Beyond plant genetics: microbiome-enhancing heterosis in plants.

Plant heterosis has been recognized as being primarily dependent on the genetics of contrasting parents. However, in recent work, Liu et al. describe 'endophytic microbiome-induced heterosis', showing distinct and diverse seed microbiomes in hybrids, which boosted seed germination compared with their parents. Here, we discuss the possible impact of this finding for sustainable agriculture.

Antimicrobial activity of eight plant essential oils having antioxidant property against spoilage microbes.

AIMS: To identify efficient, broad-spectrum, and non-toxic preservatives for natural agricultural products, eight essential oils were screened for high inhibitory and antioxidant activities against spoilage microbes. METHODS AND RESULTS: The zone of inhibition test and minimum inhibitory concentration (MIC) assay were performed to assess the antimicrobial activity of eight essential oils against B. subtilis, S. aureus, Penicillium, Saccharomyces, and E. coli. Among the eight essential oils, garlic and rose essential oils exhibited the best inhibitory effects, their MICs against the spoilage microbes were 40-640 µL/L and 10-320 µL/L, respectively. In addition, the antioxidant activities of eight essential oils were compared using the DPPH and ABTS radical-scavenging assays and the reducing power assay. eight essential oils had antioxidant capacity, among which rosemary, thyme, rose, and tea tree essential oils performed best. Moreover, the combination of thyme and rose exerted stronger antioxidant activity. Therefore, the concentrations of rose and garlic, and thyme essential oils were optimized using response surface methodology to obtain the optimal composite ratios, which were 1254 µL/L, 640 µL/L, and 1228 µL/L for rose, garlic, and thyme, respectively. The DPPH free radical-scavenging rate detected using this formulation was 50.2%, basically consistent with the prediction. Zone of inhibition diameters with the compound essential oil, against five spoilage microbes, were all greater than 45 mm. CONCLUSIONS: The essential oil combination had high antimicrobial, against agricultural product spoilage microbes, and antioxidant activities.

Various microbes used for the recovery of rare earth elements from mine wastewater.

Microbes used for the recovery of rare earth elements (REEs) from mining wastewater indicated traces of Escherichia coli (E. coli, 2149.6 µg/g), Bacillus sphaericus (1636.6 µg/g), Bacillus mycoides (1469.3 µg/g), and Bacillus cereus (1083.9 µg/g). Of these, E. coli showed an affinity for REEs than non-REEs (Mn and Zn). The amount of heavy REEs adsorbed (1511.1 µg/g) on E. coli was higher than light REEs (638.0 µg/g) due to the process of increasing adsorption with decreasing ionic radius. Additionally, E. coli demonstrated stability in the recovery of REEs from mining wastewater, as evidenced by 4 cycles. SEM-EDS, XPS and FTIR showed that REEs had a disruptive effect on cells, REEs absorbed and desorbed on the cell surface including ion exchange with ions such as Na+, ligand binding with functional groups like -NH2. Finally, the cost assessment confirmed the economically feasible of E. coli in recovery of REEs from mining wastewater.

The potential role of Akkermansia muciniphila in liver health.

Akkermansia muciniphila (A. muciniphila) is a 'star strain' that has attracted much attention in recent years. A. muciniphila can effectively regulate host metabolism, significantly affect host immune function, and play an important role in balancing host health and disease. As one of the organs most closely related to the gut (the two can communicate through the hepatic portal vein and bile duct system), liver is widely affected by intestinal microorganisms. A growing body of evidence suggests that A. muciniphila may alleviate liver-related diseases by improving the intestinal barrier, energy metabolism and regulating inflammation through its protein components and metabolites. This paper systematically reviews the key roles of A. muciniphila and its derivatives in maintaining liver health and improving liver disease.

[Box: see text].

Airborne microbes: sampling, detection, and inactivation.

The human living environment serves as a habitat for microorganisms and the presence of ubiquitous airborne microbes significantly impacts the natural material cycle. Through ongoing experimentation with beneficial microorganisms, humans have greatly benefited from airborne microbes. However, airborne pathogens endanger human health and have the potential to induce fatal diseases. Tracking airborne microbes is a critical prerequisite for a better understanding of bioaerosols, harnessing their potential advantages, and mitigating associated risks. Although technological breakthroughs have enabled significant advancements in accurately monitoring airborne pathogens, many puzzles about these microbes remain unanswered due to their high variability and environmental diffusibility. Consequently, advanced techniques and strategies for special identification, early warning, and efficient eradication of microbial contamination are continuously being sought. This review presents a comprehensive overview of the research status of airborne microbes, concentrating on the recent advances and challenges in sampling, detection, and inactivation. Particularly, the fundamental design principles for the collection and timely detection of airborne pathogens are described in detail, as well as critical factors for eliminating microbial contamination and enhancing indoor air quality. In addition, future research directions and perspectives for controlling airborne microbes are also suggested to promote the translation of basic research into real products.

