Abundance Of Microbial Genes Research Articles

Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.

Unpredictable chemotherapy side effects are a major barrier to successful treatment. Cell culture and mouse experiments indicate that the gut microbiota is influenced by and influences anti-cancer drugs. However, metagenomic data from patients paired to careful side effect monitoring remains limited. Herein, we focus on the oral fluoropyrimidine capecitabine (CAP). We investigate CAP-microbiome interactions through metagenomic sequencing of longitudinal stool sampling from a cohort of advanced colorectal cancer (CRC) patients. We established a prospective cohort study including 56 patients with advanced CRC treated with CAP monotherapy across 4 centers in the Netherlands. Stool samples and clinical questionnaires were collected at baseline, during cycle 3, and post-treatment. Metagenomic sequencing to assess microbial community structure and gene abundance was paired with transposon mutagenesis, targeted gene deletion, and media supplementation experiments. An independent US cohort was used for model validation. CAP treatment significantly altered gut microbial composition and pathway abundance, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation confirmed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Microbial menaquinol biosynthesis genes were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted hand-foot syndrome and dose reductions in an independent cohort. These results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells, with implications for toxicities outside the gastrointestinal tract. We provide a proof-of-concept for the use of microbiome profiling and machine learning to predict drug toxicities across independent cohorts. These observations provide a foundation for future human intervention studies, more in-depth mechanistic dissection in preclinical models, and extension to other cancer treatments.

Midseason draining of paddy water suppresses microbial arsenic methylation in soil and alleviates rice straighthead disease

Arsenic (As) methylation is an important component of As biogeochemical cycle. Microbial As methylation is enhanced under anoxic conditions in paddy soil, producing dimethylarsenate (DMA) which can cause physiological straighthead disease in rice. We conducted field experiments at two sites to test the effect of midseason draining of paddy water on microbial As methylation and the incidence of straighthead disease. Compared to continuous flooding, midseason draining increased soil Eh, decreased the abundances of microbial genes for arsenate reduction (arsC and arrA) and arsenite methylation (arsM), and lowered the concentrations of both inorganic As and DMA in soil porewater. Draining shifted microbial composition, resulting in decreases in the relative abundance of 17–132 amplicon sequence variants. Draining decreased the accumulation of DMA in rice husk and of inorganic As and DMA in rice grain, decreased the incidence of straighthead disease, and increased grain yield by 20–45 %. Further experiments were conducted at eight field sites to assess the effect of midseason draining in a split field design. Draining decreased husk DMA concentration by 40–65 % and increased grain yield by 25–209 %. This study demonstrates that midseason draining can effectively suppress microbial As methylation and alleviate rice straighthead disease, benefiting both grain yield and safety.

Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease

BackgroundThis study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes. MethodsIn this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls. ResultsSignificant differences were found in the gut microbiome of body-first PD patients (n = 15) compared to both brain-first PD patients (n = 9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently. ConclusionsOur findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.

Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn’s disease development

BackgroundH2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.ResultsOur analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.ConclusionsOur study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD.Dka3P5uGJeBhH66pkNJcogVideo

New insights for simultaneous nitrogen removal and greenhouse gas reduction by biological-electrolysis constructed wetland in the treatment of aquaculture wastewater under varied C/N

Aiming to address the challenges of poor nitrogen (N) removal and greenhouse gas (GHG) emissions in aquaculture wastewater treatment, biological-electrolysis constructed wetland (BECW) and constructed wetland (CW) were established to comparatively evaluate the N removal efficiency, the greenhouse gas (GHG) emissions, and specific microbial gene abundances under various influent C/N ratios. Increasing influent C/N ratio markedly enhanced the removal rates of COD, NH4+-N, NO3−-N, and TN, while markedly reduced N2O fluxes in CW and BECW. The integration of an electric field with CW (BECW) significantly compensated for the shortcomings of the poor NO3−-N removal efficiency and high N2O emissions when C/N < 6. However, this compensating effect gradually weakened with the continue increase of C/N. BECW simultaneously achieved the high COD (89.26 ± 6.08 %), NO3−N (97.03 ± 1.22 %), and TN (83.17 ± 3.19 %) removal rates, and low GHG emissions (486.00 ± 36.61 mg/m2/h) at C/N = 6. The BECW significantly decreased the abundance of mcrA and pmoA genes while increased the abundance of nirK, nirS, and nosZ genes, and the ratios of pmoA/mcrA and nosZ/(nirS + nirK) across all C/N condition. The emission flux of CH4 in BECW was positively correlated with C/N and the mcrA abundance but significantly negatively correlated with pmoA abundance and pmoA/mcrA. The emission flux of N2O was positively correlated with nirS and nirK abundance but significantly negatively correlated with C/N, NO3−-N removal rates, nosZ abundance, and the index of nosZ/(nirS + nirK). This research offers an innovative approach to get both low GHG emissions and high NO3−-N removal rate in aquaculture wastewater treatment.

Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix.

Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.

Inflammatory bowel disease associated with primary sclerosing cholangitis is associated with an altered gut microbiome and bile acid profile.

Primary sclerosing cholangitis associated with inflammatory bowel disease (IBD-PSC) carries significant morbidity compared to IBD without PSC. Alterations in microbial composition and bile acid (BA) profiles have been shown to modulate chronic inflammation in IBD, but data in IBD-PSC is scarce. We aimed to assess the differences in gut microbiome composition as well as in the BA profile and BA-related microbial functions between IBD-PSC and IBD-only. 54 IBD-PSC and 62 IBD-only subjects were enrolled from 2012 to 2021. Baseline samples were collected for fecal DNA shotgun metagenomic sequencing, fecal and serum BA quantitation using mass spectrometry and fecal calprotectin. Liver fibrosis measured by transient elastography (TE) was assessed in the IBD-PSC group. Data was analyzed using general linear regression models and Spearman rank correlation tests. Patients with IBD-PSC had reduced microbial gene richness (p=0.004) and significant compositional shifts (PERMANOVA: R2=0.01, p=0.03) compared to IBD-only. IBD-PSC was associated with altered microbial composition and function, including decreased abundance of Blautia obeum, increased abundance of Veillonella atypica, Veillonella dispar and Clostridium scindens (q<0.05 for all), and increased abundance of microbial genes involved in secondary BA metabolism. Decreased serum sulfated and increased serum conjugated secondary BA were associated with IBD-PSC and increased liver fibrosis. We identified differences in microbial species, functional capacity and serum BA profiles in IBD-PSC compared with IBD-only. Our findings provide insight into the pathophysiology of IBD associated with PSC and suggest possible targets for modulating the risk and course of IBD in subjects with PSC.

Microplastics in granular sequencing batch reactors: Effects on pollutant removal dynamics and the microbial community

This study investigated the relationship between microplastic (MP) presence and pollutant removal in granular sludge sequencing batch reactors (GSBRs). Two types of MPs, polyethylene (PE) and polyethylene terephthalate (PET), were introduced in varying concentrations to assess their effects on microbial community dynamics and rates of nitrogen, phosphorus, and organic compound removal. The study revealed type-dependent variations in the deposition of MPs within the biomass, with PET-MPs exhibiting a stronger affinity for accumulation in biomass. A 50 mg/L dose of PET-MP decreased COD removal efficiency by approximately 4 % while increasing P-PO4 removal efficiency by around 7 % compared to the control reactor. The rate of nitrogen compounds removal decreased with higher PET-MP dosages but increased with higher PE-MP dosages. An analysis of microbial activity and gene abundance highlighted the influence of MPs on the expression of the nosZ and ppk1 genes, which code enzymes responsible for nitrogen and phosphorus transformations. The study also explored shifts in microbial community structure, revealing alterations with changes in MP dose and type. This research contributes valuable insights into the complex interactions between MP, microbial communities, and pollutant removal processes in GSBR systems, with implications for the sustainable management of wastewater treatment in the presence of MP.

