First report of diazotrophic Brevundimonas spp. as growth enhancer and root colonizer of potato

Integrated microbiome and metabolome approaches reveal the regulatory mechanism of pumpkin pollination

The fruit set in the Cucurbitaceae family is a critical determinant of fruit production and development. However, limited information is available regarding the regulatory mechanisms relating to pumpkin fruit sets. To elucidate the interplay between pumpkin fruit setting and endophytic microorganisms, we conducted a comparative analysis of the endophytic microbiota and metabolite profiles in the stems of naturally pollinated and non-pollinated pumpkin using microbiome and untargeted metabolomics approaches. The results showed that both the alpha- (reduced by 18.33∼21.88 % and 16.63∼24.08 %) and beta-diversities (reduced by 12.40 % and 40.00 %) of endophytic microorganisms (bacteria and fungi) in stems of pollinated pumpkins were significantly reduced which were significantly reduced compared to those in non-pollinated pumpkins. Meanwhile, in comparison with pollinated pumpkins, the deficiency of endophytic bacterial genera that regulate endogenous hormones and metabolites, such as Pantoea, Staphylococcus, Brevundimonas, Tatumella, and Gluconobacter, and the weak metabolic pathways, viz, the relatively stable homeostasis, such as flavone and flavonol biosynthesis, alanine, aspartate, and glutamate metabolism, and phenylpropanoid biosynthesis in stems of non-pollinated pumpkin were important reasons why fruits could not bear fruits without pollination. All above results reveal that endophytic microorganisms are closely related to the growth and development of pumpkins, also, the endophytic microbial community structures in stems of pumpkins can be reshaped by man-made measures, such as pollination.

Effect of increased cathodic nitrogen levels on anodic COD removal efficiency and bioelectricity generation in microbial fuel cells

Simultaneous nitrification and denitrification (SND) of nitrogen-rich wastewater in microbial fuel cells (MFCs) is a new-age technology capable of treating wastewater and concurrently generating bioelectricity. Compared to the conventionally used biological nitrogen elimination processes, SND in MFC is much more energy and cost-efficient because it uses less organic carbon and excludes the nitrified liquid circulation process. In this work with a dual-chambered MFC, carbon-rich synthetic wastewater (CRSW) with an invariable glucose concentration of 2 g/L has been treated in the anodic chamber and nitrogen-rich synthetic wastewater (NRSW) containing 1 g/L, 2 g/L, and 3 g/L ammonium chloride (NH4Cl) concentration has been treated in the cathodic chamber and concurrently bioelectricity has been generated. Results showed that CCV-2 with 2 g/L NH4Cl load in closed circuit (CCV) mode generated the highest cell voltage, current density, and volumetric power density of 80.56 mV, 23.69 mA/m2, and 12.97 mW/m3. Removal of chemical oxygen demand (COD), total Kjeldahl nitrogen (TKN), nitrite, and nitrate was also highest in CCV-2 being 90.25%, 92.18%, 85.78%, and 86.53% respectively. With further increment of NH4Cl concentration to 3 g/L concentration there was a decrement in COD, TKN, nitrite, nitrate, and power generation output because TKN concentration higher than 3 g/L slowed down the growth of exoelectrogenic bacteria and decreased organic and nitrogen removal rate along with power output. All experiments in CCV mode gave better results than their counterparts operated in open circuit (OCV) mode. In microbial community structure analysis, the dominant genus was found to be Brevendimonas, Sphingomonadaceae, and Achromobacter in the cathodic chamber treating NRSW.

