Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Advancing two-stage hydrogen production from corn stover via dark fermentation: Contributions of thermally modified maifanite to microbial proliferation and pH self-regulation

This study introduces a two-stage hydrogen production enhancement mechanism using natural particle additives, with a focus on the effects of thermally modified maifanite (TMM) and pH self-regulation on dark fermentation (DF). Initial single-factor experiments identified preliminary parameters for the addition of TMM, which were further optimized using a Box-Behnken design. The established optimal conditions which include mass of 5.5 g, particle size of 120 mesh, and temperature of 324 °C, resulted in a 28.7 % increase in cumulative hydrogen yield (CHY). During the primary hydrogen production stage, TMM significantly boosted the growth and activity of Clostridium_sensu_stricto_1, enhancing hydrogen output. Additionally, a pH self-regulating phenomenon was observed, capable of initiating secondary hydrogen production and further augmenting CHY. These findings presented a novel and efficient approach for optimizing biohydrogen production, offering significant implications for future research and application in sustainable energy technologies.

Soil microbial communities' contributions to soil ecosystem multifunctionality in the natural restoration of abandoned metal mines

On a global scale, the restoration of metal mine ecosystem functions is urgently required, and soil microorganisms play an important role in this process. Conventional studies frequently focused on the relationship between individual functions and their drivers; however, ecosystem functions are multidimensional, and considering any given function in isolation ignores the trade-offs and interconnectedness between functions, which complicates obtaining a comprehensive understanding of ecosystem functions. To elucidate the relationships between soil microorganisms and the ecosystem multifunctionality (EMF) of metal mines, this study investigated natural restoration of metal mines, evaluated the EMF, and used high-throughput sequencing to explore the bacterial and fungal communities as well as their influence on EMF. Bacterial community diversity and composition were more sensitive to mine restoration than fungal community. Bacterial diversity exhibited redundancy in improving N-P-K-S multifunctionality; however, rare bacterial taxa including Dependentiae, Spirochaetes, and WPS-2 were important for metal multifunctionality. Although no clear relationship between fungal diversity and EMF was observed, the abundance of Glomeromycota had a significant effect on the three EMF categories (N-P-K-S, carbon, and metal multifunctionality). Previous studies confirmed a pronounced positive association between microbial diversity and multifunctionality; however, the relationship between microbial diversity and multifunctionality differs among functions' categories. In contrast, the presence of critical microbial taxa exerted stronger effects on mine multifunctionality.

Organic fertilizer facilitates the soil microplastic surface degradation and enriches the diversity of bacterial biofilm

The land-use of organic fertilizers is considered as an important sustainable method for resource utilization, which may have an impact on the microplastic behaviors in the soil. Here, a 240-d dark culture experiment was conducted to reveal the degradation and biofilm characteristics of degradable and refractory granule microplastics in soil and soil-fertilizer systems. The results indicated that microplastics generally exhibited a weak weight loss as well as a specific etiolation on the surface after the culture, especially polyvinyl-chloride and polyhydroxyalkanoates (PHA). Increase in carbon-oxygen functional groups and the changes of oxygen/carbon ratios were noticed, which implied that oxidation and degradation occurred on the surface of microplastics during the cultural process. The changes were more intense on the degradable PHA, and the fertilized-soil treatment than those of the refractory microplastics and the pure soil. Moreover, the addition of organic fertilizers enriched the community diversity of bacterial biofilm on multiple microplastic surfaces. In this regard, the animal fertilizers provided a stronger effect than the plant fertilizers. Overall, the soil, fertilizer and microplastic types affected the community structure and diversity of bacterial biofilm. The outcomes of this study would provide a theoretical basis for the utilization of organic matters for agricultural soil applications.

Thermally modified tourmaline enhances hydrogen production by influencing hydrolysis acidification in two stages during dark fermentation of corn stover

This study investigated the influence of thermally modified tourmaline (Tur) on hydrogen production during the dark fermentation of corn stover. Single-factor experimental results revealed influencing factors of particle size, mass, and temperature. Optimization of the experimental process was achieved using the Box-Behnken design, reaching optimum at conditions of 407 °C, 910-mesh, and 6.2 g. The principle analysis experiment showed that the Tur-enhanced group (Tur_En) amplified cumulative hydrogen production by elevating hydrogen production during the sugar-production stage. The Tur_En group's cumulative hydrogen production was measured at 396.2 ± 40.3 (mL/g VS), marking a 34.2% increase compared to the control group. Analysis of microbial diversity indicated that Firmicutes and Bacteroidota emerged as dominant colonies in both stages. Tur facilitated hydrogen production by stimulating the activity of Firmicutes. This study suggests a highly effective Tur-enhanced technology for hydrogen production from corn stover and elucidates the principles underpinning this method from two stages.

