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Plant growth-promoting rhizobacteria (PGPR) has been detailed to affect soil microbial exercises or community composition. There is a lack of information on the degree to which PGPR as a biofertilizer concurrently influences the action, estimate, and composition of the soil microbial community. This research investigated the impacts of the timing and frequency of PGPR application as biofertilizers on the rhizosphere bacteria community in arable soil. We compared four treatments in an experimental field site, namely: one-time treatment of PGPR at the beginning of planting (P1), twice treatment of PGPR (P2), 15-days of planting (DP), and 30-DP (P3); and without treatment of PGPR (WP). A total rhizosphere bacteria community fingerprint was surveyed using ribosomal intergenic spacer analysis (RISA) using a culture-dependent and culture-independent approach. The rhizosphere bacteria community was surveyed during 80 DP. The unweighted pair-group method with arithmetic mean (UPGMA) clustering showed that the rhizosphere bacteria community in three-frequency applications of PGPR was more abundant than without PGPR application and one or two PGPR applications. This study revealed that the rhizosphere bacteria community was increased in soil with PGPR application, especially in P3, three dosages of PGPR application. Increasing the rhizosphere bacteria community could strongly influence the clay foam soil nutrient.

ABSTRACT Skeletonema costatum, a cosmopolitan diatom primarily inhabiting coastal ecosystems, exhibits a typically close yet variable relationship with heterotrophic bacteria. The increasing temperature of surface seawater is expected to substantially affect the viability and ecological dynamics of S. costatum, potentially altering its relationship with bacteria. However, it remains unclear to what extent the elevated temperature could change these relationships. Here, the relationship between axenic S. costatum and natural seawater bacteria underwent a dramatic shift from mutualism to antagonism as the co-culture temperature increased from 20°C to 25°C. The co-occurrence network indicated significantly increased complexity of interaction between S. costatum and bacteria community after temperature elevation, especially with Flavobacteriaceae, implying their potential role in eliminating S. costatum under higher temperatures. Additionally, a Flavobacteriaceae isolate, namely MS1 identified as Tamlana genus, was isolated from the co-culture system at 25°C. MS1 had a remarkable ability to eliminate S. costatum, with the mortality rate at 25°C steadily rising from 30.2% at 48 h to 92.4% at 120 h. However, it promoted algal growth to some extent at 20°C. These results demonstrated that increased temperature promotes MS1 shifts from mutualism to antagonism with S. costatum. According to the comparative genomics analysis, changes in the lifestyle of MS1 were attributed to the increased gliding motility and attachment of MS1 under elevated temperature, enabling it to exert an algicidal effect through direct contact with alga. This investigation provided an advanced understanding of interactions between phytoplankton and bacteria in future warming oceanic ecosystems.IMPORTANCEOcean warming profoundly influences the growth and metabolism of phytoplankton and bacteria, thereby significantly reshaping their interactions. Previous studies have shown that warming can change bacterial lifestyle from mutualism to antagonism with phytoplankton, but the underlying mechanism remains unclear. In this study, we found that high temperature promotes Tamlana sp. MS1 adhesion to Skeletonema costatum, leading to algal lysis through direct contact, demonstrating a transition in lifestyle from mutualism to antagonism with increasing temperature. Furthermore, the gliding motility of MS1 appears to be pivotal in mediating the transition of its lifestyle. These findings not only advance our understanding of the phytoplankton-bacteria relationship under ocean warming but also offer valuable insights for predicting the impact of warming on phytoplankton carbon sequestration.

The goal of this study was to investigate the bacterial community associated with biogas production from food waste and rumen content. Anaerobic mono-digestion and co-digestion were performed using mixture design within Design Expert, resulting in 100 experimental runs. Parameters such as food waste and rumen content, water content, temperature, pH, number of digester agitation per day and retention time were varied during the anaerobic digestion processes. Classical microbiological techniques were used to isolate and identify strict anaerobic and facultative anaerobic bacteria from the food waste and rumen content before and after anaerobic digestion. Sixteen bacterial species belonging to 12 different generae were isolated and identified from the food waste, rumen content and composite digestates obtained from the 100 bio-digesters. These generae included Acetobacterium, Bacteroides, Clostridium, Enterobacter, Escherichia, Lactobacillus, Pseudomonas, Ruminococcus, Staphylococcus, Streptococcus, Syntrophomonas and Syntrophobacter. With the exception of Escherichia coli and Pseudomonas sp., all other bacterial species identified in the substrates were also found in samples of the composite digestates, suggesting that they may have played important roles in the anaerobic digestion process inside the 100 bio-digesters. Overall, this study provides valuable insights into the microbial community structure and function during biogas production from food waste and rumen content. The results could contribute to the development of more efficient and sustainable biogas production processes.