Editing microbes to mitigate enteric methane emissions in livestock.

Livestock production significantly contributes to greenhouse gas (GHG) emissions particularly methane (CH4) emissions thereby influencing climate change. To address this issue further, it is crucial to establish strategies that simultaneously increase ruminant productivity while minimizing GHG emissions, particularly from cattle, sheep, and goats. Recent advancements have revealed the potential for modulating the rumen microbial ecosystem through genetic selection to reduce methane (CH4) production, and by microbial genome editing including CRISPR/Cas9, TALENs (Transcription Activator-Like Effector Nucleases), ZFNs (Zinc Finger Nucleases), RNA interference (RNAi), Pime editing, Base editing and double-stranded break-free (DSB-free). These technologies enable precise genetic modifications, offering opportunities to enhance traits that reduce environmental impact and optimize metabolic pathways. Additionally, various nutrition-related measures have shown promise in mitigating methane emissions to varying extents. This review aims to present a future-oriented viewpoint on reducing methane emissions from ruminants by leveraging CRISPR/Cas9 technology to engineer the microbial consortia within the rumen. The ultimate objective is to develop sustainable livestock production methods that effectively decrease methane emissions, while maintaining animal health and productivity.

Global distribution pattern of soil phosphorus-cycling microbes under the influence of human activities.

Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle.

Chromolaena odorata affects soil nitrogen transformations and competition in tropical coral islands by altering soil ammonia oxidizing microbes.

Invasive plants can change the community structure of soil ammonia-oxidizing microbes, affect the process of soil nitrogen (N) transformation, and gain a competitive advantage. However, the current researches on competition mechanism of Chromolaena odorata have not involved soil nitrogen transformation. In this study, we compared the microbially mediated soil transformations of invasive C. odorata and natives (Pisonia grandis and Scaevola taccada) of tropical coral islands. We assessed how differences in plant biomass and tissue N contents, soil nutrients, N transformation rates, microbial biomass and activity, and diversity and abundance of ammonia oxidizing microbes associated with these species impact their competitiveness. The results showed that C. odorata outcompeted both native species by allocating more proportionally biomass to aboveground parts in response to interspecific competition (12.92 % and 22.72 % more than P. grandis and S. taccada, respectively). Additionally, when C. odorata was planted with native plants, the available N and net mineralization rates in C. odorata rhizosphere soil were higher than in native plants rhizosphere soils. Higher abundance of ammonia-oxidizing bacteria in C. odorata rhizosphere soil confirmed this, being positively correlated with soil N mineralization rates and available N. Our findings help to understand the soil N acquisition and competition strategies of C. odorata, and contribute to improving evaluations and predictions of invasive plant dynamics and their ecological effects in tropical coral islands.

Green manuring combined with zeolite reduced nitrous oxide emissions in maize field by targeting microbial nitrogen transformations.

Green manure is a crucial strategy for increasing cereal yield and mitigating environmental burden while reducing chemical N fertilizer. To effectively tackle climate change, finding ways to reduce nitrous oxide (N2O) emissions from green manuring systems is vital. Herein, field and 15N labeled microcosm experiments were arranged to investigate the effect and mechanisms of green manuring and zeolite application on N2O emission. Both experiments comprised four treatments: conventional chemical N (N100), 70 % chemical N (N70), N70 with green manure (N70 + CV), and N70 + CV combined with zeolite (N70 + CV + Z). Compared with N100, both N70 + CV and N70 + CV + Z maintained maize yield, cumulative N2O emissions decreased by 37.7 % and 34.9 % in N70 + CV + Z in 2022-yr and 2023-yr, and by 12.8 % in N70 + CV in 2022-yr. Moreover, the reduction of N2O emission primarily occurred after incorporating green manure. The N100 and N70 + CV demonstrated a similar transformed proportion of chemical N to N2O (i.e., 4.9 % and 4.7 %) while reducing it to 2.7 % in N70 + CV + Z. Additionally, a mere 0.7 % of green manure N was transformed to N2O in both N70 + CV and N70 + CV + Z treatments. Compared with N100, both N70 + CV and N70 + CV + Z decreased the relative abundances of ammonia oxidation microbes, increased denitrifier and the ratios of (nirK + nirS)/nosZ and norBC/nosZ. Furthermore, compared with N70 + CV, N70 + CV + Z decreased the relative abundances of N2O-producer and the ratios of (nirK + nirS)/nosZ and norBC/nosZ in denitrification. These findings revealed that the reduction of N2O emissions resulting from green manure replaced chemical N was mainly due to weakened nitrification, while zeolite reduced N2O emissions attributed to enhanced conversion of N2O to N2. Moreover, certain key N-cycling functional bacteria, such as Phycisphaerae, Rubrobacteria, and Thermoflexia, were positively correlated with N2O emission. In contrast, Dehalococcoidia, Gammaproteobacteria, and Betaproteobacteria were negatively correlated with N2O emission. This investigation uncovered the underlying mechanisms for effectively reducing N2O emissions through green manure combined with zeolite.

