Soil Bacteria Research Articles

Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist.

Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium's utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.

Fabrication and characterisation of B-ZnO nanoparticles for photodegradation of ciprofloxacin antibiotic and textile dyes

ABSTRACT The study is centred on the synthesis of B-ZnO photocatalysts via a straightforward mechanochemical combustion method using various weight percentages of B. The synthesised photocatalysts were characterised by XRD, FTIR, FESEM, TEM, XPS, UV-DRS, and BET. Biopersistent ciprofloxacin (CIP) degradation efficiency was investigated with the synthesised B-ZnO. Among the compositions, 4%B-ZnO exhibited the highest photocatalytic efficiency in degrading CIP under both natural sunlight and UV-C. The excellent catalytic activity was attributed to the increased surface area of 4% B-ZnO determined through BET analysis. Under optimised conditions (CIP: 10 mg/L, pH: 6.3, photocatalyst dose: 0.4 g/L), the highest CIP photodegradation efficiency was 92.05% over only 60 min of sunlight irradiation and 90.95% under 80 min of UV-C irradiation. The degradation products of CIP exhibited no antibacterial activity against random soil bacteria. The degradation of CIP followed pseudo-first-order kinetics, with a rate constant of 0.023 min−1. Scavenger tests implied •O2 − radicals’ involvement in photodegradation. CIP mineralisation by 48.53% over 3 h under sunlight was observed. After undergoing four cycles of sunlight exposure, the degradation efficiency reached 84.89%. Additionally, during 80 min of UV-C irradiation, the photodegradation efficiency of the dyes turquoise blue and Congo red was 77.91% and 98.92%, respectively.

Reuse of biogas sludge for the slow-release fertilizer production to improve fertilizer use efficiency and soil fertility

Fertilizer overuse causes negative impacts on the environment and crop yields. Therefore, the production of slow-release fertilizers from biogas sludge is a potential solution for waste reuse and sustainable use of fertilizers. Granular fertilizers containing primary macronutrients (N, P and K) were formulated using biogas sludge and supplementary chemical compounds before coating with a thin film of glutaraldehyde cross-linked gelatin. The coating films reduced the release rates of N and P effectively. The application of formulated biogas fertilizers resulted in the competitive yield and growth rate of mustard greens over the 45-days cultivation compared to the application of commercial fertilizers. Particularly, the application of coated biogas fertilizers led to less nutrient losses in drainage water while maintained a balanced supply of available nutrients and beneficial bacteria in soils. This study emphasizes the feasibility to reuse biogas sludge for slow-release fertilizers production in improving fertilizer use efficiency and soil fertility.

Comparing the population density, colony diversity, and phosphate solubilization ability between rice root endophytic and rice rhizospheric soil bacteria from organic wetland

Abstract Phosphate-solubilizing bacteria (PSB) play important roles in the agricultural systems. The present study aims to compare the population density, colony diversity, and phosphate solubilization ability between rice root endophytic bacteria (RRoEB) and rice rhizospheric soil bacteria (RRzSB) from organic wetland. By spread plate method, bacteria were isolated directly using Pikovskaya’s agar and indirectly through other media, namely Nutrient Agar (NA), Starch Casein Agar (SCA), Jensen, and Yeast Extract Mannitol Agar (YEMA). Each distinct colony based on the morphology on the respective media was screened for phosphate solubilization ability by subculturing on Pikovskaya’s agar. The phosphate solubilizing index (PSI) was measured from the halo zone formation. The results showed that by direct isolation, 6 RRoEB and 5 RRzSB were able to phosphate solubilization. By indirect isolation from NA, SCA, Jensen, and YEMA, 2, 3, 1, and 3 isolates of RRoEB and 4, 3, 1, and 3 isolates of RRzSB showed the capability as phosphate solubilizer. Although the highest colony diversity of PSB was obtained from direct isolation, however the highest PSI was yielded from indirect isolation, namely isolates J1R1 (3.53) and Y1S1 (2.48). The highest PSI from direct isolation was obtained by P1R5 (1.90) and P1S1 (1.51).

