Weaned Piglets.

Since essential oils-such as cinnamaldehyde, thymol, carvacrol, and eugenol-have antibacterial, antioxidant, and anti-inflammatory properties, this study aimed to examine the supplementation of different essential oil mixtures together with 1600 mg/kg zinc oxide (ZnO) on growth performance, incidence of diarrhea, serum immune indices, fecal volatile fatty acids, and microflora structure in weaned piglets. A total of 240 weaned piglets (Duroc × Landrace × Yorkshire) with an average body weight of 8.85 ± 0.21 kg were randomly allocated to 30 pens (6 pens per diet, 4 males and 4 females per pen). Five different experimental diets were prepared and administered for 28 days: (i) a control diet (C), a corn-soybean basal diet without antibiotics, ZnO, or a supplementation of growth promoters; (ii) a control diet with 400 mg/kg essential oil mixtures 1 (EOM1); (iii) a control diet supplemented with ZnO at 1600 mg/kg (Z); (iv) a diet incorporating the Z diet with the addition of essential oil mixtures 1 at 400 mg/kg (ZOM1); and (v) a diet incorporating the Z diet with the addition of essential oil mixtures 2 at 400 mg/kg (ZOM2). During day (d) 14-28 and d 1-28 of the experiment, the average daily gain (ADG) in piglets in the ZOM1 and ZOM2 groups were higher (p < 0.05) compared to the C group. The diarrhea incidence of the Z, ZOM1, and ZOM2 groups were significantly decreased (p < 0.05), and the piglets of the ZOM1 group exhibited the lowest diarrhea incidence throughout the trial period. Additionally, the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF), acid detergent fiber (ADF), ash, organic matter (OM), and ether extract (EE) were higher than those fed the Z diet, and higher levels of NDF, ADF, and crude protein (CP) were observed in groups other than those fed the ZOM1 diet (p < 0.01). On d 14, the pigs fed EOM1 and ZOM2 diets showed a somewhat lower (p < 0.1) immunoglobulin G (lgG) level in serum than those fed the C diet. Additionally, the IL-8 level in serum in the ZOM1 group tended to be higher than that in the other groups (p < 0.1). The piglets fed the ZOM1 diet showed a tendency of lower (p = 0.05) acetate concentration in feces on d 14. Principal co-ordinates analysis (PCoA) showed significant differences (p < 0.05) in the composition of fecal microbial communities among the groups. Dietary EOM1 significantly increased the number of fecal bacteroides (p < 0.05) and tended to increase the number of Prevotella (p < 0.1). Therefore, EOM1 combined with 1600 mg/kg ZnO tends to reduce diarrhea incidence, tends to improve the fecal microbial community structure and growth performance of weaned piglets, and has the potential to replace pharmacological dosages of ZnO.

[Microbiome of therapeutic muds used in Tatarstan]. / Mikrobiom lechebnykh gryazei, primenyaemykh v Tatarstane.

Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied. OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants. MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform. RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins. CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.

Effects of chromate on nitrogen removal and microbial community in two-stage vertical-flow constructed wetlands.

Nitrogen and chromium (Cr(VI)) pollution in waterbodies pose great threats to human health, and a cost-effective alternative with Cr(VI) and nitrogen simultaneous removal is still needed. This study investigated the influence of Cr(VI) on nitrogen removal in the two-stage vertical-flow constructed wetlands (TS-VFCWs) along with iron ore and woodchip, and explored relationship between Cr(VI) and nitrogen removal. The results showed that efficient Cr(VI) and nitrogen removal were simultaneously achieved in TS-VFCWs together with iron-ore and woodchip under 2 mg/L-Cr(VI), whereas 10 mg/L-Cr(VI) gave significant and recoverable inhibition of nitrogen removal. Cr(VI) supplementation promoted the beneficiation of Cr(VI)-reducing/resistant bacteria IMCC26207 and Bryobacter on iron-ore. Woodchip enriched Cr(VI)-reducing bacteria Streptomyces and Thiobacillus. XRD and XPS showed that abundant bound-Cr existed in the surface of iron ore and woodchip, and Cr(III) precipitation/oxide was the major product. High abundances of nitrifying and autotrophic/heterotrophic denitrifying bacteria ensured good nitrogen removal at Cr(VI) stress.

A biodegradable chitosan-based polymer for sustained nutrient release to stimulate groundwater hydrocarbon-degrading microflora.