Effects of complex sulphur substrates on sludge bioleaching to improve heavy metal removal and microbial community diversity

In this study, H2S was used as a partial replacement nutrient substrate for sludge bioleaching. The effects of different combinations of H2S/sludge load and monomeric sulphur on heavy metal removal and microbial communities were investigated. Changes in pH, oxidation-reduction potential (ORP), SO42- concentration, heavy metal removal, and the content of heavy metal states during bioleaching were investigated, and community diversity analysis was performed. Daily introduction of H2S three times (at an interval of 8 h) at a gas flow rate of 2 ml/min and an H2S/sludge load of 15 ml/L with 5 g/L FeSO4·7H2O and 2 g/L monomeric sulphur as a nutrient substrate significantly accelerated both the bioleaching process and the pH drop in the sludge system, promoted the production of SO42-, and maintained a higher redox potential. The combination of H2S and monomeric sulphur had a significant effect on the leaching of heavy metals. Compared with the experimental group containing only H2S or monomeric sulphur, the removal rates of Zn, Ni, Pb, and Cr increased by 4.63%/13.8%, 8.5%/20.07%, 3.84%/9.5%, and 4.24%/8.02% respectively, while promoting the transformation of various heavy metal states to labile states, improving heavy metal stability, and reducing sludge ecotoxicity. High-throughput sequencing analysis showed that introducing the H2S gaseous matrix accelerated the decreasing trend of species number, bacterial abundance, and community diversity in the sludge system, promoting Proteobacteria as the dominant phylum, Acidithiobacillus, Metallibacterium, and Thiomonas as the dominant genera, and improving the bioleaching treatment effect.

Investigating the effects of organic amendments on soil microbial composition and its linkage to soil organic carbon: A global meta-analysis

Understanding the dynamics of soil microbial communities responsible for soil element cycling is vital to understanding organic amendments' mechanisms in agricultural soil. However, several studies show inconsistencies in whether and how organic amendments affect the taxonomic composition of soil microbial communities compared to the application of sole chemical fertilizers. This first global meta-analysis demonstrated that organic amendments increased the bacterial diversity indices (Shannon and Chao1) but had no significant effect on fungal diversity indices. When considering both bulk and rhizosphere soils, only copiotrophic strategies such as Proteobacteria, Bacteroidetes, and Zygomycota phylum demonstrated a significant increase in response to organic amendments, mainly because the environment with a significant increase in nutrients content preferentially supports the growth of copiotrophic species after the use of organic amendments. Additionally, the factors influencing the response of different dominant microbial phyla to organic amendments varied. Besides soil pH, the effect of organic amendments on different microbial phyla was significantly influenced by soil texture, organic fertilizer type, crop type, and climate type, providing insights into the diverse responses of microbial communities to organic amendments under varying conditions. Organic amendments significantly increased soil organic carbon (SOC) content and enzyme activities related to nitrogen (N) and phosphorus (P) decomposition but had no significant effect on enzymes related to carbon (C) decomposition. Notably, the effect of organic amendments on the relative abundance of three dominant phyla (Mortierellomycota, Nitrospirae, and Firmicutes) was related to the effect on SOC, where the increase in the relative abundance of Firmicutes was significantly positively associated with the increase in SOC. This result has implications for understanding the relationship between the dynamics of microbial community composition and C turnover in agroecosystems.

Ketogenic diet ameliorates autism spectrum disorders-like behaviors via reduced inflammatory factors and microbiota remodeling in BTBR mice

Autism spectrum disorder (ASD) is increasing, but its complete etiology is still lacking. Recently, application of ketogenic diet (KD) has shown to reduce abnormal behaviors while improving psychological/sociological status in neurodegenerative diseases. However, KD role on ASD and underlying mechanism remains unknown. In this work, KD administered to BTBR and C57BL/6 J (C57) mice reduced social deficits (p = 0.002), repetitive behaviors (p < 0.001) and memory impairments (p = 0.001) in BTBR. Behavioral effects were related to reduced expression levels of tumor necrosis factor alpha, interleukin-1β, and interleukin-6 in the plasma (p = 0.007; p < 0.001 and p = 0.023, respectively), prefrontal cortex (p = 0.006; p = 0.04 and p = 0.03) and hippocampus (p = 0.02; p = 0.09 and p = 0.03). Moreover, KD accounted for reduced oxidative stress by changing lipid peroxidation levels and superoxide dismutase activity in BTBR brain areas. Interestingly, KD increased relative abundances of putatively beneficial microbiota (Akkermansia and Blautia) in BTBR and C57 mice while reversing the increase of Lactobacillus in BTBR feces. Overall, our findings suggest that KD has a multifunctional role since it improved inflammatory plus oxidative stress levels together with remodeling gut-brain axis. Hence, KD may turn out be a valuable therapeutic approach for ameliorating ASD-like conditions even though more evidence is required to evaluate its effectiveness especially on a long term.

Study on potential microbial community to the waste water treatment from bauxite desilication process

Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.

Temperate Coastal Microbial Communities Rapidly Respond to Low Concentrations of Partially Weathered Diesel

Diesel is frequently encountered in coastal ecosystems due to land run-off from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a run-off event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel run-off can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.

Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

The current trend of using nanotechnology products in all spheres of human life, including for crop improvement may have a possible impact on soil microorganisms which influence soil and plant health. Nanopore-based metagenomic study reported here used full-length 16S rRNA gene sequences to assess shifts in community composition of soil microorganisms when treated with silver, titanium dioxide and zinc oxide nanoparticles (S-NP, T-NP, Z-NP, respectively). Firmicutes and Proteobacteria were the two dominant phyla in this soil, and there were no significant differences (p < 0.05) observed in these phyla across treatments. However, in the phylum Firmicutes, the abundance of the order Clostridiales showed a significant decrease (p < 0.05) in the presence of S-NP. Similarly, in the phylum Proteobacteria, a significant decrease in the presence of S-NP was seen for two orders, Vibrionales (p < 0.05) and Rhodobacterales (p < 0.01). Analysis at a further depth revealed that abundance of the genus Clostridium (order Clostridiales) decreased in the presence of both S-NP (p < 0.01) and T-NP (p < 0.05). The abundance of the genus Vibrio (order Vibrionales) was likewise impacted in the presence of all the three NPs — S-NP (p < 0.01), T-NP (p < 0.05) and Z-NP (p < 0.05). Analyses at high taxon ranks such as phyla may not give a good representation of the nature of microbial community shifts, and at times may paint an erroneous picture. The use of full-length 16S rRNA gene sequences here yielded a greater taxonomic depth, and some shifts at the lower ranks were discernible.

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

A key aspect of global forest management, woodland use intensity (WUI) greatly affects the composition and diversity of soil microbial communities, thereby affecting multiple ecosystem functions and services. However, the effects of WUI on soil microbial community composition and enzymatic activities remains unclear. The effects of anthropomorphic alterations to a natural monsoon evergreen broad-leaved forest in terms of the composition and diversity of soil fungal and bacterial communities, was investigated at a site in Yunnan Province, Southwest China. Soil microbial communities were assessed under four levels of disturbance with increasing levels of WUI: (i) none, undisturbed forest (control), (ii) light, naturally-regenerated Pinus kesiya Royle ex Gordon forest, (iii) intermediate, shrub and grassland communities formed through grazing, and (iv) severe, continuously managed coffee (Coffea arabica L.) plantations. With increasing WUI, the diversity of soil fungal and bacterial communities increased, while similarities in community composition decreased for fungi but increased for bacteria. Among fungal functional guilds, ectomycorrhizal fungi decreased significantly with increasing WUI, whereas saprotrophic fungi (undefined, wood, and soil saprotrophs) increased significantly. The species richness of woody plants remarkably affected fungal functional guilds. Ectomycorrhizal fungi interacted in a synergistic manner with the fungal network structure. Significantly affecting microorganismal network structure, WUI increases led to more homogeneous networks with less integration within modules within the microbial community. The WUI strongly altered hub identity and module composition in the microbial community. According to structural equation models, WUI had direct positive effects on soil fungal community composition via its effects on plant species richness. The diversity of bacterial and fungal communities and composition of bacterial communities were jointly regulated by the indirect effects of plant species richness and soil nutrients (including enzyme activity). Deterministic processes largely determined the composition of soil fungal and bacterial communities. This study highlights the importance of maintaining the diversity of soil fungal and bacterial communities despite changes in woodland use to sustain ecosystem functions. These results can be used to develop management practices in subtropical forests and help sustain plant and soil microbial diversity at levels sufficient to maintain long-term ecosystem function and services.

16S rRNA genes- and metagenome-based confirmation of syntrophic butyrate-oxidizing methanogenesis enriched in high butyrate loading

The understanding and enrichment of consortia formed by syntrophic butyrate-oxidizing bacteria and methanogens in the complex environment are crucial for effectively degrading butyrate and preventing acid inhibition. In this study, the better butyrate-tolerated and highly efficient microbial consortia were domesticated and enriched through adding butyric acid ranging from 0.2 to 4.4 g/(L·d). The volumetric biogas production continuously increased to 1.65 L/(L·d). Microbial community diversity showed that a dramatic shift of bacterial structure occurred at BAL of 1.6 g/(L·d) and the structure presented better stability at high BAL. The syntrophic consortia and the main metabolic pathways were revealed through combination of the 16S rDNA and metagenome sequencing analyses. Syntrophomonas was the major butyrate-oxidizing bacterium and oxidized butyrate mainly through β-oxidaiton. Synergistaceae and Mesotoga acted as the main acetate-oxidizing bacteria. IHT and methanogenesis pathways were strongly enhanced by DMER64 and Methanosarcina as the main H₂ carrier and dominant methanogen, respectively.

Efficient decolorization of azo dye wastewater with polyaniline/graphene modified anode in microbial electrochemical systems

Azo dye pollution has become a worldwide issue, and the current treatment methods can hardly meet the expected emission standards. Microbial electrochemical systems (MESs) show promising applications for decolorization, but their performance critically depends on the microorganisms. Electrode modification is an interesting method of improving decolorization performance. However, the mechanisms of how the modification can affect microbial communities and the decolorization process remain unclear. Here, a modified anode with polyaniline (PANI) and graphene was fabricated via electro-deposition. Consequently, the highest decolorization efficiency was obtained. The Congo red (CR) decolorization rate of the MESs with the PANI/graphene-modified electrode (PG) reached 90% at 54 h. By contrast, the CR decolorization rates of the MESs with the PANI-modified electrode (P) and those of the MESs with the unmodified electrode (C) only reached 68% and 79%, respectively. Results of the microbial community analysis showed abundant Methanobrevibacter arboriphilus in PG (11%), which was 5.5 times that in C (2%) at 18 h. This phenomenon may be related to the rapid decolorization. The upregulated metabolism pathways, including arginine and proline metabolism, purine metabolism, arginine biosynthesis, and riboflavin metabolism, provided more electron shuttles and redox mediators that facilitated the extracellular electron transfer. Therefore, the PG-modified electrode facilitated the decolorization by altering certain metabolic pathways. This study can help to improve the guideline on the potential application of MESs for wastewater treatment.