The Composition and Function of Bacterial Communities Associated with the Northern Root-Knot Nematode (Meloidogyne hapla) Populations Showing Parasitic Variability

The co-existence of microbial communities and Meloidogyne hapla populations showing high, medium, and low levels of parasitic variability (PV) in mineral and muck soils with different soil health conditions in Michigan vegetable production fields is established. However, if PV relates or not to bacterial communities is unknown. This study characterized bacterial communities present on and in the body of nine M. hapla field and greenhouse sub-populations isolated from the mineral and muck fields. We utilized a high throughput sequencing of 16S rDNA. Results showed a variable composition (or abundance) of 65 genera in the field and 61 genera in the greenhouse isolates, with 12 genera of unknown and the rest belonging to 14 known functional groups. The medium- and low-PV populations shared more bacterial composition than either one with the high-PV population. Thus, laying a foundation for an in-depth understanding of if the observed associations have any role in cause-and-effect relationships with M. hapla PV.

Omics-centric evidences of fipronil biodegradation by Rhodococcus sp. FIP_B3

The widespread use of the pesticide fipronil in domestic and agriculture sectors has resulted in its accumulation across the environment. Its use to assure food security has inadvertently affected soil microbiome composition, fertility and, ultimately, human health. Degradation of residual fipronil present in the environment using specific microbial species is a promising strategy for its removal. The present study delves into the omics approach for fipronil biodegradation using the native bacterium Rhodococcus sp. FIP_B3. It has been observed that within 40 days, nearly 84% of the insecticide gets degraded. The biodegradation follows a pseudo-first-order kinetics (k = 0.0197/d with a half-life of ∼11 days). Whole genome analysis revealed Cytochrome P450 monooxygenase, peroxidase-related enzyme, haloalkane dehalogenase, 2-nitropropane dioxygenase, and aconitate hydratase are involved in the degradation process. Fipronil-sulfone, 5-amino-1-(2-chloro-4-(trifluoromethyl)phenyl)-4- ((trifluoromethyl)sulfonyl)-1H-pyrazole-3-carbonitrile, (E)-5-chloro-2-oxo-3- (trifluoromethyl)pent-4-enoic acid, 4,4,4-trifluoro-2-oxobutanoic acid, and 3,3,3- trifluoropropanoic acid were identified as the major metabolites that support the bacterial degradation of fipronil. In-silico molecular docking and molecular dynamic simulation-based analyses of degradation pathway intermediates with their respective enzymes have indicated stable interactions with significant binding energies (-5.9 to -9.7 kcal/mol). These results have provided the mechanistic cause of the elevated potential of Rhodococcus sp. FIP_B3 for fipronil degradation and will be advantageous in framing appropriate strategies for the bioremediation of fipronil-contaminated environment.

Deficit irrigation differentially modulates rhizosphere microbial community and metabolites of two potato genotypes differing in drought tolerance

Beneficial interactions between plant root exudates and the rhizosphere microbial community can alleviate the adverse effects of environmental stress on crop yields, but these interactions remain poorly understood in potato growing in drying soil. We investigated the responses of rhizosphere soil microorganisms and metabolites, and biochemical and physiological responses of two potato genotypes with contrasting drought tolerance (drought tolerant 'C93' and drought sensitive 'Favorita'), to two different irrigation treatments imposing contrasting soil water availability in the field. Deficit irrigation altered rhizosphere soil bacterial communities and metabolites of C93 more than Favorita. While the abundance of Nitrosospira and Nitrobacter belonging to the Proteobacteria increased in C93, in Favorita the Streptomyces and Nocardioides belonging to the Actinobacteria increased. These microbial changes were significantly correlated with rhizosphere organic acid concentrations, with 3-phenyllactic acid increasing in C93, and citric acid increasing in Favorita. Although deficit irrigation restricted shoot growth of C93 at the tuber initiation stage (unlike Favorita), its specific root length was 41% greater than Favorita irrespective of irrigation treatment. Deficit irrigation significantly increased foliar chlorophyll and proline accumulation of both genotypes, with the latter 28% higher in Favorita. Independent of irrigation treatment, yield of the more vigorous C93 (producing 22 and 89% more shoot biomass under deficit and full irrigation respectively) was 84% higher than Favorita. It was concluded that different potato genotypes selectively recruit beneficial microorganisms by secreting different organic acids to alleviate the adverse effects of deficit irrigation.

