Microbial Bacterial Community Research Articles

Effects of soil microbial ecology on ginsenoside accumulation in Panax ginseng across different cultivation years

The quality of ginseng is greatly influenced by ecological factors, especially soil factors. However, there are few reports on the association between the physicochemical properties of ginseng rhizosphere soil, enzyme activity, microbial bacterial community, and ginsenoside content accumulation in ginseng planted at different ages. In order to investigate the relationship between the soil microbial ecology of ginseng and the content of ginsenosides, this study compared the differences in the rhizosphere soil microecological environment and ginsenoside accumulation between ginseng planted for one, two, and three years, using soil without ginseng cultivation as a control. The results showed that monomer saponins Ro, Re, Rf, Rb1, and total ginsenoside content increased significantly (P < 0.05), while monomer saponins Rb2, Rd, Rh2, and Rg3 content decreased significantly in three-year-old ginseng, (P < 0.05). And soil pH, soil bulk weight and soil enzyme activity in ginseng rhizosphere soils altered the abundance and diversity of rhizosphere soil bacterial community. Redundancy analysis and Pearson correlation analysis revealed that soil pH, soil bulk density, soil urease, and protease were the primary factors influencing the bacterial community in the soil around roots of one, two, three years old ginseng. Co-occurrence network visualization analysis indicated that seven bacterial communities, Planctomycetota, Methylomirabilota, Verrucomicrobiota and Acidobacteriota at the phylum level, Vicinamibacterales_unclassified, Vicinamibacteraceae_unclassified and Candidatus_Udaeobacter at the genus level, had a significant effect on the synthesis of ginsenosides. In summary, soil urease, pH, and soil bulk density in agricultural soils can regulate soil physicochemical properties, soil enzymatic activities, and soil bacterial community abundance. These factors are key drivers of the ginseng soil microbial ecology in ginseng cultivation. These studies will provide a scientific basis for subsequent optimization of soil improvement techniques for cultivated ginseng in farmland by improving the soil microbial ecology.

Impact of pH-mediated in situ enzymatic pretreatment on food waste decomposition and biomethane production: Performance, mechanism, and key metabolic pathways

pH value universally presents the great influence on hydrolysis efficiency of food waste (FW) by in situ enzymatic pretreatment, while the influencing mechanism of pH value on enzymatic decomposition of FW is not clear at present. This study innovatively in situ prepared a microbial-based compound enzyme (MCE) from FW, as well as systematically deciphered the impact and underlying mechanism of pH-mediated MCE pretreatment on FW decomposition and biomethane production. The dissolution, biodegradability and monomer formation of FW were found to be promoted by MCE pretreatment, and the highest hydrolysis efficiency was obtained at pH 5, while the biomethane yield was accordingly increased by 30.89 % compared to the control. The dissection of Fourier transform infrared spectroscopy (FTIR) results unraveled that the reaction order of FW components was protein → lipid → starch → cellulose in the acid-enhanced process, while the order shifted to starch → protein → cellulose → lipid in the alkali-enhanced process. Moreover, the looser protein structure was obtained after MCE pretreatment due to α-helix/(β-sheet + random coil) value was declined from 60.35 % to 57.01 %-49.03 %. These changes induced by pH-mediated MCE pretreatment reshaped the bacterial microbial community in favor of biomethane production, and the metagenomic analysis further demonstrated that MCE pretreatment had the highest abundances of genes related to metabolic functions of level 2 and 3 at pH 5, while the abundances of over 90 % key enzyme-encoding genes associated with hydrolysis, acidogenesis and methanogenesis were also increased during the anaerobic digestion process, therefore harvesting the highest biomethane yield.

Analysis of Microbial Diversity in Rhizosphere Soil of Panax notoginseng under Different Water and Microbial Fertilizer Conditions

