Bacterial Community Richness Research Articles

What shapes a microbiome? Differences in bacterial communities associated with helminth-amphipod interactions

The fast technological advances of molecular tools have enabled us to uncover a new dimension hidden within parasites and their hosts: their microbiomes. Increasingly, parasitologists characterise host microbiome changes in the face of parasitic infections, revealing the potential of these microscopic fast-evolving entities to influence host-parasite interactions. However, most of the changes in host microbiomes seem to depend on the host and parasite species in question. Furthermore, we should understand the relative role of parasitic infections as microbiome modulators when compared with other microbiome-impacting factors (e.g., host size, age, sex). Here, we characterised the microbiome of a single intermediate host species infected by two parasites belonging to different phyla: the acanthocephalan Plagiorhynchus allisonae and a dilepidid cestode, both infecting Transorchestia serrulata amphipods collected simultaneously from the same locality. We used the v4 hypervariable region of the 16S rRNA prokaryotic gene to identify the hemolymph bacterial community of uninfected, acanthocephalan-infected, and cestode-infected amphipods, as well as the bacteria in the amphipods’ immediate environment and in the parasites infecting them. Our results show that parasitic infections were more strongly associated with differences in host bacterial community richness than amphipod size, presence of amphipod eggs in female amphipods, and even parasite load. Amphipods infected by acanthocephalans had the most divergent bacterial community, with a marked decrease in alpha diversity compared with cestode-infected and uninfected hosts. In accordance with the species-specific nature of microbiome changes in parasitic infections, we found unique microbial taxa associating with hosts infected by each parasite species, as well as taxa only shared between a parasite species and their infected hosts. However, there were some bacterial taxa detected in all parasitised amphipods (regardless of the parasite species), but not in uninfected amphipods or the environment. We propose that shared bacteria associated with all hosts parasitised by distantly related helminths may be important either in helping host defences or parasites’ success, and could thus interact with host-parasite evolution.

Improving the value of planting and breeding waste compost in agricultural applications: A zucchini cultivation case and circular agricultural models analysis

An important way of utilizing agricultural wastes to improve soil quality is the use of planting and breeding waste compost (PBWC). However, the impact of compost on agricultural production systems is unclear. Therefore, in order to study the effect of PBWC on crop growth, soil environment, and circular agriculture, PBWC [sheep manure (SM): tail vegetable (TV): corn straw (CS) = 6: 3: 1] was used based on chemical fertilizer reduction for zucchini production. In zucchini production systems, R9 (chemical fertilizer reduction by 30 % + 9,000 kg ha−1 PBWC) treatment was most effective in improving the quality and yield of zucchini fruits, mainly by improving the soil microenvironment, manifested in (1) increasing soil alkali-hydrolyzable nitrogen (AN) available potassium(AK), and soil organic matter (SOM), reducing EC, and improving C/N. (2) Increasing the richness and metabolic capacity of bacterial community. (3) Increasing the abundance of Proteobacteria, a phylum with absolute dominance (up to 32.46 %). Then, an optimization model of “summer corn − greenhouse zucchini − fattened sheep” was constructed to analyze the effect of changes in fertilizer dosage usage on the whole model. Compared with the local traditional recycling model, the optimized system reduced the ratio of inorganic to organic nitrogen input from 2.8:1 to 1.4:1, increased the recycling rate of nitrogen (N), phosphorus (P), and potassium (K) by 31.28 %, 50.84 %, and 30.25 %, respectively, and the net energy yield ratio (EYR) increased by 1.04. The optimized recycling system had significant economic and environmental benefits, which would become the basis for moving towards more sustainable farming. Overall, the circular agriculture model with PBWC returning as the core achieves sustainable production by improving material recycling and soil microenvironment. Therefore, chemical fertilizer reduction by 30 % combined with 9000 kg ha−1 PBWC can be used in practical production to improve the productivity of the circular agriculture model and achieve high yield and high quality crops.

