Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth

Community dynamics in rhizosphere bacteria affected the adaptive growth of wheat in cadmium-contaminated soils

Soil cadmium (Cd) contamination in agriculture has intensified due to industrial development and human activities, which seriously affected the safety production in wheat. There are increasing evidences that rhizosphere bacteria contributed to alleviating Cd stress in plants, but the mechanism of how rhizosphere bacteria affecting the adaptive growth of wheat exposed to Cd contamination has not been extensively explored. Therefore, the rhizosphere bacterial community dynamics and plant growth for wheat were investigated under different levels of soil Cd contamination in accordance with risk control standard for soil contamination of agricultural land. The results showed that there was no significant difference in transport coefficient of Cd in wheat plants grown in different levels of soil Cd contamination conditions. Soil Cd contamination led to a decrease in soil pH value and an increase in exchangeable Cd content in rhizosphere soil. Although rhizosphere bacterial richness and diversity had no significant difference between soil Cd contamination conditions, as its community composition changed significantly. Under Cd contamination of risk screening value, Actinobacteria, Chloroflexi, and Nitrospira showed higher abundance, but Bacteroidetes, Patescibacteria, Sphingomonas, ADurbBin063-1 and Bryobacter were more prevalent under Cd contamination of risk intervention value. The enrichment of Patescibacteria, Proteobacteria and Acidobacteria was beneficial for Cd fixation, while Nitrospira enhanced nutrient uptake and utilization. Furthermore, Cd contamination with risk screening value enhanced the relationship among rhizosphere bacterial communities, and Cd contamination with risk intervention value increased the cooperative relationship among rhizosphere bacterial species. Additionally, soil Cd content showed a significantly positive correlation with Patescibacteria and ADurbBin063-1, and a significantly negative correlation with pH. Altogether, the shift in the community structures of rhizosphere bacterial was crucial for farmland protection and food safety in Cd polluted soil.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01532-8.

Accumulation of coumaric acid is a key factor in tobacco continuous cropping obstacles

Introduction

Phenolic acids are believed to play a significant role in tobacco continuous cropping obstacles, but the strength and potential mechanisms of different phenolic acids remain unclear.

Methods

This study evaluated the allelopathic effects of six phenolic acids that exhibited cumulative effects in our previous research. Different concentrations of phenolic acids with the strongest allelopathic effects were added to potting soil to explore their impacts on tobacco growth and physiological characteristics, as well as on soil chemical properties and microbial community structure.

Results

The results showed that coumaric acid exhibited the strongest direct allelopathic effect. Exogenous coumaric acid significantly reduced soil pH and shifted the soil microbial community from bacteria-dominated to fungi-dominated. Simultaneously, the abundance of bacteria related to nutrient utilization (e.g., Flavisolibacter, Methylobacterium) and fungi related to disease resistance (e.g., Fusicolla, Clonostachys) gradually decreased, along with a reduction in soil catalase, urease, invertase, and acid phosphatase activities. Leaf MDA levels increased continuously with higher concentrations of coumaric acid, while the root resistance hormone (jasmonic acid and the jasmonate-isoleucine complex) levels show the opposite trend.

Discussion

Coumaric acid may inhibit tobacco growth by influencing the physiological processes in tobacco plants directly and the broader soil microecological balance indirectly. This study provides theoretical guidance for precise mitigation of continuous cropping obstacles in future tobacco cultivation.

Coal mining activities driving the changes in bacterial community

The mechanism of the difference in bacterial community composition caused by environmental factors in the underground coal mine is unclear. In order to reveal the influence of coal mining activities on the characteristics of bacterial community structure in coal seam, 16S rRNA gene amplicon sequencing technology was used to determine the species abundance, biodiversity, and gene abundance of bacterial community in a coal mine in Shanxi Province, and the environmental factors such as metal elements, non-metal elements, pH value, and gas concentration of coal samples were determined. The results showed that environmental factors and bacterial communities had obvious regional characteristics. Mining activities greatly affected the α diversity of bacterial communities, mining working face > main airway > roadway roof > unexposed coal seam > tunneling roadway. The bacterial community composition of each sample point is also very different. The main airway, roadway roof, and unexposed coal seam are dominated by Actinobacteria while the mining working face and tunneling roadway are dominated by Proteobacteria. Among the gene abundances of metabolic pathways in each site, Citrate cycle had the greatest difference, followed by glycine, serine and threonine metabolism, and oxidative phosphorylation and methane metabolism had little difference. RDA analysis showed that the environmental factors affecting the bacterial community were mainly cadmium, oxygen, hydrogen, and gas content. CCA analysis divided the bacterial community into three categories. Degradation functional bacteria are located in mining working face, bacteria that tolerate poor environments are located in main airway and tunneling roadway, and human pathogens are mostly located in roadway roof and unexposed coal seam. The research results would provide support for realizing green and safe mining in coal mines.

Insights into the microbiota of raw milk from seven breeds animals distributing in Xinjiang China

Owing to its high nutritional content, raw milk contains a rich microbiota. Thus, to study microorganisms present in raw milk available in Xinjiang China, 142 raw milk samples from seven animal breeds (cow, sheep, goat, donkey, horse, camel, and yak) and four regions (Hami, Tarbagatay, Kashgar, and Ili) were analyzed by high-throughput DNA sequencing. These microorganisms were characterized by 10 dominant phyla. Proteobacteria (68.33%) was the major phylum, followed by Firmicutes (18.80%) and Thermi (3.16%). Horse milk contained more Bacteroidetes, sheep milk contained more Gammaproteobacteria, and donkey milk contained more unclassified sequences. Camel and donkey milk contained the highest and lowest bacterial diversity compared with that contained by the remaining milk samples, respectively. Additionally, spoilage microorganisms, including Chryseobacterium, Propionibacterium, and Flavobacterium, and pathogenic bacteria, including Ochrobactrum anthropi and Sphingomonas, were more prevalent in horse and yak milk, whereas probiotic lactic acid bacteria (LAB), such as Leuconostoc, Lactococcus, or Lactobacillus, were more prevalent in goat, donkey, and camel milk. Furthermore, Moraxella was abundantly present in goat, camel, and yak milk, Acinetobacter was more abundant in camel milk, and Pseudomonas was relatively abundant in sheep and donkey milk. Overall, specific harmful microorganisms and probiotic lactic acid bacteria were found in the raw milk samples obtained from different animals, which provided a basis for preventing and controlling the growth of harmful bacteria, as well as investigating probiotic resources in raw milk.