Effects of different additives on the chemical composition and microbial diversity during composting of Camellia oleifera shell

The influence of three additives including Camellia oleifera meal, C. oleifera seed cake and goat dung during the C. oleifera shell composting was evaluated. The result of physic-chemical parameters indicated that compost of C. oleifera shell with one of additives could achieve the effect of maturity.16S rDNA sequencing suggested that Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Tenericutes, Deinococcus-Thermus, Patescibacteria, Fibrobacteres and Acidobacteria were the dominant microorganisms in all compost piles, and their abundances varied with compost additive and composting phase. Goat dung significantly increased the microbial diversity at the mesophilic phase. The microbial composition was most diverse at the end of composting for all piles. No pathogens were detected in the compost products of all three groups, and thus were safe for utilization in plant cultivation. This work considered that compost was best way to address the contamination problem of C. oleifera shell, where goat dung was best additive for compost.

Appropriate human intervention stimulates the development of microbial communities and soil formation at a long-term weathered bauxite residue disposal area

Bauxite residue discharged to disposal areas, which could generate environmental pollution issues. Long-term natural restoration may improve the physicochemical properties of the residues, in turn supporting vegetation establishment, and effectively managing pollution. Nevertheless, the effects of short-term human intervention on soil formation in the weathered disposal areas are still relatively unknown. Thus, residue samples with different depths from different regions including no vegetation, sparse vegetation, complete vegetation coverage, and complete vegetation coverage following sewage sludge treatment were selected to analyze microbial community using Illumina high-throughput sequencing technology and evaluate soil formation process. Long-term weathering changed pH, the fraction of water-stable aggregates and nutrient concentrations, whilst promoting Proteobacteria, Chloroflexi, Acidobacteria and Planctomycete populations. Sewage sludge addition enhanced aggregate stability and significantly changed microbial community diversity. Sewage sludge application enriched the relative abundances of Proteobacteria and Bacteroidetes, whilst decreasing the relative abundance of Acidobacteria, which may be due to variation in environmental factors. Canonical correspondence analysis revealed that pH and EC were the main factors affecting microbial structure, followed by organic carbon content and aggregate stability. The results enhance the understanding of soil formation in bauxite residue and reveal the potential benefit of human intervention in ecological reconstruction at disposal areas.

Abundance and diversity of epiphytic microbiota on forage crops and their fermentation characteristic during the ensiling of sterile sudan grass

This study aimed to evaluate the effects of exogenous epiphytic microbiota inoculation on the fermentation quality and microbial community of sudan grass silage. Gamma irradiated sudan grass was ensiled with distilled water (STR), epiphytic microbiota of sudan grass (SUDm), forage sorghum (FSm), napier grass (NAPm) and whole crop corn (WCCm). The FSm inoculated silage have significantly lower lactic acid (LA) concentration and higher pH during early ensiling, while LA concentration gradually and significantly increased with the progression of ensiling and have lower pH in relation to other treatments for terminal silage. Inoculation of NAPm resulted in lower LA and higher acetic acid (AA) concentrations, higher pH, ammonia-N and dry matter losses for terminal silage, followed by SUDm silage. Inoculations of WCCm significantly increased LA production and pH decline during early ensiling and have higher LA and pH then NAPm and SUDm silages during final ensiling. The early fermentation of SUDm silage was dominated by genus of Pediococcus. The genera of Lactobacillus were predominant in WCCm and NAPm silages during 3 days of ensiling, while Weissella dominated initial microbial community of FS silage. The terminal silage of NAPm was dominated by Enterobacter and Rosenbergiella, while Enterobacter and Lactobacillus dominated terminal SUDm silage. The final silage of FSm was dominated by Lactobacillus, Weissella and Pediococcus, while Lactobacillus and Acetobacter dominated terminal WCCm silages. The results demonstrated that among the four forages the epiphytic microbiota from forage sorghum positively influenced the microbial community and fermentability of sudan grass silage.

Bioaugmentation potential evaluation of a bacterial consortium composed of isolated Pseudomonas and Rhodococcus for degrading benzene, toluene and styrene in sludge and sewage

Bioaugmentation was conducted using a bacterial consortium of Pseudomonas putida SW-3 and Rhodococcus ruber SS-4, to test their ability to degrade benzene, toluene, and styrene (BTS). SW-3 and SS-4 were isolated from domestic sludge and sewage samples to establish a synthetic consortium with an optimized ratio of 2:1 to reach a degradation efficiency of 82.5-89.8% of BTS. The bacterial consortium was inoculated with sludge and sewage samples at a ratio of 2:1, resulting in a degradation efficiency of 97.9% and 92.7%, respectively, at a BTS concentration of 1800 mg·L^-1. Analysis of bacterial community structure following bioaugmentation indicated an increase in abundance of BTS-degrading bacteria, particularly Acinetobacter and Pseudoxanthomonas in sludge and Pseudomonas in sewage, enhancing the collective BTS degradation ability of the bacterial community. Principal component analysis demonstrated that a more balanced bacterial community structure was established following intervention. This indicated that the selected bacteria are excellent candidates for bioaugmentation.