Characteristics of the Soil Microbial Community Structure under Long-Term Chemical Fertilizer Application in Yellow Soil Paddy Fields

To compare the differences in the soil microbial community structure in yellow soil paddy fields after the long-term application of chemical fertilizer, the role and mechanism of chemical fertilizer in maintaining soil microbial diversity were analyzed, and a theoretical basis for fertilization management in farmlands was provided. In this study, long-term experiments were conducted at the Scientific Observation and Experimental Station of the Arable Land Conservation and Agricultural Environment (Guizhou), Ministry of Agriculture and Rural Affairs. Soil samples were collected from five treatments: fertilizer N, P, and K (NPK); fertilizer P and K (PK); fertilizer N and K (NK); fertilizer N and P (NP); and no fertilizer (CK). High-throughput sequencing technology was used to analyze the microbial composition and diversity of the colonies, and the influencing factors are discussed. An analysis of the soil bacterial α diversity indices under the different fertilization treatments revealed that the long-term application of NPK fertilizers had less of an effect on the soil bacterial α diversity indices than did the CK. The long-term application of chemical fertilizers significantly reduced the soil bacterial Chao1, Shannon, and Simpson indices, while there was no significant difference in the bacterial Pielou e index among the treatments. The long-term application of chemical fertilizers significantly increased the soil fungal Chao1 index, but the effects on the other indices were not significant (p < 0.05). An analysis of the bacterial and fungal species under different fertilization treatments showed found that compared with CK, the long-term application of chemical fertilizer increased the relative abundance of Proteobacteria to varying degrees while reducing the relative abundance of Chloroflexi. The impact of other phyla was relatively small, and the difference in the relative abundance of fungi was not significant (p < 0.05). Principal component analysis revealed that, at the genus level, the bacterial and fungal community structures in the CK and NK treatments were relatively independent, while those in the NPK, PK, and NP treatments were similar. Random forest analysis revealed that OM, TP, and TK are the dominant factors that affect soil bacteria α diversity. The dominant factors affecting fungi α diversity are pH, OM, and AK. Redundancy analysis indicated that AK and TP were the main factors affecting bacterial community structure, while AP, AK, and pH were the main factors affecting fungal community structure. The conclusion drawn from this study is that the long-term application of nitrogen, phosphorus, and potassium fertilizer; phosphorus and potassium fertilizer; and nitrogen and phosphorus fertilizer can improve soil fertility, alter the soil environment, enhance microbial diversity, and improve the microbial community structure in yellow soil paddy fields, promoting soil ecosystem stability and health.

Biological activities and metabolomic profiles of extracts from the marine sediment bacterium Nocardiopsis alba DP1B cultivated in different media

The soil bacterium DP1B was isolated from a marine sediment collected off the coast of Randayan Island, Kalimantan Barat, Indonesia and identified based on 16S rDNA as Nocardiopsis alba. The bacterium was cultivated in seven different media (A1, ISP1, ISP2, ISP4, PDB, PC-1, and SCB) with three different solvents [distilled water, 5 % NaCl solution, artificial seawater (ASW)] combinations, shaken at 200 rpm, 30 °C, for 7 days. The culture broths were extracted with ethyl acetate and each extract was tested for its antimicrobial activity and brine shrimp lethality, and the chemical diversity was assessed using thin-layer chromatography (TLC), gas chromatography (GC), and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The result showed that almost all extracts showed antibacterial but not antifungal activity, whereas their brine shrimp toxicity levels vary from high to low. The best medium/solvent combinations for antibacterial activity and toxicity were PC-1 (in either distilled water, 5% NaCl solution, or ASW) and SCB in ASW. Different chemical diversity profiles were observed on TLC, GC-MS, and LC-MS/MS. Extracts from the PC-1 cultures seem to contain a significant number of cyclic dipeptides, whereas those from the SCB cultures contain sesquiterpenes, indicating that media and solvent compositions can affect the secondary metabolite profiles of DP1B. In addition, untargeted metabolomic analyses using LC-MS/MS showed many molecular ions that did not match with those in the Global Natural Products Social Molecular Networking (GNPS) database, suggesting that DP1B has great potential as a source of new natural products.