Rumen Microbiota Transplantation Alleviates Gossypol Diet-Induced Reproductive, Liver, and Intestinal Damage in Male Mice.

Ruminants exhibit stronger tolerance to gossypol, an anti-nutritional factor, compared to monogastric animals. We transplanted Hu sheep rumen microbiota into male mice to investigate the role of rumen microbiota in animal gossypol tolerance. Thirty specific-pathogen-free (SPF) male C57BL/6 mice were randomly divided into three groups: normal diet (CK group), gossypol diet (FG group), and rumen microbiota transplantation (FMT group, gossypol diet). The pathological changes in the liver and small intestine of the mice, the organ coefficient, and sperm parameters were analyzed. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels in the blood and lactate dihydrogen-X (LDH-X) levels in the testicular tissue were also measured. The results showed that body weight, feed intake, sperm concentration, sperm motility, and LDH-X levels in the FMT group increased (p < 0.05) compared with the FG group, while the enzyme activities of ALT, AST, and AST/ALT decreased (p < 0.05). In the FMT group, the injury to liver cells was alleviated, the structure of the small intestine was intact, and the villus height and the ratio of villus height to crypt depth (V/C) were higher than those in the FG group (p < 0.05). And there were no differences in various organ coefficients and sperm deformity rates among the three groups (p > 0.05), but compared with the FG group, mice in the FMT group showed tendencies closer to those in the CK group. Rumen microbiota transplantation relieved the reproductive toxicity and liver damage induced by gossypol in male mice and improved the tolerance of recipient animals to gossypol. Additionally, rumen microbes improved the intestinal structural integrity of recipients.

The role of cattle manure-driven polysaccharide precursors in humus formation during composting of spent mushroom substrate.

The study examined the impact of adding cattle manure to the composting process of Agaricus bisporus mushroom substrate on compost humification. A control group CK comprised entirely of Agaricus bisporus mushroom substrate, while the experimental group CD (70 percent Agaricus bisporus mushroom substrate and 30 percent cattle manure) comprised the two composting treatments that were established. The study determined that the addition of cow dung has promoted the formation of humus components. Particularly, humic substance (HS-C) and humic acid (HA) increased by 41.3 and 74.7%, respectively, and the ratio of humic acid to fulvic acid (HA/FA) also increased by 2.78. It showed that the addition of cow dung accelerated the synthesis and decomposition of precursors, such as polysaccharides, polyphenols, and reducing sugars. Thereby promoting the formation of humic acid. Network analysis revealed that adding cow dung promoted microbial interactions increased the complexity and stability of the bacterial and fungal symbiotic network, enhanced cooperation and reciprocity among microbes, and assisted in transforming fulvic acid (FA) components. Structural equation modeling (SEM) is a multivariate data analysis method for analyzing complex relationships among constructs and core indicators. SEM illustrated that introducing cattle manure into the composting process resulted in alterations to the correlation between physicochemical parameters and the microbial community, in addition to humus formation. Polysaccharides are the primary precursors for polymerization to form HA, which is an essential prerequisite for the conversion of fulvic acid to humic acid. Additionally, microbes affected the formation of humus, with bacteria substantially more influential than fungi. These findings provide new ideas for regulating the degree of humification in the composting process and have important practical implications for optimizing mushroom cultivation and composting techniques today.

Association of dietary live microbe intake with prevalence of osteoporosis in US postmenopausal women: a cross-sectional study.