Effect of tobacco-radish rotation for different years on bacterial wilt and rhizosphere microbial communities

Tobacco bacterial wilt is a major limiting factor for tobacco production and development, and it is more likely to occur under perennial single cropping of tobacco. In recent years, the rotation of tobacco-radish has gradually become popular. Therefore, we studied the effects of years of tobacco-radish rotation on tobacco bacterial wilt occurrence and rhizosphere microorganisms. The results indicated that both SY and TY could significantly reduce the risk of tobacco bacterial wilt occurrence, and SY had the lowest disease index. The rotation of radish plants significantly increased the soil pH but decreased the contents of alkali-hydrolysed nitrogen and organic matter in the soil. Alkali-hydrolysed nitrogen and pH are the key factors affecting the composition of the bacterial community. Furthermore, radish rotation changed the composition of the soil microbial community, increased the diversity of the bacterial community, and significantly altered the bacterial community structure. At the genus level, the abundance of Sphingomonas species negatively correlated with Ralstonia increased significantly, while the relative abundance of Rhodanobacter species positively correlated with Ralstonia decreased significantly. Disease index, pH and available phosphorus were the main factors affecting the variation in different bacterial genera. The network analysis results showed that Ralstonia was less connected in the network than in the CK group, and the SY treatment group had a more complex bacterial network structure. Overall, 2 years of tobacco and radish rotation improved the bacterial community structure of the rhizosphere soil and alleviated the harm caused by tobacco bacterial wilt, which is highly important for the stability and health of the rhizosphere soil ecosystem.

Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations

BACKGROUND

The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing.

RESULTS

We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections.

CONCLUSIONS

Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. Video Abstract.

Reshaping the root endophytic microbiota in plants to combat mercury-induced stress

Emerging evidence suggests that plants experiencing abiotic stress actively seek help from soil microbes. However, the empirical evidence supporting this strategy is limited, especially in response to heavy metal stress. We used integrated microbial community profiling and culture-based methods to investigate the interaction between mercury (Hg) stress, the entophytic root microbiome, and maize seedlings. The results of the pot experiment showed that soil Hg (20 mg/kg) strongly inhibited maize growth, indicating its strong phytotoxicity. Furthermore, Hg stress significantly altered the structure of the bacterial and fungal communities and enriched the potentially pathogenic Fusarium sp., suggesting that soil Hg stress may enhance the bio-stress induced by Fusarium species in maize. Additionally, soil Hg also led to the enrichment of beneficial bacterial members of Streptomyces, Lysobacter, and Sphingomonas (defined as differential species), which were also identified as keystone species in the Hg treatment by the analysis of co-occurrence networks. Therefore, it can be postulated that the members of Streptomyces, Lysobacter, and Sphingomonas function as stress-alleviating microbes. We successfully isolated the representatives of these stress-alleviating microbes. As expected, these strains mitigated the detrimental effects of Hg stess for the maize seedlings, suggesting that plants recruit the stress-alleviated microbiota to combat Hg stress. This study provides insights into the potential of manipulating the root microbiome to enhance plant growth in polluted environments.

Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida

Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon's gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon's defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b.

Genome-based taxonomy and functional prediction of Sphingomonas fuzhouensis sp. nov. and Massilia phyllosphaerae sp. nov. isolated from Pennisetum sp. with plant growth-promoting potential

Two facultatively aerobic strains, designated SGZ-02T and SGZ-792T, were isolated from plant Pennisetum sp., exhibiting the highest 16S rRNA gene sequence similarities with the type strains of Sphingomonas zeae LMG 28739T (98.6%) and Massilia forsythiae NBRC 114511T (98.4%), respectively. SGZ-02T grew between 5 and 45 °C, pH 5.0-11.0 and tolerated NaCl concentrations of 0-4% (w/v), whereas SGZ-792T thrived at 5-40 °C, pH 5.0-11.0 and NaCl tolerance to 0-3.5% (w/v). The major quinone of SGZ-02T was ubiquinone-10, with the dominant fatty acids being C16:0 (13.5%), Summed Feature 3 (6.3%), C14:02-OH (5.3%) and Summed Feature 8 (66.3%). SGZ-792T predominantly contained ubiquinone-8, with major fatty acids being C16:0 (20.3%), Summed Feature 3 (5.0%) and Summed Feature 8 (54.7%). Average nucleotide identity and digital DNA-DNA hybridization values between two strains and their closest references strains were below the bacterial species threshold. Based on genotypic and phenotypic characteristics, strains SGZ-02T and SGZ-792T are proposed as novel species within the genera Sphingomonas and Massilia, respectively. The suggested names for the new species are Sphingomonas fuzhouensis sp. nov. (SGZ-02T = GDMCC 1.4033T = JCM 36769T) and Massilia phyllosphaerae sp. nov. (SGZ-792T = GDMCC 1.4211T = JCM 36643T), respectively.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling

Introduction

In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied.

Methods

This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities.

Results

Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth.

Discussion

In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds

Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot

BACKGROUND

Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health.

RESULTS

Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease.