The effect of botanical pesticide application and mycorrhiza on colonization of mycorrhiza, soil microbial communities, growth and yield of maize on Ultisols

An experiment to study the effect of synthetic and botanical pesticide and arbuscular mycorrhizae (AMF) on mycorrhizal colonization, population of soil microbes, growth and yield of maize on Ultisols was carried out in green house of Agriculture Faculty, Universitas Padjadjaran at Jatinangor, Sumedang District, West Java Indonesia The experiment design used was Factorial Randomized Block, consisted two factors. The first factor was pesticide consisted five levels i.e. without pesticide; neem (Azadirachta indica A. Juss) pesticide; Annona muricata pesticide ; furadan and regent. The second factor was mycorrhiza consisted two levels i.e. without AMF inoculation and AMF inoculation. The experiment consisted two units with three replications; the first unit was harvested in the end of vegetative period to observe percentage of mycorrhizal infection, population of soil bacteria and fungi, fosfor uptake and dry weight of shoot, and the second unit was harvested in the end of generative period to find out the yield of maize. The results of this experiment showed that there was no interaction effect between pesticide and AMF on percentage of mycorrhizal infection, population of soil bacteria and fungi, fosfor uptake, dry weight of shoot and yield of maize. Pesticide decreased percentage of mycorrhizal infection and population of soil bacteria and increased yield of maize. Furthermore, AMF increased fosfor uptake and yield of maize.

Microplastics alter cadmium accumulation in different soil-plant systems: Revealing the crucial roles of soil bacteria and metabolism

Cadmium (Cd) and microplastics (MPs) gradually increased to be prevalent contaminants in soil, it is important to understand their combined effects on different soil-plant systems. We studied how different doses of polylactic acid (PLA) and polyethylene (PE) affected Cd accumulation, pakchoi growth, soil chemical and microbial properties, and metabolomics in two soil types. We found that high-dose MPs decreased Cd accumulation in plants in red soil, while all MPs decreased Cd bioaccumulation in fluvo-aquic soil. This difference was primarily attributed to the increase in dissolved organic carbon (DOC) and pH in red soil by high-dose MPs, which inhibited Cd uptake by plant roots. In contrast, MPs reduced soil nitrate nitrogen and available phosphorus, and weakened Cd mobilization in fluvo-aquic soil. In addition, high-dose PLA proved detrimental to plant health, manifesting in shortened shoot and root lengths. Co-exposure of Cd and MPs induced the shifts in bacterial populations and metabolites, with specific taxa and metabolites closely linked to Cd accumulation. Overall, co-exposure of Cd and MPs regulated plant growth and Cd accumulation by driving changes in soil bacterial community and metabolic pathways caused by soil chemical properties. Our findings could provide insights into the Cd migration in different soil-plant systems under MPs exposure. Environmental ImplicationMicroplastics (MPs) and cadmium (Cd) are common pollutants in farmland soil. Co-exposure of MPs and Cd can alter Cd accumulation in plants, and pose a potential threat to human health through the food chain. Here, we investigated the effects of different types and doses of MPs on Cd accumulation, plant growth, soil microorganisms, and metabolic pathways in different soil-plant systems. Our results can contribute to our understanding of the migration and transport of Cd by MPs in different soil-plant systems and provide a reference for the control of combined pollution in the future research.

Effects of Organic Fertilizer Addition to Vegetation and Soil Bacterial Communities in Saline-Alkali-Degraded Grassland with Photovoltaic Panels.