Petroleum hydrocarbon-contaminated groundwater often has a low indigenous microorganism population and lacks the necessary nutrient substrates for biodegradation reaction, resulting in a weak natural remediation ability within the groundwater ecosystem. In this paper, we utilized the principle of petroleum hydrocarbon degradation by microorganisms to identify effective nutrients (NaH2PO4, K2HPO4, NH4NO3, CaCl2, MgSO4·7H2O, FeSO4·7H2O, and VB12) and optimize nutrient substrate allocation through a combination of actual surveys of petroleum hydrocarbon-contaminated sites and microcosm experiments. Building on this, combining biostimulation and controlled-release technology, we developed a biodegradable chitosan-based encapsulated targeted biostimulant (i.e., YZ-1) characterized by easy uptake, good stability, controllable slow-release migration, and longevity to stimulate indigenous microflora in groundwater to efficiently degrade petroleum hydrocarbon. Results showed that YZ-1 extended the active duration of nutrient components by 5-6 times, with a sustainable release time exceeding 2 months. Under YZ-1 stimulation, microorganisms grew rapidly, increasing the degradation rate of petroleum hydrocarbon (10 mg L-1) by indigenous microorganisms from 43.03% to 79.80% within 7 d. YZ-1 can easily adapt to varying concentrations of petroleum hydrocarbon-contaminated groundwater. Specifically, in the range of 2-20 mg L-1 of petroleum hydrocarbon, the indigenous microflora was able to degrade 71.73-80.54% of the petroleum hydrocarbon within a mere 7 d. YZ-1 injection facilitated the delivery of nutrient components into the underground environment, improved the conversion ability of inorganic electron donors/receptors in the indigenous microbial community system, and strengthened the co-metabolism mechanism among microorganisms, achieving the goal of efficient petroleum hydrocarbon degradation.

Effect of microbial communities on nitrogen and phosphorus metabolism in rivers with different heavy metal pollution.

Small urban and rural rivers usually face heavy metal pollution as a result of urbanization and industrial and agricultural activities. To elucidate the metabolic capacity of microbial communities on nitrogen and phosphorus cycle in river sediments under different heavy metal pollution backgrounds, this study collected samples in situ from two typical rivers, Tiquan River and Mianyuan River, with different heavy metal pollution levels. The microbial community structure and metabolic capacity of nitrogen and phosphorus cycles of sediment microorganisms were analyzed by high-throughput sequencing. The results showed that the major heavy metals in the sediments of the Tiquan River were Zn, Cu, Pb, and Cd with the contents of 103.80, 30.65, 25.95, and 0.44 mg/kg, respectively, while the major heavy metals in the sediments of the Mianyuan River were Cd and Cu with the contents of 0.60 and 27.81 mg/kg, respectively. The dominant bacteria Steroidobacter, Marmoricola, and Bacillus in the sediments of the Tiquan River had positive correlations with Cu, Zn, and Pb while are negatively correlated with Cd. Cd had a positive correlation with Rubrivivax, and Cu had a positive correlation with Gaiella in the sediments of the Mianyuan River. The dominant bacteria in the sediments of the Tiquan River showed strong phosphorus metabolic ability, and the dominant bacteria in the sediments of the Mianyuan River showed strong nitrogen metabolic ability, corresponding to the lower total phosphorus content in the Tiquan River and the higher total nitrogen content in the Mianyuan River. The results of this study showed that resistant bacteria became dominant bacteria due to the stress of heavy metals, and these bacteria showed strong nitrogen and phosphorus metabolic ability. It can provide theoretical support for the pollution prevention and control of small urban and rural rivers and have positive significance for maintaining the healthy development of rivers.

Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head".

Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.

Nano hydroxyapatite pre-treatment effectively reduces Cd accumulation in rice (Oryza sativa L.) and its impact on paddy microbial communities.

Cadmium (Cd) contamination in paddy soil has become a worldwide concern and severely endangered human health. Nano hydroxyapatite (n-HAP) is a practical material to manage paddy Cd pollution, but its dosage should not be excessive. Based on previous studies, we validated the effect of n-HAP pre-treatment on rice Cd uptake in pot and field experiments. The results indicated that n-HAP pre-treatment effectively restricted Cd translocation in the soil-rice system. In pot experiment, when soil n-HAP concentration was 5000 mg/kg, the Cd content in the grains of n-HAP pre-treated rice was 0.171 mg/kg, decreased by 29.3% compared with normal rice (0.242 mg/kg). In field experiment, when soil n-HAP concentration was 20,000 mg/kg, the Cd content in the grains of n-HAP pre-treated rice was 0.156 mg/kg, decreased by 35.3% compared with normal rice (0.241 mg/kg). The primary mechanism was that n-HAP pre-treatment altered the formation and composition of iron plaque and therefore enhanced the Cd binding ability of iron plaque. The available N and P content and urease activity in paddy field were increased. We further investigated the impact of n-HAP on the diversity and structure of paddy microbial communities. The Chao1 and Shannon diversity indices showed no significant difference. The relative abundance of Actinobacteria and Proteobacteria was significantly decreased by n-HAP, indicating that Cd pollution might be alleviated. Desulfobacterota, Gemmatimonadota, and Geobacteraceae were significantly enriched by n-HAP. The declining relative abundance of Basidiomycota and the increasing relative abundance of other fungal taxa also suggested that n-HAP could alleviate Cd toxicity in soil.

Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation.