Enhanced nitrogen removal by simultaneous nitrification-denitrification and further denitrification (SND-DN) in a moving bed and constructed wetland (MBCW) integrated bioreactor

With the main objective of improving the removal of nitrogen from domestic wastewater and more sustainably, a moving bed and constructed wetland (MBCW) integrated bioreactor was fabricated and evaluated with continuous and intermittent aeration operations. The hybrid system achieves average removal efficiencies up to 90.4 ± 0.8% of chemical oxygen demand (COD), 91.8 ± 1.2% of ammonia nitrogen (NH₄⁺-N), and 77.0 ± 2.6% of total nitrogen (TN), respectively, through a simultaneous nitrification-denitrification and further denitrification (SND-DN) process. This occurs through an intermittent aeration operation followed by continuous aeration with a dissolved oxygen (DO) of 4.0 mg L^-1 due to the complementary and coordinated action of mixed biocarriers. It has resulted in the improvement of the efficiency of SND from 5.9 to 35.3% and in the removal via wetland for DN, between 2.42 and 2.45 g m^-2·d^-1, respectively. The analysis of extracellular polymeric substances (EPS) and high-throughput sequencing demonstrated the enhanced SND mechanism and the evolution of microbial species within the biofilm structure. The total relative abundance of nitrifying bacteria, more aggregated outside the biofilm, decreased by 7.66% compared to denitrifying bacteria, mostly accumulated inside, which increased by 5.49%, respectively.

Liraglutide modulates gut microbiome and attenuates nonalcoholic fatty liver in db/db mice

AIMS

Liraglutide, a glucagon-like peptide-1(GLP-1) analog, is effective for the treatment of type II diabetes and nonalcoholic fatty liver disease (NAFLD). It was proved that gut microbiome plays a role in the development of NAFLD. This study aims to observe the therapeutic effect of liraglutide on nonalcoholic fatty liver (NAFL) in mice and effect on the gut microbial community.

MAIN METHODS

The db/db mice were used as the NAFL model, and lactulose was used as the positive control drug. Hepatic triglyceride, liver histopathology, and indices of glucolipid metabolism, including fasting blood glucose, fasting insulin, insulin resistance index and blood lipids were evaluated after treatment of liraglutide or lactulose for four weeks. The colonic microbiome of the mice was analyzed by 16S rRNA gene sequencing.

KEY FINDINGS

Liraglutide significantly reduced the hepatic triglyceride (TG) content, alanine aminotransferase (ALT) activity, fasting blood glucose, insulin resistance and serum low density lipoprotein (LDL) in the db/db mice. In terms of hepatic pathologies, hepatic steatosis was significantly improved after liraglutide treating. Microbiome analysis revealed that liraglutide significantly increased the abundance of Akkermansia, Romboutsia, norank_f_Bacteroidales_S24-7_group, and decreased the abundance of Klebsiella, Anaerotruncus, Bacteroides, Lachnospiraceae_UCG-001, Lachnospiraceae_NK4A136_group, Ruminiclostridium, uncultured_f__Ruminococcaceae, and Desulfovibrio.

SIGNIFICANCE

The results of the present study suggested that liraglutide had a certain therapeutic effect on fatty liver in db/db mice and had an impact on the composition of the intestinal microflora, especially some bacteria related to glucolipid metabolism and intestinal inflammation. Affecting gut microbiome might be a potential mechanism of liraglutide in treating NAFL.

Drought is a stronger driver of soil respiration and microbial communities than nitrogen or phosphorus addition in two Mediterranean tree species

The drivers of global change, such as increasing drought and nutrient deposition, are affecting soils and their microbial communities in many different habitats, but how these factors interact remains unclear. Quercus ilex and Pinus sylvestris are two important tree species in Mediterranean montane areas that respond differently to drought, which may be associated with the soils in which they grow. We measured soil respiration and physiologically profiled microbial communities to test the impact of drought and subsequent recovery on soil function and diversity for these two species. We also tested whether the addition of nitrogen and phosphorus modified these effects. Drought was the stronger driver of changes to the soil communities, decreasing diversity (Shannon index), and evenness for both species and decreasing soil respiration for Q. ilex when N was added. Soil respiration for P. sylvestris during the drought period was positively affected by N addition but was not affected by water stress. P addition during the drought period did not affect soil respiration for either tree species but did interact with soil-water content to affect community evenness for P. sylvestris. The two species also differed following the recovery from drought. Soil respiration for Q. ilex recovered fully after the drought treatment ended but decreased for P. sylvestris, whereas the soil community was more resilient for P. sylvestris than Q. ilex. Nutrient addition did not affect respiration or community composition or diversity during the recovery period. Soil respiration was generally weakly positively correlated with soil diversity. We demonstrate that short-term water stress and nutrient addition can have variable effects on the soil communities associated with different tree species and that the compositions of the communities can become uncoupled from soil respiration. Overall, we show that drought may be a stronger driver of changes to soil communities than nitrogen or phosphorus deposition.

Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw

Background

Chinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere.

Methods

We examined the rhizosphere's methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw.

Results

Rice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.

Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)

Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.

Unraveling microbial community diversity and succession of Chinese Sichuan sausages during spontaneous fermentation by high-throughput sequencing

The microbial community diversity and succession of Chinese Sichuan sausages during the spontaneous fermentation were demonstrated using high-throughput sequencing technology. The bacterial diversity was abundant and the succession of bacterial community along the direction of Lactobacillus spp. increased and Weissella spp. decreased. While fungal diversity was single and trace fungal population was detected. The core functional microbiota were lactic acid bacteria, including Lactobacillus spp., Weissella spp. and Pediococcus spp. In initial fermentation, Weissella spp. was the dominant bacteria and its relative abundance was 49.84%, but then its relative abundance decreased to 11.96% during fermentation before recovering to 26.74% at the end of fermentation. Meanwhile, Lactobacillus spp. rose from 24.70 to 55.74% and became the dominant genus. Moreover, Pediococcus spp. increased from 0.06 to 18.05% on day 20 but then decreased to 1.89% on day 30. These results revealed that the primary microorganisms contributing to spontaneous fermentation of Chinese Sichuan sausages were bacteria, while eukaryotic microorganisms such as yeast scarcely contributed to fermentation.

Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos

Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F-1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.

Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos

Microbes on aging flue-cured tobaccos (ATFs) improve the aroma and other qualities desirable in products. Understanding the relevant organisms would picture microbial community diversity, metabolic potential, and their applications. However, limited efforts have been made on characterizing the microbial quality and functional profiling. Herein, we present our investigation of the bacterial diversity and predicted potential genetic capability of the bacteria from two AFTs using 16S rRNA gene sequences and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) software. The results show that dominant bacteria from AFT surfaces were classified into 48 genera, 36 families, and 7 phyla. In addition, Bacillus spp. was found prevalent on both ATFs. Furthermore, PICRUSt predictions of bacterial community functions revealed many attractive metabolic capacities in the AFT microbiota, including several involved in the biosynthesis of flavors and fragrances and the degradation of harmful compounds, such as nicotine and nitrite. These results provide insights into the importance of AFT bacteria in determining product qualities and indicate specific microbial species with predicted enzymatic capabilities for the production of high-efficiency flavors, the degradation of undesirable compounds, and the provision of nicotine and nitrite tolerance which suggest fruitful areas of investigation into the manipulation of AFT microbiota for AFT and other product improvements.

Insights into the role of earthworms on the optimization of microbial community structure during vermicomposting of sewage sludge by PLFA analysis

In this study, the influences of earthworms on the structure of microbial community as well as the metabolic function in vermicomposting (VPs, with earthworms) for excess sludge stabilization were investigated. Comparison between the dynamic variation of PLFA profiles in VPs and common composting (CPs, with no earthworms) was conducted. The Shannon index was increased in VPs, while it was decreased in CPs with time, indicating earthworm activity enhanced microbial community diversity. The fungal and protozoal biomasses were significantly increased in VPs compared with CPs. Further researches by principal component analysis (PCA) indicated that earthworms benefited certain microorganisms containing biomarkers of 18:1ω9c, 18:3ω3, 18:3ω6, 20:1ω9, 20:2ω6 and 20:3ω6. Moreover, the ratios of monounsaturated to branched PLFAs in VPs were larger than those in CPs, suggesting the aeration condition was promoted by the burrowing behaviors of earthworms and therefore facilitated the growth and propagation of aerobic microorganisms, such as protozoa. Those results indicated that earthworm activity led to the general optimization of vermicomposting for excess sludge stabilization.

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment

Microbial communities in the functional areas of biofilm reactors with large height-diameter ratio using the anaerobic-aerobic (A/O) reflux process was investigated to treat heavy oil refinery wastewater without pretreatment. In the process, chemical oxygen demand (COD) and total nitrogen (TN) removal reached 93.2% and 82.8%, and the anaerobic biofilm reactor was responsible for 95% and 99%, respectively. Areas for hydrolysis acidification and acetic acid production, methane production, and COD recovery were obvious in the anaerobic reactor. Among all areas, area for hydrolysis acidification and acetic acid production was the key factor to improve COD removal efficiency. High throughput sequencing of 16S rDNA gene showed that the native community was mainly composed of functional groups for hydrocarbon degradation, syntrophic bacteria union body, methanogenesis, nitrification, denitrification, and sulfate reduction. The deviations between predicted values and actual COD and TN removal were less than 5% in the optimal prediction model.

