Chujaibacter soli gen. nov., sp. nov., isolated from soil

Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery

Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling

Introduction

In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied.

Methods

This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities.

Results

Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth.

Discussion

In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Composition and Diversity of Endophytic Rhizosphere Microbiota in Apple Tree with Different Ages

In order to determine the underlying mechanism of the senescence occurring in older apple trees, the effects of tree age on the community structure and dominant genus of endophytic rhizosphere bacteria in apple were investigated. The diversity and structure of the bacterial communities and corresponding changes in the dominant genera of endophytic rhizosphere bacteria of apple at different ages (2, 8, 16, 22 years) were compared based on 16S rRNA high-throughput sequencing technology. The results revealed that the longer the tree age, the less the number of ASV in the endophytic bacteria. Moreover, the number of ASV in the endophytic bacteria gradually decreased as the tree age increased, however no significant changes were observed in the alpha diversity. At the phyla level, the relative abundance of Actinobacteria increased, while that of Proteobateria decreased. At the genus level, the relative abundance of Mycobacterium, Chujaibacter, and other genera increased, while the relative abundance of Aquabacterium, Ralstonia, Streptomyces, Asticcacaulis, Hyphomicrobium, Pseudomonas, and Sphingomonas decreased. The reduced relative abundance of endophytic rhizosphere bacteria associated with plant growth and disease resistance may thus be the cause of tree senescence. This work acts as a reference to increases the understanding of plant-microbe interactions.

Chicken manure-derived biochar enhanced the potential of Comamonas testosteroni ZG2 to remediate Cd contaminated soil

The combined remediation of Cd-contaminated soil using biochar and microorganisms has a good application value. In this study, the effect of chicken manure-derived biochar on CdCO3 precipitation induced by Comamonas testosteroni ZG2 was investigated. The results showed that biochar could be used as the carrier of strain ZG2, enhance the resistance of strain ZG2 to Cd, and reduce the toxicity of Cd to bacterial cells. Cd adsorbed by biochar could be induced by strain ZG2 to form CdCO3 precipitation. Strain ZG2 could also induce CdCO3 precipitation when biochar was added during precipitation formation and fermentation broth formation. The CdCO3 precipitation could enter the pores of the biochar and attach to the surface of the biochar. The single and combined effects of strain ZG2 and biochar could realize the remediation of Cd-contaminated soil to a certain extent. The overall effect was in the order of strain ZG2 with biochar > biochar > strain ZG2. The combination of strain ZG2 and biochar reduced soil available Cd by 48.2%, the aboveground biomass of pakchoi increased by 72.1%, and the aboveground Cd content decreased by 73.3%. At the same time, it promoted the growth and development of the root system and improved the microbial community structure of the rhizosphere soil. The results indicated that chicken manure-derived biochar could enhance the stability of CdCO3 precipitation induced by strain ZG2, and strain ZG2 combined with biochar could achieve a more stable remediation effect on Cd-contaminated soil.

Biodegradation of microplastics derived from controlled release fertilizer coating: Selective microbial colonization and metabolism in plastisphere

Coated controlled-release fertilizers (CRFs) are widely used in agriculture, and the persistent presence of residual polymer coating has raised environmental concerns. This study investigates the underlying degradation dynamics of microplastics (MPs) derived from three typical materials used in CRFs, including polyethylene (PE), epoxy (EP), and polyurethane (PU), through a soil degradation test. The formation of surface biofilm, the succession process, and metabolic characteristics of microbial community are revealed by laser scanning confocal microscope, 16S rRNA sequencing, and non-targeted metabolomics analysis. The weight loss rates of PE, EP, and PU after 807 days of degradation were 16.70 %, 2.79 %, and 4.86 %, respectively. Significant secondary MPs were produced with tears and holes appeared in the coating cross sections and pyrolysis products were produced such as ethers, acids, and esters for PE; alkanes, olefins and their branched-chain derivatives for EP; and short-chain fatty acids and benzene molecules for PU. The coating surface selectively recruited the bacteria of Chujaibacter and Ralstonia and fungus of Fusarium and Penicillium, forming biofilm composed of lipids, proteins, and living cells. The metabolism of amino acids and polymers was enhanced to protect against MP-induced stress. The metabolites or intermediates of organic acids and derivatives, oxygen-contained organic compounds, and benzenoids on CRF surface increased significantly compared with soil, but there were no significant differences among different coating types. This study provides insights to the underlying mechanisms of biodegradation and microenvironmental changes of MPs in soil.