Panax notoginseng is a highly regarded medicinal plant that has obstacles associated with continuous cropping. Understanding soil microorganisms is crucial, as they play a major role in this regard. However, soil microorganisms are affected by multiple factors; therefore, we need to conduct more in-depth research. This study investigated the combined effects of irrigation and microbial fertilizer treatments (J1F1, J1F2, J2F1, J2F2, J3F1, J3F2, and CK) on the diversity of bacterial and fungal microbial communities in the rhizosphere of Panax notoginseng. The bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences were sequenced using Illumina HiSeq. The results showed that, without microbial fertilizer (CK), the microbial community abundance and diversity were significantly lower than in the other treatments; moreover, among the microbial fertilizer treatments, the microbial abundance in F1 was higher than that in F2. Under the same microbial fertilizer application, the incidence rate of Panax notoginseng root rot was J2 &gt; J1 &gt; J3, and the yield of Panax notoginseng was J3 &gt; J2 &gt; J1. Under the same irrigation conditions, the incidence rate of Panax notoginseng root rot was F1 &gt; F2, and the yield of Panax notoginseng was F2 &gt; F1. This study provides important guidance for Panax notoginseng plant microbiota and sustainable agriculture.

Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions.

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

Stochastic Processes Dominate Soil Microbial Community Assembly during the Restoration of Degraded Karst Forests

The mechanisms underpinning the soil microbial community assembly are important, particularly in the fragile karst forest ecosystem. Despite such significance, relevant topics remain limited. We investigated a typical karst area, the Maolan National Nature Reserve in China. For this purpose, 30 forest dynamics plots were established on three restoration gradients in degraded karst forests, namely shrub, pioneer tree, and climax communities. Using vegetation surveys, we explored the diversity patterns, driving factors, and community assembly of the soil microbial communities during the restoration of degraded karst forest ecosystems. In addition, the soil physicochemical properties and macrogenomic sequencing data were examined. One-way analysis of variance and principal coordinates analysis showed no significant changes in soil microbial α-diversity during restoration, and the opposite pattern was observed for β-diversity. Variation partitioning analysis revealed that the combined effect of both soil microbial β-diversity and soil was significant (28% and 32% for bacteria and fungi, respectively). Pearson correlation analyses showed that plant species diversity and soil multifunctionality correlated significantly with soil microbial β-diversity. In contrast, the direct effect of plants was smaller (2% and 3% for bacteria and fungi, respectively). According to the dispersal–niche continuum index, stochastic processes were responsible for the assembly of the bacterial and fungal soil microbial communities. During restoration, the dominant influence of stochastic effects on the assembly of bacterial communities intensified. In contrast, the reverse tendency was observed in soil fungi. The investigation of the diversity pattern of soil microbial communities and their assembly can provide theoretical references for the restoration of degraded ecosystems.

Interplay of biotic and abiotic factors shapes tree seedling growth and root-associated microbial communities

Root-associated microbes can alleviate plant abiotic stresses, thus potentially supporting adaptation to a changing climate or to novel environments during range expansion. While climate change is extending plant species fundamental niches northward, the distribution and colonization of mutualists (e.g., arbuscular mycorrhizal fungi) and pathogens may constrain plant growth and regeneration. Yet, the degree to which biotic and abiotic factors impact plant performance and associated microbial communities at the edge of their distribution remains unclear. Here, we use root microscopy, coupled with amplicon sequencing, to study bacterial, fungal, and mycorrhizal root-associated microbial communities from sugar maple seedlings distributed across two temperate-to-boreal elevational gradients in southern Québec, Canada. Our findings demonstrate that soil pH, soil Ca, and distance to sugar maple trees are key drivers of root-associated microbial communities, overshadowing the influence of elevation. Interestingly, changes in root fungal community composition mediate an indirect effect of soil pH on seedling growth, a pattern consistent at both sites. Overall, our findings highlight a complex role of biotic and abiotic factors in shaping tree-microbe interactions, which are in turn correlated with seedling growth. These findings have important ramifications for tree range expansion in response to shifting climatic niches.

Effect of Bacillus amyloliquefaciens QST713 on Inter-Root Substrate Environment of Cucumber under Low-Calcium Stress

