Bacterial Community Richness Research Articles

Production of polyhydroxybutyrate with photosynthetic bacteria treating artificial kitchen waste: Effect of light intensity

Kitchen waste can be used as a cheap carbon source for photosynthetic bacteria (PSB) to produce polyhydroxybutyrate (PHB). Light intensity is one of the most important factors in PSB growth. This paper investigated the efficiency and mechanism of PSB growth and PHB production from fermented kitchen waste under different light intensities. Results showed that PSB could grow well and produce PHB within the light intensity range of 1000-4000 lux using fermented kitchen waste as substrate. The 2000 lux was the optimal for PHB production, and PHB content and concentration reached 41.6% dry cell weight and 675.3mg/L, respectively, much higher than other light intensities. The corresponding PHB yield and productivity were 0.33g PHB/g chemical oxygen demand (COD) and 51.9mg/L/d, respectively. Removal of COD and NH4+ were 89.6% and 44.7%, respectively. Microbial community analysis showed that diversity and richness of bacterial community increased with time, and Rhodopseudomona and unclassified_f_Enterobacteriaceae were the dominant bacterial genera at the 2000 lux. Metabolic characteristics in fatty acid degradation, tricarboxylic acid cycle, pyruvate metabolism, photosynthesis, and pyruvate metabolism increased at the 2000 lux. Also, the key enzyme (PhaC, butyryl-CoA dehydrogenase, etc.) for synthesizing PHB was highly expressed, which corresponded to the large amount of PHB accumulation. This study provides a theoretical reference for treatment of kitchen waste with PSB for PHB production.

The Synergistic Impact of a Novel Plant Growth-Promoting Rhizobacterial Consortium and Ascophyllum nodosum Seaweed Extract on Rhizosphere Microbiome Dynamics and Growth Enhancement in Oryza sativa L. RD79

This study investigated the combined effects of novel plant growth-promoting rhizobacteria (PGPR)—Agrobacterium pusense NC2, Kosakonia oryzae WN104, and Phytobacter sp. WL65—and Ascophyllum nodosum seaweed extract (ANE) as biostimulants (PGPR-ANE) on rice growth, yield, and rhizosphere bacterial communities using the RD79 cultivar. The biostimulants significantly enhanced plant growth, shoot and root length, and seedling vigour; however, seed germination was not affected. In pot experiments, biostimulant application significantly increased the richness and evenness of bacterial communities in the rhizosphere, resulting in improvements in rice growth and yield, with increases in plant height (9.6–17.7%), panicle length (14.3–17.9%), and seeds per panicle (48.0–53.0%). Notably, biostimulant treatments also increased post-harvest soil nutrient levels, with nitrogen increasing by 7.7–19.2%, phosphorus by 43.4–161.4%, and potassium by 16.9–70.4% compared to the control. Principal coordinate analysis revealed distinct differences in bacterial composition between the tillering and harvesting stages, as well as between biostimulant treatments and the control. Beneficial bacterial families, including Xanthobacteraceae, Beijerinckiaceae, Acetobacteraceae, Acidobacteriaceae, and Hyphomicrobiaceae, increased in number from the tillering to harvesting stages, likely contributing to soil health improvements. Conversely, methanogenic bacterial families, such as Methanobacteriaceae and Methanosarcinaceae, decreased in number compared to the control. These findings highlight the dynamic responses of the rhizosphere microbiome to biostimulant treatments and underscore their potential benefits for promoting sustainable and productive agriculture.

Atractylodes macrocephala Root Rot Affects Microbial Communities in Various Root-Associated Niches

Atractylodes macrocephala, a perennial herb widely used in traditional Chinese medicine, is highly prone to root rot, which significantly reduces its yield and quality. This study compared the physicochemical properties of soil from healthy and diseased A. macrocephala plants and analyzed the microbial diversity in the endophytic, rhizosphere, and root zone soils. The results showed that the diseased plants had higher levels of available potassium and electrical conductivity in the rhizosphere, both positively correlated with the severity of root rot, while soil pH was negatively correlated. The diversity and richness of endophytic bacterial and fungal communities were significantly reduced in diseased plants. Additionally, root rot led to major changes in the rhizosphere microbial community, with an increased abundance of Proteobacteria and Ascomycota, and a decrease in Firmicutes, Bacteroidetes, Actinobacteria, and Basidiomycota. Fusarium oxysporum, Fusarium solani, and Fusarium fujikuroi were identified as key pathogens associated with root rot. This study enhances our understanding of the microbial interactions in soils affected by root rot, offering a foundation for developing soil improvement and biological control strategies to mitigate this disease in A. macrocephala cultivation.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene.