First Insights into the Bacterial Diversity of Mount Etna Volcanic Caves

While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world.

Non-targeted metabolomics and 16s rDNA reveal the impact of uranium stress on rhizosphere and non-rhizosphere soil of ryegrass

As a radioactive heavy metal element with a long half-life, uranium causes environmental pollution when it enters the surrounding soil. This study analyzed the changes about soil enzyme activity, non-targeted metabolomics, microbial community structure and function microbial community structure and function to assess the differences in the effects of uranium stress on rhizosphere and non-rhizosphere soil. Results showed that uranium stress significantly inhibited the activities of urease and sucrase in rhizosphere and non-rhizosphere, which had less effect on rhizosphere. Compare to the non-rhizosphere soil, the uranium stress induced the production of gibberellin A1, to promoted several metabolic pathways, such as nitrogen and PTS (Phosphotransferase system) metabolic in rhizosphere soil. The species and abundance of Aspergillus, Acidobacter, and Synechococcus in both rhizosphere and non-rhizosphere soil were decreased by uranium stress. However, the microorganisms in rhizosphere soil were less inhibited according to the soil metabolism and microbial network map analysis. Furthermore, the Chujaibacter in rhizosphere soil under uranium stress was found significantly positively correlated with lipid and organic oxygen compounds. Overall, the results indicated that ryegrass roots significantly alleviated the effects of uranium stress on soil microbial activity and population abundances, thus playing a protective role. The study also provided a theoretical basis for in-depth understanding of the biological effects, prevention and control mechanisms of uranium-contaminated soil.

Biodegradation of 1,4-dioxane by a native digestate microbial community under different electron accepting conditions

The potential of a native digestate microbial community for 1,4-dioxane (DX) biodegradation was evaluated under low dissolved oxygen (DO) concentrations (1-3 mg/L) under different conditions in terms of electron acceptors, co-substrates, co-contaminants and temperature. Complete DX biodegradation (detection limit of 0.01 mg/L) of initial 25 mg/L was achieved in 119 days under low DO concentrations, while complete biodegradation happened faster at 91 and 77 days, respectively in nitrate-amended and aerated conditions. In addition, conducting biodegradation at 30 ˚C showed that the time required for complete DX biodegradation in unamended flasks reduced from 119 days in ambient condition (20-25 °C) to 84 days. Oxalic acid, which is a common metabolite of DX biodegradation was identified in the flasks under different treatments including unamended, nitrate-amended and aerated conditions. Furthermore, transition of the microbial community was monitored during the DX biodegradation period. While the overall richness and diversity of the microbial community decreased, several families of known DX-degrading bacteria such as Pseudonocardiaceae, Xanthobacteraceae and Chitinophagaceae were able to maintain and grow in different electron-accepting conditions. The results suggested that DX biodegradation under low DO concentrations, where no external aeration was provided, is possible by the digestate microbial community, which can be helpful to the ongoing research for DX bioremediation and natural attenuation.

Thermomonas paludicola sp. nov., isolated from a lotus wetland

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated IMCC34681^T, was isolated from a lotus wetland in the Republic of Korea. Cellular growth occurred at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and with 0-2 % (w/v) NaCl (optimum, 0.5 % NaCl). The results of 16S rRNA gene sequence analysis indicated that IMCC34681^T represented a member of the genus Thermomonas, sharing 95.3-96.9 % similarities with type strains of species of the genus. The whole-genome sequence of IMCC34681^T was 2.72 Mbp in size with 66.2 % DNA G+C content. The IMCC34681^T genome shared the highest average nucleotide identity (ANI) value, 82.8 %, with that of Thermomonas brevis KACC 16975^T among species of the genus Thermomonas, indicating that the strain represents a novel genomic species. The major respiratory quinone of the strain was ubiquinone-8 (Q-8) and the predominant cellular fatty acids were iso-C_15 : 0 (25.7 %) and iso-C_14 : 0 (20.8 %). The strain harboured diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as major fatty polar lipids. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, IMCC34681^T was assigned to the genus Thermomonas as the type strain of a novel species, for which the name Thermomonas paludicola sp. nov. is proposed. The type strain is IMCC34681^T (=KACC 21793^T=NBRC 114635^T).