High dosage of exogenous glycine in cross-feeding breaks the equilibrium of anammox system

Strategies to break the cross-feeding equilibrium by dosing essential metabolites and thus enriching and isolating anammox bacteria (AnAOB) have been proposed, but amino acids have not been investigated as important cross-feeding pathways in anammox consortia. In this study, long-term experiments were designed to verify the effect of exgenous glycine on anammox consortia and changes in the bacterial community and metabolic activity after the addition of glycine in a highly active anammox system were investigated. The results showed that the impact of glycine on the activity of anammox highly depended on glycine concentrations, which was manifested as a promotive effect at low concentrations (0–150 mg/L) and an inhibitory effect at high concentrations (300–600 mg/L). The addition of low concentrations of glycine not only enhanced the diversity and richness of bacterial communities but also promoted the enrichment of Candidatus Kuenenia. The qPCR results showed that the content of functional genes Hzs, NirS and anammox 16S rRNA increased while the expression of amoA and NrfA genes was suppressed when glycine acted positively on AnAOB; Hzs and amoA were suppressed when glycine acted negatively on AnAOB, while the expression of NirS and NrfA genes increased dramatically. Specific anammox activity (SAA) experimental results show that 50–150 mg/L glycine was the optimal amount for promoting the activity of AnAOB. Analysis of community metabolic functions indicated that the addition of exogenous glycine resulted in a imbalance of glycine cross-feeding and promoted AnAOB enrichment mainly by affecting pathways such as other glycan degradation and Lysosome. Overall, this study provided new insights into understanding the glycine cross-feeding, which is essential for improving anammox-based technologies.

Shift in Bacterial Community Structure in the Biodegradation of Benzene and Toluene under Sulfate-Reducing Condition.

Groundwater contaminated by benzene and toluene is a common issue, posing a threat to the ecosystems and human health. The removal of benzene and toluene under sulfate-reducing condition is well known, but how the bacterial community shifts during this process remains unclear. This study aims to evaluate the shift in bacterial community structure during the biodegradation of benzene and toluene under sulfate-reducing condition. In this study, groundwater contaminated with benzene and toluene were collected from the field and used to construct three artificial samples: Control (benzene 50 mg/L, toluene 1.24 mg/L, sulfate 470 mg/L, and HgCl2 250 mg/L), S1 (benzene 50 mg/L, toluene 1.24 mg/L, sulfate 470 mg/L), and S2 (benzene 100 mg/L, toluene 2.5 mg/L, sulfate 940 mg/L). The contaminants (benzene and toluene), geochemical parameters (sulfate, ORP, and pH), and bacterial community structure in the artificial samples were monitored over time. By the end of this study (day 90), approximately 99% of benzene and 96% of toluene could be eliminated in both S1 and S2 artificial samples, while in the Control artificial sample the contaminant levels remained unchanged due to microbial inactivation. The richness of bacterial communities initially decreased but subsequently increased over time in both S1 and S2 artificial samples. Under sulfate-reducing condition, key players in benzene and toluene degradation were identified as Pseudomonas, Janthinobacterium, Novosphingobium, Staphylococcus, and Bradyrhizobium. The results could provide scientific basis for remediation and risk management strategies at the benzene and toluene contaminated sites.

High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China

The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3− accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.

Variations in different preceding crops on the soil environment, bacterial community richness and diversity of tobacco-planting soil.

Tobacco (Nicotiana tabacum L.) is a major cash crop, and soil quality played a significant role in the yield and quality of tobacco. Most farmers cultivate tobacco in rotation with other crops to improve the soil characteristics. However, the effects of different previous crops on the soil's nutrient status and bacterial community for tobacco cultivation still need to be determined. Three treatments were assessed in this study, i.e., tobacco-planting soil without treatment (CK), soil with barley previously cultivated (T1), and soil with rapeseed previously cultivated (T2). The soil physical and chemical properties and the 16S rRNA gene sequence diversity of the bacterial community were analyzed. The effects of different crops on the physical and chemical properties of tobacco-planting soil and the diversity and richness of the bacterial community were comprehensively discussed. The results of this study showed that different previously cultivated crops altered the nutrient status of the soil, with changes in the ratio of NH4 +-N to NO3 --N having the most significant impact on tobacco. In CK, the ratio of NH4 +-N to NO3 --N was 1:24.2, T1-1:9.59, and T2-1:11.10. The composition of the bacterial community in tobacco-planting soil varied significantly depending on the previously cultivated crops. The richness and diversity of the bacterial community with different crops were considerably higher than without prior cultivation of different crops. The dominant bacteria in different treatments were Actinobacteriota, Proteobacteria, and Chloroflexi with their relative abundance differed. In conclusion, our study revealed significant differences in nutrient status, bacterial community diversity, and the richness of tobacco-planting soil after the preceding cultivation of different crops. Suitable crops should be selected to be previously cultivated in tobacco crop rotations in near future for sustainable agriculture.