(1) Background: Low-calcium stress can have adverse effects on the rhizosphere environment of cucumber, subsequently impacting cucumber growth. However, plant-growth-promoting rhizobacteria can directly or indirectly enhance plant growth and induce plant tolerance, thereby mitigating the detrimental effects of low-calcium stress on cucumber growth. This study aims to elucidate the role of Bacillus amyloliquefaciens QST713 in the rhizosphere environment of cucumber under low-calcium stress, providing a theoretical basis for the application and promotion of Bacillus amyloliquefaciens. (2) Methods: This study used the ‘JinYou NO.4′ cucumber variety as test material, setting four treatments of CK, CK+Q, LCa, LCa+Q. We conducted measurements of plant height and stem diameter for four groups of cucumber plants: before treatment (0 d), and at 10 d, 20 d, 30 d, and 60 d after treatment. Additionally, we determined the biomass of cucumber plants under different treatments during the peak fruiting period. Inter-root matrix samples of cucumber were collected during the fruiting late period, and the physical and chemical properties and nutrient contents of the inter-root matrix of cucumber were determined, and bacterial microbial diversity and bacterial microbial communities were analysed using Illumina-MiSeq high-throughput sequencing technology. (3) Results: Low-calcium stress significantly inhibits the growth of cucumber plants. However, the application of Bacillus amyloliquefaciens QST713 effectively mitigates the inhibitory effects of low-calcium stress on cucumber growth. The application of Bacillus amyloliquefaciens QST713 was able to improve the physicochemical environment of the matrix and enhanced the absorption and utilisation of matrix nutrients in cucumber. The high-throughput sequencing analysis showed that the richness and diversity of bacterial communities and the number of bacteria decreased significantly under low-calcium stress, and increased significantly after the application of Bacillus amyloliquefaciens QST713. The composition of the dominant bacterial groups of the inter-root matrix of cucumber was basically the same among the four treatments, and the main difference was in the abundance of bacteria. The application of Bacillus amyloliquefaciens QST713 increased the relative abundance of bacteria that decreased under low-calcium stress, and decreased the relative abundance of bacteria that increased under low-calcium stress. (4) Conclusions: The results of this study elucidated the positive effects of Bacillus amyloliquefaciens QST713 on the growth and inter-root environment of cucumber under low-calcium stress, and provided a theoretical basis for in-depth research on the resistance of Bacillus amyloliquefaciens and its popularised application.

An inquiline mosquito modulates microbial diversity and function in an aquatic microecosystem.

Understanding microbial roles in ecosystem function requires integrating microscopic processes into food webs. The carnivorous pitcher plant, Sarracenia purpurea, offers a tractable study system where diverse food webs of macroinvertebrates and microbes facilitate digestion of captured insect prey, releasing nutrients supporting the food web and host plant. However, how interactions between these macroinvertebrate and microbial communities contribute to ecosystem functions remains unclear. We examined the role of the pitcher plant mosquito, Wyeomyia smithii, in top-down control of the composition and function of pitcher plant microbial communities. Mosquito larval abundance was enriched or depleted across a natural population of S. purpurea pitchers over a 74-day field experiment. Bacterial community composition and microbial community function were characterized by 16S rRNA amplicon sequencing and profiling of carbon substrate use, bulk metabolic rate, hydrolytic enzyme activity, and macronutrient pools. Bacterial communities changed from pitcher opening to maturation, but larvae exerted minor effects on high-level taxonomic composition. Higher larval abundance was associated with lower diversity communities with distinct functions and elevated nitrogen availability. Treatment-independent clustering also supported roles for larvae in curating pitcher microbial communities through shifts in community diversity and function. These results demonstrate top-down control of microbial functions in an aquatic microecosystem.

Nitrogen Removal Mechanism and Microbial Community Changes of the MBR Bioaugmented with Two Novel Fungi Pichia kudriavzevii N7 and Candida tropicalis N9

Ammonia nitrogen wastewater causes dissolved oxygen concentrations to decrease and the content of harmful substances to increase. To characterize the application properties of two novel strains of highly efficient ammonium transforming fungi—Pichia kudriavzevii N7 and Candida tropicalis N9—this study used both as compound microbial agents to treat nitrogenous wastewater. Here, we investigated the bioaugmentation effect of compound fungi N7 and N9 in the MBR bioreactor and the effect of N7 and N9 on the fungal and bacterial microbial communities in the system. The results revealed that in the first week after inoculation of N7 and N9, the average removal rate of ammonium in the experimental and control groups were 89.43% and 82.86%, respectively, and the NO3−-N accumulation concentrations were 12.56 mg·L−1 and 17.73 mg·L−1, respectively. The average transformation rate of total nitrogen in the experimental and control groups were 46.32% and 30.6%, respectively. ITS sequencing results indicated that N9 could be a dominant fungus in the complex MBR system. The results of 16S rRNA sequencing showed that the dominant bacterial communities in the system were changed by the inoculation of compound fungi. Therefore, the compound fungi can be applied to strengthen the treatment of nitrogenous wastewater due to its compatibility.