The Songnen grassland is an important resource for livestock production in China. Due to the intensification of anthropogenic activities in recent years, vegetation degradation has worsened, and the salinization of grassland has become increasingly serious, which severely affects the sustainable development of grassland animal husbandry. In this study, organic fertilizer addition was carried out at saline-and-alkaline-degraded Songnen grassland sites with photovoltaic panels, and we investigated the effects of organic fertilizer treatments on the vegetation and soil bacteria in these areas. The results showed that both organic fertilizer treatments increased the community composition and diversity indices of plants (p < 0.05); they also had significant effects on soil electrical conductivity and rapidly available potassium (p < 0.05). In the dominant phylum of bacteria, the relative abundance of Firmicutes increased without adding organic fertilizer under the photovoltaic panel; the addition of organic fertilizer had a significant effect on the relative abundance of Firmicutes and Desulfobacterota (p < 0.05), reducing their relative abundance, respectively. There were differences in the number of bacteria at the genus level under different treatments compared to the control, with the highest enrichment of bacteria occurring at the OFE position, and a significant difference (p < 0.05) being found between the control and the other four groups at the genus level of g_norank_f_norank_o_Actinomarinales. Organic fertilizer had a significant effect on the bacterial Simpson diversity index, with the most significant increasing trend found in OFE (the front eaves of the photovoltaic panel in fertilization area). The results of a correlation analysis showed that pH, electrical conductivity, and total nitrogen were the main factors affecting the soil bacterial community.

Effects of Organic Fertilizer with Different Degrees of Maturity on Bacteria in Saline–Alkali Soil

Soil microorganisms are important components of soil ecosystems, and their diversity plays an important role in maintaining their functional stability. Organic fertilizer is an important measure for improving soil fertility in agronomic practice. The effects of organic fertilizer on soil microbial diversity and community structure are different with different degrees of maturation. In this study, uncomposted organic fertilizer (R), high-temperature organic fertilizer (H), cooling organic fertilizer (C), and decomposed organic fertilizer (D) were applied, and the 16S rRNA gene sequences of bacteria in soil were analyzed via high-throughput sequencing technology to understand the effects of organic fertilizer with different degrees of maturation on bacterial diversity and community structure in saline soil. Compared with no fertilization, the uncomposted organic fertilizer, high-temperature organic fertilizer, and decomposed organic fertilizer treatments significantly reduced soil bacterial diversity: the decomposed organic fertilizer treatment significantly reduced soil bacterial richness, the cooling organic fertilizer treatment had no significant effect on soil bacterial diversity and bacterial richness, Proteobacteria representing soil nutrients significantly increased under the cooling organic fertilizer treatment, and the relative abundance of Firmicutes significantly decreased. These four organic fertilizers, with different degrees of maturation, significantly increased the beneficial bacterium Bacillus and nitrile-based degrading bacteria but also significantly increased the potential pathogenicity of the soil, and there was no significant difference between the four treatments. In addition, during a cooling period, the organic fertilizer treatment helped to increase the population of oxidative-stress-tolerant bacteria. The application of organic fertilizer during a cooling period to saline–alkali soil is more helpful in improving its nutrient levels.

Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

Identification of Growth-Promoting Bacterial Resources by Investigating the Microbial Community Composition of Polyporus umbellatus Sclerotia.

The sclerotium of the edible mushroom Polyporus umbellatus (Zhuling) exhibits various medicinal properties. However, given its long growth cycle and overexploitation, wild resources are facing depletion. Macrofungal growth depends on diverse microbial communities; however, the impact of soil bacteria on P. umbellatus development is unknown. Here, we combined high-throughput sequencing and pure culturing to characterize the diversity and potential function of bacteria and fungi inhabiting the P. umbellatus sclerotium and tested the bioactivities of their isolates. Fungal operational taxonomic units (OTUs) were clustered and classified, revealing 1275 genera. Bacterial OTUs yielded 891 genera. Additionally, 81 bacterial and 15 fungal strains were isolated from P. umbellatus sclerotia. Antagonism assays revealed three bacterial strains (FN2, FL19, and CL15) promoting mycelial growth by producing indole-3-acetic acid, solubilizing phosphate, and producing siderophores, suggesting their role in regulating growth, development, and production of active compounds in P. umbellatus. FN2-CL15 combined with bacterial liquid promoted growth and increased the polysaccharide content of P. umbellatus mycelia. This study reports new bioactive microbial resources for fertilizers or pesticides to enhance the growth and polysaccharide accumulation of P. umbellatus mycelia and offers guidance for exploring the correlation between medicinal macrofungi and associated microbial communities.