Soil microbial communities are essential drivers of ecosystem functions, yet the factors shaping their structure and function, particularly at different altitudes and between invasive and native plants, remain insufficiently understood. Using high-throughput Illumina sequencing, we assessed the composition, diversity, impact factors, and functional potential of the microbial communities associated with Galinsoga quadriradiata (an invasive species) and Artemisia lavandulifolia (a native species) across an altitudinal gradient ranging from 896 m to 1889 m in the Qinling Mountains. The results revealed that both plant species and altitude significantly influenced soil bacterial diversity and community structure. Actinobacteriota, Proteobacteria, and Acidobacteriota accounted for higher proportions in the soils of G. quadriradiata and A. lavandulifolia. A linear discriminant analysis showed that the two species hosted distinct microbial communities, with variations driven by species-specific traits and environmental factors. Compared with plant parameters, environmental factors had a greater impact on plant soil bacterial abundance. Functional analysis indicated that A. lavandulifolia soils were more associated with nitrogen cycling processes, while G. quadriradiata soils contributed more to organic matter decomposition. Therefore, invasive and native plants harbored microbial flora with different nutritional preferences and metabolic characteristics. These findings advance our understanding of plant–microbe interactions along altitudinal gradients, and they have practical implications for managing invasive species and supporting ecosystem resilience.

Pharmaceutical usage has led to the widespread detection of these compounds in aquatic ecosystems worldwide, raising concerns about the selective pressure they can exert on microbial communities. To aid in tackling this global emergency, we undertook an initial step in identifying potential hotspots of bacterial resistance arising from the occurrence of antibiotics in the environment. This was conducted by performing a risk assessment based on the measured environmental concentrations of selected antibiotics, acquired from an international pharmaceutical database, and the respective no-effect concentrations for bacterial resistance of such antibiotics. We identified untreated industrial and hospital sewage as the aquatic matrices of most concern. Regarding treated effluent from wastewater treatment plants, the antibiotic ciprofloxacin and Tunisia exhibit a high-risk quotient. For surface water matrices (rivers and streams), both ciprofloxacin and amoxicillin warrant attention and the countries with the highest risk medians were India, South Africa, and the United States of America. Our study provides an initial basis for highlighting the antibiotics, countries, and aquatic matrices that warrant more attention regarding bacterial resistance. This approach can be applied at national or regional scales for more detailed environmental evaluation and decision-making. Nonetheless, we encourage further investigations to confirm the occurrence of antibiotic-resistant bacteria and antibiotic-resistance genes in the potential hotspots identified in this study.

AbstractThe richness and diversity of bacterial community in the fermented pit mud from the new and old distilleries of Shedian Liquor were analysed via the Illumina Miseq PE300 high-throughput sequencing technology, so as to further understand the differences of bacterial community structure in fermented pit muds with different pit ages. The results show that the bacterial community is mainly distributed into five dominant phyla (> 1.0%): Firmicutes, Synergistes, Bacteroidetes, Proteobacteria and Verrucomicrobia. There are 13 dominant genera (> 1.0%), of which Lactobacillus is dominant in both samples with a higher content in the new pit (61.12%) and lower in the old pit (1.15%). Caproiciproducens accounting for 43.53% and Syntrophomonas accounting for 6.20%, norank_f__Family_XIV (17.68%), Aminobacterium (17.68%), Sedimentibacter (1.89%), Caldicoprobacter (1.52%) and Sporanaerobacter (1.29%) are the dominant bacteria in the old pit mud. Bacillus accounting for 6.02%, Bacteroides (6.27%), Akkermansia (1.51%), Hydrogenispora (2.15%) and norank_f__Bacteroidales_S24-7_group (1.15%) are the dominant bacteria in the new pit mud. The results showed that there is a great difference in the bacterial community structure of in the new and old pit mud. In addition, compared with the bacterial community composition in the pit mud of Luzhou flavour Baijiu in Sichuan, it was found that the microorganisms that formed caproic acid and butyric acid were different.

Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil (“MP kit”) and the DNeasy PowerSoil Pro Kit (“PowerSoil kit”). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642–37,805 16S rRNA gene sequence reads and 30,380–42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.

Abstract The gut microbiome is essential for processing complex food compounds and synthesizing nutrients that the host cannot digest or produce, respectively. New model systems are needed to study how the metabolic capacity provided by the gut microbiome impacts the nutritional status of the host, and to explore possibilities for altering host metabolic capacity via the microbiome. Here, we colonized the nematode Caenorhabditis elegans gut with cellulolytic bacteria that enabled C. elegans to utilize cellulose, an otherwise indigestible substrate, as a carbon source. Cellulolytic bacteria as a community component in the worm gut can also support additional bacterial species with specialized roles, which we demonstrate by using Lactobacillus plantarum to protect C. elegans against Salmonella enterica infection. This work shows that engineered microbiome communities can be used to endow host organisms with novel functions, such as the ability to utilize alternate nutrient sources or to better fight pathogenic bacteria.