Amino-functionalized graphene oxide affects bacteria–phage interactions in aquatic environments

The widespread use of graphene family nanomaterials (GFNs) in mass production has resulted in their release into the atmosphere, soil and water environment through various processes. Among these, the water environment is particularly affected by GFN pollution. Our previous study has demonstrated the impact of graphene oxide (GO) on bacteria–phage interactions in natural systems. However, the effects of amino-functionalized GO with a positive charge on bacteria–phage interactions in aquatic environments remain unclear. In the present study, we found that amino-functionalized graphene oxide (AGO) (0.05 mg/mL) inhibited the growth of Pseudomonas aeruginosa Y12. Furthermore, treating P. aeruginosa Y12 and phage with AGO (0.05 mg/mL) led to a reduced ratio of phage to bacteria, indicating that AGO can inhibit phage infection of bacteria. Additionally, the acidic environment exacerbated this effect by promoting electrostatic adsorption between the positively charged AGO and the negatively charged phage. Finally, a field water body intervention experiment showed that the richness and diversity of bacterial communities in six water samples changed due to AGO exposure, as revealed by Illumina analysis based on the bacterial 16S rRNA gene. These findings offer valuable insights into the environmental impacts of GFNs.

Temporal Variation and Phylogeny of Air and Surface Microflora in Relation to Occupancy Patterns in a Higher Education Institution (HEI)

People not only inhale life-sustaining oxygen but also traces of bacteria and even inanimate surfaces introduce microorganisms to one’s bodies. However, the diversity and richness of bacterial communities both indoor and outdoor in a Philippine HEI in relation to human occupancy patterns remain relatively unexplored. Hence, the study aimed to bridge this gap. Microflora were collected using settle plates and swabbing method and identified by comparing their 16s rRNA gene amplicons using the Basic Local Alignment Tool. Several isolates were found to have biological implications in health (e.g. Staphylococcus haemolyticus and Bacillus clarus) and biotechnology (e.g. Rhodococcus pyridinivorans and Bacillus altitudinis). The phylogeny of samples exhibited close cohesion from the genus level, hence forming monophyletic taxa – under the classes Bacilli, Gammaproteobacteria, and Actinomycetes. Furthermore, statistical results established the significant relationship between indoor air and outdoor surface microbial load with the volume of occupants, as opposed to outdoor air and indoor surfaces. The analysis also revealed a strong correlation between the volume of occupants and indoor air microbial concentration (p = 0.002, R = 0.998), likewise in the case of indoor and outdoor surface bacterial contamination (p = 0.036, R = 0.664). Additionally, there was a significant difference in the indoor and outdoor air microbial load following human occupancy patterns in the area (p = 0.018). Findings of the study provide a foundation for understanding air and surface-borne flora, as well as a basis for the enhancement of health and safety standards for building inhabitants.

Commensal bacteria in raw milk, the reservoirs for antibiotic resistance genes during cold chain transportation

The emergence and prevalence of antibiotic resistance genes (ARGs) in food pose a great threat to public health and have attracted globally attention. Shotgun metagenomics sequencing is widely used to characterize ARGs in the environment. However, the distribution, co-occurrence patterns, and host information of ARGs in raw milk to the cold chain transportation duration with shotgun metagenomics sequencing, are not fully understood in China. In this study, species annotation and ARG annotation were performed on 40 raw milk samples collected from Beijing (BJ), Hebei (HB), Inner Mongolia (NMG), Shanghai (SH), and Guangdong (GD) using shotgun sequencing based on the Illumina platform. A total of 4731 bacterial species were annotated, of which 37 were dominant (relative abundance >1%). And also, 259 ARGs were annotated, corresponding to 69 kinds of antibiotic resistance. The NMG samples, which had the lowest bacterial community richness and bacterial diversity, were annotated with the highest number of ARGs, revealing the potential risk of bacterial resistance in NMG samples. Spearman correlation analysis and network analysis were showed that the probable bacterial hosts of multiple highly abundant ARGs (MacB and VanRC) in samples from provinces except for the BJ samples were Pseudomonas and Serratia, rather than conventionally known foodborne pathogens. It is noteworthy that the relative abundance of Pseudomonas fluorescens conformed to the Allometricl function with the cold chain transportation duration, the finding that could provide a reference for assessing the freshness and the risk assessment of antibiotic resistance genes of raw milk. In addition, the dairy industry should be aware of the risk of ARGs transferring from highly abundant commensal bacteria. Raw milk for transportation by cold chain, higher abundance of Pseudomonas in some samples should be kept in mind, and the roles of ARGs carried by these bacteria should be further investigated.