Response of Soil Microbial Community Structure and Diversity to Mixed Proportions and Mixed Tree Species in Bamboo–Broad-Leaved Mixed Forests

Bamboo and broad-leaved mixed forests have been widely recognized for their advantages in maintaining ecological balance, improving soil fertility, and enhancing biodiversity. To understand the effects of mixed broad-leaved tree species and mixing ratios on soil microbial communities in bamboo and broad-leaved mixed forests, we quantified the structure and diversity responses of soil microbial communities to tree species and mixing ratios using high-throughput sequencing of the 16 S rRNA gene. Three bamboo and broad-leaved tree mixed forests were studied, including bamboo–Castanopsis chinensis Hance mixed forest (CCB), bamboo–Alniphyllum fortune (Hemsl.) Makino mixed forest (AFB), and bamboo–Choerospondias axillaris (Roxb.) B. L. Burtt &amp; A. W. Hill mixed forest (CAB). We assessed the impact of tree species and mixing ratios on soil microbial communities by measuring soil properties and the diversity and composition of soil microbes. The results indicate that soil properties and the diversity and composition of microbial communities are highly dependent on broad-leaved tree species in mixed forests. The mixing ratios had a more pronounced effect on microbial diversity than on richness. In CAB, diversity peaked at mixing ratios of 10%–20% and 20%–40%. The presence of broad-leaved trees significantly altered the relationships among soil bacteria, with CAB showing the highest stability, likely due to the increased diversity and quantity of litter from Choerospondias axillaris. Our results show that the choice of broad-leaved tree species and their mixing ratios significantly influence soil microbial diversity and composition in bamboo–broad-leaf mixed forests. An optimal mixing ratio in CAB can maximize bacterial diversity and stability, providing insights for forest management and promoting ecosystem health and sustainability.

CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme.

The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this study, we employed QM/MM calculations to investigate whether the reaction mechanism of the silver-substituted enzyme is similar to that of the native enzyme. Our results suggest that the Ag-substituted enzyme can oxidize CO and release CO2 following the same reaction steps as the native enzyme, with a computed rate-limiting step of 10.4 kcal/mol, consistent with experimental findings. Surprisingly, lower activation energies for C-O bond formation have been found in the presence of silver. Furthermore, comparison of rate constants for reduction of copper- and silver-containing enzymes suggests a discrepancy in the transition state stabilization upon silver substitution. We also evaluated the effects that differences in the water-active site interaction may exert on the overall energy profile of catalysis. Finally, the formation of a thiocarbonate intermediate along the catalytic pathway was found to be energetically unfavorable for the Ag-substituted enzyme. This finding aligns with the hypothesis proposed for the wild-type form, suggesting that the creation of such species may not be necessary for the enzymatic catalysis of CO oxidation.

The effects of straw return on soil bacterial diversity and functional profiles: A meta-analysis

