Microbial Function Research Articles

Multifunctional effects of nitrification and urease inhibitors: decreasing soil herbicide residues and reducing nitrous oxide emissions simultaneously

Glyphosate pollution and greenhouse gas emissions are major problem in achieving sustainable soil management. It is necessary to develop effective strategies to simultaneously reduce herbicide residues and nitrous oxide (N2O) emissions in soil. This study aimed to: (1) quantitative analyze the effects of nitrogen (N) cycle inhibitors (nitrification inhibitors 3,4 dimethylpyrazole phosphate (DMPP) and dicyandiamide (DCD) and urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT)) on glyphosate degradation and reduction of N2O under different soil moistures; (2) identify the functional microbes and genes associated with glyphosate degradation and N2O emissions; and (3) decipher the main mechanisms of N cycle inhibitors affecting glyphosate degradation at different soil water contents. Compared to the control, the application of DMPP, DCD and NBPT reduced glyphosate residues in soil by 33.0%, 60.3% and 35.7%, respectively, under 90% water holding capacity (WHC). The application of DCD stimulated Acidobacteria and the phnX gene to degrade soil glyphosate. Further, soil glyphosate residues were significantly and negatively related to soil N2O emissions at both 60% and 90% WHC. Compared to the control, NBPT application decreased cumulative N2O emissions by 91.4% at 90% WHC by decreasing soil nitrate N (NO3--N) and inhibiting amoC and narG genes at 90%. The application of N cycle inhibitors could be a potential strategy to simultaneously reduce glyphosate residues and soil N2O emissions. Our study could provide technical support to reduce the risks of herbicide exposure and reduce greenhouse gas emissions.

Synchronous bioremediation of vanadium(V) and chromium(VI) using straw in a continuous-flow reactor

Vanadium (V) and chromium (Cr) are key resources widely used in industrial production. However, mining causes V(V) and Cr(VI) contamination in groundwater, posing health and environmental risks. Straw is an important byproduct and considered waste, however, it could be a solid carbon source. Therefore, the feasibility of V(V) and Cr(VI) bioremediation in groundwater was determined using straw as the carbon source in this study. A continuous-flow reactor able to resist fluctuations in pollutant concentrations in groundwater was constructed. V(V) and Cr(VI) were completely removed (100%, 10-34 d) in the reactor, and the maximum Cr(VI) removal rate from effluent was 1.19 mg/(L·h) (34-64 d). After long-term reactor operation (114 d), the V(V) and Cr(VI) removal rates reached almost 100%. Moreover, the formation of humus and tryptophan contributed to V(V) and Cr(VI) bioremediation. The extracellular polymeric substance content increased from 108.28 to 113.98 mg/g VSS, and combined with V(V) and Cr(VI) to reduce their concentrations. Moreover, functional microbes associated with heavy metal removal (Bacillus and Pseudobacteroides) and straw decomposition (Paludibacter) were found. The findings of this study offer empirical evidence that support the utilization of straw for mitigating composite heavy metal pollution, thereby laying a foundation for its practical engineering applications.

Advanced anaerobic digestion by co-immobilization of anaerobic microbes and conductive particles in hydrogel for enhanced methane production performance

Recent research has increasingly focused on the enhancement of anaerobic digestion (AD) through direct interspecies electron transfer (DIET) facilitated by conductive particles (CP). Although this approach can significantly accelerate the AD process, the contact efficiency between CPs and AD microbes is relatively low due to the flow of water in a dispersed condition, leading to possible DIET inefficiency. In this study, a unique approach involving the “co-immobilization” of anaerobic microbes and multi-walled carbon nanotubes (MWCNTs) as CP into a hydrogel matrix was developed to improve the AD process. The advantages of this method include improved contact efficiency between microbes and CPs for enhanced DIET, and increased CP retention within the reactor, thereby omitting the need to compensate for CP washout. The methane production rate for the co-immobilized hydrogel was 2.5-fold and 1.9-fold faster than that of the control (dispersed sludge) and conventional DIET (dispersed sludge with MWCNT addition), respectively. Microbial analysis indicated the enrichment of functional microbes such as Anaerolineacea, Sedimentibacteraceae, Rhodocyclaceae, and Methanothrichaceae, which could be involved in the DIET under co-immobilized conditions. These results demonstrate the potential of the proposed method for realizing an advanced continuous AD process through improved DIET.