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

Enhanced bioremediation of bensulfuron-methyl contaminated soil by Hansschlegelia zhihuaiae S113: metabolic pathways and bacterial community structure

Bensulfuron-methyl (BSM), a widely used herbicide, can persist in soil and damag sensitive crops. Microbial degradation, supplemented with exogenous additives, provides an effective strategy to enhance BSM breakdown. Hansschlegelia zhihuaiae S113 has been shown to efficiently degrade this sulfonylurea herbicide. However, depending solely on a single strain for degradation proves inefficient and unlikely to achieve ideal remediation in practical applications. This study assessed the impact of various carbon sources on the degradation efficiency of S113 in BSM-polluted soil. Among these, glucose was the most effective, achieving a 98.7% degradation rate after 9 d of inoculation. In addition, seven intermediates were detected during BSM degradation in soil through the cleavage of the phenyl ring ester bond, the pyrimidine rings, and urea bridge peptide bond, among other pathways. 2-amino-4,6-dimethoxy pyrimidine (ADMP), and 2-(aminosulfonylmethyl)-methyl benzoate(MSMB) were the primary intermediates. These metabolites were less toxic to maize, sorghum, and bacteria than the BSM. Community structure analysis indicated that variations in exogenous carbon sources and environmental pollutants significantly improved the ecological functions of soil microbial communities, enhancing pollutant degradation. Addition of carbon sources notably affected soil microbial community structure, modifying metabolic activities and interaction patterns. Specifically, glucose substantially increased the richness and diversity of soil bacterial communities. These findings offer valuable insights for field remediation practices and contributed to the development of more robuste soil pollution management strategies.

Ingesting Stellera chamaejasme Significantly Impacts the Gastrointestinal Tract Bacterial Community and Diversity in Plateau Zokors (Eospalax baileyi)

Intestinal bacteria are considered the “second genome” of the host, playing a crucial physiological role in assisting the host in degrading plant secondary compounds, nutrient absorption, immune regulation, and other aspects. To explore the effects of Stellera chamaejasme on the bacterial community of the gastrointestinal tract of plateau zokor, this study uses the 16S rRNA gene high-throughput sequencing technology, and the biodiversity and the community structure of gut bacteria in different gastrointestinal tract segments (the stomach and cecum) of plateau zokors. The results showed that at the phylum level, the dominant flora in the stomach and cecum of plateau zokors before and after ingesting Stellera chamaejasme were Firmicutes and Bacteroidetes. In plateau zokors that ingested Stellera chamaejasme, the relative abundance of Firmicutes in the stomach and cecum decreased, the relative abundance of Bacteroidetes increased, and the ratio of Firmicutes to Bacteroidetes decreased. After plateau zokors ingested Stellera chamaejasme, the ACE index demonstrated a significant reduction in the richness of the stomach bacterial community, while cecal bacterial community richness showed no significant change. Stellera chamaejasme exhibits significantly different effects on the bacterial communities in different segments of the gastrointestinal tract. Beta diversity analysis revealed that, after plateau zokors ingested Stellera chamaejasme, there were notable distinctions in the bacterial communities within both the stomach and cecum, alongside a marked reduction in the variability of the intestinal bacterial profiles across individuals. The results show that ingesting Stellera chamaejasme has a significant impact on the composition and structure of the gastrointestinal tract bacterial community in plateau zokors.