Returning straw directly to agricultural fields increases soil carbon sequestration and influences soil microbial activities. However, the precise impacts of straw return on soil bacterial diversity, composition, and function profiles remain unclear, necessitating a comprehensive synthesis and standardized analysis. In this study, we conducted a meta-analysis of 729 original bacterial sequencing samples from fields with and without straw return to elucidate how soil bacteria respond to different experimental conditions after straw return (e.g., straw and fertilizer management practices and return duration). Our analysis revealed that overall straw return slightly increased the Chao 1 index while the Shannon index remained unaffected. However, we found strong responses depending on the experimental conditions of straw return. Particularly, bacterial community diversity increased significantly, particularly under high nitrogen, low straw addition, or continuous straw return. Furthermore, straw return altered bacterial community composition, elvating the abundance of Proteobacteria and Bacteroidetes, while decreasing Chloroflexi, Firmicutes, and Nitrospirae. Straw return also increased modularity in bacterial co-occurrence networks. Functional annotation analysis highlighted that straw return substantially enriched microbes involved in chemoheterotrophy, nitrogen fixation, and functional groups related to straw decomposition (chitinolysis, cellulolysis, xylanolysis), while inhibiting microbes associated with nitrification and nitrate reduction. Surprisingly, straw return did not impact the relative abundance of plant pathogens. Overall, our findings offer an in-depth understanding the effects of straw return on soil bacterial communities, including increased diversity, modified structure, and enhanced functional profiles related to straw decomposition.

Evaluation of the Rhizosphere Resistome of Cultivated Soils Polluted with Antibiotics from Reclaimed Wastewater

The use of reclaimed wastewater to irrigate crops is a valuable option due to water scarcity. However, the presence of antibiotics residues that are not removed in the tertiary treatments reaches crop soils when irrigated and it poses a serious concern for human health. Crops rhizosphere is considered a hotspot of antibiotic resistant genes (ARG) being in addition a link to plant phyllosphere and human microbiome. Understanding the structure of the soil microbiota is crucial before applying any bioremediation or biostimulation strategy. The aim of this work was firstly to confirm the presence of antibiotics residues in soil and fruits in two greenhouses at the south of Spain irrigated with reclaimed water. Secondly, to characterize the rhizosphere microbiome of three crops (Capsicum annuum, Cucumis melo and Solanum melongena) cultured in those greenhouses. Finally, a predictive functional analysis was done using PICRUSt2 to figure out the rhizosphere resistome. The presence of residues of antibiotics was confirmed both soil and fruits. Antibiotics absorbed by plants correlated with those on soil. The most abundant resistance gene was the multidrug in all the three crops tested. Compatibility of basidiomycete fungi (i.e., Pleurotus) with soil bacteria could be indicative of their possible use for restoration of agricultural soils polluted with antibiotics.

Optimizing Irrigation and Fertilization to Simultaneously Improve Potato Tuber Yield, Water and Fertilizer Use Efficiency and Net Income in Northwest China

Irrigation, fertilization, and variety are important factors affecting potato production in northwest China. Field experiments (2021 and 2022) were performed to investigate the effects of irrigation and fertilization on the plant growth and soil microbial population of different potato varieties. Three irrigation levels were used, i.e., 100% ETc (W1), 80% ETc (W2), and 60% ETc (W3), with ETc standing for crop evapotranspiration. Three fertilization levels were used (N-P-K), i.e., 240-120-300 kg ha−1 (F1), 180-90-225 kg ha−1 (F2), and 120-60-150 kg ha−1 (F3). Three variety types were used, i.e., Feiurita (V1), Longshu 7 (V2), and Qingshu 9 (V3). These factors significantly influenced tuber yield (TY), net income (NI), and water productivity (WP). TY, NI, WP, total nitrogen accumulation (TNA), and nitrogen use efficiency (NUE) peaked at F2. Fertilization significantly impacted soil bacteria quantity (SBQ), fungi quantity (SFQ), and actinomycetes quantity (SAQ). TY, NI, SBQ, SFQ, and SAQ were highest at W2. Soil microbial population was strongly correlated with TY, NI, WP, TNA, and NUE. Comprehensively, this study suggests that irrigation that is varied from 248 to 266 mm, and fertilization (N-P-K) that is varied from 149.09-74.55-186.36 to 212.73-106.36-265.91 kg ha−1 can promote the potato industry’s sustainable development and provide important references for the optimal field management of potato cultivation in northwest China.

The activity of CobB1 protein deacetylase contributes to nucleoid compaction in Streptomyces venezuelae spores by increasing HupS affinity for DNA.