Based on the low content of water-soluble carbohydrate (WSC) and lactic acid bacteria (LAB) attachment in oat raw materials, we assumed that the neutral detergent fiber (NDF) content of oat can be reduced by adding cellulase or xylanase. The concentration of metabolizable sugars will be increased, which will assist the oat’s bacterial community in fermentation and obtain a better quality of oat silage. After wilting the oat, it was treated as follows: (1) distributed water (CK); (2) silages inoculated with xylanase (X); and (3) silages inoculated with cellulase (C), ensiling for 3, 7, 14, 30, and 60 days. Cellulase and xylanase treatments both alter the fermentation and nutritional quality of ensiled oat, resulting in lower NDF, acid detergent fiber (ADF), cellulose, and hemicellulose contents, increased lactic acid and acetic acid contents, and a significant decrease in ensiling environment pH. The bacterial community undergoes significant changes with cellulase and xylanase treatments, with a significant increase in Lactobacillus abundance in the C_14, X_30, C_30, X_60, and C_60 treatment groups, while Weissella abundance gradually decreases with longer ensiling times. Two exogenous fibrolytic enzymes also alter the bacterial diversity of ensiled oat, with different bacterial species and abundances observed in different treatment groups. Ensiled oat treated with cellulase and xylanase experiences significant changes in its own bacterial community, particularly in the abundance of Lactobacillus. These changes result in improved fermentation and nutritional quality of oat, but the higher metabolism levels observed after 60 days of ensiling with cellulase treatment may lead to energy loss.

As the global human population continues to increase, the use of saline–alkali land for food production is an important consideration for food security. In addition to breeding or cultivating salt-tolerant crop varieties, microorganisms are increasingly being evaluated for their ability to improve plant salt tolerance. Barley is one of the most important and salt-tolerant cereal crops and is a model system for investigating the roles of microorganisms in improving plant salt tolerance. However, a comprehensive review of the mechanisms by which microorganisms improve barley salt tolerance remains lacking. In this review, the mechanisms of barley salt tolerance improvement by microorganisms are summarized, along with a discussion of existing problems in current research and areas of future research directions. In particular, with the development of sequencing technology and the great reduction of prices, the use of omics can not only comprehensively evaluate the role of microorganisms but also evaluate the impact of the microbiome on plants, which will provide us with many opportunities and challenges in this research area.

Abstract Background Previous studies have found that coastal eutrophication increases the influence of homogeneous selection on bacterial community assembly. However, whether seasonal changes affect the dominance of homogenous selection in bacterial community assembly in eutrophic bays remains unclear. Sansha Bay is an enclosed bay with ongoing eutrophication, located in the southeast coast of China. We investigated the bacterial community composition at two depths of the enclosed bay across seasons and the seasonal variation in community assembly processes. Results Diversity analyses revealed that the bacterial community composition among seasons differed significantly. By contrast, there was little difference in the community composition between the two depths. The temperature was the key environmental factor influencing the community composition. The null model indicated that the relative importance of homogeneous selection decreased in the following order: spring > winter > autumn > summer. Homogeneous selection did not always dominate the community assembly among seasons in the eutrophic bay. The effects of pure spatial variables on the community assembly were prominent in autumn and winter. Conclusions Our results showed the seasonal influence of eutrophication on bacterial community diversity. The seasonal variation in composition and structure of bacterial communities eclipsed the vertical variability. Eutrophication could enhance the importance of homogeneous selection in the assembly processes, but the seasonal environmental differences interfered with the steady-state maintained by ongoing eutrophication and changed the community assembly processes. Homogeneous selection was not always important in bacterial community in the eutrophic enclosed bay. The bacterial community was the most complex in summer, because the composition differed from other seasons, and the assembly process was the most intricate. These findings have contributed to understanding bacterial community composition and assembly processes in eutrophic coastal ecosystems.

Imbalance in the microbiota has been identified in Crohn's disease (CD). We explored the difference of the microbiota in fecal and intestinal mucosa (including ileocecal junction, terminal ileum and transverse colon) in pediatric patients with active CD, CD patients in remission, nonspecific enteritis (NE) and the healthy children. Seven children had active CD, 5 cases of patients achieve remission (CDR), 19 were NE patients, and 11 were healthy controls (Col). A total of 168 samples were collected. Microbiota compositions were analyzed using 16 ​S rRNA sequencing. The results showed that, in fecal samples, Clostridium_sensu_stricto, Enterobacter and Akkermansia had a higher relative abundance in the CD group than that in CDR, Col and NE groups. Fusobacterium and Streptococcus showed a higher abundance in both CD and CDR than that in Col group. In intestinal mucosa samples, the bacterial communities of the three sampling sites were extremely similar. Escherichia-Shigella was the most abundant mucosal bacteria in the CD group, and the abundance of Bacillus, Ruminococcus_torques_group, Streptococcus, Faecalibacterium and Blautia was lower in the CD group than in other groups. In conclusion, as a very characteristic bacteria, the abundance of Escherichia-Shigella in the intestinal mucosa can be used as a diagnostic criterion for CD patients. Also, the Bacilus and Blautia, which were not as prominent as Escherichia-Shigella could still be used as a diagnostic candidate due to their neatness in CD patients. Mucosal samples may be better than stool samples when assessing the community and diversity of patients' intestinal microbes.