Composting feasibility of organic solid waste ratio of CELSS and associated microbial enhancement effects

Due to the unique environment of the Controlled Ecological Life Support System (CELSS), the type and quantity of organic solid wastes produced during long-term space missions are fixed. However, these mixed materials do not meet the indicators of conventional composting, and the vacuum in CELSS limits bio-degradation due to a shortage of functional microbes. In order to explore the feasibility of the organic solid waste ratio of CELSS and its microbial enhancement effect, composting experiments were setup to compare the actual and optimized material ratios on composting and polluted gaseous emissions, and to investigate the enhancement of microbial inoculation. The results demonstrated that the actual material ratio can be used for composting, whose degradation degree of crude protein, soluble sugar, cellulose, hemicellulose and lignin was better than the optimized treatment. The actual material ratio can also reduce 26.1% of ammonia (NH3) and 66.8% of methane (CH4) emissions. They were attributed to the carbon source in the actual materials, which resulted in higher species abundance, uniformity, and dominance of the microbial community and a stronger overall utilization ability. Moreover, the inoculation of VT microbial agent can further increase the diversity of microorganisms and prolong the duration of high activity, which helps to strengthen the degradation of crude fat, cellulose and lignin, and reduced 50.7% of hydrogen sulfide (H2S) and 33.2% of nitrous oxide (N2O) emissions. Therefore, it is recommended that the aerobic composting technology in CELSS use the proportion of actual organic solid waste to match the material and add VT microbial agent.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m−2·yr−1; N1, 100 g m−2·yr−1; N2, 200 g m−2·yr−1; N3, 300 g m−2·yr−1; and N4, 400 g m−2·yr−1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100–300 g m−2·yr−1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m−2·yr−1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing

Animals form functional units with their microbial communities, termed metaorganisms. Despite extensive research on some model animals, microbial diversity in many species remains unexplored. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod using a shotgun DNA sequencing approach. We focused on the mucus to determine if its microbial composition differs from that of the fecal microbiota, which could reveal unique microbial interactions and functions. Metagenomes from six individuals were analyzed, revealing three different taxonomic profiles: Type I is dominated in numbers by Pseudomonadaceae (44%) and Xanthomonadaceae (13%), Type II by Vibrionaceae (65%), and Type III by Enterobacteriaceae (76%). This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, Type II within the Photobacterium phosphoreum clade, and Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod’s intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient microbiota. This suggests that the intestine contains two separate and distinct microbial populations.

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues

The interactive pathway of the gut-liver axis underscores the significance of microbiome modulation in the pathogenesis and progression of various liver diseases, including hepatocellular carcinoma (HCC). This study aims to investigate the disparities in the composition and functionality of the hepatic microbiota between tumor tissues and adjacent normal liver tissues, and their implications in the etiology of HCC. We conducted a comparative analysis of the hepatic microbiome between adjacent normal liver tissues and tumor tissues from HCC patients. Samples were categorized according to the modified Union for International Cancer Control (mUICC) staging system into Non-tumor, mUICC stage I, mUICC stage II, and mUICC stage III groups. Microbial richness and community composition were analyzed, and phylogenetic profiles were examined to identify significantly altered microbial taxa among the groups. Predicted metabolic pathways were analyzed using PICRUSt2. Our analysis did not reveal significant differences in microbial richness and community composition with the development of HCC. However, phylogenetic profiling identified significantly altered microbial taxa among the groups. Sphingobium, known for degrading polychlorinated biphenyls (PCBs), exhibited a significantly negative correlation with clinical indices in HCC patients. Conversely, Sphingomonas, a gut bacterium associated with various liver diseases, showed a positive correlation. Predicted metabolic pathways suggested a correlation between atrazine degradation and valine, leucine, and isoleucine biosynthesis with mUICC stage and tumor size. Our results underscore the critical link between hepatic microbial composition and function and the HCC tumor stage, suggesting a potentially pivotal role in the development of HCC. These findings highlight the importance of targeting the hepatic microbiome for therapeutic strategies in HCC.