Distribution of Microorganisms and Antibiotic Resistance Genes in Production Wastewater During Pumped Storage Power Station Construction

The construction period of pumped storage power stations (PSPS) generates amounts of production wastewater, which may contain pathogenic bacteria and antibiotic resistance genes (ARGs) in these bacteria, potentially posing environmental and health risks. This study used the metagenome approach to analyze the distribution of microorganisms, ARGs and their correlation with water quality indicators in wastewater collected from two typical PSPSs. Coagulation system wastewater exhibits strong alkalinity (11.88), and aggregate system wastewater has high suspended solids (SS, 8 × 104 mg/L), resulting in lower richness and diversity of bacterial communities. Serpentinimonas, a kind of alkaliphilic bacteria, had the highest relative abundance (48.58–99.7%). The ARG subtypes obtained conferred wastewater resistance to tetracycline, macrolide, fluoroquinolone and so on, but wastewater treatment has limited removal effect on ARGs. The results indicate that resistant bacteria and resistance genes can still be present and distributed under highly alkaline conditions, and the removal efficiency of ARGs by wastewater treatment in PSPS is limited. Attention should be given to the environmental and health risks posed by production wastewater, thereby providing a theoretical basis for the sustainable development of the PSPS industry.

Using fungal-bacterial community analysis to explore potential microbiomes to manage Meloidogyne incongnita.

Rhizosphere microbial communities strongly affect outbreaks of root-knot nematode (RKN) disease. However, little is known about the interactions among fungi, bacteria and RKN. The bacterial and fungal community compositions in the rhizospheres of four representative tobacco varieties, both resistant and susceptible to RKN, were characterized using 16S rRNA gene sequencing for bacteria and internal transcribed spacer gene sequencing for fungi. Our findings revealed that the fungi played crucial roles in facilitating the cross-kingdom and symbiotic fungal-bacterial interactions to suppress RKN. Moreover, our investigation suggested Microbacterium as a potential microbial antagonist against RKN based on its enhanced presence in RKN-resistant tobacco genotypes, and the relative abundance of Microbacterium was 34.49% greater in the rhizosphere of resistant tobacco than that of susceptible tobacco significantly. Notably, the richness of fungal community enhanced tobacco's microbe-associated resistance to RKN through the positive regulation of the richness and diversity of bacterial community and the relative abundance of Microbacterium. This study underscores the critical role of the fungus-dominated fungal-bacterial community in bolstering tobacco resistance against RKN. The potential antagonistic role of Microbacterium presents promising avenues for innovative RKN management strategies.

The Effects of Acid-Modified Biochar and Biomass Power Plant Ash on the Physiochemical Properties and Bacterial Community Structure of Sandy Alkaline Soils in the Ancient Region of the Yellow River

The application of biochar can effectively enhance soil organic matter (SOM) and improve soil structure. Biomass power plant ash (BPPA) is also rich in essential nutrients for plants, with similar carbon content. Considering production cost and agricultural waste recycling, it is beneficial to apply BPPA to improve soil fertility and quality. However, it remains unclear whether its ameliorative effects surpass those of biochar in alkaline soils. In the study, we set up seven pot experiments of faba beans in sandy alkaline soils from the ancient region of the Yellow River, including the controls (CK), different amounts of acid-modified BPPA (A1, A2, A3), and the same amounts of acid-modified biochar (B1, B2, B3), to compare their effects on soil physiochemical properties and bacterial community structure. The results indicate that the application of both biochar and BPPA can improve soil physiochemical properties. At the same dosage, the biochar application outperformed BPPA treatment in terms of soil physical properties such as bulk density (BD), maximum water-holding capacity (FC), and soil capillary porosity (SP2). Conversely, BPPA treatment displayed advantages in chemical properties such as readily oxidizable organic carbon (ROOC), total nitrogen (TN), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), and electrical conductivity (EC). All the treatments enhanced the richness and diversity of bacterial communities, increasing the relative abundance of eutrophic groups such as Bacteroidota and Firmicutes while decreasing that of oligotrophic groups like Actinobacteriota. BPPA also increased the relative abundance of Proteobacteria, while the opposite was observed for biochar. Correlation analysis showed that the environmental factors such as soil pH, EC, TN, AK, SOM, and SP2 emerged as primary factors influencing the bacterial community structure of alkaline soils, significantly affecting their diversity and abundance. Among them, SP2 and SOM were the dominant physical and chemical factors, respectively. Overall, the application of both acid-modified BPPA and biochar can enhance the physiochemical properties of sandy alkaline soils, while the application of BPPA is superior for improving soil nutrient content and enhancing bacterial community structure. The study explores the potential mechanisms through which the application of acid-modified BPPA affects soil characteristics and microbial features, providing new insight into developing optimizing fertilization strategies for enhancing soil quality in the ancient region of the Yellow River.

Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae).

Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment. Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR. Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.

Reclamation of co-pyrolyzed dredging sediment as soil cadmium and arsenic immobilization material: Immobilization efficiency, application safety, and underlying mechanisms

The safe management of toxic metal-polluted dredging sediment (DS) is imperative owing to its potential secondary hazards. Herein, the co-pyrolysis product (DS@BC) of polluted DS was creatively applied to immobilize soil Cd and As to achieve DS resource utilization, and the efficiency, safety, and mechanism were investigated. The results revealed that the DS@BC was more effective at reducing soil Cd bioavailability than the DS was (58.9–73.2% vs. 21.8–27.4%), except for the dilution effect, whereas the opposite phenomenon occurred for soil As (25.5–35.7% vs. 35.7–42.8%). The DS@BC immobilization efficiency was dose-dependent for both Cd and As. Soil labile Cd and As were transformed to more stable fractions after DS@BC immobilization. DS@BC immobilization inhibited the transfer of soil Cd and As to Brassica chinensis L. and did not cause excessive accumulation of other toxic metals in the plants. The appropriate addition of the DS@BC (8%) sufficiently alleviated the oxidative stress response of the plants and enhanced their growth. These findings indicate that the DS@BC was safe and effective for soil Cd and As immobilization. DS@BC immobilization decreased the diversity and richness of the rhizosphere soil bacterial community because of the dilution effect. The DS@BC immobilized soil Cd and As via direct adsorption, and indirect increasing soil pH, and regulating the abundance of specific beneficial bacteria (e.g., Bacillus). Therefore, the use of co-pyrolyzed DS as a soil Cd and As immobilization material is a promising resource utilization method for DS. Notably, to verify the long-term effects and safety of DS@BC immobilization, field trials should be conducted to explore the effectiveness and risk of harmful metal release from DS@BC immobilization under real-world conditions.

Are bacterial communities and aggregation in fragile soils influenced by the management system?

Light-textured soils are widely distributed globally and, despite their limitations, have been integrated into agricultural production systems. This study aimed to assess how management systems—conventional tillage (CT) and no-till (NT)—affect aggregate formation pathways (physicogenic and biogenic) and bacterial communities. Two management systems (NT and CT) and three cover crops were evaluated: CJ: Crotalária (Crotalaria juncea (40 ​kg ​ha−1); M: Millet (Pennisetum glaucum - 60 ​kg ​ha−1); and C: Cocktail (Crotalária - Crotalaria juncea - 10 ​kg ​ha−1, Jack bean - Canavalia ensiformis - 75 ​kg ​ha−1, and Millet - Pennisetum glaucum - 30 ​kg ​ha−1). Undisturbed soil samples were collected from the crop row at a depth of 0.00–0.10 ​m. Aggregates with diameters between 9.7 and 8.0 ​mm were classified as biogenic or physicogenic. In addition to the chemical attributes of the aggregates, total organic carbon (TOC) and its fractions (mineral-associated organic carbon, MAOC; particulate organic carbon, POC; and free light fraction carbon, FLFC) were quantified. The structure and bacterial composition of the aggregates were also characterized. A higher proportion of biogenic aggregates (53–64%) was observed compared to physicogenic aggregates (36–47%). Cover crops exhibited significant differences in pH, calcium (Ca2+), base saturation, phosphorous (P), and percentage of base saturation. The management systems differed significantly for Ca2+ and P, with CT showing higher values than NT. The management system influenced organic matter accumulation and stabilization in the aggregates, with MAOC content being significantly lower in CT. POC and TOC were also significantly lower in physicogenic aggregates under CT. Bacterial community richness, diversity, and structure were significantly influenced by the management system, with greater richness and diversity in NT compared to CT. Network analysis revealed NT had more nodes and edges (65 and 406, respectively) than CT (52 and 357, respectively. Phyla abundance differed between the systems, with Firmicutes and Entotheonellaeota more abundant in CT, while WPS_2, GAL15, Bdellovibrionota, and Myxococcota were more abundant in NT. Despite the relatively short period of NT implementation (5 years), it had a positive effect on the bacterial community, which may subsequently influence nutrient and carbon content and their fractions in the aggregates.