The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction

The Lanzhou reach of the Yellow River, located at the upstream of Lanzhou, has been contaminated by heavy metals and polycyclic aromatic hydrocarbons over a long-time. We hypothesized that indigenous microbial communities would remediate those contaminants and some unique populations could play an important role in this process. In this study, we investigated the sediment microbial community structure and function from the Lanzhou reach. Sediment samples were collected from two nearby sites (site A and site B) in the Lanzhou reach along the Yellow River. Sediment geochemical property data showed that site A sediment samples contained significantly (p < 0.05) higher heavy metals than site B, such as chromium (Cr), manganese (Mn), and copper (Cu). Both site A and B samples were incubated with or without hexavalent chromium (Cr (VI)) for 30 days in the laboratory, and Cr (VI) reduction was only observed in site A sediment samples. After incubation, MiSeq sequencing of 16S rRNA gene amplicons revealed that the phylogenetic composition and structure of microbial communities changed in both samples, and especially Proteobacteria, as the most abundant phylum increased from 45.1 % to 68.2 % in site A, and 50.1 % to 71.3 % in site B, respectively. Some unique OTUs and populations affiliated with Geobacter, Clostridium, Desulfosporosinus and Desulfosporosinus might be involved in Cr (VI) reduction in site A. Furthermore, GeoChip 4.0 (a comprehensive functional gene array) data showed that genes involved in carbon and nitrogen cycling and metal resistance significantly (p < 0.05) increased in site A sediment samples. All the results indicated that indigenous sediment microbial communities might be able to remediate contaminants like Cr (VI), and this information provides possible strategies for future bioremediation of the Lanzhou reach.

Treatment of turtle aquaculture effluent by an improved multi-soil-layer system

Concentrated turtle aquaculture effluent poses an environmental threat to water bodies, and therefore needs to be treated prior to disposal. This study was conducted to assess the effect of multi-soil-layer (MSL) systems treating turtle aquaculture effluent with adding different amounts of sludge. Four MSL systems were constructed with dry weight ratios of sludge with 0%, 5%, 10%, and 20% (MSL 1, MSL 2, MSL 3, and MSL 4, respectively). The turtle aquaculture effluent had an average chemical oxygen demand (COD), ammonia nitrogen (NH4(+)-N) and total nitrogen (TN) concentration of 288.4, 213.4, and 252.0 mg/L, respectively. The COD/TN (C/N) ratio was 1.2. The results showed that the four MSL systems could effectively treat the COD, NH4(+)-N, and TN, and MSL 4 showed significantly improved NH4(+)-N removal efficiency, suggesting the potential of sludge addition to improve the turtle aquaculture effluent treatment. The average COD, TN, and NH4(+)-N removal efficiencies of MSL 4 were 70.3%, 66.5%, and 72.7%, respectively. To further interpret the contribution of microorganisms to the removal, the microbial community compositions and diversities of the four MSL systems were measured. Comparisons of the denaturing gradient gel electrophoresis (DGGE) profiles revealed that the amount of nitrifying bacteria and diversity in MSL 4 were higher than those in the other three systems. We concluded that adding 20% of sludge improved the NH4(+)-N removal and stability of the system for nitrification, due to the enrichment of the nitrifying bacteria in MSL 4.

Microbial reduction and precipitation of vanadium (V) in groundwater by immobilized mixed anaerobic culture

Vanadium is an important contaminant impacted by natural and industrial activities. Vanadium (V) reduction efficiency as high as 87.0% was achieved by employing immobilized mixed anaerobic sludge as inoculated seed within 12h operation, while V(IV) was the main reduction product which precipitated instantly. Increasing initial V(V) concentration resulted in the decrease of V(V) removal efficiency, while this index increased first and then decreased with the increase of initial COD concentration, pH and conductivity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the decreased microbial diversity. V(V) reduction was realized through dissimilatory reduction process by significantly enhanced Lactococcus and Enterobacter with oxidation of lactic and acetic acids from fermentative microorganisms such as the enriched Paludibacter and the newly appeared Acetobacterium, Oscillibacter. This study is helpful to detect new functional species for V(V) reduction and constitutes a step ahead in developing in situ bioremediations of vanadium contamination.

Diversity change of microbial communities responding to zinc and arsenic pollution in a river of northeastern China

Pollution discharge disturbs the natural functions of water systems. The environmental microbial community composition and diversity are sensitive key indicators to the impact of water pollutant on the microbial ecology system over time. It is meaningful to develop a way to identify the microbial diversity related to heavy metal effects in evaluating river pollution. Water and sediment samples were collected from eight sections along the Tiaozi River where wastewater and sewage were discharged from Siping City in northeastern China. The main pollutants contents and microbial communities were analyzed. As the primary metal pollutants, zinc (Zn) and arsenic (As) were recorded at the maximum concentrations of 420 and 5.72 μg/L in the water, and 1704 and 1.92 mg/kg in the sediment, respectively. These pollutants posed a threat to the microbial community diversity as only a few species of bacteria and eukaryotes with strong resistance were detected through denaturing gradient gel electrophoresis (DGGE). Acinetobacter johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii were the dominant bacteria in the severely polluted areas. The massive reproduction of Limnodrilus hoffmeisteri almost depleted the dissolved oxygen (DO) and resulted in the decline of the aerobic bacteria. It was noted that the pollution reduced the microbial diversity but the L. hoffmeisteri mass increased as the dominant community, which led to the overconsuming of DO and anaerobic stinking water bodies. Water quality, concentrations of heavy metals, and the spatial distribution of microbial populations have obvious consistencies, which mean that the heavy metals in the river pose a serious stress on the microorganisms.