CONCLUSIONS

Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Analysis of rhizosphere soil microbial diversity and its functions between Dahongpao mother tree and cutting Dahongpao

Dahongpao mother tree (Camellia sinensis (L.) O. Ktze) is a representative of Wuyi rock tea. Whether there is a difference in rhizosphere soil microbial diversity and function between asexually propagated cuttings of Dahongpao (PD) and the parent Dahongpao mother tree (MD) has not been reported. In this study, high throughput sequencing technology was used to analyze rhizosphere soil microbial diversity, functions and their relationship with soil available nutrients and enzyme activities in MD and PD. The results showed that available nitrogen, phosphorus and potassium contents and urease, protease, acid phosphatase and sucrase activities of rhizosphere soils in MD were significantly higher than those in PD. Both bacterial and fungal diversity were higher in rhizosphere soils in MD than in PD, and secondly, the bacterial community structure was less stable while the fungal community structure was more stable in PD compared to MD. There were significant differences between MD and PD tea tree rhizosphere soils in 6 genera of characteristic bacteria and 4 genera of characteristic fungi. The results of function and interaction effect analysis showed that the rhizosphere soil available nutrient content and enzyme activities in MD were significantly higher than those in PD, and their contributions mainly originated from Pirellula and Acidisphaera of characteristic bacteria and Alatospora of characteristic fungi. Secondly, MD maybe had a stronger ability to inhibit soil pathogens than PD, with the main contribution coming from Scopulariopsis and Tolypocladium of characteristic fungi. Overall, compared with PD, soil texture in MD was relatively better, and its soil nutrient cycling-related enzyme activities were stronger, which was more favorable to soil nutrient cycling and increased the available nutrient content of the soil, which in turn promoted the growth of tea trees. This study provides an important reference for the planting and management of tea tree cuttings and microbial regulation of tea tree growth.

Role of bacterial pathogens in microbial ecological networks in hydroponic plants

Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.

Insights into the airborne microorganisms in a Sichuan south-road dark tea pile fermentation plant during production

Introduction

Sichuan south-road dark tea (SSDT) is generally produced through a series of processes, including fixing, rolling, pile fermentation, and drying, with microbial action during pile fermentation playing a crucial role in determining tea quality. The air within the SSDT pile fermentation plant (SSDTPP) is considered an important source of these microbes, but research in this area has been limited.

Methods

In this study, air samples from SSDTPP were collected on the 1st (SSDT1), 12th (SSDT2), and 24th (SSDT3) days of pile fermentation and comprehensively analyzed by high-throughput sequencing.

Results and discussion

The results revealed the presence of 2 and 24 phyla, 9 and 49 classes, 18 and 88 orders, 28 and 153 families, 38 and 253 genera, and 47 and 90 species of fungi and bacteria, respectively, across all samples. SSDT1 and SSDT2 individually had the highest fungal and bacterial diversity, while Aspergillus was the dominant genus throughout the pile fermentation with an abundance of 34.6%, 91.17%, and 67.86% in SSDT1, SSDT2, and SSDT3, respectively. Microbial populations in SSDT1 were predominantly involved in xenobiotic biodegradation and metabolism, amino acid metabolism, the biosynthesis of other secondary metabolites, etc. However, SSDT2 exhibited a higher prevalence of human disease-related functions. SSDT3 primarily focused on the metabolism of other amino acids and carbohydrate metabolism. Additionally, 104 genera and 22 species coexisted in both SSDTPP air and piled SSDT, suggesting that frequent microbial exchange may occur between them. These findings pave the way for microbial traceability during SSDT production and provide a foundation for further functional microbial research.

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

Deciphering the core microbiota in open environment solid-state fermentation of Beijing rice vinegar and its correlation with environmental factors

BACKGROUND

Rice vinegar is a popular cereal vinegar worldwide and is typically produced in an open environment, and the ecosystem of solid-state fermentation is complicated and robust. The present study aimed to reveal the shaping force of the establishment of the ecosystem of Beijing rice vinegar, the core function microbiota and their correlation with critical environmental factors. [Correction added after first online publication on 29 May 2024; the word "worldwide" has been removed from the first sentence under the section Background.] RESULTS: The experimental findings revealed the changes in environmental factors, major metabolites and microbial patterns during Beijing rice vinegar fermentation were obtained. The major metabolites accumulated at the middle and late acetic acid fermentation (AAF) periods. Principal coordinates and t-test analyses revealed the specific bacterial and fungal species at corresponding stages. Kosakonia, Methlobacterium, Sphingomonas, unidentified Rhizobiaceae, Pseudozyma and Saccharomycopsis dorminated during saccharification and alcohol fermentation and early AAF, whereas Lactococcus, Acetobacter, Rhodotorula and Kazachstania dominated the later AAF stages. Canonical correspondence analysis of environmental factors with core microbiota. Temperature and total acid were the most significant factors correlated with the SAF bacterial profile (Pediococcus, Weissella, Enterococcus and Kosakonia). Ethanol was the most significant factor between AAF1 and AAF3, and mainly affected Acetobacter and Lactobacillus. Conversely, ethanol was the most significant factor in the SAF, AAF1 and AAF3 fungi communities; typical microorganisms were Saccharomyces and Malassezia. Furthermore, the predicted phenotypes of bacteria and their response to environmental factors were evaluated.

CONCLUSION

In conclusion, the present study has provided insights into the process regulation of spontaneous fermentation and distinguished the key driving forces in the microbiota of Beijing rice vinegar fermentation. © 2024 Society of Chemical Industry.

Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development

This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1 year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m3 ha-1 year-1, installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m3 ha-1 year-1 doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.

Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

The biotechnological industry faces a crucial demand for novel bioactive compounds, particularly antimicrobial agents, to address the rising challenge of bacterial resistance to current available antibiotics. Traditional strategies for cultivating naturally occurring microorganisms often limit the discovery of novel antimicrobial producers. This study presents a protocol for targeted selection of bacterial strains using the supernatant of Paenibacillus elgii, which produces abundant signal molecules and antimicrobial peptides. Soil samples were inoculated in these enriched culture media to selectively cultivate bacteria resistant to the supernatant, indicating their potential to produce similar compounds. The bacterial strains isolated through this method were assessed for their antibacterial activity. In addition, the functional annotation of the genome of one of these strains revealed several gene clusters of biotechnological interest. This study highlights the effectiveness of using this approach for selective cultivation of microorganisms with potential for biotechnological applications.

Enhanced phytoremediation of cadmium-contaminated soil using chelating agents and plant growth regulators: effect and mechanism

The heavy metal cadmium (Cd) is a major threat to food safety and human health. Phytoremediation is the most widely used remediation technology, and how to improve the remediation efficiency of phytoremediation has become a key issue. In this study, we constructed an intensive phytoremediation technology for remediation of Cd-contaminated soil with biodegradable chelating agent and plant growth regulator combined with maize and investigated the mechanism of this technology. The results showed that the best remediation effect was achieved in the treatment with 10-6 mol l-1 gibberellic acid (GA3) and 6 mmol kg-1 aspartate diethoxysuccinic acid (AES) combined with maize. In this treatment, the total biomass and extraction efficiency of maize were 3.6 and 8.67 times higher than those of the control, respectively, and the antioxidant enzyme activities of maize were also increased. The soil was enriched with dominant bacterial genera that promote plant growth and metabolism and tolerance to heavy metal stress, which in turn promoted maize growth and Cd accumulation. Structural equation modelling results indicated a large effect of plant Cd concentration and plant antioxidant enzyme activity on plant Cd extraction. The enhanced phytoremediation technology showed good potential for safe use of Cd-contaminated soil.