Diversity of Bacterial Communities in Sediment in Inland Water Bodies in Relation to Environmental Factors and Human Impacts: A Case Study on Typical Regions in Vietnam

Environmental changes and human impact can alter biodiversity in negative manners that affect mankind’s sustainable development. Particularly, such effects on inland waters are even more concerning, as those ecosystems play essential roles in sustaining human life as well as relevant wildlife. Thus, in this study, we investigated such effects on microbial diversity in inland waters in Vietnam using bacterial communities in sediment as indicators. To do this, we collected sediment samples from various locations in three respective regions (Red river in the north, Ba river in the central area, and Mekong delta flood zone in the south) using standard methods, extracted their total DNA, sequenced their V3-V4 16S rRNA gene fragments using an Illumina Miseq platform and analyzed the sequences to infer the diversity of the bacterial communities in the samples. These communities were compared in terms of richness (alpha diversity) and composition (beta diversity), and the correlations between their diversity levels and environmental factors, as well as human activities, were analyzed by using standard statistical tools. Our results showed that the communities were different from each other solely by region, in richness and critically in composition, although there were some communities distinctively different from all the others. Among environmental factors, only water salinity (and conductivity) had negative correlations with alpha-diversity indices of the bacterial communities, and phosphate concentration and turbidity had positive correlations, while the other factors had almost no correlations, which partially explains the region-specific diversity. These results also suggest that climate change incidences, especially sea intrusion, can have significant effects on microbial diversity in inland waters. The impact of human activities did not appear severe, solely affecting bacterial community richness, but not significantly affecting bacterial community composition. However, apparently reduced bacterial diversity in several sites with intense human impacts and distinct environmental conditions should be noted and deserve further investigation.

Exploring changes in microplastic-associated bacterial communities with time, location, and polymer type in Liusha Bay, China

Microplastics have become a widespread concern within marine environments and are particularly evident in aquaculture regions that are characterized by plastic accumulation. This study employed 16 S rDNA sequencing to investigate the dynamic succession of microbial communities colonizing polyvinyl chloride (PVC), polystyrene (PS), and polyamide (PA) microplastics in seawater, when subjected to varying exposure durations in the Liusha Bay aquaculture region. Results revealed that the composition of microplastics microbial communities varied remarkably across geographical locations and exposure times. With an increase in exposure duration, both the diversity and richness of bacterial communities colonizing microplastics significantly increased, microbial communities show adaptations to the plastisphere. The type of microplastics had a significant effect on the community structure characteristicsof bacteria attached to their surfaces, with inconsistent trends in the relative abundance of different genera on different substrates. Notably, microplastic surfaces harbored a significant abundance of hydrocarbon-degrading bacteria, exemplified by Erythrobacter. These findings underscore the potential of microplastics as unique microbial niches. Meanwhile, long-term exposure experiments also offer the possibility of screening for plastic-degrading bacteria. In addition, the presence of the pathogenic bacterium Vibrio was detected in all microplastic samples, implying that microplastics could serve as carriers for pathogenic dissemination. This underscores the urgency of addressing the risk posed by the proliferation of harmful bacteria on microplastic surfaces. Overall, this study enhances our understanding of microbial community dynamics on microplastics under diverse conditions. It contributes to the broader comprehension of plastisphere microbial ecosystems in the marine environment, thereby addressing critical environmental implications.

Effects of community ecological network construction on physicochemical, microbial, and quality characteristics of inoculated northeast sauerkraut: A new insight in food fermentation processes

The enhancement of the quality of northeast sauerkraut can be achieved by inoculation with lactic acid bacteria. However, a comprehensive ecological understanding of the intricate dynamic processes involved is currently lacking, which could yield valuable insights for regulating sauerkraut fermentation. This study compares spontaneously sauerkrauts with the sauerkrauts inoculated with autochthonous Lactiplantibacillus plantarum SC-MDJ and commercial L. plantarum, respectively. We examine their physicochemical properties, quality characteristics, bacterial community dynamics, and ecological network interactions. Inoculation with L. plantarum leads to reduced bacterial community richness and niche breadth, but an increase in robustness, interactions, and assembly processes. Notably, there appears to be a potential correlation between bacterial community structure and quality characteristics. Particularly, sauerkraut inoculated with L. plantarum SC-MDJ may produce a sourness more quickly, possibly attributed to the enhanced ecological role of L. plantarum SC-MDJ. This study establishes a foundation for the targeted regulation of sauerkraut fermentation.