It is a two-way interaction between algae bloom events and nutrient cycles in aquatic environments. In Meiliang bay of Taihu Lake, phosphorus (P) forms in the water, sediment and pore water, and bacterial community structures in the sediment were investigated in June 2021 (the algae bloom period) and December 2021 (the algae collapse period). The aim of this study is to clarify the periodic variations of P migration and transformation driven by algae bloom and collapse. Results showed that concentrations of total P and total particulate P in the water during the algae bloom period (.13–.25 mg/L) were much higher than those during the algae collapse period (0–.13 mg/L), which was mainly caused by the uptake of phosphate (PO43-) by algae in the surface water. Compared with the algae bloom period, there were higher concentrations of organic P (OP), iron-bound P (FeP) and inorganic P in the sediments during the algae collapse period. The propositions of OP and FeP in total P in the sediments increased from 19% to 17% during the algae bloom period to 27% and 33% during the algae collapse period. These suggest the cumulative trend of OP and FeP in the sediments during the algae collapse period, and FeP might be formed through the processes of OP mineralization and P adsorption by iron oxides/hydroxides in the sediments. Different routes of sediment P regeneration existed over the two periods. During the algae bloom period, the similar vertical variations of labile PO43- and labile Fe2+ in the sediments provided in situ, high-resolution evidence for FeP reductive dissolution driven by FRBs activities. During the algae collapse period, OP mineralization driven by organic P-solubilizing bacteria activities and accelerated by the sulfate reduction process was confirmed by the similar vertical variations of labile PO43- and labile S2- in the sediments. Therefore, treatment approaches and management practices should consider the periodic variations of internal P cycles in aquatic environments during the algae bloom and algae collapse periods to avoid inefficient treatments of lake eutrophication and algae bloom.

Community and composition of dust-borne microbes would affect human health and are regulated by microbial community assembly. The dust in kindergarten is always collected to evaluate the microbial exposure of children, yet the microbial assembly, their interactions, and potential pathogens in kindergarten dust remain unclear. Here, we aim to investigate the microbial community assembly and structures, and potential bacterial pathogens in outdoor dust of kindergartens, and reveal the factors influencing the assembly and composition of microbial community. A total of 118 urban dust samples were collected on the outdoor impervious surfaces of 59 kindergartens from different districts of Xiamen in January and June 2020. We extracted microbial genomic DNA in these dusts and characterized the microbial (i.e., bacteria and fungi) community compositions and diversities using target gene-based (16S rRNA genes for bacterial community and ITS 2 regions for fungal community) high-throughput sequencing. Potential bacterial pathogens were identified and the interactions between microbes were determined through a co-occurrence network analysis. Our results showed the predominance of Actinobacteria and α-Proteobacteria in bacterial communities and Capnodiales in fungal communities. Season altered microbial assembly, composition, and interactions, with both bacterial and fungal communities exhibiting a higher heterogeneity in summer than those in winter. Although stochastic processes predominated in bacterial and fungal community assembly, the season-depended environmental factors (e.g., temperature) and interactions between microbes play important roles in dust microbial community assembly. Potential bacterial pathogens were detected in all urban dust, with significantly higher relative abundance in summer than that in winter. These results indicated that season exerted more profound effects on microbial community composition, assembly, and interactions, and suggested the seasonal changes of potential risk of microbes in urban dust. Our findings provide new insights into microbial community, community assembly, and interactions between microbes in the urban dust, and indicate that taxa containing opportunistic pathogens occur commonly in urban dust.

Raw camel milk is generally contaminated with varied microbiota, including antibiotic–resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high–throughput quantitative PCR and 16S rRNA gene–based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β–lactamas and multidrugs. The ARGs’ profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co–occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.

This study investigated the performance of thermophilic–mesophilic (T-M) and mesophilic–thermophilic (M-T) two-phase sludge anaerobic digestion at different inoculation proportions after a change in digestion temperature. After temperature change, the pH, total ammonia nitrogen (TAN), free ammonia nitrogen (FAN), solubility chemical oxygen demand (SCOD), and total alkalinity (TA) levels of two-phase digesters were between thermophilic control digesters and mesophilic control digesters. However, the volatile fatty acid (VFA) levels of two-phase digesters were higher than those of thermophilic or mesophilic control digesters. The bacteria communities of M-T two-phase digesters were more diverse than those of T-M. After a change in digestion temperature, the bacterial community was dominated by Coprothermobacter. After a change of digestion temperature, the relative abundance (RA) of Methanobacterium, Methanosaeta, and Methanospirillum of M-T two-phase digesters was higher than that of T-M two-phase digesters. In comparison, the RA of Methanosarcina of T-M two-phase digesters was higher than that of M-T two-phase digesters. The ultimate methane yields of thermophilic control digesters were greater than those of mesophilic control digesters. Nevertheless, the ultimate methane yield levels of M-T two-phase digesters were greater than those of T-M two-phase digesters. The ultimate methane yields of all two-phase digesters presented an earlier increase and later decrease trend with the increasing inoculation proportion. Optimal methane production condition was achieved when 15% of sludge (T-M15) was inoculated under mesophilic–thermophilic conditions, which promoted 123.6% (based on mesophilic control) or 27.4% (based on thermophilic control). An optimal inoculation proportion (about 15%) balanced the number and activity of methanogens of high-solid sludge anaerobic digestion.