Land use intensity is a major driver of soil microbial and carbon cycling across an agricultural landscape

Soil carbon (C) storage is a critical ecosystem function that underpins human health and well-being. The acceleration of human-driven land use change, such as agricultural intensification, is a major driver of soil C loss globally. Developing sustainable land use practices that enhance agricultural productivity whilst protecting essential ecosystem functions such as soil C storage is vital. The soil microbiome has a critical role in regulating soil biogeochemical cycling processes, including soil C cycling. Examining the impacts of land use intensity on the soil microbiome enables us to assess the potential effects on long-term soil C stocks. Using metagenomic DNA sequencing and phospholipid fatty acid analysis, we investigated differences in the activity, diversity, and function of the soil microbiome associated with five contrasting land uses across an agricultural landscape. The land uses covered a gradient of disturbance intensities and included remnant native forest, regenerating native bush, exotic plantation forest, dryland pasture, and irrigated pasture. We identified pronounced differences in the soil microbiome associated with each land use, including the diversity and abundance of microbial C and nitrogen (N) cycling genes. Notably, intensive agricultural land uses had a significantly higher diversity and abundance of microbial C-degrading genes, whilst land uses of remnant native forest had the lowest diversity and abundance of microbial C-degrading genes. Our findings suggest that intensive agricultural land use may increase the functional potential of the soil microbiome to mineralize soil C, potentially resulting in a greater loss of soil C as respired CO2 into the atmosphere. This research may be used to support the development of sustainable management practices that promote the persistence of soil C across agricultural landscapes, such as the protection of remnant native forest fragments and greater incorporation of regenerating native vegetation.

Impact of two acquisitive plants on N cycle on different soils: The invasive Fallopia japonica does it and so does the native Dactylis glomerata!

Invasive plants may alter ecological and ecosystem processes, including the N-cycle. The Fallopia species complex is a well-studied invasive species whose N-resource acquisition traits define it as an acquisitive species. However, the study of the impacts of invasive plants on the N-cycle never considers the N-acquisition strategy as a reference for choosing another suitable plant control. The purpose of this study is to assess the impacts of an invasive species (Fallopia japonicaFJ) on the N-cycle and to compare with those caused by a native acquisitive species (Dactylis glomerataDG), all compared to unplanted soils. A four-months mesocosm experiment was conducted by growing FJ and DG on nine different soils and measuring their impacts on N-cycle microbial activities (free-living nitrogen fixation FLNF, denitrification DEA, nitrification NEA), on N-mineral forms and on functional N-cycle gene abundance (nifH, AOA, AOB, nirS, nirK) as well as the total bacterial community gene (rRNA 16S). The nine soils differ in microbial enzymatic activities, N-mineral form concentrations, physico-chemical factors, texture, and gene abundances. Plant effects on FLNF, NEA and DEA are only soil dependent and no effect of invasive status was found. In addition, the native plant DG generally affected microbial parameters over a wider range of soils than the invasive plant. Stronger impacts of the native DG on microbial gene abundances were found compared to the invasive FJ. A stronger effect of the invasive plant was found for the soil NO3− concentration, with a significant decrease under the FJ than under the DG. Under both FJ and DG, NH4+ concentrations were not significantly affected. In conclusion, the invasive status in the ecosystem of the two plants studied cannot be explained through their impacts on microbial enzymatic activities and gene abundances of the soil N-cycle and the soil N mineral pools.

The pivotal role of phosphorus level gradient in regulating nitrogen cycle in wetland ecosystems

Phosphorus (P) is one of key drivers in Earth's nitrogen (N) cycle, however, the global overview of the P-regulated microbial community structure and gene abundance carrying wetland N process remains to be investigated. The key environmental factors that influenced wetland N cycle were initially screened, verifying the central role P. More complex and stable community interaction can be established in rich (20 mg/kg < P ≤ 100 mg/kg) and surplus P groups (P > 100 mg/kg) compared to that in deficient P group (P ≤ 20 mg/kg), with enhanced participation of betaproteobacteria and actinobacteria (i.e., changed hub microorganisms). Accordingly, P-mediated variations in gene expression patterns can be expected. On the one hand, the gene responses to carbon (C), N, and P factors presented nearly synchronous variation, highlighting the potential C-N-P coupling cycle in wetland ecosystem. On the other hand, the gene sensitivity towards environmental factors was changed at different P levels. Overall, the P level gradient can influence N cycle in direct (i.e., influences on gene abundances) and indirect (i.e., influences on gene response to environmental factors) manners. These findings provide important insights for controlling the N cycle in wetland ecosystems, particularly in cases where P levels are limiting factors.