Phyllosphere bacterial composition from Brassica oleracea and Raphanus sativus, the feeding food for Plutella xylostella

The diamondback moth (DBM) is involved in great amount of predominant gut bacterium Enterococcus mundtii. Radish seedlings and cabbage leaves are natural suitable foods to feed the pest in laboratory. Leaf microbiome could be reshaped by insect herbivory. In this study, phyllosphere bacterial composition on radish seedlings with and without DBM herbivory in the chamber, and on cabbage leaves in the field with no DBM herbivory were investigated by high-throughput sequencing technology. Results showed that Proteobacteria and Bacteroidota were two common predominant phyla for both radish seedlings and cabbage leaves, while Firmicutes was only detected in phyllosphere of radish seedlings. Pseudomonas was the only common shared phyllosphere genus; Alkanindiges and Delftia were the unique dominant bacterial genera in cabbage and in radish, respectively. More bacterial varieties and higher bacterial community diversity was also found in cabbages leaves than that of radish seedlings. The bacterial community diversity and richness in radish seedlings fed by DBM was higher than that of not fed. Gut bacterium Enterococcus was only found on radish seedlings leaves that fed by DBM, while neither in radish seedlings nor in cabbage leaves not fed by the pest. As one survey in origin of predominant gut bacterium Enterococcus from DBM, this study offers new insights into the phyllosphere bacterial composition and diversity from the feeding food of DBM in field cabbage leaves and in laboratory radish seedlings.

Soil bacterial community characteristics and its effect on organic carbon under different fertilization treatments.

By implementing small-scale and efficient fertilization techniques, it is possible to enhance the activity of microorganisms, thereby improving soil carbon sequestration and ecological value in agriculture. In this study, field experiments were conducted using various types of fertilizers: organic fertilizer, microbial fungal fertilizer, composite fertilizer, and an unfertilized control (CK). Additionally, different dosages of compound fertilizers were applied, including 0.5 times compound fertilizers, constant compound fertilizers, 1.5 times compound fertilizers and CK. Using advanced technologies such as Illumina MiSeq high-throughput sequencing, PICRUSt2 prediction, Anosim analysis, redundancy analysis, canonical correlation analysis, and correlation matrix, soil organic carbon (SOC) content and components, bacterial diversity, metabolic functions, and interaction mechanisms were examined in different fields. The results showed pronounced effects of various fertilization modes on SOC and the bacterial community, particularly in the topsoil layer (0-20 cm). Organic fertilizer treatments increased the richness and diversity of bacterial communities in the soil. However, conventional doses and excessive application of compound fertilizers reduced the diversity of soil bacterial communities and SOC content. Additionally, different fertilization treatments led to an increase in easily oxidizable organic carbon (EOC) contents. Interestingly, the relationship between SOC components and soil bacteria exhibited inconsistency. EOC was positively correlated with the bacterial diversity index. Additionally, Chloroflexi exhibited a negative correlation with both SOC and its components. The influence of metabolismon primary metabolic functions on the content of SOC components in the soil was more notable. It included seven types of tertiary functional metabolic pathways significantly correlated with SOC components (p < 0.05). These findings enhance the understanding of the relative abundance of bacterial communities, particularly those related to the carbon cycle, by adjusting agricultural fertilization patterns. This adjustment serves as a reference for enhancing carbon sinks and reducing emissions in agricultural soils.

Comparison of Rhizosphere Bacterial Communities of Pinus squamata, a Plant Species with Extremely Small Populations (PSESP) in Different Conservation Sites.