The Role of Nutrient and Energy Limitation on Microbial Decomposition of Deep Podzolized Carbon: A Priming Experiment

AbstractSoil carbon decomposition is primarily driven by microbial activities and is regulated by factors which stimulate or impede microbial functions. Deep podzolized carbon (DPC), found in the United States Southeastern Coastal Plain, is situated well below the soil surface in horizons isolated from active plant input. This carbon is characterized by high C:N ratios (>30) which could reflect nutrient limitation of microbial decomposition. To uncover the energy or nutrient limitation on DPC degradation, a 90‐day priming experiment was performed with soils from the surface horizon and DPC horizons (i.e., Bh1 and Bh2) received the additions of 13C‐labeled alanine and glucose. This resulted in prominent priming effects: addition of alanine increased basal decomposition of soil organic carbon by 918 ± 51% and 737 ± 7% in Bh2 and Bh1, respectively. Glucose relative priming was 505 ± 28% in Bh1 and 606 ± 77% of basal respiration in Bh2. These strong responses to substrate input highlight the susceptibility of DPC to loss when microbial carbon and nutrient constraints are alleviated. After 90 days, glucose addition increased the microbial biomass in DPC horizons relative to alanine addition, with the latter showing no difference from ultrapure‐water control. The response of the microbial biomass indicates constraint by a lack of energy sources both by the paucity of labile substrates and reduced availability of organic matter as a result of podzolization. Our study has important implications for predicting the response of DPC in Coastal Plain soils in the context of land management and global change.

What Is a Biofilm? Lessons Learned from Interactions with Immune Cells.

Biofilms are unique, multicellular life forms that challenge our understanding of the microbial functioning. The last decades of research on biofilms have allowed us to better understand their importance in the context of both health and various pathologies in the human body, although many knowledge gaps hindering their correct comprehension still exist. Biofilms are classically described as mushroom-shaped structures attached to the substrate; however, an increasing body of evidence shows that their morphology in clinical conditions may differ significantly from that classically presented. Although this may result partly from the unique physicochemical conditions within the host, the interaction between microbes and immune cells during development of a biofilm should not be underestimated. The current Opinion confronts the classical view on biofilms with the latest scientific research describing the vitality of interactions with immune cells as a modulator of the biofilm phenotype and behavior in clinical conditions.

Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants

ABSTRACT To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella , Rhizophagus , Rhizobacter , Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio , Syntrophorhabdus , Syntrophus , Chlorobium , Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium , Ideonella , Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus , may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further. IMPORTANCE Previous studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.

Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED

ABSTRACT Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans . In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED in vivo results in a higher abundance of transcripts for methyltransferases ( mtaC2, mtaB3, mtaC3 ), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability. IMPORTANCE Methanosarcina is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.

Fecal Microbiome Composition Correlates with Pathologic Complete Response in Patients with Operable Esophageal Cancer Treated with Combined Chemoradiotherapy and Immunotherapy.

Background: Preclinical and clinical data indicate that chemoradiotherapy (CRT) in combination with checkpoint inhibitors may prime an anti-tumor immunological response in esophageal cancer. However, responses to neoadjuvant therapy can vary widely and the key biomarkers to determine response remain poorly understood. The fecal microbiome is a novel and potentially modifiable biomarker of immunotherapy response, and both fecal and tumor microbes have been found to associate with outcomes in esophageal cancer. Methods: Fecal and tumor samples were collected from patients with stage II-III resectable esophageal or gastroesophageal junction carcinoma treated with neoadjuvant immune checkpoint inhibitors (ICIs) plus CRT prior to surgical resection. Microbiome profiles were analyzed by 16S rRNA amplicon sequencing and taxonomic data were integrated with fecal metabolite analysis to assess microbial function. Results: The fecal microbiome of patients with pathological complete response (PCR) grouped in distinct clusters compared to patients with residual viable tumor (RVT) by Bray-Curtis diversity metric. Integrated taxonomic and metabolomic analysis of fecal samples identified a sphingolipid and primary bile acid as enriched in the PCR, the levels of which correlated with several bacterial species: Roseburis inulinivorans, Ruminococcus callidus, and Fusicantenibacter saccharivorans. Analysis of the tumor microbiome profiles identified several bacterial genera previously associated with esophageal tumors, including Streptococcus and Veillonella. Conclusions: These results further characterize the fecal and tumor microbiome of patients with operable esophageal cancer and identify specific microbes and metabolites that may help elucidate how microbes contribute to tumor response with neoadjuvant CRT combined with ICI.

Mice colonized with the defined microbial community OMM19.1 are susceptible to Clostridioides difficile infection without prior antibiotic treatment.