Metal-tolerant morganella morganii isolates can potentially mediate nickel stress tolerance in Arabidopsis by upregulating antioxidative enzyme activities

Plant growth-promoting rhizobacteria (PGPRs) have been utilized to immobilize heavy metals, limiting their translocation in metal contaminated settings. However, studies on the mechanisms and interactions that elucidate how PGPRs mediate Nickel (Ni) tolerance in plants are rare. Thus, in this study we investigated how two pre-characterized heavy metal tolerant isolates of Morganella morganii (ABT9 and ABT3) improve Ni stress tolerance in Arabidopsis while enhancing its growth and yield. Arabidopsis seedlings were grown for five weeks in control/Ni contaminated (control, 1.5 mM and 2.5 mM) potted soil, in the presence or absence of PGPRs. Plant growth characteristics, quantum yield, and antioxidative enzymatic activities were analyzed to assess the influence of PGPRs on plant physiology. Oxidative stress tolerance was quantified by measuring MDA accumulation in Arabidopsis plants. As expected, Ni stress substantially reduced plant growth (shoot and root fresh weight by 53.25% and 58.77%, dry weight by 49.80% and 57.41% and length by 47.16% and 64.63% over control), chlorophyll content and quantum yield (by 40.21% and 54.37% over control). It also increased MDA content by 84.28% at higher (2.5 mM) Ni concentrations. In contrast, inoculation with M. morganii led to significant improvements in leaf chlorophyll, quantum yield, and Arabidopsis biomass production. The mitigation of adverse effects of Ni stress on biomass observed in M. morganii-inoculated plants was attributed to the enhancement of antioxidative enzyme activities compared to Ni-treated plants. This upregulation of the antioxidative defense mechanism mitigated Ni-induced oxidative stress, leading to improved performance of the photosynthetic machinery, which, in turn, enhanced chlorophyll content and quantum yield. Understanding the underlying mechanisms of these tolerance-inducing processes will help to complete the picture of PGPRs-mediated defense signaling. Thus, it suggests that M. morganii PGPRs candidate can potentially be utilized for plant growth promotion by reducing oxidative stress via upregulating antioxidant defense systems in Ni-contaminated soils and reducing Ni metal uptake.

Phosphate solubilization and plant growth properties are promoted by a lactic acid bacterium in calcareous soil

On the basis of good phosphate solubilization ability of a lactic acid bacteria (LAB) strain Limosilactobacillus sp. LF-17, bacterial agent was prepared and applied to calcareous soil to solubilize phosphate and promote the growth of maize seedlings in this study. A pot experiment showed that the plant growth indicators, phosphorus content, and related enzyme activity of the maize rhizospheric soils in the LF treatment (treated with LAB) were the highest compared with those of the JP treatment (treated with phosphate solubilizing bacteria, PSB) and the blank control (CK). The types of organic acids in maize rhizospheric soil were determined through LC-MS, and 12 acids were detected in all the treatments. The abundant microbes belonged to the genera of Lysobacter, Massilia, Methylbacillus, Brevundimonas, and Limosilactobacillus, and they were beneficial to dissolving phosphate or secreting growth-promoting phytohormones, which were obviously higher in the LF and JP treatments than in CK as analyzed by high-throughput metagenomic sequencing methods. In addition, the abundance values of several enzymes, Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology, and Carbohydrate-Active Enzymes (CAZys), which were related to substrate assimilation and metabolism, were the highest in the LF treatment. Therefore, aside from phosphate-solubilizing microorganisms, LAB can be used as environmentally friendly crop growth promoters in agriculture and provide another viable option for microbial fertilizers. KEY POINTS: • The inoculation of LAB strain effectively promoted the growth and chlorophyll synthesis of maize seedlings. • The inoculation of LAB strain significantly increased the TP content of maize seedlings and the AP concentration of the rhizosphere soil. • The inoculation of LAB strain increased the abundances of the dominant beneficial functional microbes in the rhizosphere soil.