#1801 Gut dysbiosis contributes to TMAO accumulation in CKD

Abstract Background and Aims Chronic kidney disease (CKD) patients face a substantial morbidity risk, especially related to cardiovascular complications. The imbalance of circulating metabolites influences inter-organ crosstalk and disease pathophysiology. In this regard, metabolites of microbial origin have gained increasing attention. Trimethylamine N-oxide (TMAO) originates from microbial Trimethylamine (TMA) metabolism and is found at high concentrations in the blood of CKD patients. A high TMAO concentration is known to be an independent risk factor for cardiovascular disease. This study aims to investigate the extent to which high concentrations of TMAO in the blood are due to increased bacterial production or are mainly a consequence of impaired renal clearance. Methods We used existing biomaterials and clinical data of a pediatric CKD cohort, consisting of patients enrolled at CKD stage G3-5, including G5 patients treated with hemodialysis (HD), as well as patients after kidney transplantation (KT) and individuals with normal kidney function. We analyzed TMAO in plasma and urine samples using LC-MS/MS and developed a novel gene targeting assay (GTA) that quantifies the abundance of the bacterial target genes (CutC, CntA) encoding for the key enzymes of microbial TMA synthesis in each fecal sample. Results Plasma TMAO levels were stage-dependently elevated in CKD, with HD patients showing the highest levels (75 ± 46 µmol/l). While urinary TMAO levels were lower in the CKD groups, TMAO/creatinine ratios and fractional excretion were not significantly different in CKD compared to controls. Fecal microbial gene abundance of both CutC and CntA genes was elevated across CKD stages and correlated with both plasma TMAO levels and eGFR. Although KT patients exhibited an eGFR range comparable to controls, they still showed higher plasma TMAO levels and elevated TMAO-associated gene abundances. In a regression analysis, this gene abundance was associated with plasma TMAO independent of eGFR in a model adjusted for age, sex, and BMI. Using a likelihood ratio test, we showed that adding fecal microbial gene abundance to the model provided a significantly better fit compared to only eGFR, age, sex, and BMI. Conclusion Our data indicate that the production of TMA by intestinal bacteria contributes significantly to the accumulation of TMAO in patients with CKD and after kidney transplantation. This finding opens the possibility for new potential interventions in the management of patients with CKD.

Seawater intrusion effects on nitrogen cycling in the regulated Nakdong River Estuary, South Korea

Research on the impact of seawater intrusion on nitrogen (N) cycling in coastal estuarine ecosystems is crucial; however, there is still a lack of relevant research conducted under in-situ field conditions. The effects of elevated salinity on N cycling processes and microbiomes were examined in situ seawater intrusion experiments conducted from 2019 to 2021 in the Nakdong River Estuary (South Korea), where an estuarine dam regulates tidal hydrodynamics. After the opening of the Nakdong Estuary Dam (seawater intrusion event), the density difference between seawater and freshwater resulted in varying degrees of seawater trapping at topographically deep stations. Bottom-water oxygen conditions had been altered in normoxia, hypoxia, and weak hypoxia due to the different degrees of seawater trapping in 2019, 2020, and 2021, respectively. Denitrification mostly dominated the nitrate (NO3-) reduction process, except in 2020 after seawater intrusion. However, denitrification rates decreased because of reduced coupled nitrification after seawater intrusion due to the dissolved oxygen limitation in 2020. Dissimilatory nitrate reduction to ammonium (DNRA) rates immediately increased after seawater intrusion in 2020, replacing denitrification as the dominant pathway in the NO3- reduction process. The enhanced DNRA rate was mainly due to the abundant organic matter associated with seawater invasion and more reducing environment (maybe sulfide enhancement effects) under high seawater-trapping conditions. Denitrification increased in 2021 after seawater intrusion during weak hypoxia; however, DNRA did not change. Small seawater intrusion in 2019 caused no seawater trapping and overall normoxic condition, though a slight shift from denitrification to DNRA was observed. Metagenomic analysis revealed a decrease in overall denitrification-associated genes in response to seawater intrusion in 2019 and 2020, while DNRA-associated gene abundance increased. In 2021 after seawater intrusion, microbial gene abundance associated with denitrification increased, while that of DNRA did not change significantly. These changes in gene abundance align mostly with alterations in nitrogen transformation rates. In summary, ecological change effects in N cycling after the dam opening (N retention or release, that is, eutrophication deterioration or mitigation) depend on the degree of seawater intrusion and the underlying freshwater conditions, which constitute the extent of seawater-trapping.

Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input

Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5, 10, and 15 g N m−2 year−1) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.

Inoculation with Stutzerimonas stutzeri strains decreases N₂O emissions from vegetable soil by altering microbial community composition and diversity.

Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N₂O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N₂O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N₂O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N₂O-mitigating effect after inoculation. Inoculation with Stutzerimonas stutzeri strains decreased N₂O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N₂O emissions from vegetable agricultural soils.

Microbial mechanisms in nitrogen fertilization: Modulating the re-mobilization of clay mineral-bound cadmium in agricultural soils

Soil cadmium (Cd) can affect crop growth and food safety, and through the enrichment in the food chain, it ultimately poses a risk to human health. Reducing the re-mobilization of Cd caused by the release of protons and acids by crops and microorganisms after stabilization is one of the significant technical challenges in agricultural activities. This study aimed to investigate the re-mobilization of stabilized Cd within the clay mineral-bound fraction of soil and its subsequent accumulation in crops utilizing nitrogen ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N), at 60 and 120 mg kg−1. Furthermore, the study harvested root exudates at various growth stages to assess their direct influence on the re-mobilization of stabilized Cd and to evaluate the indirect effects mediated by soil microorganisms. The results revealed that, in contrast to the NO3−-N treatment, the NH4+-N treatment significantly enhanced the conversion of clay mineral-bound Cd in the soil to NH4NO3-extractable Cd. It also amplified the accumulation of Cd in edible amaranth, with concentrations in roots and shoots rising from 1.7–6.0 mg kg−1 to 4.3–9.8 mg kg−1. The introduction of NH4+-N caused a decrease in the pH value of the rhizosphere soil and stimulated the production and secretion organic and amino acids, such as oxalic acid, lactic acid, stearic acid, succinic acid, and l-serine, from the crop roots. Furthermore, compared to NO3−-N, the combined interaction of root exudates with NH4+-N has a more pronounced impact on the abundance of microbial genes associated with glycolysis pathway and tricarboxylic acid cycle, such as pkfA, pfkB, sucB, sucC, and sucD. The effects of NH4+-N on crops and microorganisms ultimately result in a significant increase in the re-mobilization of stabilized Cd. However, the simulated experiments showed that microorganisms only contribute to 3.8–6.6 % of the re-mobilization of clay mineral-bound Cd in soil. Therefore, the fundamental strategy to inhibit the re-mobilization of stabilized Cd in vegetable cultivation involves the regulation of proton and organic acid secretion by crops.

Abstract P199: Oral Microbiome Potentially Modifies the Cardiometabolic Benefits of Nitrate Consumption: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS)

Background: Dietary nitrate consumption is associated with cardiometabolic health in many but not all studies. The enterosalivary nitrate-nitrite-nitric oxide (NO 3 - NO 2 - NO) pathway requires the oral microbiome for NO production (a signaling molecule beneficial to cardiometabolic health) following nitrate intake. We hypothesize that the oral microbiome modifies the cardiometabolic benefits of nitrate intake. Methods: We analyzed cross-sectional data from 657 ORGINS participants. Dietary nitrate intakes and alternative healthy eating index (AHEI) scores were calculated from food frequency questionnaire responses and a US food database. Subgingival 16S rRNA microbial genes (Illumina, MiSeq) were sequenced, and PICRUSt2 estimated metagenomic content. The Microbiome Induced Nitric oxide Enrichment Score (MINES) was calculated as a microbial gene abundance ratio representing enhanced net capacity for NO generation. Cardiometabolic biomarker (systolic and diastolic blood pressure, HbA1C, glucose, insulin, and HOMA-IR) Z-scores were averaged to form a cardiometabolic Z-score (CMZ). Adjusted multivariable linear models regressed CMZ and individual Z-scores on nitrate intake tertiles. Results: Participants were mean age 31±9, 72% female, 31% White, 14% Black, and 28% Hispanic. Mean nitrate intake was 189±171 mg/day. Higher nitrate intake was significantly associated with lower CMZ, glucose, insulin, and HOMA-IR. Mean CMZ(SE) across dietary nitrate tertiles were 0.53(0.30), 0.35(0.31), and -0.11(0.30), p for trend=0.04; findings were attenuated after adjustment for AHEI (p for trend=0.12). In subgroup analysis by MINES level, higher nitrate intake was only associated with lower cardiometabolic biomarker levels among participants with a &lt;median MINES even after AHEI adjustment (Table). Conclusion: Higher dietary nitrate intake was associated with lower cardiometabolic risk biomarker levels only among those with reduced potential for oral microbiome-dependent NO generation.