Diverse gut microorganisms present in humans and mice are essential for the prevention of microbial pathogen colonization. However, antibiotic-induced dysbiosis of the gut microbiome reduces microbial diversity and allows Clostridioides difficile (C. difficile) to colonize the intestine. The Oligo-Mouse-Microbiota 19.1 (OMM19.1) is a synthetic community that consists of bacteria that are taxonomically and functionally designed to mimic the specific pathogen-free mouse gut microbiota. Here, we examined the susceptibility of OMM19.1 colonized mice to C. difficile infection (CDI) at a range of infectious doses (103, 105, and 107 spores) without prior antibiotic treatment. We found that mice colonized with OMM19.1 were susceptible to CDI regardless of the dose. The clinical scores increased with increasing C. difficile dosage. Infection with C. difficile was correlated with a significant increase in Ligilactobacillus murinus and Escherichia coli, while the relative abundance of Bacteroides caecimuris, Akkermansia muciniphila, Extibacter muris, and Turicimonas muris was significantly decreased following CDI. Our results demonstrate that the OMM19.1 community requires additional bacteria to enable C. difficile colonization resistance.IMPORTANCEThe human gut microbiota consists of a wide range of microorganisms whose composition and function vary according to their location and have a significant impact on health and disease. The ability to generate and test the defined microbiota within gnotobiotic animal models is essential for determining the mechanisms responsible for colonization resistance. The exact mechanism(s) by which healthy microbiota prevents Clostridioides difficile infection is unknown, although competition for nutrients, active antagonism, production of inhibitory metabolites (such as secondary bile acids), and microbial manipulation of the immune system are all thought to play a role. Here, we colonized germ-free C57BL/6 mice with a synthetic bacterial community (OMM19.1) that mimics the specific pathogen-free mouse microbiota. Following breeding, to enable immune system development, F1 mice were infected with three different doses of C. difficile. Our research suggests that there are additional essential microbial functions that are absent from the current OMM19.1 model.

Microbial Inoculants Modify the Functions of Resident Soil Microbes to Expedite the Field Restoration of the Abandoned Mine

ABSTRACTGlobal‐scale mining activities have had significant deleterious impacts on local ecosystems and the overall environment, which will necessitate robust restoration efforts. A practical approach includes combining microbial inoculants with the technology of external soil spray seeding. This approach holds the potential for sustainable abandoned mine site restoration by enhancing plant growth through the modulation of soil nutrients and microbial communities. Nonetheless, the detailed effects of microbial inoculants on specific aspects of soil microbial community functions and their complex interactions with plant growth remain underexplored, particularly in the context of restoration efforts. To bridge this gap, we performed a four‐year field study at an abandoned carbonate mine location, using metagenomic sequencing to evaluate the influence of microbial inoculants on soil microbial functionality. Our research revealed that introducing microbial inoculants greatly enhanced essential soil parameters and notably increased plant biomass. Additionally, these inoculants altered the functional gene makeup of the microbial community, significantly boosting the relative abundance of processes such as nitrogen fixation, nitrification, denitrification, assimilatory nitrate reduction (ANRA), dissimilatory nitrate reduction (DNRA), and organic phosphorus mineralization. Conversely, there was a decrease in the relative abundance of carbon degradation, phosphorus regulation, and transport processes. We observed strong correlations between the abundance of nitrogen and phosphorus cycles and plant biomass. Crucially, microbial inoculants affect plant biomass by initially altering soil properties and subsequently coordinating nitrogen and phosphorus cycles. These findings provide valuable insights into the role of microbial inoculants in mine site restoration and offer a theoretical foundation for their broader practical application.

Impact of tidal fluctuations on bacterial community structure in Wuyuan Bay: A comparative analysis of waters inside and outside the tidal barrage.

The tidal barrage at Wuyuan Bay effectively mitigated the odor from the tidal flat during ebb tide, however, its effect on bacterial community structure in waters are still unclear. In this study, high-throughput sequencing was used to analyze the structure of the microbial community in waters inside and outside the tidal barrage during flood and ebb tides. Results showed bacterial diversity was higher in water outside the barrage during flood tide. The dominated species at phylum and genus levels were various in waters inside and outside the tidal barrage during flood and ebb tides. The water inside during ebb tide (E1) were dominated by two cyanobacterial genera, Cyanobium_PCC-6307 (42.90%) and Synechococcus_CC9902 (12.56%). The microbial function, such as porphyrin and chlorophyll metabolism and photosynthesis, were increased in E1. Norank_f__Nitriliruptoraceae was identified as differential microorganism in waters inside the barrage. Inorganic nitrogen and nonionic ammonia were significantly high in E1, and were negatively correlated with norank_f__Nitriliruptoraceae. These results suggest tidal barrage blocks water exchange, resulting in the accumulation of nutrients in Wuyuan Bay. Consequently, the environment became favorable for the growth of cyanobacteria, leading to the dominance of algae in the water inside the barrage and posing the risk of cyanobacterial bloom. Higher Nitriliruptoraceae inside the barrage might be a cue for the change of water quality.