The response of root-zone soil bacterial community, metabolites, and soil properties of Sanyeqing medicinal plant varieties to anthracnose disease in reclaimed land, China

Objectives

To enhance the utilization of reclaimed land, Sanyeqing (SYQ) has been extensively cultivated in Zhejiang province, China. However, the prevalence of anthracnose has significantly hindered SYQ growth, emerging as a primary obstacle to its production. This study aimed to elucidate SYQ's responses to anthracnose in reclaimed land environments by comprehensively analyzing root-zone bacterial community structure, metabolites, and soil properties.

Methods

The experiment was conducted on reclaimed land in Chun'an, China. In order to evaluate the responses of SYQ to anthracnose, the fresh and dry weight of SYQ tubes, the soil properties, the high-throughput sequencing, and metabolomics assay were carried out.

Results

Significant differences were observed between an anthracnose-resistant variety (A201714) and an anthracnose-susceptibile variety (B201301). Fresh and dry weight increased 131.53 % and 144.82 % for A201714 compared to B201301.Lacibacterium (39.85 %), Gp6 (21.83 %), Gp5 (21.49 %), and Sphingomonas (18.84 %) were more prevalent, whereas Gp3 (22.71 %), WPS-1 (18.88 %), Gp4 (15.60 %), Subdivision3 (14.70 %), Chryseolinea (14.37 %), and Nitrospira (0.76 %) were less prevalent in A201714 than B201301. A total of 24 bacterial biomarkers were detected in all soil samples, while the network suggests a more stable soil bacterial community in A201714 than in B201301. Eight differentially expressed metabolites (DEMs) that belonged to lipids and lipid-like molecules, organic acids and derivatives, benzenoids, nucleosides, nucleotides, and analogues were found between two soil samples, and all these eight DEMs were downregulated in A201714 and had a strong correlation with 12 genera of bacteria. Moreover, the data from the redundancy analysis indicated that the main variables affecting changes in the bacterial communities were pH, available phosphorus (AP), available potassium (AK), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN).

Conclusion

This research offers new insights into the SYQ response to anthracnose in reclaimed land and provides valuable recommendations for the high-quality SYQ cultivation and production.

Microbial diversity across tea varieties and ecological niches: correlating tea polyphenol contents with stress resistance

Introduction

Microorganisms exhibit intricate interconnections with tea plants; however, despite the well-established role of microorganisms in crop growth and development, research on microbes within the tea plant remains insufficient, particularly regarding endophytic microorganisms.

Methods

In this study, we collected samples of leaves and rhizosphere soils from 'Zhuyeqi', 'Baojing Huangjincha#1', 'Baiye#1', and 'Jinxuan' varieties planted.

Results

Our analyses revealed significant variations in tea polyphenol contents among tea varieties, particularly with the 'Zhuyeqi' variety exhibiting higher levels of tea polyphenols (>20% contents). Microbiome studies have revealed that endophytic microbial community in tea plants exhibited higher host specificity compared to rhizospheric microbial community. Analyses of across-ecological niches of the microbial community associated with tea plants revealed that soil bacteria serve as a significant reservoir for endophytic bacteria in tea plants, Bacillus may play a crucial role in shaping the bacterial community across-ecological niche within the tea plants with higher tea polyphenol levels. In the aforementioned analyses, the microbial community of 'Zhuyeqi' exhibited a higher degree of host specificity for leaf endophytic microorganisms, the topological structure of the co-occurrence network is also more intricate, harboring a greater number of potential core microorganisms within its nodes. A closer examination was conducted on the microbial community of 'Zhuyeqi', further analyses of its endophytic bacteria indicated that its endophytic microbial community harbored a greater abundance of biomarkers, particularly among bacteria, and the enriched Methylobacterium and Sphingomonas in 'Zhuyeqi' may play distinct roles in disease resistance and drought resilience in tea plants.

Conclusion

In summary, this study has shed light on the intricate relationships of tea plant varieties with their associated microbial communities, unveiling the importance of microorganisms and tea varieties with higher tea polyphenols, and offering valuable insights to the study of microorganisms and tea plants.

Isolation of highly copper-resistant bacteria from deep-sea hydrothermal fields and description of a novel species Marinobacter metalliresistant sp. nov

Introduction

Hydrothermal vents, rich in heavy metals, provided a unique niche for heavy metal resistant microbes. However, knowledge about copper resistant microbes in deep sea hydrothermal vents is still limited.

Methods

The copper-resistant bacteria were isolated from deep-sea hydrothermal vent samples and conducted thorough physical, phylogenetic, and genomic analyses to elucidate their copper resistance capability and related genes.

Results

Twelve highly copper-resistant bacteria (up to 6-10 mM) were isolated from deep sea hydrothermal fields They were affiliated with the Pseudoalteromonas (4), Marinobacter (3), Halomonas (2), Psychrobacter (1), and Pseudomonas (1) genus in the α-Proteobacteria, and the Sphingomonas (1) genus in the β-Proteobacteria. The presence of copper in the medium obviously induced the amount of polysaccharides and proteins in the crude extracellular polymeric substances (EPS) produced by Halomonas sp. CuT 3-1, Pseudoalteromonas sp. CuT 4-3 and Marinobacter metalliresistant CuT 6, which could absorb 40 to 50 mg•g-1 copper. We further described a novel species, Marinobacter metalliresistant sp. nov. CuT 6T, which exhibited a higher copper resistance and encoded more heavy metal resistance-related genes than other Marinobacter species.

Discussion

It revealed that the copper resistance capability exhibited by these strains in hydrothermal fields is likely attributed to the production of exopolymeric substances, such as polysaccharides and proteins, as well as active transport or efflux mechanisms for heavy metals.

