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A novel bacterium, designated DCY112T, was isolated from the rhizospheric soil of a ginseng-cultivated field in Gochang-gun, Republic of Korea. Based on 16S rRNA gene sequence analysis, this isolate was assigned to the genus Rhodanobacter and is closely related to Rhodanobacter soli DCY45T (98.0%) and R. umsongensis GR24-2T (98.0%). Strain DCY112T is Gram-negative, catalase- and oxidase-positive, aerobic, non-motile, rod-shaped, and produces yellow-pigmented colonies on R2A medium. Q-8 was the predominant respiratory quinone. The major cellular fatty acids were iso-C15:0, iso-C17:0, and summed feature 9 (iso-C17:1ω9c and/or 10-methyl-C16:0). The major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unknown amino lipid (AL1), and an unidentified polar lipid (L3). The genomic DNA G + C content was 65.2 mol%. DNA–DNA homology values between strain DCY112T and related strains were lower than 55%. The low DNA relatedness data in combination with phenotypic and genotypic tests indicated that strain DCY112T could not be assigned to a recognized species. Strain DCY112T showed antagonistic activity against the fungal pathogen Fusarium solani (KACC 44891T), which causes ginseng root rot. The results of this study support that strain DCY112T is a novel species belonging to the genus Rhodanobacter, for which the name Rhodanobacter ginsengiterrae is proposed. The type strain is DCY112T (= KCTC 62018T = JCM 32167T).

Denitrifying nitrous oxide (N 2 O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N 2 O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N 2 O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N 2 O production ( nirS and nirK ) to the gene responsible for N 2 O reduction ( nosZ ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N 2 O-generating bacteria in BF and a higher abundance of N 2 O-reducing bacteria in FF. High accumulation of N 2 O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N 2 O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N 2 O and thus less N 2 O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N 2 O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N 2 O accumulation. This knowledge would help to develop a strategy for mitigating N 2 O emissions in agricultural soils by regulating the phenotypes of N 2 O metabolism.

In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO 2 2+ , Mn 2+ , Al 3+ , Cd 2+ , Zn 2+ , Co 2+ , and Ni 2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter -dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.

Aims Plants host communities of fungal and bacterial endophytes, establishing a complex network of multipartite interactions, but the mechanisms whereby they interact are poorly understood. Some fungi, such as the beneficial mycorrhiza-like fungus Serendipita (= Piriformospora ) indica , can be helped by bacteria for establishment, survival and colonization. Although this fungus harbors a Rhizobium as an endofungal bacterium, we hypothesized that other bacteria might also establish associations with the fungus and combining S. indica with bacteria might enhance plant growth and health. Methods The interactions among S. indica and four endophytic Proteobacteria belonging to Methylobacterium , Tardiphaga , Rhodanobacter and Trinickia spp. were characterized in vitro and for their effect on tomato growth and biocontrol of Fusarium oxysporum and Rhizoctonia solani . Possible mechanisms behind these interactions were described based on genome and microscopic analyses, using fungal and bacterial strains tagged with fluorescent markers. Results All bacteria stimulated S. indica growth in vitro. Moreover, several of the bacteria stimulated growth of tomato plants, but co-inoculations with S. indica and bacteria did not perform better than single inoculations. Contrarily, combinations of S. indica and bacteria significantly reduced disease progression of fungal pathogens. These microbes seem to cooperate in the process of root colonization for instance by increasing fungal sporulation and hyphae expansion, showing multipartite interaction between microbes and plants. Interestingly, the strain of Trinickia internally colonizes spores of S. indica as an endofungal bacterium during in vitro-co-culturing, suggesting further that the fungus might acquire formerly unrecognized genera of bacteria and genome analysis of the bacteria revealed many genes potentially involved in fungal and plant growth stimulation, biocontrol and root colonization, highlighting putative mechanisms of plant-fungal-bacterial interaction. Conclusions Our study represents an important step towards unraveling the complex interactions among plants, S. indica , endophytic bacteria and fungal pathogens, and indicates that adding bacteria to fungal inoculum could have a remarkable impact on the plant- S. indica symbiosis.

This study evaluated the effects of two surfactants (i.e., Tween 80 and SDS) on biodegradation of crude oil by mixed bacterial consortium in soil-aqueous system. The mixed bacterial consortium was domesticated from the activated sludge of cooking plant through a progressive domestication process. High-throughput sequencing analysis revealed that Rhodanobacter sp. was the dominant bacteria. The higher CMC eff value for two surfactants was observed in soil-aqueous system compared with that in aqueous system, which was likely due to their adsorption onto soil particles. Either Tween 80 or SDS can be utilized as carbon source and promote the growth of mixed bacterial consortium. Further findings evidenced that the degradation of crude oil can be enhanced by adding either Tween 80 or SDS. The performance of Tween 80 was generally superior to SDS for the crude oil degradation. The highest crude oil degradation efficiency was 42.2 and 31.0% under the conditions of 5 CMC eff of Tween 80 and 2 CMC eff of SDS, respectively. Furthermore, the degradation efficiency of crude oil in remediation experiment (i.e., 77%) evidenced that the integration of adding Tween 80 and inoculating mixed bacterial consortium was effective for crude oil-contaminated soil decontamination.