Characterization of the bacterial communities of aerobic granules in a 2-fluorophenol degrading process

Aerobic granular sludge constitutes a novel technology for wastewater treatment. This study focused on the effect of 2-fluorophenol (2-FP) shock loadings on the microbial community diversity present in aerobic granules before and after inoculation with a bacterial strain able to degrade 2-FP, Rhodococcus sp. strain FP1. After bioaugmentation, apart from strain FP1, five culturable bacteria were isolated from the 2-FP degrading granules, belonging to the following genera: Serratia, Chryseobacterium, Xanthomonas, Pimelobacter and Rhodococcus. The latter two isolates are able to degrade 2-FP. Changes in the aerobic granules' bacterial communities related to 2-FP shock loadings were examined using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene pool. Numerical analysis of the DGGE profiles showed high diversity with an even distribution of species. Based on cluster analysis of the DGGE profiles, the bacterial communities present in the aerobic granules changes were related to the sampling time and the 2-FP concentration fed.

Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation in microbial fuel cells

Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation were realized in microbial fuel cells (MFCs). With initial V(V) concentrations of 75 mg/l and 150 mg/l in anolyte and catholyte, respectively, stable power output of 419±11 mW/m(2) was achieved. After 12h operation, V(V) concentration in the catholyte decreased to the value similar to that of the initial one in the anolyte, meanwhile it was nearly reduced completely in the anolyte. V(IV) was the main reduction product, which subsequently precipitated, acquiring total vanadium removal efficiencies of 76.8±2.9%. Microbial community analysis revealed the emergence of the new species of Deltaproteobacteria and Bacteroidetes as well as the enhanced Spirochaetes mainly functioned in the anode. This study opens new pathways to successful remediation of vanadium contamination.

Support vector regression model of wastewater bioreactor performance using microbial community diversity indices: effect of stress and bioaugmentation

The relationship between microbial community structure and function has been examined in detail in natural and engineered environments, but little work has been done on using microbial community information to predict function. We processed microbial community and operational data from controlled experiments with bench-scale bioreactor systems to predict reactor process performance. Four membrane-operated sequencing batch reactors treating synthetic wastewater were operated in two experiments to test the effects of (i) the toxic compound 3-chloroaniline (3-CA) and (ii) bioaugmentation targeting 3-CA degradation, on the sludge microbial community in the reactors. In the first experiment, two reactors were treated with 3-CA and two reactors were operated as controls without 3-CA input. In the second experiment, all four reactors were additionally bioaugmented with a Pseudomonas putida strain carrying a plasmid with a portion of the pathway for 3-CA degradation. Molecular data were generated from terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S rRNA and amoA genes from the sludge community. The electropherograms resulting from these T-RFs were used to calculate diversity indices - community richness, dynamics and evenness - for the domain Bacteria as well as for ammonia-oxidizing bacteria in each reactor over time. These diversity indices were then used to train and test a support vector regression (SVR) model to predict reactor performance based on input microbial community indices and operational data. Considering the diversity indices over time and across replicate reactors as discrete values, it was found that, although bioaugmentation with a bacterial strain harboring a subset of genes involved in the degradation of 3-CA did not bring about 3-CA degradation, it significantly affected the community as measured through all three diversity indices in both the general bacterial community and the ammonia-oxidizer community (α = 0.5). The impact of bioaugmentation was also seen qualitatively in the variation of community richness and evenness over time in each reactor, with overall community richness falling in the case of bioaugmented reactors subjected to 3-CA and community evenness remaining lower and more stable in the bioaugmented reactors as opposed to the unbioaugmented reactors. Using diversity indices, 3-CA input, bioaugmentation and time as input variables, the SVR model successfully predicted reactor performance in terms of the removal of broad-range contaminants like COD, ammonia and nitrate as well as specific contaminants like 3-CA. This work was the first to demonstrate that (i) bioaugmentation, even when unsuccessful, can produce a change in community structure and (ii) microbial community information can be used to reliably predict process performance. However, T-RFLP may not result in the most accurate representation of the microbial community itself, and a much more powerful prediction tool can potentially be developed using more sophisticated molecular methods.

Microbial community structure and metabolic property of biofilms in vermifiltration for liquid-state sludge stabilization using PLFA profiles

To investigate effects of earthworms on microbial community structure and metabolic properties of biofilms in vermifiltration for liquid-state sludge stabilization, a vermifilter (VF) with earthworms and a conventional biofilter (BF) without earthworms were compared. The Shannon index of fungi in VF was 16% higher than that in BF, which indicated earthworm activities significantly enhanced fungi diversity. The ratio of monounsaturated to saturated (mono:sat) PLFAs of VF biofilms was higher than that of BF biofilms, which indicated the physiological and nutritional stress for microbial community in VF was relieved due to the increasing of soluble substances caused by the earthworm ingestion. Further investigation showed that the burrowing action of earthworms promoted the aeration condition and led to aerobic microorganisms were predominant in VF. Those results indicated earthworms improved microbial community structure and metabolic properties of biofilms and thus resulted in the overall optimization of the vermifiltration system for liquid-state sludge stabilization.