Nano-biofertilizers: utilizing nanopolymers as coating matrix-a comprehensive review

In modern agriculture, nanotechnology was recognized as a potentially transformative innovation. Nanopolymers as coating matrix in nano-biofertilizer has a massive impact on agricultural productivity. The integration of nanotechnology with biofertilizers has led to the creation of nano-biofertilizer formulations that enhance nutrient delivery, improve plant growth, and increase resistance to environmental stress. Nanopolymers, both synthetic and biogenic, including chitosan, cellulose, gelatin, sodium alginate, starch, and polyvinyl alcohol, are utilized as encapsulating materials. They are effective in ensuring controlled nutrient release and shielding beneficial microorganisms from external environmental conditions. Studies indicate that nano-biofertilizers improve soil quality, raise crop yields, and reduce the usage of chemical fertilizers to enhance sustainable agricultural practices. The review also addresses the microbial encapsulation methodology, release kinetics, phytotoxicity, challenges and future prospects of nano-biofertilizer technology, including nanoparticle-bacteria interaction, scalability, and regulatory considerations. This paper elaborates the potential and limitations of nano-biofertilizers, providing insights for future advancements in the agriculture field.

The Colonization of Synthetic Microbial Communities Carried by Bio-Organic Fertilizers in Continuous Cropping Soil for Potato Plants

Synthetic microbial communities (SynComs) play significant roles in soil health and sustainable agriculture. In this study, bacterial SynComs (SCBs) and fungal SynComs (SCFs) were constructed by selecting microbial species that could degrade the potato root exudates associated with continuous cropping obstacles. SCBs, SCFs, and SCB + SCF combinations were then inoculated into organic fertilizers (OFs, made from sheep manure) to produce three bio-organic fertilizers (BOFs), denoted by SBFs (BOFs of inoculated SCBs), SFFs (BOFs of inoculated SCFs), and SBFFs (BOFs of inoculated SCB + SCF combinations), respectively. The OF and three BOFs, with a chemical fertilizer (CK) as the control, were then used in pot experiments involving potato growth with soil from a 4-year continuous cropping field. Microbial diversity sequencing was used to investigate the colonization of SCBs and SCFs into the rhizosphere soil and the bulk soil, and their effects on soil microbial diversity were evaluated. Source Tracker analysis showed that SCBs increased bacterial colonization from the SBFs into the rhizosphere soil, but at a relatively low level of 1% of the total soil bacteria, while SCFs increased fungi colonization from the SFF into the bulk soil at a much higher level of 5-18% of the total soil fungi. In combination, SCB + SCF significantly increased fungi colonization from the SBFF into both the bulk soil and the rhizosphere soil. Overall, the soil fungi were more susceptible to the influence of the BOFs than the bacteria. In general, the application of BOFs did not significantly change the soil microbial alpha diversity. Correlation network analysis showed that key species of bacteria were stable in the soils of the different groups, especially in the rhizosphere soil, while the key species of fungi significantly changed among the different groups. LEfSe analysis showed that the application of BOFs activated some rare species, which were correlated with improvements in the function categories of the tolerance of stress, nitrogen fixation, and saprotroph functions. Mantel test analysis showed that the BOFs significantly affected soil physicochemical properties, influencing bacterial key species, and core bacteria, promoting potato growth. It was also noted that the presence of SynCom-inoculated BOFs may lead to a slight increase in plant pathogens, which needs to be considered in the optimization of SynCom applications to overcome continuous cropping obstacles in potato production.

Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae)

Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.