Whilst biodegradation of different hydrocarbon components has been widely demonstrated to occur by specialist oil-degrading bacteria, less is known about the impact on microbial communities as a function of oil composition by comparing the biodegradation of chemically complex fuels to synthetic products. The objectives of this study were (i) to assess the biodegradation capacity and succession of microbial communities isolated from Nigerian soils in media with crude oil or synthetic oil as sole sources of carbon and energy, and (ii) to assess the temporal variability of the microbial community size. Community profiling was done using 16 S rRNA gene amplicon sequencing (Illumina), and oil profiling using gas chromatography. The biodegradation of natural and synthetic oil differed probably due to the content of sulfur that may interfere with the biodegradation of hydrocarbons. Both alkanes and PAHs in the natural oil were biodegraded faster than in the synthetic oil. Variable community responses were observed during the degradation of alkanes and more simple aromatic compounds, but at later phases of growth they became more homogeneous. The degradation capacity and the size of the community from the more-contaminated soil were higher than those from the less-contaminated soil. Six abundant organisms isolated from the cultures were found to biodegrade oil molecules in pure cultures. Ultimately, this knowledge may contribute to a better understanding of how to improve the biodegradation of crude oil by optimizing culturing conditions through inoculation or bioaugmentation of specific bacteria during ex-situ biodegradation such as biodigesters or landfarming.

Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis.

In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.

Strip intercropping with local crops increased Aconitum carmichaeli yield and soil quality.

Aconitum carmichaeli Debx. is a traditional Chinese medicine that is cultivated in China and Japan. However, the monoculturing of this herb substantially decreases soil quality. Therefore, scientific planting management is crucial for resolving the current problems in the cultivation of A. carmichaeli. In this study, we conducted a comparative study on the soil environmental characteristics, herb growth and quality of A. carmichaeli intercropping with five local crops in two different areas. Herb growth and quality, including biomass and secondary metabolites, and rhizosphere soil environmental characteristics were measured. The results showed that the intercropping with the five local crops substantially improved the A. carmichaeli biomass and polysaccharide content, decreased the disease index, and altered three monoester diterpenoid alkaloids and three diester diterpenoid alkaloids accumulations. The intercrops also increased the soil pH, nitrogen-cycling-gene abundances, and potentially beneficial microorganism abundances, and it also changed the soil nutrient levels. Moreover, these intercropping patterns could alleviate the continuous cropping obstacles of A. carmichaeli. According to a comprehensive evaluation of the A. carmichaeli growth and quality, as well as the soil quality, the best intercropping systems were the A. carmichaeli intercropping with rice, maize, and peanut. In summary, the strip-intercropping systems could improve the A. carmichaeli growth and soil quality, and be beneficial to the sustainable ecological planting of A. carmichaeli.

Isotopic and microbial evidence for biodegradation of diluted bitumen in the unsaturated zone.

The oil sands region in Western Canada is one of the world's largest proven oil reserves. To facilitate pipeline transport, highly viscous oil sands bitumen is blended with lighter hydrocarbon fractions to produce diluted bitumen (dilbit). Anticipated increases in dilbit production and transport raise the risk of inland spills. To understand the behaviour of dilbit in the unsaturated or vadose zone following a surface spill, we ran parallel dilbit and conventional heavy crude exposures, along with an untreated control, using large soil-filled columns over 104 days. Phospholipid fatty acids (PLFAs), biomarkers for the active microbial population, were extracted from column soil cores. Stable carbon isotope contents (δ13C) of individual PLFAs and radiocarbon contents (Δ14C) of bulk PLFAs were characterized over the course of the experiment. The Δ14CPLFA values in soils impacted by dilbit (-221.1 to -54.7‰) and conventional heavy crude (-259.4 to -97.9‰) indicated similar levels of microbial uptake of fossil carbon. In contrast, Δ14CPLFA values in the control column (-46.1 to +53.7‰) reflected assimilation of more recently fixed organic carbon. Sequencing of 16S ribosomal RNA genes extracted from soil cores revealed a significant increase in the relative abundance of Polaromonas, a known hydrocarbon-degrader, following exposure to both types of oil. This study demonstrates that in the first several months following a surface spill, dilbit has a similar potential for biodegradation by a native shallow subsurface microbial community as conventional heavy crude oil.

Cold sediment microbial community shifts in response to crude oil water-accommodated fraction with or without dispersant: a microcosm study.

In cold environments, the low temperature slows down microbial metabolisms, such as the biodegradation processes of hydrocarbons, which are often stimulated by the addition of dispersants in oil spill disasters. In this study, we investigated the effects of hydrocarbon water-accommodated fraction (WAF) prepared with and without dispersant on benthic microbial communities in a microcosm experiment in which hydrocarbon removal was observed. Both WAFs contained similar polycyclic aromatic hydrocarbon (PAH) content. The microcosm experiment, set up with either pristine or contaminated sediments, was conducted for 21 days at 4 °C under WAF and WAF + dispersant conditions. The behavior of bacterial communities in response to WAF and WAF + dispersant was examined at both DNA and RNA levels, revealing the effect of WAF and WAF + dispersant on the resident and active communities respectively. The contaminated sediment showed less taxa responsive to the addition of both WAF and WAF + dispersant than the pristine sediment, indicating the legacy effect by the presence hydrocarbon-degrading and dispersant-resistant taxa inhabiting the contaminated sediment.