Programming rumen microbiome development in calves with the anti-methanogenic compound 3-NOP

The aim of this study was to establish a distinctive rumen microbial and fermentation profile using the anti-methanogenic compound 3-NOP to assess dam effect, and nutritional intervention of the juvenile offspring on microbial structure and function of rumen up to 12 months of age, once the treatment was withdrawn. Forty-eight pregnant heifers (H) and their future offspring (C) were allocated to either Control (-) or 3-NOP (+) treatment resulting in four experimental groups: H+/C+, H+/C-, H-/C + and H-/C-. Animals were treated from 6 weeks prior to calving until weaning, with the offspring monitored until 12 months of age. Rumen fluid samples and methane measurements using the Greenfeed system were collected during the trial. Results supported the mode of action of the compound, with a shift in fermentation from acetate to propionate, increases in branched chain fatty acids and formic acid in the 3-NOP treated animals. Similar shifts in microbial populations occurred in 3-NOP treated animals with lower abundances of rumen methanogen populations, increases of bacterial groups Succiniclasticum spp, Candidatus Saccharimonas. Fibrobacter and the families Prevotellaceae and Succinivibrioacea. and the protozoa Entodinium. Early life intervention had an enduring impact on the rumen microbial structure of young animals up to 28 weeks post weaning, however the effect was diminished once 3-NOP was withdrawn. Interestingly, a group of young animals emitted significantly less methane (15%) than the animals that did not receive the treatment during their juvenile stage. Our results suggest a higher resemblance of the young calf microbiome to a low methane adult and that early life colonisation of the rumen persists through to later life with the pre-weaning microbiome comprising ~ 65% of the yearling animal. Further research needs to be performed to determine the timing and dose of 3-NOP for new-born calves that can sustain a reduction in methane emissions after the treatment is withdrawn, under extensive grazing or controlled conditions.

Elucidating the synergic mechanism of sodium pyrophosphate assisted enzymolysis on the waste activated sludge fermentation enhancement: Insights from organic conversion and metagenomic analysis

Lysozyme has been identified as a promising approach for enhancing waste activated sludge (WAS) anaerobic fermentation. However, the extracellular polymeric substance (EPS), functioning as a ‘protective shell’ for microbial cells, hindered the lysozyme transfer and subsequent interaction with cell wall, resulting in excessive dosage and limited efficiency in practical engineering applications. This study innovatively proposed a sodium pyrophosphate (SP) assisted lysozyme treatment, aiming to overcome such limitations and enhance the solubilization and hydrolysis efficiency. As a result, 3583.5 mg COD/L short-chain fatty acids (SCFAs) and 23.1 % acidification rate were achieved after 2-day anaerobic fermentation within SP-lysozyme treatment. Mechanism investigation revealed that SP facilitated EPS disruption by inducing a loosening of the protein structure, leading to the enhanced solubilization of organic matter within the EPS and microbial cells. Consequently, the release of substantial substrates contributed to the enrichment of functional microbes associated with hydrolysis and acidogenesis, accompanied by the augmentation of corresponding metabolic functions. Besides, the key functional genes analysis demonstrated the amino acid metabolism, glycolysis, pyruvate metabolism and SCFAs transport were facilitated and the methanogenesis was inhibited on the contrary with SP-lysozyme treatment, which was undoubtedly responsible for the superior SCFAs accumulation in anaerobic fermentation process. Considering the carbon resource recovery in SCFAs form, such novel SP-lysozyme treatment exhibited 325.1 CNY /ton SS (45.5 USD / ton SS) economic benefit and avoided 0.12 CO2/ton SS carbon emission, suggesting its promising application potential in future WAS management.

Effects of filling substrates on remediation performance and sulfur transformation of sulfate reducing packed-bed bioreactors treating acid mine drainage