This study aimed to investigate the behavioral shifts of constructed wetland (CW) when the treated water was changed from domestic wastewater to mariculture wastewater. The results showed that the average removal efficiencies of ammonium nitrogen (), total nitrogen and chemical oxygen demand (COD) were 29.54, 46.07 and 57.15% in mariculture wastewater, respectively, which were significantly lower than those in domestic wastewater (71.35, 66.34 and 74.98%, respectively). While there was no significant difference in the removal efficiency of nitrate and phosphate (P > 0.05) between the two systems. Based on the analysis of bacterial community and adsorption properties, the results further indicated that the removal mechanism of between both systems was mainly due to substrate adsorption: the maximum adsorption capacity of on the substrate in mariculture wastewater was 5,432 mg kg−1, whereas that in domestic wastewater was 18,033 mg kg−1. In terms of bacterial communities, the dominant bacteria at the family level were Victivallaceae (18.63%) in domestic wastewater and Porphyromonadaceae (18.37%) in mariculture wastewater, which showed the significant alteration to the bacterial community. In conclusion, this study showed that conventional CW could be used for treating wastewater from land-based marine aquaculture, while the operating conditions needed to be optimized in the process of application. HIGHLIGHTS We addressed changes in the reuse of constructed wetlands for treating mariculture wastewater.; Significant inhibitive effects on , total nitrogen and COD removal occurred during the wastewater transformation.; Substrate adsorption negatively affected removal efficiency in constructed wetland-treatment of mariculture wastewater.;

The microorganisms that inhabit the gastrointestinal tract are responsible for multiple chains of reactions that affect their environment and modify the internal metabolism, their study receives the name of microbiome, which has become more relevant in recent years. In the near future, the challenges related to feeding are anticipated to escalate, encompassing the nutritional needs to sustain an overpopulated world. Therefore, it is expected that a better understanding of the interactions between microorganisms within the digestive tract will allow their modulation in order to provide an improvement in the immune system, feed efficiency or the promotion of nutritional characteristics in production animals, among others. In the present study, the main effects of experimental diets in production animals were described, emphasizing the diversity of the bacterial populations found in response to the diets, ordering them between polygastric and monogastric animals, and then describing the experimental diets used and their effect on the microorganisms. It is hoped that this study will help as a first general approach to the study of the role of the microbiome in production animals under different diets.

Most oat forage has low water-soluble carbohydrates (WSC), which may be the main limited factor for silage fermentation safely, but oat is rich in cellulose and hemicellulose; therefore, we assume that xylanase and cellulase as additives can reduce the content of cellulose and xylan in oat silage, increase the microbial fermentable sugar content, and improve the fermentation quality of the silage. After wilting, oats were treated as follows: (i) distributed water (CK); (ii) silages inoculated with xylanase (X); (iii) silages inoculated with cellulase (C), ensiling for 3 days (early stage of silage) and 60 days (late stage of silage), respectively, after ensiling 60 days for a 5-day aerobic exposure study. The pH, neutral detergent fiber (NDF), and acid detergent fiber (ADF) were significantly reduced by xylanase and cellulase treatment during the late stage of silage, and the concentration of lactic acid, acetic acid, and ammonia nitrogen increased remarkably. The WSC content reached its peak with xylanase treatment during the late stage of silage. The content of crude protein (CP) was not affected by additives but by the silage period; CP and ether extract (EE) significantly increased during the late stage of silage compared to the early stage. After ensiling, the bacterial community showed that xylanase and cellulase treatment increased the relative abundance of lactic acid bacteria. Lactobacillus has a higher relative abundance with cellulase treatment after 60 days of ensiling; this can effectively reduce the pH of silage and ensure long-term, stable storage of silage. Cellulase and xylanase increased bacterial diversity during aerobic exposure and improved the aerobic stability of silage significantly. This study indicated that different additives and silage periods had significant effects on chemical compositions, fermentation quality, and bacterial community; meanwhile, both additives improved the aerobic stability of silage. In summary, when the WSC of oat is low, cellulase and xylanase have good effects as silage additives, and the comprehensive effect of cellulase is more prominent.

Nettle (Urtica cannabina) is an excellent feed resource widely distributed worldwide. Phyllosphere microbes are important as they have living conditions similar to those of the above-ground parts of host plants. Exploring amino acids (AA) and microorganisms can further understand the growth of plants in different seasons. The present study investigated the content of AA and phyllosphere microbes’ structure of nettle plants in different seasons. The results found that AA contents varied significantly with the season, such as alanine, aspartate, cysteine, glutamate, glycine, and methionine contents decreased significantly from spring to winter (p < 0.05), the contents of arginine, histidine, serine, and lysine were highest in summer (p < 0.05). The results suggested that the diversity of bacteria and fungi both increased during winter. During winter, Sphingomonas (relative abundance 25.22–28.45%) and Filobasidum (27.6–41.14%) became dominant. According to the redundancy analysis (RDA) of the correlation between AA and microbes, these two microbes were both the most important factors and showed a negative correlation with AA during winter. Thus, seasons could significantly affect the distribution of phyllosphere microbial communities on the nettle, especially in winter. According to the function prediction(PICRUS2 (KEGG pathway) and FUNGuild) results, the bacteria in the phyllosphere of U. cannabina mainly participated in metabolism. Pathogenic fungi were relatively high in autumn. The present study reveals the influence of seasonal change on the phyllosphere microbial community in U. cannabina.