Can Functional Micro-organisms Associated with Pumpkin Sizes Be Sought Out from the Soil?-A Comparison of Soil Microbial Community Structures in Rhizospheres between Giant- and Small-Sized Pumpkin Varieties

To elucidate the biological mechanisms driving the growth of various pumpkin varieties to different sizes under identical management conditions while in the same field, the soil microbial community structures in the rhizospheres of giant-pumpkin (GP) and small-pumpkin (SP) varieties were analyzed. The results revealed that a significantly higher abundance of bacterial communities could be detected in the rhizospheres of the giant pumpkin varieties, such as Gemmatimonadota, norank__f__norank__o_Gaiellales, norank__f__Gemmatimonadaceae, Bryobacter, Sphingomonas, norank__f__JG30-KF-AS9, and norank__f__norank__o___Elsterales, than in those of the small-sized pumpkins. Additionally, norank_f__norank_o__Elsterale, Ellin6067, norank_f__67-14, and Chujaibacter were unique dominant soil bacteria genera in the rhizospheres of the giant pumpkins. By contrast, Arthrobacter, norank_f__Roseiflexaceae, unclassified_f__Rhizobiaceae, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Nocardioides, Mycobacterium, norank_f__norank_o__Vicinamibacterales, and Burkholderia-Caballeronia-Paraburkholderia were the unique dominant soil bacterial genera in the rhizospheres of the small pumpkins. Moreover, at the fungal genus level, unclassified_c__Chytridiomycetes, Podosphaera, and Colletotrichum presented significant differences between the giant-pumpkin (GP) and small-pumpkin (SP) rhizospheres. In addition, unclassified__p__Rozellomycota, unclassified__c__Chytridiomycetes, Penicillium, and unclassified__f__Chaetomiaceae were unique dominant soil fungal genera in the rhizospheres of the giant pumpkins (GPs). By contrast, Podosphaera, Colletotrichum, unclassified__f__Plectosphaerellaceae, unclassified__o_Boletales, Scytalidium, unclassified__p__Rozellomycota, and unclassified__o_Agaricales were the unique dominant soil fungal genera in the rhizospheres of the small pumpkins (SPs). PICRUSt and FUNGuild functional prediction analyses revealed that the giant-pumpkin rhizosphere microbial community had significantly increased translation, ribosomal structure and biogenesis, nucleotide transport and metabolism, defense mechanisms, replication, recombination and repair, wood saprotroph, and undefined saprotroph levels. The above results suggest that the soil microbial compositions differed between the rhizospheres of the giant- (GP) and small-pumpkin (SP) varieties, even though the plants were grown in the same field under identical management conditions. Meanwhile, bacterial genera such as norank_f__norank_o__Elsterale, Ellin6067, norank_f__67-14, and Chujaibacter, in addition to fungal genera such as unclassified__p__Rozellomycota, unclassified__c__Chytridiomycetes, Penicillium, and unclassified__f__Chaetomiaceae, can be speculated as potential soil functional micro-organisms associated with improved pumpkin size.

Unraveling the spatio-temporal dynamics of soil and root-associated microbiomes in Texas olive orchards

Understanding the structure and diversity of microbiomes is critical to establishing olives in non-traditional production areas. Limited studies have investigated soil and root-associated microbiota dynamics in olives across seasons or locations in the United States. We explored the composition and spatiotemporal patterns of the olive-associated microbial communities and specificity in two niches (rhizosphere and root endosphere), seasons (spring, summer, and fall), and domains (bacteria and fungi) in the microbiome of the olive cultivar Arbequina across three olive orchards in Texas. Phylum Proteobacteria, followed by Actinobacteriota, dominated the bacterial populations in the rhizosphere and endosphere. Rubrobacter and Actinophytocola were dominant taxa in the rhizosphere and root endosphere at the genus level. Among fungal communities, phylum Ascomycota was prevalent in the rhizosphere and endosphere, while members of the Chaetomiaceae family outnumbered other taxa in the root endosphere. As per the alpha diversity indices, the rhizosphere at Moulton showed much higher richness and diversity than other places, which predicted a significant difference in rhizosphere between locations for bacterial diversity and richness. There was no significant variation in the bacterial diversity in the niches and the fungal diversity within the root endosphere between locations. Beta diversity analysis confirmed the effect of compartments-in influencing community differences. Microbial diversity was apparent within the endosphere and rhizosphere. The seasons influenced only the rhizosphere fungal diversity, contrasting the bacterial diversity in either niche. The research provided a comprehensive overview of the microbial diversity in olive trees' rhizosphere and root endosphere. The abundance and composition of OTUs associated with the rhizosphere soil of Arbequina suggest its role as a source reservoir in defining the potential endophytes.

Molecular characterization and in-depth genomic analysis to unravel the pathogenic features of an environmental isolate Enterobacter sp. S-33

Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.

Emerald Ash Borer Infestation-Induced Elevated Negative Correlations and Core Genera Shift in the Endophyte Community of Fraxinus bungeana

Endophytes, prevalent in plants, mediate plant-insect interactions. Nevertheless, our understanding of the key members of endophyte communities involved in inhibiting or assisting EAB infestation remains limited. Employing ITS and 16S rRNA high-throughput sequencing, along with network analysis techniques, we conducted a comprehensive investigation into the reaction of endophytic fungi and bacteria within F. bungeana phloem by comparing EAB-infested and uninfected samples. Our findings reveal that EAB infestation significantly impacts the endophytic communities, altering both their diversity and overall structure. Interestingly, both endophytic fungi and bacteria exhibited distinct patterns in response to the infestation. For instance, in the EAB-infested phloem, the fungi abundance remained unchanged, but diversity decreased significantly. Conversely, bacterial abundance increased, without significant diversity changes. The fungi community structure altered significantly, which was not observed in bacteria. The bacterial composition in the infested phloem underwent significant changes, characterized by a substantial decrease in beneficial species abundance, whereas the fungal composition remained largely unaffected. In network analysis, the endophytes in infested phloem exhibited a modular topology, demonstrating greater complexity due to an augmented number of network nodes, elevated negative correlations, and a core genera shift compared to those observed in healthy phloem. Our findings increase understanding of plant-insect-microorganism relationships, crucial for pest control, considering endophytic roles in plant defense.

Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta

Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.

Comparison of Bacterial Communities in Five Ectomycorrhizal Fungi Mycosphere Soil

Ectomycorrhizal fungi have huge potential value, both nutritionally and economically, but most of them cannot be cultivated artificially. To better understand the influence of abiotic and biotic factors upon the growth of ectomycorrhizal fungi, mycosphere soil and bulk soil of five ectomycorrhizal fungi (Calvatia candida, Russula brevipes, Leucopaxillus laterarius, Leucopaxillus giganteus, and Lepista panaeola) were used as research objects for this study. Illumina MiSeq sequencing technology was used to analyze the community structure of the mycosphere and bulk soil bacteria of the five ectomycorrhizal fungi, and a comprehensive analysis was conducted based on soil physicochemical properties. Our results show that the mycosphere soil bacteria of the five ectomycorrhizal fungi are slightly different. Escherichia, Usitatibacter, and Bradyrhizobium are potential mycorrhizal-helper bacteria of distinct ectomycorrhizal fungi. Soil water content, soil pH, and available potassium are the main factors shaping the soil bacterial community of the studied ectomycorrhizal fungi. Moreover, from the KEGG functional prediction and LEfSe analysis, there are significant functional differences not only between the mycosphere soil and bulk soil. 'Biosynthesis of terpenoidsand steroids', 'alpha-Linolenic acid metabolism', 'Longevity regulating pathway-multiple species', 'D-Arginine and D-ornithine metabolism', 'Nitrotoluene degradation' and other functions were significantly different in mycosphere soil. These findings have pivotal implications for the sustainable utilization of ectomycorrhizal fungi, the expansion of edible fungus cultivation in forest environments, and the enhancement of derived economic benefits.

Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere

Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.

Almond shell-derived biochar decreased toxic metals bioavailability and uptake by tomato and enhanced the antioxidant system and microbial community

The effectiveness of almond shell-derived biochar (ASB) in immobilizing soil heavy metals (HMs) and its impact on soil microbial activity and diversity have not been sufficiently studied. Hence, a pot study was carried out to investigate the effectiveness of ASB addition at 2, 4, and 6 % (w/w) on soil biochemical characteristics and the bioavailability of Cd, Cu, Pb, and Zn to tomato (Solanum lycopersicum L.) plants, as compared to the control (contaminated soil without ASB addition). The addition of ASB promoted plant growth (up to two-fold) and restored the damage to the ultrastructure of chloroplast organelles. In addition, ASB mitigated the adverse effects of HMs toxicity by decreasing oxidative damage, regulating the antioxidant system, improving soil physicochemical properties, and enhancing enzymatic activities. At the phylum level, ASB addition enhanced the relative abundance of Actinobacteriota, Acidobacteriota, and Firmicutes while decreasing the relative abundance of Proteobacteria and Bacteroidota. Furthermore, ASB application increased the relative abundance of several fungal taxa (Ascomycota and Mortierellomycota) while reducing the relative abundance of Basidiomycota in the soil. The ASB-induced improvement in soil properties, microbial community, and diversity led to a significant decrease in the DTPA-extractable HMs down to 41.0 %, 51.0 %, 52.0 %, and 35.0 % for Cd, Cu, Pb, and Zn, respectively, as compared to the control. The highest doses of ASB (ASB6) significantly reduced the metals content by 26.0 % for Cd, 78.0 % for Cu, 38.0 % for Pb, and 20.0 % for Zn in the roots, and 72.0 % for Cd, 67.0 % for Cu, 46.0 % for Pb, and 35.0 % for Zn in the shoots, as compared to the control. The structural equation model predicts that soil pH and organic matter are driving factors in reducing the availability and uptake of HMs. ASB could be used as a sustainable trial for remediation of HMs polluted soils and reducing metal content in edible plants.

Exploring the diversity and potential functional characteristics of microbiota associated with different compartments of Schisandra chinensis

Introduction

Symbiotic microbial have a significant impact on the growth and metabolism of medicinal plants. Schisandra chinensis is a very functionally rich medicinal herb; however, its microbial composition and diversity have been poorly studied.

Methods

In the present study, the core microbiomes associated with the rhizospheric soil, roots, stems, leaves, and fruits of S. chinensis from six geographic locations were analyzed by a macro-genomics approach.

Results

Alpha and beta diversity analyses showed that the diversity of microbial composition of S. chinensis fruits did not differ significantly among the geographic locations as compared to that in different plant compartments. Principal coordinate analysis showed that the microbial communities of S. chinensis fruits from the different ecological locations were both similar and independent. In all S. chinensis samples, Proteobacteria was the most dominant bacterial phylum, and Ascomycota and Basidiomycota were the most dominant fungal phyla. Nitrospira, Bradyrhizobium, Sphingomonas, and Pseudomonas were the marker bacterial populations in rhizospheric soils, roots, stems and leaves, and fruits, respectively, and Penicillium, Golubevia, and Cladosporium were the marker fungal populations in the rhizospheric soil and roots, stems and leaves, and fruits, respectively. Functional analyses showed a high abundance of the microbiota mainly in biosynthesis.

Discussion

The present study determined the fungal structure of the symbiotic microbiome of S. chinensis, which is crucial for improving the yield and quality of S. chinensis.

Microplastics change soil properties, plant performance, and bacterial communities in salt-affected soils

Microplastics (MPs) are emerging contaminants found globally. However, their effects on soil-plant systems in salt-affected habitats remain unknown. Here, we examined the effects of polyethylene (PE) and polylactic acid (PLA) on soil properties, maize performance, and bacterial communities in soils with different salinity levels. Overall, MPs decreased soil electrical conductivity and increased NH4+-N and NO3--N contents. Adding NaCl alone had promoting and inhibitive effects on plant growth in a concentration-dependent manner. Overall, the addition of 0.2% PLA increased shoot biomass, while 2% PLA decreased it. Salinity increased Na content and decreased K/Na ratio in plant tissues (particularly roots), which were further modified by MPs. NaCl and MPs singly and jointly regulated the expression of functional genes related to salt tolerance in leaves, including ZMSOS1, ZMHKT1, and ZMHAK1. Exposure to NaCl alone had a slight effect on soil bacterial α-diversity, but in most cases, MPs increased ACE, Chao1, and Shannon indexes. Both MPs and NaCl altered bacterial community composition, although the specific effects varied depending on the type and concentration of MPs and the salinity level. Overall, PLA had more pronounced effects on soil-plant systems compared to PE. These findings bridge knowledge gaps in the risks of MPs in salt-affected habitats.

Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii

Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.

Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation

Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation

Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na+ and enhancing K+). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.

The effects of different impeller combinations in the Sphingan WL gum fermentation process

The fermentation of the high-viscosity polysaccharide WL gum has always been associated with poor mass transfer. Appropriate impeller configurations are key factors in maintaining homogeneity and sufficient mass transfer conditions. Therefore, a flat-folded disc turbine impeller (FFDT) taking into account both the reduced cavitation effect and the increased contact area was designed. Besides, a curved cross impeller (CC) and a fishbone-shaped impeller (FS) generating axial flow were also designed. The energy consumption and efficiency of the designed impellers and eight reported impellers were evaluated through fermentation and principal component analysis (PCA). Compared to the commonly-used six-blade flat-blade disc turbine (FBDT), the ungassed power number of FFDT was reduced by 50 %. Combinations of six-blade Brumajin impeller (BM) + FFDT and CC + FFDT produced high WL gum production and viscosity (34.0 g/L, 35.50 g/L, and 62.64 Pa·s, 61.68 Pa·s, respectively) and were suitable impellers for WL biosynthesis. WL gum from BM + FFDT showed higher viscosity, viscoelasticity, and molecular weight than that from FBDT + FBDT. In addition, fewer amino acids and pyruvic acid intermediates were formed using BM + FFDT, indicating a greater metabolic flux towards WL gum synthesis. This work provided an important reference for the design of impellers in high-viscosity fermentation systems.

Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in the phytoremediation of heavy metals. However, limited access to tailing dams and inadequate assessment of plants' phytoremediation potential limit the characterization of native accumulators, hindering the effectiveness of local remediation efforts. This study evaluates the heavy metal sequestration potentials of Pennisetum purpureum, Leucaena leucocephala, and Pteris vittata and their associated rhizospheric microbial communities at the Marlu and Pompora tailing dams in Ghana. The results indicate shoot hyperaccumulation of Cd (334.5 ± 6.3 mg/kg) and Fe (10,647.0 ± 12.6 mg/kg) in P. purpureum and L. leucocephala, respectively. Analysis of rhizospheric bacterial communities revealed the impact of heavy metal contamination on bacterial community composition, associating Fe and Cd hyperaccumulation with Bacillus, Arthrobacter, and Sphingomonas species. This study reports the hyperaccumulation potentials of L. leucocephala and P. purpureum enhanced by associated rhizosphere bacterial communities, suggesting their potential application as an environmentally friendly remediation process of heavy metals contaminated lands.

Comparative analysis of the microbiomes of strawberry wild species Fragaria nilgerrensis and cultivated variety Akihime using amplicon-based next-generation sequencing

Fragaria nilgerrensis is a wild strawberry species widely distributed in southwest China and has strong ecological adaptability. Akihime (F. × ananassa Duch. cv. Akihime) is one of the main cultivated strawberry varieties in China and is prone to infection with a variety of diseases. In this study, high-throughput sequencing was used to analyze and compare the soil and root microbiomes of F. nilgerrensis and Akihime. Results indicate that the wild species F. nilgerrensis showed higher microbial diversity in nonrhizosphere soil and rhizosphere soil and possessed a more complex microbial network structure compared with the cultivated variety Akihime. Genera such as Bradyrhizobium and Anaeromyxobacter, which are associated with nitrogen fixation and ammonification, and Conexibacter, which is associated with ecological toxicity resistance, exhibited higher relative abundances in the rhizosphere and nonrhizosphere soil samples of F. nilgerrensis compared with those of Akihime. Meanwhile, the ammonia-oxidizing archaea Candidatus Nitrososphaera and Candidatus Nitrocosmicus showed the opposite tendencies. We also found that the relative abundances of potential pathogenic genera and biocontrol bacteria in the Akihime samples were higher than those in the F. nilgerrensis samples. The relative abundances of Blastococcus, Nocardioides, Solirubrobacter, and Gemmatimonas, which are related to pesticide degradation, and genus Variovorax, which is associated with root growth regulation, were also significantly higher in the Akihime samples than in the F. nilgerrensis samples. Moreover, the root endophytic microbiomes of both strawberry species, especially the wild F. nilgerrensis, were mainly composed of potential biocontrol and beneficial bacteria, making them important sources for the isolation of these bacteria. This study is the first to compare the differences in nonrhizosphere and rhizosphere soils and root endogenous microorganisms between wild and cultivated strawberries. The findings have great value for the research of microbiomes, disease control, and germplasm innovation of strawberry.

An updated view of bacterial endophytes as antimicrobial agents against plant and human pathogens

Bacterial endophytes are a crucial component of the phytomicrobiome, playing an essential role in agriculture and industries. Endophytes are a rich source of bioactive compounds, serving as natural antibiotics that can be effective in combating antibiotic resistance in pathogens. These bacteria interact with host plants through various processes such as quorum sensing, chemotaxis, antibiosis, and enzymatic activity. The current paper focuses on how plants benefit extensively from endophytic bacteria and their symbiotic relationship in which the microbes enhance plant growth, nitrogen fixation, increase nutrient uptake, improve defense mechanisms, and act as antimicrobial agents against pathogens. Moreover, it highlights some of the bioactive compounds produced by endophytes.