The association between live microbe intake and osteoporosis in postmenopausal women remains unknown. The research findings indicated that an increased intake of live microbes through dietary sources was associated with a low prevalence of osteoporosis among postmenopausal women. PURPOSE: To investigate the relationship between the consumption of live microbes in the diet and osteoporosis in postmenopausal women. METHODS: A cross-sectional investigation using data obtained from the National Health and Nutrition Examination Survey was conducted. Participants were classified into three groups by using the dietary live microbe classification system developed by Sanders. Dual x-ray absorptiometry was used to measure body mineral density, and osteoporosis was diagnosed according to the World Health Organization criteria. We conducted a crude and adjusted multivariate logistic regression analysis, and utilized the restricted cubic splines model to assess the correlation between the consumption of live microbes in the diet and osteoporosis in postmenopausal women. RESULTS: A total of 1378 women who had undergone menopause were enrolled in the study. After controlling for potential covariates, individuals with a high consumption of live microbes in their diet exhibited a notably low prevalence of osteoporosis in comparison to those with a low intake of dietary live microbes (odd ratio: 0.46, 95% confidence interval: 0.23, 0.93, P = 0.03). Subgroup analysis showed the stability of the results, and restricted cubic splines showed an approximate L-shape curve. CONCLUSIONS: In this research, a higher consumption of live microbes in the diet was linked to a low prevalence of osteoporosis in postmenopausal women.

Evaluation of Neuroprotective Effect of Gut Microbe in Parkinson's Disease: An In Silico and In Vivo Approach.

Parkinson's disease is a progressive neurodegenerative disorder marked by the death of dopaminergic neurons in the substantia nigra region of the brain. Aggregation of alpha-synuclein (α-synuclein) is a contributing factor to Parkinson's disease pathogenesis. The objective of this study is to investigate the neuroprotective effects of gut microbes on α-synuclein aggregation using both in silico and in vivo approaches. We focussed on the interaction between α-synuclein and metabolites released by gut bacteria that protect from PD. We employed three probiotic microbe strains against α-synuclein protein: Lactobacillus casei, Escherichia coli, and Bacillus subtilis, with their chosen PDB IDs being Dihydrofolate reductase (3DFR), methionine synthetase (6BM5), and tryptophanyl-tRNA synthetase (3PRH), respectively. Using HEX Dock 6.0 software, we examined the interactions between these proteins. Among the various metabolites, methionine synthetase produced by E. coli showed potential interactions with α-synuclein. To further evaluate the neuroprotective benefits of E. coli, an in vivo investigation was performed using a rotenone-induced Parkinsonian mouse model. The motor function of the animals was assessed through behavioural tests, and oxidative stress and neurotransmitter levels were also examined. The results demonstrated that, compared to the rotenone-induced PD mouse model, the rate of neurodegeneration was considerably reduced in mice treated with E. coli. Additionally, histopathological studies provided evidence of the neuroprotective effects of E. coli. In conclusion, this study lays the groundwork for future research, suggesting that gut bacteria may serve as potential therapeutic agents in the development of medications to treat Parkinson's disease. fig. 1.

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila.

This study used berberine hydrochloride to treat the Asian paddle crab, Charybdis japonica infected with the Gram-negative bacterium Aeromonas hydrophila at concentrations of 0, 100, 200 and 300 mg/L. The effect of berberine hydrochloride on the survival rate and gut microbiota of C. japonica was investigated. Berberine hydrochloride improved the stability of the intestinal flora, with an increase in the abundance of probiotic species and a decrease in the abundance of both pathogenic bacteria after treatment with high concentrations of berberine hydrochloride. Berberine hydrochloride altered peroxidase activity (POD), malondialdehyde (MDA), and lipid peroxidation (LPO) in the intestinal tract compared to the control. Berberine hydrochloride could modulate the energy released from the enzyme activities of hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK) in the intestinal tract of C. japonica infected with A. hydrophila. Zona occludens 1 (ZO-1), Zinc finger E-box binding homeobox 1 (ZEB1), occludin and signal transducer, and activator of transcription5b (STAT5b) expression were also increased, which improved intestinal barrier function. The results of this study provide new insights into the role of berberine hydrochloride in intestinal immune mechanisms and oxidative stress in crustaceans.

Elucidating microbial iron corrosion mechanisms with a hydrogenase-deficient strain of Desulfovibrio vulgaris.

Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure. There is substantial debate over their corrosion mechanisms. We investigated Fe0 corrosion with Desulfovibrio vulgaris, the sulfate reducer most often employed in corrosion studies. Cultures were grown with both lactate and Fe0 as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes. Fe0 was corroded in cultures of a D. vulgaris hydrogenase-deficient mutant with the 1:1 correspondence between Fe0 loss and H2 accumulation expected for Fe0 oxidation coupled to H+ reduction to H2. This result and the extent of sulfate reduction indicated that D. vulgaris was not capable of direct Fe0-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous sulfide. Corrosion in the hydrogenase-deficient mutant cultures was greater than in sterile controls, demonstrating that H2 removal was not necessary for the enhanced corrosion observed in the presence of microbes. The parental H2-consuming strain corroded more Fe0 than the mutant strain, which could be attributed to H2 oxidation coupled to sulfate reduction, producing sulfide that further stimulated Fe0 oxidation. The results suggest that H2 consumption is not necessary for microbially enhanced corrosion, but H2 oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction. The finding that D. vulgaris was incapable of direct electron uptake from Fe0 reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes.