Abstract Background Minqin is suffering from a serious desertification, whereas the knowledge about its bacterial community is limited. Herein, based on Nitraria tangutorum and Haloxylon ammodendron from Minqin, the bacterial community diversities in fixed sandy land, semi-fixed sandy land and shifting sandy land were investigated by combining with culture-dependent and culture-independent methods. Results Minqin stressed with high salinity and poor nutrition is an oligotrophic environment. Bacterial community in Minqin was shaped primarily by the presence of host plants, whereas the type of plant and sandy land had no marked effect on those, which displayed a better survival in the rhizospheres of N. tangutorum and H. ammodendron. The dominant groups at phyla level were Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria and Candidate_division_TM7. The abundance of Firmicutes with ability of desiccation-tolerance was significantly higher in harsh environment, whereas Bacteroidetes were mainly distributed in areas with high nutrient content. The abundances of Proteobacteria and Bacteroidetes were relatively high in the rhizospheres of N. tangutorum and H. ammodendron, which had more plant-growth promoting rhizobacteria. A large number of Actinobacteria were detected, of which the most abundant genus was Streptomyces. The physicochemical factors related to the diversity and distribution of the bacterial community were comprehensively analyzed, such as pH, electrical conductivity, soil organic matter, C/N and sand, and the results indicated that Minqin was more suitable for the growth of N. tangutorum, which should be one of most important sand-fixing plants in Minqin. Conclusions The bacterial community diversities in different types of sandy lands of Minqin were comprehensively and systematically investigated by culture-dependent and culture-independent approaches, which has a great significance in maintaining/restoring biological diversity.

The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.

This study aimed to evaluate the fermentation quality, bacterial community, and nitrate content of sorghum-sudangrass silage with two ensiling densities [550 kg fresh weight (FW)/m3 (low density, LD) and 650 kg FW/m3 (high density, HD)] stored at two temperatures [10°C (low temperature, LT) and 25°C (normal temperature, NT)] for 60 days. The fermentation parameters, microbial counts, bacterial community, nutritional composition, and nitrate and nitrite levels were assessed. The pH and ammonia nitrogen (N) in all silages were below 4.0 and 80 g/kg total N, respectively. Compared with LT treatments, NT treatments had lower pH and lactic acid (LA) bacteria and yeasts counts and contained higher LA and LA/acetic acid (LA/AA) (p < 0.05). The LT-LD contained more ammonia–N than LT-HD (p < 0.05) and had higher nitrate and lower nitrate degradation than other treatments (p < 0.05). Lactobacillus was the most dominant genus with all treatments (57.2–66.9%). The LA, LA/AA, and abundances of Pantoea, Pseudomonas, and Enterobacter in the silage negatively correlated with nitrate concentration and positively correlated with nitrate degradation (p < 0.05). Moreover, pH and ammonia–N were positively correlated with nitrate concentration and negatively correlated with nitrate degradation (p < 0.05). Overall, all silage had satisfactory fermentation quality, and the silage with HD and NT had better fermentation quality and higher nitrate degradation. The bacterial communities in all silages were dominated by Lactobacillus. The nitrate degradation during the fermentation process might be related to the fermentation quality and the activity of Pantoea, Pseudomonas, and Enterobacter in silage.

The physicochemical and biological characteristics of milli-microbubbles were compared to evaluate their performance on hydrogenotrophic denitrification (HD) for groundwater treatment in remote areas. The hydrogen supply was controlled at 1.14 L/d with 40 mgN/L of NO3-N. The microbial community structure in two bubble reactors was investigated by high throughput sequencing. Microbubbles enhanced biodegradation in the HD system, providing a maximum nitrogen removal efficiency of 99%. Approximately 50% of total hydrogen was utilized for biological nitrate removal with the highest hydrogen effectiveness achieved at 1.21 g N/g H2. In contrast, millibubbles achieved less than 10% efficiency and 9.9% of total hydrogen was consumed for biological nitrogen removal. Thaueraspp., Hydrogenophagaspp. and Rhodocyclaceaeof Proteobacteriaphylum were the dominant bacteria in the microbubble reactor, whereas Methyloversatilis spp.was dominant in the millibubble reactor, in which a relatively low amount of hydrogen (0.6 mg/L) was dissolved. The differences can be attributed to the higher hydrogen transfer efficiency (45×10-3s-1) and lower rising velocity (0.31 mm/s) of the microbubbles system than the millibubbles system (2×10-3s-1and 480 mm/s). The micro-hydrogen bubble technology affords increased hydrogen effectiveness, reduced energy consumption, and modified system design. Therefore, it is more appropriate for enhancing HD.