Microplastics stimulated soil bacterial alpha diversity and nitrogen cycle: A global hierarchical meta-analysis

Microplastics (MPs) pollution is recognized as a global emerging threat with serious potential impacts on ecosystems. Our meta-analysis was conducted based on 117 carefully selected publications, from which 2160 datasets were extracted. These publications described experiments in which MPs were added to soil (in laboratory or greenhouse experiments or in the field) after which the soil microbial community was analyzed and compared to a control group. From these publications, we extracted 1315 observations on soil bacterial alpha diversity and richness indices and 845 datasets on gene abundance of bacterial genes related to the soil nitrogen cycle. These data were analyzed using a multiple hierarchical mixed effects meta-analysis. The mean effect of microplastic exposure was a significant decrease of soil bacterial community diversity and richness. We explored these responses for different regulators, namely MPs addition rates, particle size and plastic type, soil texture and land use, and study type. Of the bacterial processes involved in the soil nitrogen cycle, MPs addition significantly promoted assimilation of ammonium, nitrogen fixation and urea decomposition, but significantly inhibited nitrification. These results suggest that MPs contamination may have considerable impacts on soil bacterial community structure and function as well as on the soil nitrogen cycle.

Enhancing compost quality through biochar and oyster shell amendments in the co-composting of seaweed and sugar residue

Aquaculture and agricultural production generate substantial amounts of waste, including seaweed (which has plant-stimulating properties), oyster shells, and sugar residues. Through composting and appropriate management, these wastes have the potential to be converted into beneficial soil amendments. However, there is a lack of research exploring the potential of composting in promoting the conversion of seaweed into more stable humified forms, as well as in assessing whether composted seaweed retains its beneficial effects on plant growth. Additionally, studies on using oyster shells as additives to reduce waste pressure and comparing their effectiveness with biochar are relatively scarce. This study examines the impact of incorporating 5% corn stover biochar (T1), 10% biochar (T2), and 10% oyster shell powder (T3) on key physicochemical properties, product quality, and microbial community dynamics during the co-composting of seaweed and sugar residues. Results indicate that organic matter (OM) loss in T1 and T2 increased by 31.2% and 26.4%, respectively, compared to the control (CK). Moreover, Excitation-emission matrix (EEM) fluorescence spectroscopy revealed that humic substances in T1 and T2 surged by 434% and 423%, respectively, far exceeding the 289% increase in CK. The 10% biochar treatment also improved alginate degradation and seed germination index, due to the presence of biostimulants in seaweed and an increased abundance of Cobetia. Microbial analysis post-composting showed that T2 and T3 significantly enhanced the diversity and richness of bacterial communities. Notably, although oyster shell powder did not improve the humification degree of compost as significantly as biochar, it achieved effective weight reduction of waste (OM loss of 43.57%, far exceeding CK's 35.34%) without hindering the composting process. All four compost treatments retained the plant-stimulating effects of seaweed and facilitated alginate degradation. These results underscore the potential of biochar to enhance composting efficiency and utilize composting to process large quantities of oyster shell waste.

Effect of inoculation with different Eurotium cristatum strains on the microbial communities and volatile organic compounds of Fu brick tea

Eurotium cristatum is the primary fungus in Fu brick tea (FBT) and plays a crucial role in its special flavor. This study investigated the effect of inoculation with different E. cristatum strains (i.e., ZJ, GX, GZ, HN, and SX) on the microbial communities and volatile organic compounds (VOCs) of FBT. A total of 113 VOCs were identified in all samples, with the concentration of VOCs (alcohols, aldehydes, and ketones) significantly higher in GXE FBT than in other samples. The core VOCs of GXE (19), GZE (16), HNE (19), SXE (15), and ZJE (13) FBT were identified using orthogonal partial least squares discriminant analysis and relative odor activity value (ROAV) analysis. Methional (a27), butanal (a41), 1-octen-3-one (a69), and ethyl acetate (a77) were key markers for inoculated FBTs, and 1-octen-3-ol, dimethyl disulfide, and acetoin-M were the specific markers of HNE. Linalool and (E)-2-octenal were particularly prominent in GXE, and isoamyl acetate-D was an important aroma component of GZE. Differences in microbial diversity were observed among the different inoculated fermented FBTs, and E. cristatum inoculation remarkably influenced the richness and diversity of bacterial communities. The VOCs were closely associated with fungi and bacteria, and 19 potentially dominant microorganisms (10 fungal and 9 bacterial genera) correlated with VOCs were identified. Among them, Aspergillus (fungi) and Pseudomonas (bacteria) exerted the greatest role. The FBT inoculated with E. cristatum from ZJ had the highest content of theaflavins and theabrownins, which intensified the red and yellow colors of the tea. E. cristatum greatly decreased the free amino acids and fatty acids, contributing to the aroma formation of FBT. Therefore, inoculating FBT with E. cristatum remarkably influenced the microbial communities and improved its flavor profile. This work provides a theoretical foundation on the role of E. cristatum in the formation and regulation of FBT flavor.