Antioxidant, Nutritional Properties, Microbiological, and Health Safety of Juice from Organic and Conventional 'Solaris' Wine (Vitis vinifera L.) Farming

This study investigated the technological parameters, microbiological, and functional properties of juice from Solaris grapes grown under conventional and organic farming systems to assess how these cultivation methods influence juice quality. The one-year study focused on key aspects such as the levels of health-promoting polyphenols, the presence of mycotoxins, and pesticide residues. Organic grapes showed greater bacterial and fungal diversity, with significant differences in dominant genera. Sphingomonas and Massilia were the predominant bacteria across both systems, while Erysiphe was more common in conventional grapes, and Aureobasidium was abundant in both. Despite the presence of genes for mycotoxin production, no mycotoxins were detected in the juice or pomace. Organic juice exhibited significantly higher levels of polyphenols, leading to enhanced antioxidant properties and improved technological characteristics, including lower acidity and higher nitrogen content. However, residues of sulfur and copper, used in organic farming, were detected in the juice, while conventional juice contained synthetic pesticide residues like cyprodinil and fludioxonil. These findings highlight that while organic juice offers better quality and safety in terms of polyphenol content and antioxidant activity, it also carries risks related to residues from organic treatments, and conventional juice poses risks due to synthetic pesticide contamination.

Microcystin-degrading bacteria reduce bioaccumulation in Fragaria vulgaris and enhance fruit yield and quality

In Morocco, red fruit production has thrived, primarily utilizing hydroponic methods to control crops, increase fruit yield and quality, and avoid soil-related problems. However, the irrigation of these expansive hydroponic farms relies heavily on water sourced from dams, many of which are contaminated with Microcystins (MCs). To address this contamination issue, ongoing research is focused on discovering effective and cost-efficient biological solutions for eliminating MCs. In this study, we isolate and identify bacterial strains capable of degrading MCs, evaluate the rate of degradation, and investigate how soil inoculated with these bacteria affects the accumulation of MCs in plant tissue. The partial 16S rRNA analyses of three bacterial sequences were conducted, identifying them through NCBI as follows: Ensifer sp. (B1) isolated from soil, Shinella sp. (B2) from a cyanobacterial bloom, and Stutzerimonas sp. (B3) from water. These bacteria exhibited the ability to degrade MCs, with approximately 34.75%, 73.75%, and 30.1% of the initial concentration (20 µg/L) being removed after a 6-day period for B1, B2, and B3, respectively. Moreover, strawberry plants were cultivated hydroponically in a greenhouse for a duration of 90 days. These plants were subjected to extracts of cyanobacteria containing 10 and 20 µg/L of Microcystins (MC), as well as water from an artificial lake contaminated with MC, both with and without the presence of isolated bacterial strains. Among these strains, Shinella sp. exhibited the highest efficacy in mitigating MC accumulation. Specifically, it resulted in a reduction of approximately 1.159 µg of MC per kilogram of root dry weight, leading to complete elimination in the leaves and fruits. The findings also indicated that the inoculation of perlite with the three MC-degrading bacterial strains significantly enhanced growth, photosynthetic pigments, yield, biochemical constituents, and quality attributes of strawberries (p ≤ 0.05). These promising outcomes suggest the potential of this approach for addressing the adverse impacts of crops irrigated with MC-contaminated water in future agricultural practices.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Newly isolated Brevundimonas naejangsanensis as a biocontrol agent against Fusarium redolens the causal of Fusarium yellows of chickpea

Three endophytic bacteria, namely BvV, BvP and BvL, were newly isolated from the root nodules of bean, pea and lentil plants respectively cultivated in Mascara the northwest of Algeria, and identified by 16S ribosomal RNA gene sequencing as Brevundimonas naejangsanensis. These strains were able to produce hydrolytic enzymes and hydrogen cyanide. All strains produced a growth-promoting hormone, indole acetic acid, varying in concentration from 83.2 to 171.7 µg/mL. The phosphate solubilizing activity of BvV, BvP and BvL varied from 25.5 to 42.02 µg/mL for tricalcium phosphate. The three antagonistic Brevundimonas spp. showed in vitro the most inhibitory effect on mycelial growth of Fusarium redolens FRC (from 78.33 to 85.55%). Strain BvV, BvP and BvL produced also volatile metabolites which inhibited mycelial FRC growth up to 39.2%. All strains showed significant disease reduction in pot experiments. Chickpea Fusarium yellows severity caused by FRC was reduced significantly from 89.3 to 96.6% in the susceptible cultivar ILC 482 treated with antagonistic B. naejangsanensis. The maximum stimulatory effect on chickpea plants growth was observed by inoculation of strain BvV. This treatment resulted in a 7.40-26.21% increase in shoot height as compared to the control plants. It is concluded that the endophytic bacterial strains of B. naejangsanensis having different plant growth promoting (PGP) activities can be considered as beneficial microbes for sustainable agriculture. To our knowledge, this is the first report to use B. naejangsanensis strains as a new biocontrol agent against F. redolens, a new pathogen of chickpea plants causing Fusarium yellows disease in Algeria.

Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications

Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.

Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings?

Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Effects of Microplastics on Endophytes in Different Niches of Chinese Flowering Cabbage (Brassica campestris)

Microplastics (MPs) are present in soil as emerging contaminants and pose a threat to soil as well as plants. Here, the effects of MPs on Chinese flowering cabbage from a microbiology perspective were explored. MP size and concentration significantly affected endophytic communities of plant root and petiole (p < 0.05). Under MP treatments, the root, petiole, and leaf exhibited a substantial abundance of pathogenic biomarkers, such as Pseudomonas, Burkholderia, Ralstonia, and Escherichia, resulting in the slow growth and morbidity of the plant. Difference analysis of metabolic pathways revealed that MPs significantly upregulated the pathogenic metabolic pathways (p < 0.05), and the presence of Vibrio infectious and pathogenic metabolic pathways was detected in all three niches of the plant. Moreover, MPs significantly inhibited the contents of carotenoids, iron, vitamin C, and calcium in edible niches of the plant (p < 0.05), and most of the high-abundant biomarkers were negatively correlated with their nutritional qualities.

Dynamic changes of endophytic bacteria in the bark and leaves of medicinal plant Eucommia ulmoides in different seasons

The bark and leaves of the Eucommia ulmoides Oliv. (E. ulmoides) have good medicinal value. Studies show endophytes play important roles in host medicinal plant secondary metabolite synthesis, with season being a key influencing factor. Therefore, we used 16 S rRNA to detect endophytic bacteria (EB) in E. ulmoides bark and leaves collected in winter, spring, summer, and autumn, and analyzed the contents of major active components respectively. The results showed that the species diversity and richness of EB of the E. ulmoides bark were higher than those of leaves in all seasons except fall. Among them, the higher species diversity and richness were found in the E. ulmoides bark in winter and spring. EB community structure differed significantly between medicinal tissues and seasons. Concurrently, the bark and leaves of E. ulmoides showed abundant characteristic EB across seasons. For active components, geniposidic acid showed a significant positive correlation with EB diversity and richness, while the opposite was true for aucubin. Additionally, some dominant EB exhibited close correlations with the accumulation of active components. Delftia, enriched in autumn, correlated significantly positively with aucubin. Notably, the impact of the same EB genera on active components differed across medicinal tissues. For example, Sphingomonas, enriched in summer, correlated significantly positively with pinoresinol diglucoside (PDG) in the bark, but with aucubin in the leaves. In summary, EB of E. ulmoides was demonstrated high seasonal dynamics and tissue specificity, with seasonal characteristic EB like Delftia and Sphingomonas correlating with the accumulation of active components in medicinal tissues.

Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae

Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.

Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach

Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.

The impact of utilizing oyster shell soil conditioner on the growth of tomato plants and the composition of inter-root soil bacterial communities in an acidic soil environment

Introduction

The objective of this study is to examine the impact of various oyster shell soil conditioners, which are primarily composed of oyster shells, on the growth of tomatoes in acidic soil. Moreover, the aim of this investigation is to analyze the variety and structure of soil bacterial populations in close proximity to tomato roots while also contributing to the understanding of the physical, chemical, and biological mechanisms of oyster shell soil conditioners.