Vitamin D and prebiotics for intestinal health in cystic fibrosis: Rationale and design for a randomized, placebo-controlled, double-blind, 2 x 2 trial of administration of prebiotics and cholecalciferol (vitamin D3) (Pre-D trial) in adults with cystic fibrosis

Individuals with cystic fibrosis (CF) have dysfunctional intestinal microbiota and increased gastrointestinal (GI) inflammation also known as GI dysbiosis. It is hypothesized that administration of high-dose cholecalciferol (vitamin D3) together with a prebiotic (inulin) will be effective, and possibly additive or synergistic, in reducing CF-related GI and airway dysbiosis. Thus, a 2 x 2 factorial design, placebo-controlled, double-blinded, pilot and feasibility, clinical trial was proposed to test this hypothesis. Forty adult participants with CF were block-randomized into one of four groups: 1) high-dose oral vitamin D3 (50,000 IU weekly) plus oral prebiotic placebo daily; 2) oral prebiotic (12 g inulin daily) plus oral placebo vitamin D3 weekly; 3) combined oral vitamin D3 weekly and oral prebiotic inulin daily; and 4) oral vitamin D3 placebo weekly and oral prebiotic placebo. The primary endpoints included 12-week changes in the microbial bacterial communities, gut and airway microbiota richness and diversity before and after the intervention. This pilot study examined whether vitamin D3 with or without prebiotics supplementation was feasible, changed airway and gut microbiota, and reduced dysbiosis, which in turn, may improve health outcomes and quality of life of patients with CF.

Effect of long-term in-row branch covering on soil microorganisms in pear orchards.

Branches covering (BC) is a way to reuse the pruned branches and save the cost of ground cloth. This study investigated the effects of BC and ground-cloth covering on the soil microcosm environment by measuring the chemical properties and microbial communities at different soil depths for 6 years. The results revealed that BC significantly improved soil chemical properties, increased the abundance of bacterial microbial communities and the diversity and homogeneity of bacteria and fungi, while decreased the abundance of fungal microbial communities. There was a threshold value for the regulation of microbial communities by BC, which decreased the high-abundance communities (Proteobacteria, Ascomycota, etc.) and increased the low-abundance communities (Acidobacteriota, Basidiomycota, etc.). Fungi were more sensitive to BC than bacteria. The stability and homogeneity of microorganisms were stronger in the 15-25 cm soil layer. The bacterial phyla were dominated by Proteobacteria, with the top 10 phyla accounting for more than 80% of the relative abundance; the genera were dominated by MND1, with the top 10 genera accounting for about 10%. The fungal phyla were dominated by Ascomycota, with the top 10 phyla accounting for 50-90%; the genera were dominated by unidentified Pyronemataceae sp., with the top 10 genera accounting for 30-60%. The phyla that differed significantly between treatments were mainly Proteobacteria, Ascomycota, Acidobacteriota, and Basidiomycota. In addition, metabolism was the predominant function in bacteria, while Saprotroph was the predominant function in fungi. Bacteroidota correlated strongly with soil chemical properties and bacterial functions, while Chytridiomycota correlated strongly with soil chemical properties and Pathogen-Saprotroph-Symbiotroph. In conclusion, BC can improve soil nutrient content and optimize microbial community structure and function. Through initially assessing the effects of BC on soil nutrients and microorganisms in pear orchard rows, this study provides a reference for excavating key microorganisms and updating the soil row management model.

Potential of novel zinc-based nanomaterials on the microbial community, antibiotic resistance genes, and DNA replication in animal manure