Synergistic biodegradation of trichloroethylene-contaminated soil using Typha angustifolia L. and an anaerobic degrading bacterial consortium

Plant-microorganism combined bioremediation is a highly efficient and environmentally sustainable method for the remediation of contaminated soils. Despite its potential, the synergistic effects of wetland plants and anaerobic microbial consortium on the removal of chlorinated hydrocarbons (CAHs) from soil remain inadequately understood. In this study, an anaerobic bacterial consortium, capable of completely dechlorinating trichloroethylene (TCE), was enriched and screened from long-term CAH-contaminated soil. Subsequently, the combined effects of the wetland plant Typha angustifolia L. and the degrading bacterial consortium on the removal of TCE from soil were investigated, along with the underlying microbial mechanisms. The results demonstrated that the bacterial consortium was able to completely convert 0.5 mM TCE to vinyl chloride (VC) within 7 days, and subsequently degrade VC to ethylene within 48 days. The integration of Typha angustifolia L. with the degrading bacterial consortium significantly enhanced both the removal and complete dechlorination of TCE from the soil compared to either treatment alone. Furthermore, this combination substantially increased the diversity and richness of soil bacterial communities, enriched dechlorinating microorganisms, and elevated the relative abundance of dehalogenating enzymes and peroxidases involved in pollutant degradation. In addition, the combination resulted in a more complex soil bacterial community, closer microbial interactions, and a more stable microbial co-occurrence network. This study extends the scope of plant-microorganism combined bioremediation for CAH- contaminated soils.

The diversity and biogeography of bacterial communities in lake sediments across different climate zones

Bacteria are diverse and play important roles in biogeochemical cycling of aquatic ecosystems, but the global distribution patterns of bacterial communities in lake sediments across different climate zones are still obscure. Here we integrated the high-throughput sequencing data of 750 sediment samples from published literature to investigate the distribution of bacterial communities in different climate zones and the potential driving mechanisms. The obtained results indicated that the diversity and richness of bacterial community were notably higher in temperate and cold zones than those in other climate zones. In addition, the bacterial community composition varied significantly in different climate zones, which further led to changes in bacterial functional groups. Specifically, the relative abundance of nitrogen cycling functional groups in polar zones was notably higher compared to other climate zones. Regression analysis revealed that climate (mean annual precipitation, MAP; and mean annual temperature, MAT), vegetation, and geography together determined the diversity pattern of sediment bacterial community on a global scale. The results of partial least squares path modeling further demonstrated that climate was the most significant factor affecting the composition and diversity of bacterial communities, and MAP was the most important climate factor affecting the composition of bacteria community (R2 = 0.443, P < 0.001). It is worth noting that a strong positive correlation was observed between the abundance of the dominant bacterial group uncultured_f_Anaerolineaceae and the normalized difference vegetation index (NDVI; P < 0.001), suggesting that vegetation could affect bacterial community diversity by influencing dominant bacterial taxa. This study enhances our understanding of the global diversity patterns and biogeography of sediment bacteria.