Abstract Potato brown rot, caused by Ralstonia solanacearum, ranked globally as the second most important bacterial plant pathogen. In the present study, the influence of different cropping programs in potato brown rot management was investigated in four infected fields in Egypt. Two districts were selected as sandy soils in Giza (Wardan) and Behera (Ganuob El-Tahrir) governorates. The other two were selected as silty clay in Minufyia (Talia) and Beni-Suef (Sids) governorates. The followed crop succession included corn, potato intercropped with cabbage, onion, cowpea, wheat, corn again, and ended by potato. The pathogen was undetectable after corn, onion, and wheat. It decreased in cowpea and cabbage rhizospheres in the clay soils. The pathogen was undetectable at all districts, except at Sids, where the pathogen was significantly decreased but was not eradicated. This was possibly attributed to the high ratio of NO3 − and Na+ at this district. Decreased R. solanacearum density after corn coincided with the high ratio of fluorescent pseudomonads, endospores, and actinomycetes, being most clear in the poor soils (Wardan) and less clear under iron excess at Ganoub El-Tahrir as well as the clay soils. Corn rhizosphere supported an array of antagonistic actinomycetes such as strains similar to Streptomyces intermedius, Streptomyces albidoflavus group, Streptomyces argenteolus group, and Streptomyces erythrogriseus. Intercropping potato with cabbage decreased the density of the pathogen in rhizosphere, which is associated with greater antagonistic fluorescent pseudomonads, Bacillus spp. and Serratia spp. Onion soil and rhizosphere associated with abundance of antagonists and fluorescent pseudomonads, followed by S. maltophilia and Bacillus spp. Wheat soil and rhizosphere supported fluorescent pseudomonads and antagonistic Streptomyces spp., especially in sandy soils. The pathogen was undetectable after planting the ending potato in the three districts, Wardan, Ganoub El-Tahrir, and Talia. This was accompanied by a general oligotrophism and increased ratio of fluorescent pseudomonads, endospores bacteria, and actinomycetes along with a diversity of R. solanacearum antagonists such as S. maltophilia, Citrobacter freundii, Acinetobacter sp., Delftia sp., and Serratia marcescens.

Microbial inoculation is a promising strategy to improve crop yields and reduce the use of chemical fertilizers, thereby creating environment-friendly agriculture. In this study, the long-term (5 years) effects of a phosphate-solubilizing bacterium Burkholderia cepacia ISOP5, a purple non-sulfur bacterium Rhodopseudomonas palustris ISP-1, and a mixed inoculation of these two bacteria (MB) on peanut yield, soil microbial community structure, and microbial metabolic functions were evaluated in a field experiment. After 5 years of inoculation, total peanut yield with B. cepacia ISOP5, R. palustris ISP-1, and MB treatments increased by 8.1%, 12.5%, and 19.5%, respectively. The treatments also significantly promoted the absorption of N and increased the protein content in peanut seeds. Nutrient content also increased to some extent in the bacteria-inoculum-treated soil. However, bacterial community diversity and richness were not significantly affected by bacterial inoculums, and only minor changes occurred in the bacterial community composition. Functional prediction revealed that bacterial inoculums reduced the relative abundance of those genes associated with P uptake and transport as well as increased the abundance of genes associated with inorganic P solubilization and organic P mineralization. Bacterial inoculums also increased the total relative abundance of genes associated with N metabolism. In addition to developing sustainable and eco-friendly agricultural practice, crop inoculation with B. cepacia ISOP5 and R. palustris ISP-1 would improve soil fertility, enhance microbial metabolic activity, and increase crop yield.

Strategies to mitigate the spread of antibiotic resistance genes (ARGs) in soils are urgently needed. Therefore, a pristine pyroligneous acid (PA) from pyrolyzing blended woody waste at 450 °C and its three fractions distilled at 98, 130, and 220 °C (F1, F2, and F3) were used to evaluate their feasibility of reducing ARGs in soil. Application of PA, F2, and F3 effectively decreased the relative ARG abundance by 22.4–75.4% and 39.7–66.7% in the rhizosphere and bulk soil relative to control, respectively, and the removal efficiency followed an order of F3 > PA > F2. Contrarily, F1 increased the abundance of ARGs. The decreased abundance of two mobile genetic elements and impaired conjugative transfer of RP4 plasmid in the presence of PA, F2 and F3 demonstrated that the weakened horizontal gene transfer (HGT) contributed to the reduced ARG level. Variation partitioning analysis and structural equation models confirmed that ARG reduction was primarily driven by the weakened HGT, followed by the decreased co-selection of heavy metals and shifted bacterial community (e.g., reduced potential host bacteria of ARGs). Our findings provide practical and technical support for developing PA-based technology in remediating ARG-contaminated soil to ensure food safety and protect human health.

Biological control agents (BCAs) are considered as one of the most important strategies for controlling Fusarium wilt, and bioorganic fertilizer, in particular, has been extensively investigated. However, little is known regarding how a biocontrol microorganism affects the suppression mechanisms when combined with different amendments. In this study, a pot experiment was performed using banana plants to investigate the different mechanisms by which the biocontrol bacterium Bacillus velezensis HN03 (isolated from our laboratory) and amendments suppress Fusarium wilt. The incidence of banana wilt was decreased under HN03 and was reduced further when HN03 was combined with compost, particularly wormcast. In the suppression of Fusarium wilt, HN03 was found to influence the soil environment in various ways. HN03 increased the peroxidase level, which improves plant defense, and was highest when combined with wormcast, being 69 times higher than when combined with cow dung compost. The high accumulation of Mg and P in the “HN03 + wormcast” and Zn and Mn in the “HN03 + cow dung” treatments was negatively correlated with disease incidence. Furthermore, HN03 re-established the microbial community destroyed by the pathogen and further increased the level of suppression in the wormcast. HN03 also enhanced the functional traits of the soil, including defensive mechanism-related traits, and these traits were further enhanced by the combination of HN03 + wormcast.