Abundance, Characterization and Diversity of Culturable Anoxygenic Phototrophic Bacteria in Manitoban Marshlands

Marshes are an important ecosystem, acting as a biodiversity hotspot, a carbon sink and a bioremediation site, breaking down anthropogenic waste such as antibiotics, metals and fertilizers. Due to their participation in these metabolic activities and their capability to contribute to primary productivity, the microorganisms in such habitats have become of interest to investigate. Since Proteobacteria were previously found to be abundant and the waters are well aerated and organic-rich, this study on the presence of anoxygenic phototrophic bacteria, purple non-sulfur bacteria and aerobic anoxygenic phototrophs in marshes was initiated. One sample was collected at each of the seven Manitoban sites, and anoxygenic phototrophs were cultivated and enumerated. A group of 14 strains, which represented the phylogenetic diversity of the isolates, was physiologically investigated further. Aerobic anoxygenic phototrophs and purple non-sulfur bacteria were present at each location, and they belonged to the α- and β-Proteobacteria subphyla. Some were closely related to known heavy metal reducers (Brevundimonas) and xenobiotic decomposers (Novosphingobium and Sphingomonas). All were able to synthesize the photosynthetic complexes aerobically. This research highlights the diversity of and the potential contributions that anoxygenic phototrophs make to the essential functions taking place in wetlands.

Response of Chinese cabbage (Brassica rapa subsp. pekinensis) to bacterial soft rot infection by change of soil microbial community in root zone

Chinese cabbage, scientifically known as Brassica rapa subsp. pekinensis, is a highly popular vegetable in China for its delectable taste. However, the occurrence of bacterial soft rot disease poses a significant threat to its growth and overall development. Consequently, this study aimed to explore the defense mechanisms employed by Chinese cabbage against bacterial soft rot disease. Specifically, the investigation focused on understanding the relationship between the disease and the microbial communities present in the soil surrounding the roots of Chinese cabbage. Significant disparities were observed in the composition of microbial communities present in the root-zone soil of healthy Chinese cabbage plants compared to those affected by Pectobacterium brasiliense-caused soft rot disease. The analysis of 16S rRNA gene high-throughput sequencing results revealed a lower abundance of Proteobacteria (8.39%), Acidobacteriot (0.85), Sphingomonas (3.51%), and Vicinamibacteraceae (1.48%), whereas Firmicutes (113.76%), Bacteroidota (8.71%), Chloroflexi (4.89%), Actinobacteriota (1.71%), A4b (15.52%), Vicinamibacterales (1.62%), and Gemmatimonadaceae (1.35%) were more prevalent in healthy plant soils. Similarly, the analysis of ITS gene high-throughput sequencing results indicated a reduced occurrence of Chytridiomycota (23.58%), Basidiomycota (21.80%), Plectosphaerella (86.22%), and Agaricomycetes (22.57%) in healthy soils. In comparison, Mortierellomycota (50.72%), Ascomycota (31.22%), Podospora (485.08%), and Mortierella (51.59%) were more abundant in healthy plant soils. In addition, a total of 15 bacterial strains were isolated from the root-zone soil of diseased Chinese cabbage plants. These isolated strains demonstrated the ability to fix nitrogen (with the exception of ZT20, ZT26, ZT41, ZT45, and ZT61), produce siderophores and indole acetic acid (IAA), and solubilize phosphate. Notably, ZT14 (Citrobacter freundii), ZT33 (Enterobacter cloacae), ZT41 (Myroides odoratimimus), ZT52 (Bacillus paramycoides), ZT58 (Klebsiella pasteurii), ZT45 (Klebsiella aerogenes), and ZT32 (Pseudomonas putida) exhibited significant growth-promoting effects as determined by the plant growth promotion (PGP) tests. Consequently, this investigation not only confirmed the presence of the soft rot pathogen in Chinese cabbage plants in Hangzhou, China, but also advanced our understanding of the defense mechanisms employed by Chinese cabbage to combat soft rot-induced stress. Additionally, it identified promising plant-growth-promoting microbes (PGPMs) that could be utilized in the future to enhance the Chinese cabbage industry.

Sphingomonas clade and functional distribution with simulated climate change

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.

Trophic interactions in microbiomes influence plant host population size and ecosystem function

Plant microbiomes that comprise diverse microorganisms, including prokaryotes, eukaryotes and viruses, are the key determinants of plant population dynamics and ecosystem function. Despite their importance, little is known about how species interactions (especially trophic interactions) between microbes from different domains modify the importance of microbiomes for plant hosts and ecosystems. Using the common duckweed Lemna minor, we experimentally examined the effects of predation (by bacterivorous protists) and parasitism (by bacteriophages) within microbiomes on plant population size and ecosystem phosphorus removal. Our results revealed that the addition of predators increased plant population size and phosphorus removal, whereas the addition of parasites showed the opposite pattern. The structural equation modelling further pointed out that predation and parasitism affected plant population size and ecosystem function via distinct mechanisms that were both mediated by microbiomes. Our results highlight the importance of understanding microbial trophic interactions for predicting the outcomes and ecosystem impacts of plant-microbiome symbiosis.

Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria

BACKGROUND

The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS

We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION

Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.

Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area

This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L-1), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L-1), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg-1·h-1), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.

Effects of sulfur nanoparticles on rhizosphere microbial community changes in oilseed rape plantation soil under mercury stress

In the present study, experiments were conducted to assess the influence of nanoscale sulfur in the microbial community structure of metallophytes in Hg-contaminated rhizosphere soil for planting rapeseed. The results showed that the richness and diversity of the rhizobacteria community decreased significantly under Hg stress, but increased slightly after SNPs addition, with a reduction in the loss of Hg-sensitive microorganisms. Moreover, all changes in the relative abundances of the top ten phyla influenced by Hg treatment were reverted when subjected to Hg + SNPs treatment, except for Myxococcota and Bacteroidota. Similarly, the top five genera, whose relative abundance decreased the most under Hg alone compared to CK, increased by 19.05%-54.66% under Hg + SNPs treatment compared with Hg alone. Furthermore, the relative abundance of Sphingomonas, as one of the dominant genera for both CK and Hg + SNPs treatment, was actively correlated with plant growth. Rhizobacteria, like Pedobacter and Massilia, were significantly decreased under Hg + SNPs and were positively linked to Hg accumulation in plants. This study suggested that SNPs could create a healthier soil microecological environment by reversing the effect of Hg on the relative abundance of microorganisms, thereby assisting microorganisms to remediate heavy metal-contaminated soil and reduce the stress of heavy metals on plants.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Microbiome-based classification models for fresh produce safety and quality evaluation

Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food.

IMPORTANCE

Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.