A hitchhiker’s guide: estimates of microbial biomass and microbial gene abundance in soil

Information on microbial biomass carbon (MBC) is crucial to assess their stocks and role for plant nutrient release in soil. Next to fumigation-extraction, molecular methods are routinely used to estimate the contribution of fungi, bacteria, and archaea to the soil microbial community. However, more information on the links between these different indices would deepen the understanding of microbial processes. The current study is based on 11 datasets, which contain MBC and MBN data obtained by fumigation-extraction and information on bacterial, archaeal, and fungal gene abundance, totalling 765 data points from agricultural, forest, and rangeland soils. Some of these datasets additionally provide information on double-stranded deoxyribonucleic acid (dsDNA) and fungal ergosterol. MBC varied around the median of 206 µg g−1 soil. MBN followed with a median MB-C/N ratio of 4.1. Median microbial gene abundance declined from bacteria (96 × 108) to archaea (4.4 × 108) to fungi (1.8 × 108). The median ratio of MBC/dsDNA was 15.8 and that of bacteria/dsDNA was 5.8 × 108 µg−1. The relationships between MBC and dsDNA as well as between bacterial gene abundance and dsDNA were both negatively affected by soil pH and positively by clay content. The median ergosterol/MBC and fungi/ergosterol ratios were 0.20% and 4.7 (n × 108 µg−1), respectively. The relationship between fungal gene abundance and ergosterol was negatively affected by soil pH and clay content. Our study suggests that combining fumigation-extraction with molecular tools allows more precise insights on the physiological interactions of soil microorganisms with their surrounding environment.

Soil microbial gene abundance rather than diversity and network complexity predominantly determines soil multifunctionality in Tibetan alpine grasslands along a precipitation gradient

Abstract The relationship between biodiversity and ecosystem functioning has mainly focused on plant communities, with comparably little known about soil microbial‐driven ecosystem functions. Climate change severely threatens soil microbial roles, but how soil microbial communities determine soil multifunctionality under climate change is poorly understood. Here, we evaluated the effects of diverse bacterial and fungal properties, including microbial gene abundance, diversity and network complexity, on soil multifunctionality (nine soil functions) across a 3000 km transect along a natural precipitation gradient in Tibetan alpine grasslands. Variation partitioning analyses were performed to disentangle the relative importance of bacterial and fungal properties to the variation of soil multifunctionality. Moreover, structural equation modelling was adopted to explore the influencing pathways of precipitation‐induced changes in plant and edaphic factors to soil microbial properties and, consequently, soil multifunctionality. Soil multifunctionality was positively associated with bacterial and fungal gene abundance, diversity and network complexity. Microbial gene abundance was the more important driver influencing soil multifunctionality than microbial diversity and network complexity. In addition, microbial gene abundance was mainly determined by precipitation‐induced changes in soil pH. Meanwhile, the effects of bacterial properties on soil multifunctionality were much larger than those of fungi. Soil multifunctionality was closely associated with different bacterial (cellulolysis, ligninolysis, nitrogen reduction, denitrification and nitrate fixation etc.) and fungal (soil saprotrophs, arbuscular mycorrhizal and plant pathogens etc.) functional guilds, which exert vital regulations on an array of soil biogeochemical cycling processes. Our results provide the large‐scale evidence of the relative contribution of soil microbial gene abundance, diversity and network complexity to the variation of soil multifunctionality in alpine grasslands with changing precipitation, which is pivotal for understanding microbial roles in modulating and predicting soil multifunctionality under future precipitation changes. Read the free Plain Language Summary for this article on the Journal blog.

Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem

Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %–35 % and 65 %–75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m−2 y−1). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %–35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %–75 % MFC) and high P-supply (5 g P m−2 y−1) treatments. However, the P-supply treatment resulted in a 12 %–22 % decrease in the soil NH4+-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4+-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.