Effects of Tetracycline and Copper on Water Spinach Growth and Soil Bacterial Community

The effects of tetracycline (TC) and copper (Cu) on the growth of water spinach and the bacterial community structure in soil were examined in this study. The results revealed that a single Cu treatment decreased water spinach development more severely than TC, and that the toxic effects of TC and Cu on water spinach were synergistic at low doses and antagonistic at high concentrations. The single Cu treatment had the largest influence on the activities of three antioxidant enzymes (Superoxide Dismutase (SOD), Peroxidase (POD), Catalase (CAT)) and the content of Malondialdehyde (MDA) in water spinach leaves, followed by the TC and Cu composed treatment, with the single TC treatment having the least effect. The results of 16Sr RNA sequence analysis showed that the richness and diversity of soil bacterial communities were reduced by either a single TC or Cu treatment. Cu had a greater effect on the composition of the microbial community at genus level than TC. In conclusion, Cu had a greater influence on the growth of water spinach and soil microbial community composition than TC. TC and Cu exhibited synergistic effects at low concentrations and antagonistic effects at high concentrations on relevant indicators when Cu concentration was fixed.

Effect of the coexistence of endosulfan on the lindane biodegradation by Novosphingobium barchaimii and microbial enrichment cultures

Organochlorine pesticides, especially lindane and endosulfan, have been demonstrated to be both biodegradable and frequently coexistent, but their inhibitory effect has never been studied. In this study, we investigated the effect of endosulfan coexistence on lindane degradation to a lindane-degrading isolate, Novosphingobium barchaimii strain LL02, and mixed enrichment cultures from two different inocula. Our results of the lindane degradation batch experiments demonstrated that endosulfan concentration above 20 mg L^-1 causes significant inhibition to the lindane degradation efficiency of the strain LL02. Besides, the acidic conditions at pH 5.0 to 6.0 further decreased its lindane degradation rate constants by 57% compared to the neutral and alkaline conditions. For the mixed microbial cultures, the lindane degradation efficiency in the lindane/endosulfan co-contamination conditions decreased by 35.7%-50.7% compared to the lindane alone conditions. From our 16S rRNA amplicon sequencing results through the PacBio platform, most of the predominant bacteria in the lindane-enriched cultures were depressed in the lindane/endosulfan-enriched cultures. Moreover, bacteria of Burkholderia australis, Chujaibacter soli, Flavitalea flava, and one Rhodanobacteraceae bacterium were relatively highly abundant in the co-contamination enrichment cultures, suggesting their potential for lindane degradation under the endosulfan stress. Our results demonstrated that endosulfan coexistence causes inhibitory impacts on lindane biodegradation toward both lindane-degrading bacteria and mixed microbial cultures. The coexistence of multiple organochlorine pesticides on the biodegradation efficiencies should be carefully considered when applying bioremediation to remove organochlorine pesticide contamination.

Soil characteristics and microbial community response in rare earth mining areas in southern Jiangxi Province, China

The microbial community and functional flora in rare earth mining areas are correlated, but the characteristics and metabolic pathways of pollutant in such mining areas are still poorly known. The heavy metals, rare earth elements, and microorganisms present after mining of rare earth mine sites were analyzed. After mining, all sampling sites exhibited low pH and low total organic carbon levels, accompanied by high iron and aluminum concentrations. The development of vegetation is closely related to the development of microorganisms. In the complex environment of rare earth mining areas, Proteobacteria exhibit an absolute competitive advantage. During mine environmental recovery, the relative abundances of Acidobacteria and Chloroflexi will increase markedly, and with further restoration the relative abundance of Firmicutes will gradually decrease. Many genera of bacteria related to the N cycle and heavy metal metabolism were detected in the study area, indicating the important metabolic pathways for ammonia nitrogen and heavy metals in rare earth mining areas. Bacterial genera that promote plant nitrogen fixation also occur in the area, further revealing the nitrogen cycle. This research is important for health assessment and recovery of rare earth mines.