Diversified crop rotations improve soil microbial communities and functions in a six-year field experiment

Diversified crop rotations can help mitigate the negative impacts of increased agricultural intensity on the sustainability of agroecosystems. However, the impact of crop rotation diversity on the complexity of soil microbial association networks and ecological functions is still not well understood. In this study, a 6-year field experiment was conducted to evaluate how six different crop rotations change the composition and network complexity of soil microbial communities, as well as their related ecological functions. Microbial traits were measured in six crop rotations with different crop diversity index (CDI) during 2016–2022, including winter wheat–summer maize (CDI 1, WM) as the control, sweet potato→winter wheat–summer maize (CDI 1.5, SpWM), peanut→winter wheat–summer maize (CDI 1.5, PWM), soybean→winter wheat–summer maize (CDI 1.5, SWM), spring maize→winter wheat–summer maize (CDI 1.5, SmWM), and ryegrass–sweet sorghum→winter wheat–summer maize (CDI 2, RSWM). The study findings indicated that diversified crop rotations significantly increased ASV richness of both bacterial and fungal communities after 6-year treatments, and the β-diversity profiles of bacterial and fungal communities significantly distinguished at the year of 2022 from 2016. The relative abundance of Acidobacteria and Chloroflexi was significantly enriched in SpWM rotation at 2022, while Basidiomycota significantly declined in five diversified rotations compared to WM. Diversified crop rotations at 2022 increased the complexity and density of bacterial and fungal networks than 2016. SpWM and PWM rotations had the highest functional groups involved in chemoheterotrophy and saprotroph, respectively. Structural equation modelling (SEM) also revealed that diversified crop rotations increased soil nutrients through improving the composition of bacterial communities and the augmented intricacy of the interconnections within both bacterial and fungal communities. This research underscores the importance of preserving the diversity and ecological functions of soil microorganisms in the nutrient-recycling processes for efficient agricultural practices.

Endophytic consortium exhibits varying effects in mitigating cadmium toxicity in rice cultivars with distinct cadmium accumulation capacities

Cadmium (Cd)-contaminated rice is the main source of Cd exposure that threatens food safety and human health. While plant growth-promoting bacteria (PGPB) have been reported to reduce Cd toxicity in rice, the effect of endophytic consortium is less understood compared to the single strain. Here, we reported that the PGPB consortium consisting of Cd-tolerant endophytic bacteria Pseudomonas sp. 4N2 and Bacillus sp. TB1 increased extracellular polymeric substance secretion and demonstrated a higher Cd removal rate compared to individual 4N2 and TB1. Further, two rice cultivar, namely the low-Cd-accumulating (LA) cultivar 728B and the high-Cd-accumulating (HA) cultivar BB, were inoculated with the 4N2-TB1 consortium. As expected, the consortium had a more pronounced effect on 728B, from which the endophytic bacteria were screened. The 4N2-TB1 consortium was found to facilitate the growth of rice seedlings and enhance their antioxidation activity. Moreover, the consortium significantly reduced Cd transfer coefficient from root to shoot through Cd immobilization in rice roots, resulting in a reduction from 30 % to 6 % in 728B and from 31 % to 13 % in BB. Furthermore, alpha-diversity analysis indicated an increased diversity and richness of the root bacterial community after 4N2-TB1 inoculation. Also, redundancy analysis confirmed a positive correlation between rice biomass and Cd content with a specific assemblage of bacteria including Bacillus and Leifsonia. These results demonstrated that the 4N2-TB1 consortium may alleviate Cd stress in rice cultivars through recruiting PGPB and Cd-binding bacteria on the root surface, thus strengthening the immobilization of Cd in rice roots.

Deciphering the differences of bacterial communities between high- and low-productive wheat fields using high-throughput sequencing.

Microbial communities have been demonstrated to be essential for healthy and productive soil ecosystems. However, an understanding of the relationship between soil microbial community and soil productivity levels is remarkably limited. In this study, bulk soil (BS), rhizosphere soil (RS), and root (R) samples from the historical high-productive (H) and low-productive (L) soil types of wheat in Hebei province of China were collected and analyzed by high-throughput sequencing. The study highlighted the richness, diversity, and structure of bacterial communities, along with the correlation networks among different bacterial genera. Significant differences in the bacterial community structure between samples of different soil types were observed. Compared with the low-productive soil type, the bacterial communities of samples from the high-productive soil type possessed high species richness, low species diversity, complex and stable networks, and a higher relative abundance of beneficial microbes, such as Pseudoxanthomonas, unclassified Vicinamibacteraceae, Lysobacter, Massilia, Pseudomonas, and Bacillus. Further analysis indicated that the differences were mainly driven by soil organic matter (SOM), available nitrogen (AN), and electrical conductivity (EC). Overall, the soil bacterial community is an important factor affecting soil health and crop production, which provides a theoretical basis for the targeted regulation of microbes in low-productivity soil types.