A 150 days (150-d) experiment was carried out to investigate the production efficiency, inorganic nitrogen syndrome and bacteria community of indoor biofloc technology (BFT) systems used to rear genetically improved farmed tilapia (Oreochromis niloticus) under 0 (S-0), 10 (S-10), and 20 salinities (S-20). The start-up period for BFT was 50, 60 and 80 d for S-0, S-10 and S-20 groups, respectively. At steady state, the total ammonium nitrogen (NH4+-N) and nitrite nitrogen (NO2−-N) were lower than 3.0 mg/L and 0.34 mg/L, respectively and no nitrate-nitrogen (NO3−-N) accumulation was observed. The fish survival rate was above 95% for all the groups. The final fish biomass of the S-10 group (35.83 ± 1.08 kg/m3) was not significantly different from the S-0 (34.79 ± 1.33 kg/m3) group but was significantly higher than S-20 (32.6 ± 1.04 kg/m3). The feed conversion ratio for the tilapia in S-20 was 1.46, which was higher than the ratio in S-0 (1.40) and S-10 (1.39) tilapia. There was no significant difference in the crude protein content of the back muscle from tilapia of the three experimental groups. No significant difference in blood parameters, except for aspartate aminotransferase and alkaline phosphatase was observed between the three groups. Evaluation of microorganisms in the three BFT systems revealed that Proteobacteria, Bacteroidetes, and Fusobacteria were the top three at the phylum level in all groups. However, a significant difference was observed at the genus level in the bacteria of the three BFTs at different salinity (P

The Asian ladybird Harmonia axyridis is an invasive insect in Europe and the Americas and is a great threat to the environment in invaded areas. The situation is exacerbated by the fact that non native species are resistant to many groups of parasites that attack native insects. However, very little is known about the complex microbial community associated with this insect. This study based on sequencing 16S rRNA genes in extracted metagenomic DNA is the first research on the bacterial flora associated with H. axyridis. Lady beetles were collected during hibernation from wind turbines in Poland. A mean ± SD of 114 ± 35 species of bacteria were identified. The dominant phyla of bacteria recorded associated with H. axyridis were Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. Representatives of these phyla are common in the environment, e.g. in the soil, and are often identified as the dominant bacteria associated with arthropods. We also identified animal pathogenic bacteria, such as Burkholderia, Rhodococcus, Chlamydiae and Anaplasmataceae spp. (Neorickettsia helminthoeca and Ehrlichia ovina). We also identified Wolbachia pipientis in a single beetle. This bacterium is a causative agent of reproductive alterations in arthropods. These results support the enemy release hypothesis in the case of this ladybird invasion. Pathogenic bacteria were recorded in only a few samples. Moreover, male-killing bacteria such as Spiroplasma spp., Wolbachia spp. and Rickettsia spp. were only recorded in single insects so they cannot be responsible for the observed alterations in the sex-ratio of the ladybird population studied.

The effects of rumen buffer agents on ruminal fermentation parameters and bacterial community composition were determined using in vitro and in vivo experiments in three rumen-cannulated, high-concentrate fed Holstein Friesian dairy cows. Experiment 1 in vitro treatments included bentonite, calcium carbonate, calcium oxide, sodium bicarbonate, sodium sesquicarbonate, and processed coral, and unbuffered samples served as the control. Experiment 2 in vitro treatments were based on the formulation of various combinations of the buffer agents used in Experiment 1. Combinations were selected for the in vivo study based on their buffering ability. Calcium oxide, sodium bicarbonate, and sodium sesquicarbonate stabilized the ruminal pH and improved in vitro rumen fermentation. The combined buffer agents had a significant effect on pH, buffering capacity, total gas, and total volatile fatty acids. Firmicutes and Bacteroidetes were the dominant phyla in both treatments and the control. Ruminococcus and Prevotella were found to be the dominant genera. Ruminococcus bromii was predominant in the treatment group. Prevotella jejuni was more abundant in the control group compared to the treatment group, in which its abundance was very low. Ruminococcus flavefaciens and Intestinimonas butyriciproducens gradually increased in abundance as cows received treatment. Overall, a high-concentrate diet administered to cows induced adverse changes in ruminal pH; however, buffer supplementation enhanced ruminal fermentation characteristics and altered bacterial community, which could contribute to preventing ruminal acidosis.

To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected strains, Lactobacillus salivarius LS358 and L. rhamnosus LR753, two type strains L. salivarius ATCC 11741T and L. rhamnosus ATCC 7469T. The ensiling temperatures were designed at 30 °C and 45 °C, and the sampling took place after 0, 3, 7, 14, and 60 days of fermentation. The higher pH and dry matter losses were observed in the silages stored at 45 °C compared to those stored at 30 °C. Silages inoculated with strains LS358 and LR753 at 30 °C had a lower ratio of lactic acid/acetic acid. The dominant bacterial genera gradually changed from Pediococcus and Lactobacillus to Lactobacillus in silages during ensiling at 30 °C, while the bacterial community became more complex and fragmented after 7 d of ensiling at 45 °C. The high temperatures significantly led to a transformation of the LAB population from homo-fermentation to hetero-fermentation. This study is the first to describe microbial population dynamics response to high temperature during corn ensiling, and the results indicate that L. rhamnosus 753 shows potential ability to improve silage fermentation in tropics and subtropics.

Background Global demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil. Methods In order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries. Results The results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed. Discussion The results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state.