The existence of Antibiotic Resistance Genes (ARGs) in diverse everyday environments, such as animal agriculture, natural surroundings, and waste products, presents potential threats to both human health and food safety. Herein, metagenomic sequencing technique was employed to investigate the impact of two zinc-based nanoparticles, Graphene Oxide-modified Zinc Oxide (GOnZnO) and Microorganism-mediated Zinc Oxide (Micro-ZnO), on the microbial community, ARGs, and DNA replication. The results showed that both GOnZnO and Micro-ZnO significantly reduced zinc levels in animal manure when compared to the control group of nano zinc oxide (nZnO). The order of ARGs copy numbers was nZnO > GOnZnO > Micro-ZnO, with a significant difference between the GOnZnO and Micro-ZnO groups. Additionally, the expression levels of various DNA replication genes, including DNA polymerase III holoenzyme, dnaB, dnaG, RNeseH, polA, and Lig, were significantly lower in the GOnZnO group compared to the nZnO group. The Micro-ZnO group exhibited even lower expression levels of these genes compared to the GOnZnO group. In contrast, GOnZnO and Micro-ZnO had no significant impact on archaeal DNA replication pathway-related genes. Specifically, the expression of RNASEH1 was significantly higher in the Micro-ZnO group compared to the GOnZnO and nZnO groups. Co-occurrence network analysis revealed changes in ARGs driven by bacterial and eukaryotic DNA replication and microbial community dynamics. However, there was no correlation observed between ARGs and archaeal DNA replication genes. Overall, these findings add to the existing literature regarding the application of GOnZnO and Micro-ZnO as potential agents for reducing ARGs pollution.

Phosphorus fertiliser application mitigates the negative effects of microplastic on soil microbes and rice growth

Soil microplastics (MPs) have attracted widespread attention recently. Most studies have explored how soil MPs affect the soil's physicochemical parameters, matter circulation, and soil microbial community assembly. Similarly, a key concern in agricultural development has been the use of phosphorus (P) fertiliser, which is essential for plant health and development. However, the relationship between MPs and phosphate fertilisers and their effects on the soil environment and plant growth remains elusive. This study assessed the influence of adding low-density polyethylene MPs (1%) with different phosphate fertiliser application rates on microbial communities and rice biomass. Our results showed that MPs changed the structure of soil bacterial and phoD-harbouring microbial communities in the treatment with P fertiliser at the same level and suppressed the interactions of phoD-harbouring microorganisms. In addition, we found that MPs contamination inhibited rice growth; however, the inclusion of P fertiliser in MP-contaminated soils reduced the inhibitory action of MPs on rice growth, probably because the presence with P fertiliser promoted the uptake of NO3--N by rice in MP-contaminated soils. Our results provide further insights into guiding agricultural production, improving agricultural management, and rationally applying phosphate fertilisers in the context of widespread MPs pollution and global P resource constraints.

Effects of Nitrogen Fertilizer on Nitrospira- and Nitrobacter-like Nitrite-Oxidizing Bacterial Microbial Communities under Mulched Fertigation System in Semi-Arid Area of Northeast China

The accumulation of nitrite is frequently overlooked, despite the fact that nitrification is the most essential phase of the entire nitrogen (N) cycle and that nitrifying bacteria play a significant role in nitrification. At present, the effects of different N application rates on soil nitrite-oxidizing bacteria (NOB) abundance, community composition, diversity, and its main influencing factors are still unclear. In this study, five N fertilizer application rates under film mulching and a drip irrigation system were studied in the semi-arid area of Northeast China. The treatments were 0 kg ha−1 (N0), 90 kg ha−1 (N1), 150 kg ha−1 (N2), 210 kg ha−1 (N3), and 270 kg ha−1 (N4). Fluorescent quantitative PCR and Illumina Miseq sequencing were used to analyze the abundance and community structure of NOB under different amounts of N application. The results showed that the increase in amounts of N application was strongly accompanied by an increase in the content of soil organic matter (SOM), total nitrogen (TN), nitrate nitrogen (NO3−-N), and ammonium nitrogen (NH4+-N), while the pH significantly reduced with an increase in N fertilization. N fertilization significantly increased soil nitrite oxidoreductase (NXR) activity, soil nitrification potential (PNR), and soil nitrite oxidation potential (PNO). A high N application rate significantly heightened the abundance of Nitrospira- and Nitrobacter-like NOB. N fertilizer considerably raised the Shannon index of Nitrospira-like NOB. The N application amount was the key factor affecting the community structure of Nitrospira-like NOB, and available nitrogen (AN) had the dominant influence on the community structure of Nitrospira-like NOB. N fertilizer can cause soil acidification, which affects NOB abundance and diversity. Nitrospira-like NOB may promote nitrite oxidation in different N application rates under a mulched fertigation system. The findings offered a crucial scientific foundation for further investigation into how nitrite-oxidizing bacteria respond to N fertilizer management strategies in farmland soil under film mulching drip irrigation in Northeast China.