Pinus squamata is one of the most threatened conifer species in the world. It is endemic to northeastern Yunnan Province, China, and has been prioritized as a Plant Species with Extremely Small Populations (PSESP). The integrated study of soil properties and rhizosphere bacteria can assist conservation to understand the required conditions for the protection and survival of rare and endangered species. However, differences between the rhizospheric bacterial communities found in the soil surrounding P. squamata at different conservation sites remain unclear. In this study, Samples were collected from wild, ex situ, and reintroduced sites. Bacterial communities in different conservation sites of P. squamata rhizosphere soils were compared using Illumina sequencing. The soil physicochemical properties were determined, the relationships between the bacterial communities and soil physicochemical factors were analyzed, and the potential bacterial ecological functions were predicted. The reintroduced site Qiaojia (RQ) had the highest richness and diversity of bacterial community. Actinobacteria, Proteobacteria, and Acidobacteriota were the dominant phyla, and Bradyrhizobium, Mycobacterium, Acidothermus were the most abundant genera. Samples were scattered (R = 0.93, p = 0.001), indicating significant difference between the different conservation sites. The abundance of Mycobacterium differed between sites (0.01 < p ≤ 0.05), and the relative abundances of Bradyrhizobium and Acidothermus differed significantly among different sites (0.001 < p ≤ 0.01). Soil total potassium (TK) and available nitrogen (AN) were the main factors driving bacterial community at the phylum level (0.01 < p ≤ 0.05). This study generated the first insights into the diversity, compositions, and potential functions of bacterial communities associated with the rhizosphere soils of P. squamata in different conservation sites and provides a foundation to assess the effect of conservation based on bacterial diversity and plant growth-promoting rhizobacteria (PGPR) to guide future research into the conservation of P. squamata.

Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum

Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.

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.

Effects of cations on biofilms in gravity-driven membrane system: Filtration performance and mechanism investigation

The gravity-driven membrane (GDM) system is desirable for energy-efficient water treatment. However, little is known about the influence of cations on biofilm properties and GDM performance. In this study, typical cations (Ca2+ and Na+) were used to reveal the combined fouling behavior and mechanisms. Results showed that Ca2+ improved the stable flux and pollutant removal efficiency, while Na+ adversely affected the flux. Compared with GDM control, the concentration of pollutants was lower in Ca-GDM, as indicated by the low biomass, proteins, and polysaccharides. A heterogeneous and loose biofilm was observed in the Ca-GDM system, with roughness and porosity increasing by 43.06 % and 32.60 %, respectively. However, Na+ induced a homogeneous and dense biofilm, with porosity and roughness respectively reduced by 17.48 % and 22.04 %. The richness of bacterial communities increased in Ca-GDM systems, while it decreased in Na-GDM systems. High adenosine triphosphate (ATP) concentration in Ca-GDM system was consistent with the abundant bacteria and their high biological activity, which was helpful for the efficient removal of pollutants. The abundance of Apicomplexa, Platyhelminthes, Annelida and Nematoda increased after adding Ca2+, which was related to the formation of loose biofilms. Computational simulations indicated that the free volumes of the biofilms in Ca-GDM and Na-GDM were 13.7 and 13.2 nm3, respectively. The addition of cations changed intermolecular forces, Ca2+ induced bridging effects led to large and loose floc particles, while the significant dehydration of hydrated molecules in the Na-GDM caused obvious aggregation. Overall, microbiological characteristics and contaminant molecular interactions were the main reasons for differences in GDM systems.

Remediation of cadmium-contaminated soil by biochar-loaded nano-zero-valent iron and its microbial community responses

At present, cadmium (Cd)-contaminated soil has been increasingly serious, which is adverse to soil health. In this study, biochar (BC) and biochar-loaded nanoscale zero-valent iron (nZVI@BC) were synthesized for remediation of Cd-contaminated soil. The effects of various factors including reaction time, dosage, nZVI loading on Cd fractionation, soil available iron, pH, CEC, and soil enzyme activity were comprehensively discussed. It can be concluded that nZVI@BC exhibited more excellent immobilization effect of Cd, and was positively correlated with dosage and reaction time, but negatively related to nZVI loading. As a result, 5% nZVI@BC(1:3) performed the best. Soil available iron, pH, and CEC were significantly enhanced with increasing nZVI loading. The immobilization mechanism was analyzed, including ion exchange, physical adsorption, surface complexation, electrostatic attraction as well as co-precipitation. Besides, nZVI@BC remarkably promoted soil catalase activity, but inhibited urease and FDA hydrolase activities. Furthermore, the effects and differences on the diversity, abundance, and species composition of soil microbial communities were deeply explored. The order of bacterial community richness in each group was CK > Cd > BC > nZVI@BC, and the bacterial community diversity was CK > nZVI@BC > Cd > BC. The greatest difference of species abundance composition was observed between nZVI@BC treatment group and the control. Additionally, forty-three biomarkers were screened, which primarily belonged to Proteobacteria, Gemmatimonadetes, Firmicutes, and Actinobacteria. This study will provide the profound theoretical basis for nZVI@BC remediation of Cd-contaminated soil and its microbial community responses.

Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing.

Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.