Streptomyces are soil bacteria with complex life cycle. During sporulation Streptomyces linear chromosomes become highly compacted so that the genetic material fits within limited spore volume. The key players in this process are nucleoid-associated proteins (NAPs). Among them, HU (heat unstable) proteins are the most abundant NAPs in the cell and the most conserved in bacteria. HupS, one of the two HU homologues encoded by the Streptomyces genome, is the best-studied spore-associated NAP. In contrast to other HU homologues, HupS contains a long, C-terminal domain that is extremely rich in lysine repeats (LR domain) similar to eukaryotic histone H2B and mycobacterial HupB protein. Here, we have investigated, whether lysine residues in HupS are posttranslationally modified by reversible lysine acetylation. We have confirmed that Streptomyces venezuelae HupS is acetylated invivo. We showed that HupS binding to DNA in vitro is controlled by the acetylation. Moreover, we identified that CobB1, one of two Sir2 homologues in Streptomyces, controls HupS acetylation levels invivo. We demonstrate that the elimination of CobB1 increases HupS mobility, reduces chromosome compaction in spores, and affects spores maturation. Thus, our studies indicate that HupS acetylation affects its function by diminishing DNA binding and disturbing chromosome organization.

Interactions between plants and bacterial communities for phytoremediation of petroleum-contaminated soil.

Plants can stimulate the microbes to degrade ubiquitous petroleum hydrocarbons (PHCs), which has prompted a novel view on rhizoremediation. In the present study, the degradation rateof PHCs was investigated and 16S rRNA gene analysis was performed to investigate the PHC-degrading bacteria in petroleum-contaminated soil with different plants. Mirabilis jalapa (M. jalapa) has a higher PHC degradation rate than Lolium perenne (L. perenne) under petroleum contamination. The bacterial diversity in rhizospheric soil was decreased but the relative abundance of Actinobacteriota, Proteobacteria, and Candidatus Saccharibacteria were significant increased on 45days petroleum-contaminated rhizospheric soil. In addition, the relative expression of PHC degradation-related genes, the content ofmalic acid and citric acid of the root exudates in the two plants was significantly increased in response to petroleum stress. The content ofcitric acid increased 11.9 times in M. jalapa and 3.4 times in L. perenne, respectively, in response to petroleum stress. These results indicate that M. jalapa changes the hydrocarbon-degrading microbial community to enhance the degradation of PHCs by root exudates and phytostimulation.

Unlocking the diversity and plant‐growth promoting potential of the bulk soil bacteria associated with the Saharan tree Vachellia tortilis subsp. raddiana

AbstractIn this study, we investigated the bacterial diversity and plant growth‐promoting (PGP) properties of bulk soil bacteria of Vachellia tortilis subsp. raddiana collected from the Taidalt and Amazloug nature preserves area in southern Morocco. Using repetitive extragenic palindromic polymerase chain reaction fingerprinting and 16S rDNA sequencing, 93 strains were identified. They belonged mainly to the genera Bacillus and Peribacillus. In vitro tests for PGP traits showed high levels of activity for strains belonging to the genera Bacillus and Pseudomonas. It was relevant that several Bacillus strains produced auxin (maximum amount 262.61 µg mL−1 for Bacillus sp. LMR1097), solubilized phosphate (maximum amount 22.10 µg mL−1), or produced siderophores, while three strains were able to fix atmospheric nitrogen (LMR1145, LMR1013, and LMR1015). Inoculation of V. tortilis subsp. raddiana plants with selected bacterial strains (LMR881 and LMR1097) increased shoot and root growth parameters. The strain Pantoea sp. LMR881 had the highest mean values for shoot and root length (24.60–14.80 cm) and shoot dry weight (1.31 g), whereas Bacillus sp. LMR1097 showed the lowest mean shoot dry weight. Overall, these results highlight the potential of using selected native bacterial inoculants for improving growth of candidate tree plants to be used in restoration programs of arid degraded areas.