Nexus Between Sarcopenia and Microbiome Research: A Bibliometric Exploration.

Despite over 30 years of microbiome and skeletal muscle research, no quantitative analysis of sarcopenia and the microbiome literature had been conducted. Our bibliometric study examined research status, hotspots, and future trends. We utilized bibliometric techniques to search the Science Citation Index Extended Database on February 27, 2023, using the Bibliometrix package in R to create a map displaying scientific production and subject categories. Collaborative network maps between countries/regions were visualized using Scimago Graphica, while VOSviewer explored collaboration modes among individuals and institutions. We analyzed the top 25 emerging keywords, top co-occurring keyword networks, and co-occurring keyword clusters using CiteSpace. A total of 997 articles were retrieved for sarcopenia and microbiome, of which 633 papers were analyzed. Both the number of publications and total citation frequency had been continuously increasing. The United States had the highest total citation frequency, while China had the highest number of publications. Research on the impact of the microbiome on sarcopenia was in its nascent stage and spans multiple disciplines, including nutrition, microbiology, geriatrics, immunology, endocrinology and metabolism, molecular biology, and sports medicine. The University of Copenhagen contributed the most to the number of publications (n=16), with Tibbett M (n=7) and Hulver MW (n=7) among the top authors. The most published journal was "Nutrients" (n=24). Analysis of keywords and clusters revealed new research hotspots in microbes and sarcopenia, such as malnutrition, dietary fiber, signaling pathways, frailty, and intestinal permeability. Research on the impact of the microbiome on sarcopenia is in its infancy and spans multiple disciplines. Malnutrition, dietary fiber, signaling pathways, frailty, and intestinal microbes are currently research hotspots. Furthermore, the visual atlas analysis of research on microbes and sarcopenia helps to track the knowledge structure in research fields related to sarcopenia and microbes, providing direction for future research.

Refocusing the microbial rare biosphere concept through a functional lens.

The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.

From super-wicked problems to more-than-human justice: new bioethical frameworks for antimicrobial resistance and climate emergency.

In this article, building on our multidisciplinary expertise on philosophy, anthropology, and social study of microbes, we discuss and analyze new approaches to justice that have emerged in thinking with more-than-human contexts: microbes, animals, environments and ecosystems. We situate our analysis in theory of and practical engagements with antimicrobial resistance and climate emergency that both can be considered super-wicked problems. In offering solutions to such problems, we discuss a more-than-human justice orientation, seeking to displace human exceptionalism while still engaging with human social justice issues. We offer anthropological narratives to highlight how more-than-human actors already play an important role in environmental and climate politics. These narratives further justify the need for new ethical frameworks, out of which we, for further development outside the scope of this article, suggest a queer feminist posthumanist one.

Effects of cadmium on the intestinal health of the snail Bradybaena ravida Benson.

The heavy metal cadmium (Cd) is a toxic and bioaccumulative metal that can be enriched in the tissues and organs of living organisms through the digestive tract. However, more research is needed to determine whether food-sourced Cd affects the homeostasis of host gut microflora. In this study, the snail Bradybaena ravida (Benson) was used as a model organism fed with mulberry leaves spiked with different concentrations of Cd (0, 0.052, 0.71, and 1.94 mg kg-1). By combining 16S rRNA high-throughput sequencing with biochemical characterization, it was found that there were increases in the overall microbial diversity and abundances of pathogenic bacteria such as Corynebacterium, Enterococcus, Aeromonas, and Rickettsia in the gut of B. ravida after exposure to Cd. However, the abundances of potential Cd-resistant microbes in the host's gut, including Sphingobacterium, Lactococcus, and Chryseobacterium, decreased with increasing Cd concentrations in the mulberry leaves. In addition, there was a significant reduction in activities of energy, nutrient metabolism, and antioxidant enzymes for gut microbiota of snails treated with high concentrations of Cd compared to those with low ones. These findings highlight the interaction of snail gut microbiota with Cd exposure, indicating the potential role of terrestrial animal gut microbiota in environmental monitoring through rapid recognition and response to environmental pollution.