The filling substrate is one of key factors influencing effectiveness of sulfate reducing packed-bed bioreactor (SRPB) treating acid mine drainage (AMD). The effects of four substrates (i.e. quartz sand, steel residue, biochar, and peanut shell) on remediation performance and sulfur transformation of SRPB treating AMD was studied. The results showed that steel residue and biochar improved sulfate reduction efficiency (61% and 49%) compared to quartz sand (32%), whereas peanut shell inhibited sulfate reduction efficiency (19%), attributed to its decomposition process leading to a severe accumulation of acetic acid. More amounts of sulfides generated in steel residue bioreactor were converted into acid volatile sulfide and elemental sulfur, resulting in a significant decrease in dissolved sulfide in the effluent. Metals (Fe, Al, Zn, Cd and Cr) except for Mn were effectively immobilized in the bioreactors, particularly for Al and Cd. Sulfate reducing bacteria and sulfide oxidizing bacteria lived symbiotically in all bioreactors which exhibited similar heterogeneity in microbial distribution and function, i.e. bacterial sulfate reduction mainly occurring in bottom-middle layers and photoautotrophic sulfide oxidation in upper layer close to outlet. The microbial response mechanism to various substrate environments was revealed through co-occurrence networks analysis. This study suggests that attention should be paid to the inhibitory effect of acetic acid accumulation on sulfate reduction when using sole lignocellulosic waste (peanut shell), and steel residue and biochar could be utilized as filling substances to promote sulfate reduction.

Bioremediation of nitrate in agricultural drainage ditches: Impacts of low-grade weirs on microbiomes and nitrogen cycle gene abundance

Artificial drainage is essential for the success of modern agriculture, but it can also accelerate the movement of nutrients, especially nitrate, from soil to surrounding and downstream water bodies. Removal of nitrate from agricultural drainage by using controlled drainage systems, such as ditches installed with low-grade weirs, has been shown to help reduce nutrient loading into watersheds. However, the effect of low-grade weirs varies greatly, likely due to the differences in climate, system designs (e.g., hydraulic characteristics), and the resulting variation in microbial structures and functions in the ditch. In this study, we analyzed the temporal and spatial dynamics of microbiomes in a paired ditch system with weir-installed and uninstalled (control) channels over two years by using the 16S rRNA gene amplicon sequencing and the high-throughput quantitative PCR targeting various N cycle-associated genes [the Nitrogen Cycle Evaluation (NiCE) chip]. The installation of the low-grade weir had a significant impact on the microbiome structure and the distribution of denitrifiers. Microbiome structures also differed significantly between the ditch inlets and the outlets. Denitrification functional genes were more abundant in the inlets than in the other locations and in the channel installed with a low-grade weir. Additionally, oxygenic denitrifiers that utilize nitric oxide dismutase (nod) to produce N2 and O2 gases from nitric oxide were detected in the ditch channels, suggesting the occurrence of nitrate removal process that bypasses the production of nitrous oxide (N2O). The ditch microbiomes sampled during high-flow seasons (i.e., spring and fall) exhibited greater similarity to each other than microbiomes sampled during low-flow seasons (i.e., summer). Taken together, this study indicates that the low-grade weirs have the potential to foster a more favorable environment for denitrifiers, resulting in an increase in the abundance of denitrification functional genes. These findings could offer valuable insights into system management and optimization strategies.

Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn’s disease location

BackgroundCrohn’s disease (CD) is characterized by chronic intestinal inflammation. Diet is a key modifiable factor influencing the gut microbiome (GM) and a risk factor for CD. However, the impact of diet modulation on GM function in CD patients is understudied. Herein, we evaluated the effect of a high-fiber, low-fat diet (the Mi-IBD diet) on GM function in CD patients. All participants were instructed to follow the Mi-IBD diet for 8 weeks. One group of CD patients received one-time diet counseling only (Gr1); catered food was supplied for the other three groups, including CD patients (Gr2) and dyads of CD patients and healthy household controls (HHCs) residing within the same household (Gr3-HHC dyads). Stool samples were collected at baseline, week 8, and week 36, and analyzed by liquid chromatography-tandem mass spectrometry.ResultsAt baseline, the metaproteomic profiles of CD patients and HHCs differed. The Mi-IBD diet significantly increased carbohydrate and iron transport and metabolism. The predicted microbial composition underlying the metaproteomic changes differed between patients with ileal only disease (ICD) or colonic involvement: ICD was characterized by decreased Faecalibacterium abundance. Even on the Mi-IBD diet, the CD patient metaproteome displayed significant underrepresentation of carbohydrate and purine/pyrimidine synthesis pathways compared to that of HHCs. Human immune-related proteins were upregulated in CD patients compared to HHCs.ConclusionsThe Mi-IBD diet changed the microbial function of CD patients and enhanced carbohydrate metabolism. Our metaproteomic results highlight functional differences in the microbiome according to disease location. Notably, our dietary intervention yielded the most benefit for CD patients with colonic involvement compared to ileal-only disease.9orssYZV9GnhTtyZm1JCtCVideo