Microbial Community Shifts with Soil Properties and Enzyme Activities in Inter-/Mono-Cropping Systems in Response to Tillage

No-till and cereal–legume intercropping have been recognized as favorable cropping practices to increase crop yields while maintaining soil quality in arid and semiarid environments, but the biological mechanisms are poorly understood. The present study aimed to determine the response of yields, soil properties, enzyme activities, and microbial community diversity and composition in mono- and inter-cropping under conventional and no-tillage conditions. We initiated a field experiment in Wuwei, a typical arid area of China, in 2014. Soil was sampled in August 2022 and, yields, soil properties, enzyme activities, and the microbial community diversity and composition were determined in the maize and pea strips in inter- and mono-cropping systems. Results revealed that the maize and pea strips in the no-till intercropping significantly increased yields, total and organic carbon stocks, decreased NO3−-N, and obtained the highest total and organic P in the soil. No-tillage significantly enhanced the Shannon index and Pielou evenness of the bacterial community and total microbial community over conventional tillage, with the α-diversity of the bacterial community and total microbial community distinctly higher in the NTIM treatment than in the CTIM treatment. The α-diversity of the total microbial community was significantly related to yield, soil IC and OC, and the α-diversity of the archaea community was significantly related to soil TC, TC/TP, TN/TP, and BX. Meanwhile, the α-diversity of the eukaryote community was significantly related to soil yield, soil TC/TP. Both no-tillage and intercropped maize significantly increased the abundance of archaea phylum Thaumarchaeota and bacterial phylum Nitrospirae, and were significantly positively associated with soil OC and NH4+-N, benefiting nitrogen fixation of intercropped pea from the atmosphere under the no-tillage cereal/legume intercropping. No-till intercropping was conducive to the accumulation of organic carbon, while decreasing the abundance of Proteobacteria, Acidobacteria, and Verrucomicrobia. Limited soil enzyme activities (ACP, ALP, DP, NAG, BG, AG, CB) led to decreases in organic carbon turnover and utilization. Intercropping altered soil microbial community diversity and composition due to changes in soil properties and enzyme activities. These findings suggest that no-tilled cereal–legume intercropping is a sustainable cropping practice for improving soil properties and enhancing microbial (archaea, bacterial, eukaryota) diversity, but the persistence is not conducive to rapid turnover of soil nutrients due to limited enzyme activities.

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.

Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.

Comprehensive insight into synergistic enhancement of nickel and iron doped lanthanum manganese oxide for biohydrogen production via anaerobic fermentation

Anaerobic fermentation offers an effective strategy to produce H2 from organic wastes, which facilitates waste utilization and the development of sustainable energy. However, the low hydrogen yield and instability of fermentation systems block the further industrial and commercial application. In this work, nickel and iron doped lanthanum manganese oxide nanoparticles (NPs) are successfully fabricated for researching their effects on H2 production and process stability. The advantages of lanthanum manganese oxides doped by nickel and iron in terms of bacterial activity and microbial community structures are studied in a fermentation system. The physicochemical properties of LaMn0.7Fe0.3O3 NPs and LaMn0.7Ni0.3O3 NPs are summarized and analyzed. The results show that the moderate addition of nanoparticles can both effectively increase the final H2 yield and stabilize the fermentation process simultaneously. The highest H2 yield of 223.08 mL/g and 246.10 mL/g correspond to 100 mg/L supplementation of LaMn0.7Fe0.3O3 NPs and LaMn0.7Ni0.3O3 NPs, respectively, which confirms that the LaMn0.7Ni0.3O3 NPs exhibit a more positive impact on anaerobic fermentation, while excess dosage nanoparticles (over 100 mg/L) may hamper the H2 production and inhibit the electron transfer to microbe. The underlying mechanism analysis reveals that Fe3+ and Ni2+ significantly improve the microbial transmembrane transportation and conversion rate of glucose into acetate, butyrate and H2 through stimulating the activity of related enzymes, leading to an enhanced H2 productivity. Meanwhile, Ni2+ and Fe3+ are helpful to the synthesis of ferredoxin and hydrogenase, which increase the activity of critical enzymes. The microbial community discloses that LaMn0.7Fe0.3O3 NPs and LaMn0.7Ni0.3O3 NPs separately make a 7.71%, 9.65% increase of Clostridium_sensu_stricto_1 compared to the control group, which is deeply involved in the sustainable H2 generation. Based on comprehensive evaluation, LaMn0.7Ni0.3O3 NPs will have a huge potential market for H2 production enhancement in anaerobic fermentation system.