Robust Nitritation Sustained by Acid-Tolerant Ammonia-Oxidizing Bacteria

Oxidation of ammonium to nitrite rather than nitrate, i.e., nitritation, is critical for autotrophic nitrogen removal. This study demonstrates a robust nitritation process in treating low-strength wastewater, obtained from a mixture of real mainstream sewage with sidestream anaerobic digestion liquor. This is achieved through cultivating acid-tolerant ammonia-oxidizing bacteria (AOB) in a laboratory nitrifying bioreactor at pH 4.5-5.0. It was shown that nitrite accumulation with a high NO₂^-/(NO₂^- + NO₃^-) ratio of 95 ± 5% was stably maintained for more than 300 days, and the obtained volumetric NH₄⁺ removal rate (i.e., 188 ± 14 mg N L^-1 d^-1) was practically useful. 16S rRNA gene sequencing analyses indicated the dominance of new AOB, "Candidatus Nitrosoglobus," in the nitrifying guild (i.e., 1.90 ± 0.08% in the total community), with the disappearance of typical activated sludge nitrifying microorganisms, including Nitrosomonas, Nitrospira, and Nitrobacter. This is the first identification of Ca. Nitrosoglobus as key ammonia oxidizers in a wastewater treatment system. It was found that Ca. Nitrosoglobus can tolerate low pH (<5.0), and free nitrous acid (FNA) at levels that inhibit AOB and nitrite-oxidizing bacteria (NOB) commonly found in wastewater treatment processes. The in situ inhibition of NOB leads to accumulation of nitrite (NO₂^-), which along with protons (H⁺) also produced in ammonium oxidation generates and sustains FNA at 3.0 ± 1.4 mg HNO₂-N L^-1. As such, robust PN was achieved under acidic conditions, with a complete absence of NOB. Compared to previous nitritation systems, this acidic nitritation process is featured by a higher nitric oxide (NO) but a lower nitrous oxide (N₂O) emission level, with the emission factors estimated at 1.57 ± 0.08 and 0.57 ± 0.03%, respectively, of influent ammonium nitrogen load.

Characterization of sludge reduction and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time

Sludge reduction performance and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time were characterized. Throughout the operation period of 281 days, the total loading sludge and the total digested sludge were 4700 and 3300 kg-MLSS. After 114 days of operation, the residual MLSS (RMLSS) in the reactors for sludge treatment was maintained at 18-25 kg-RMLSS m^-3, and the sludge reduction efficiency achieved 95% under the F/M ratio (kg-loading MLSS kg-RMLSS^-1) of less than 0.018. Also, among the sludge components, both fixed suspended solids and volatile suspended solids were reduced. Based on the sludge reduction performance and the RNA-based bacterial community characteristics, the combined action of the maintenance metabolism, lysis-cryptic growth, and particulate inorganic matter is proposed as the sludge reduction mechanism in the multi-stage sludge treatment process.

Long-term fertilization regimes change soil nitrification potential by impacting active autotrophic ammonia oxidizers and nitrite oxidizers as assessed by DNA stable isotope probing

Chemoautotrophic ammonia-oxidizers and nitrite-oxidizers are responsible for a significant amount of soil nitrate production. The identity and composition of these active nitrifiers in soils under different long-term fertilization regimes remain largely under-investigated. Based on that soil nitrification potential significantly decreased in soils with chemical fertilization (CF) and increased in soils with organic fertilization (OF), a microcosm experiment with DNA stable isotope probing was further conducted to clarify the active nitrifiers. Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were found to actively respond to urea addition in soils with OF and no fertilizer (CK), whereas only AOB were detected in soils with CF. Around 98% of active AOB were Nitrosospira cluster 3a.1 in all tested soils, and more than 90% of active AOA were Nitrososphaera subcluster 1.1 in unfertilized and organically fertilized soils. Nitrite oxidation was performed only by Nitrospira-like bacteria in all soils. The relative abundances of Nitrospira lineage I and VI were 32% and 61%, respectively, in unfertilized soils, and that of Nitrospira lineage II was 97% in fertilized soils, indicating long-term fertilization shifted the composition of active Nitrospira-like bacteria in response to urea. This finding indicates that different fertilizer regimes impact the composition of active nitrifiers, thus, impacting soil nitrification potential.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.