PurposeSoil pH and microbial community composition are crucial determinates of plant health. However, their contributions to the success or failure of plant pathogen colonization and the underlying mechanisms are still unknown.MethodsWe used real-time PCR and Miseq sequencing to investigate the colonization efficiency of Ralstonia solanacearum, a typical plant pathogen, in diverse pH values (6.2, 7.0, and 7.8) and residential microbial communities created by soil sterilization and microbial re-inoculation.ResultsBoth pH and microbial re-inoculation significantly influenced the composition of soil bacterial community, while the relative importance of pH (86.44%) far outweighed that of microbial re-inoculation (4.32%). The abundance of R. solanacearum was significantly lower and the complexity of soil microbial network was higher in soils with a higher pH value, and meanwhile the relative abundances of key pathogen-antagonistic microbes were significantly increased in these soils. Structural equation modeling and an independent verification test further suggested that the indirect effect of soil pH, or the effect of soil pH on bacterial community composition, was the primary driver of the success or failure of R. solanacearum colonization. The incidence of bacterial wilt disease was highly variable, but the disease incidence was lowest in low pH soils. Low disease incidence was mainly attributed to the significant increase of key microbes, such as Firmicutes, Paenibacillus, Luteibacter, Chitinophagaceae, and Rhodanobacter, which are known to induce systemic resistance in plant.ConclusionsOur results suggest that soil pH indirectly determines plant pathogen colonization through its impact on soil microbial community composition.

Mine activities leaked heavy metals into surrounding soil and may affected indigenous microbial communities. In the present study, the diversity and composition of the bacterial community in soil collected from three regions which have different pollution degree, heavy pollution, moderate pollution, and non-pollution, within the catchment of Chao River in Beijing City, were compared using the Illumina MiSeq sequencing technique. Rarefaction results showed that the polluted area had significant higher bacterial alpha diversity than those from unpolluted area. Principal component analysis (PCA) showed that microbial communities in the polluted areas had significant differences compared with the unpolluted area. Moreover, PCA at phylum level and Matastats results demonstrated that communities in locations shared similar phyla diversity, indicating that the bacterial community changes under metal pollution were not reflected on phyla structure. At genus level, the relative abundance of dominant genera changed in sites with degrees of pollution. Genera Bradyrhizobium , Rhodanobacter , Reyranella , and Rhizomicrobium significantly decreased with increasing pollution degree, and their dominance decreased, whereas several genera (e.g., Steroidobacter , Massilia , Arthrobacter , Flavisolibacter , and Roseiflexus ) increased and became new dominant genera in the heavily metal-polluted area. The potential resistant bacteria, found within the genera of Thiobacillus , Pseudomonas , Arthrobacter , Microcoleus , Leptolyngbya , and Rhodobacter , are less than 2.0 % in the indigenous bacterial communities, which play an important role in soil ecosystem. This effort to profile the background diversity may set the first stage for better understanding the mechanism underlying the community structure changes under in situ mild heavy metal pollution.

Background The ginseng endophyte Paenibacillus polymyxa Pp-7250 (Pp-7250) has multifaceted roles such as preventing ginseng diseases, promoting growth, increasing ginsenoside accumulation, and degrading pesticide residues, however, these effects still have room for improvements. Composite fungicides are an effective means to improve the biocontrol effect of fungicides, but the effect of Pp-7250 in combination with its symbiotic bacteria on ginseng needs to be further investigated, and its mechanism of action has not been elucidated. In this study, a series of experiments was conducted to elucidate the effect of Paenibacillus polymyxa and Bacillus cereus co-bacterial agent on the yield and quality of understory ginseng, and to investigate their mechanism of action. Results The results indicated that P. polymyxa and B. cereus co-bacterial agent (PB) treatment improved ginseng yield, ginsenoside accumulation, disease prevention, and pesticide degradation. The mechanism is that PB treatment increased the abundance of beneficial microorganisms, including Rhodanobacter , Pseudolabrys , Gemmatimonas , Bacillus , Paenibacillus , Cortinarius , Russula , Paecilomyces , and Trechispora , and decreased the abundance of pathogenic microorganisms, including Ellin6067 , Acidibacter , Fusarium , Tetracladium , Alternaria , and Ilyonectria in ginseng rhizosphere soil. PB co-bacterial agents enhanced the function of microbial metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of antibiotics, biosynthesis of amino acids, carbon fixation pathways in prokaryotes, DNA replication, and terpenoid backbone biosynthesis, and decreased the function of microbial plant pathogens and animal pathogens. Conclusion The combination of P. polymyxa and B. cereus may be a potential biocontrol agent to promote the resistance of ginseng to disease and improve the yield, quality, and pesticide degradation.

Background Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau. Results The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter , Acidobacterium , Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N 2 O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K + as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles. Conclusions These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.

Biofilms aid bacterial adhesion to surfaces via direct and indirect mechanisms, and formation of biofilms is considered as an important strategy for adaptation and survival in suboptimal environmental conditions. However, the molecular underpinnings of biofilm formation in subsurface sediment/groundwater ecosystems where microorganisms often experience fluctuations in nutrient input, pH, and nitrate or metal concentrations are underexplored. We examined biofilm formation under different nutrient, pH, metal, and nitrate regimens of 16 Rhodanobacter strains isolated from subsurface groundwater wells spanning diverse levels of pH (3.5 to 5) and nitrates (13.7 to 146 mM). Eight Rhodanobacter strains demonstrated significant biofilm growth under low pH, suggesting adaptations for survival and growth at low pH. Biofilms were intensified under aluminum stress, particularly in strains possessing fewer genetic traits associated with biofilm formation, findings warranting further investigation. Through random barcode transposon-site sequencing (RB-TnSeq), proteomics, use of specific mutants, and transmission electron microscopy analysis, we discovered flagellar loss under aluminum stress, indicating a potential relationship between motility, metal tolerance, and biofilm growth. Comparative genomic analyses revealed the absence of flagella and chemotaxis genes and the presence of a putative type VI secretion system in the highly biofilm-forming strain FW021-MT20. In this study we identified genetic determinants associated with biofilm growth under metal stress in a predominant environmental genus, Rhodanobacter, and identified traits aiding survival and adaptation to contaminated subsurface environments.