Tetracycline inhibits tick host reproduction by modulating bacterial microbiota, gene expression and metabolism levels.

Ticks are disease vectors that are a matter of worldwide concern. Antibiotic treatments have been used to explore the interactions between ticks and their symbiotic microorganisms. In addition to altering the host microbial community, antibiotics can have toxic effects on the host. In the tick Haemaphysalis longicornis, engorged females showed reproductive disruption after microinjection of tetracycline. Multi-omics approaches were implemented to unravel the mechanisms of tick reproductive inhibition in this study. There were no significant changes in bacterial density in the whole ticks on Day (D)2 or D4 after tetracycline treatment, whereas the bacterial microbial community was significantly altered, especially on D4. The relative abundances of the bacteria Staphylococcus, Bacillus and Pseudomonas decreased after tetracycline treatment, whereas the relative abundances of Coxiella and Rhodococcus increased. Ovarian transcriptional analysis revealed a cumulative effect of tetracycline treatment, as there was a significant increase in the number of differentially expressed genes with treatment time and a higher number of downregulated genes. The tick physiological pathways including lysosome, extracellular matrix (ECM)-receptor interaction, biosynthesis of ubiquinone and other terpenoids-quinones, insect hormone biosynthesis, and focal adhesion were significantly inhibited after 4 days of tetracycline treatment. Metabolite levels were altered after tetracycline treatment and the differences increased with treatment time. The differential metabolites were involved in a variety of physiological pathways; the downregulated metabolites were significantly enriched in the nicotinate and nicotinamide metabolism, galactose metabolism, and ether lipid metabolism pathways. These findings indicate that tetracycline inhibits tick reproduction through the regulation of tick bacterial communities, gene expression and metabolic levels. The results may provide new strategies for tick control. © 2023 Society of Chemical Industry.

Effects of Water Control and Nitrogen Addition on Functional Traits and Rhizosphere Microbial Community Diversity of Haloxylon ammodendron Seedlings

Water and nitrogen sources have always been the primary limiting factors for vegetation growth in arid and semi-arid regions and play an important role in the physiological ecology of vegetation. In this work, we studied the effects of water deficit and nitrogen addition on the physiological traits and rhizosphere bacterial microbial community of Haloxylon ammodendron seedlings in sterilized and non-sterilized soil habitats. A pot experiment was conducted to control the water and nitrogen sources of H. ammodendron seedlings. The water deficit treatment was divided into two groups based on gradient: a normal water group (CK, 70% field water holding capacity) and water deficit group (D, 30% field water holding capacity). The nitrogen addition treatment was divided into a no addition group (CK, 2.8 mg·kg−1) and addition group (N, 22.4 mg·kg−1). At the end of the growing season, the biochemical indexes of H. ammodendron seedlings were measured, and the rhizosphere soil was subjected to 16S rDNA-high-throughput sequencing to determine the rhizosphere bacterial community composition of H. ammodendron seedlings under different treatments. The results showed that the root-to-crown ratio of H. ammodendron seedlings increased significantly (p &lt; 0.05) under the water deficit treatment compared to the control and nitrogen addition treatments, indicating that H. ammodendron seedlings preferred to allocate biological carbon to the lower part of the ground. In contrast, plant height and root length were significantly lower (p &lt; 0.05) under water deficit treatment compared to the control, and no significant change was observed under water deficit and nitrogen addition compared to the control, indicating that water deficit inhibited the growth of H. ammodendron seedlings and nitrogen addition mitigated the effect of water deficit on the growth of H. ammodendron seedlings. Under sterilized soil conditions, both water deficit and nitrogen addition significantly increased the abundance and diversity of bacterial communities in H. ammodendron seedlings (p &lt; 0.05). Conversely, under non-sterilized conditions, both inhibited the diversity of microbial bacterial communities, and the microbial characteristic species under different controls were different. Therefore, in the short-term experiment, H. ammodendron seedlings were affected by water deficit and allocated greater quantities of biomass to the underground part, especially in the non-sterile microbial environment; different initial soil conditions resulted in divergent responses of rhizosphere bacterial communities to water deficit and nitrogen addition. Under different initial soil conditions, the same water deficit and nitrogen addition treatment will lead to the development of distinct differences in rhizosphere bacterial community composition.