Methods

Tomato plants were grown in acidic red soil in three groups: a control group and a treatment group that used two types of oyster shell soil conditioners, OS (oyster shell powder) and OSF (oyster shell powder with organic microbial fertilizer). A range of soil physicochemical properties were measured to study differences in inter-soil physicochemical parameters and the growth of tomato plantings. In addition, this study utilized the CTAB (Cetyltrimethylammonium Bromide) technique to extract DNA from the soil in order to investigate the effects of oyster shell soil conditioner on the composition and diversity of bacterial populations. Utilizing high-throughput sequencing technologies and diversity index analysis, the composition and diversity of bacterial populations in the soil adjacent to plant roots were then evaluated. Ultimately, correlation analysis was used in this study to explore the relationship between environmental factors and the relative abundance of soil bacteria in the inter-root zone of tomato plants.

Results

The findings indicated that the oyster shell soil conditioners were capable of modifying the physicochemical characteristics of the soil. This was evidenced by significant increases in soil total nitrogen (16.2 and 59.9%), soil total carbon (25.8 and 27.7%), pH (56.9 and 55.8%), and electrical conductivity (377.5 and 311.7%) in the OS and OSF groups, respectively, compared to the control group (p < 0.05). Additionally, data pertaining to tomato seed germination and seedling growth biomass demonstrated that both oyster shell soil conditioners facilitated the germination of tomato seeds and the growth of seedlings in an acidic red clay soil (p < 0.05). On the other hand, the application of two oyster shell soil conditioners resulted in a modest reduction in the diversity of inter-root soil bacteria in tomato plants. Specifically, the group treated with OSF exhibited the most substantial fall in the diversity index, which was 13.6% lower compared to the control group. The investigation carried out on the soil between tomato plant roots yielded findings about the identification of the ten most abundant phyla. These phyla together represented 91.00-97.64% of the overall abundance. In the inter-root soil of tomatoes, a study identified four major phyla, namely Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, which collectively accounted for up to 85% of the total abundance. At the general level, the relative abundance of Massilia increased by 2.18 and 7.93%, Brevundimonas by 5.43 and 3.01%, and Lysobacter by 3.12 and 7.49% in the OS and OSF groups, respectively, compared to the control group. However, the pathogenic bacteria unidentified_Burkholderiaceae decreased by 5.76 and 5.05%, respectively. The correlation analysis yielded conclusive evidence indicating that, which involved the use of CCA (Canonical Correlation Analysis) graphs and Spearman correlation coefficients, pH exhibited a positive correlation (p < 0.05) with Shewanella and a negative correlation (p < 0.05) with Bradyrhizobium. The relative abundance of Lysobacter and Massilia exhibited a positive correlation with the levels of total soil nitrogen.

Discussion

The utilization of oyster shell soil conditioner on acidic red soil resulted in several positive effects. Firstly, it raised the pH level of the inter-root soil of tomato plants, which is typically acidic. This pH adjustment facilitated the germination of tomato seeds and promoted the growth of seedlings. In addition, the application of oyster shell soil conditioner resulted in changes in the structure of the bacterial community in the inter-root soil, leading to an increase in the relative abundance of Proteobacteria and Bacteroidetes and a decrease in the relative abundance of Acidobacteria. Furthermore, this treatment fostered the proliferation of genera of beneficial bacteria like Massilia, Brevundimonas, and Lysobacter, ultimately enhancing the fertility of the red soil.

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.

Diversity of potential nitrogen-fixing bacteria from rhizosphere of the Coffea arabica L. and Coffea canephora L

Coffea arabica L. and Coffea canephora L. are coffee species most consumed and marketed in the world. The coffee crop requires a large amount of nitrogen, which shows the importance of knowledge of the population of nitrogen-fixing bacteria (NFB) from the rhizosphere of these crops. These microorganisms may help the reduction of nitrogen fertilizing. However, there is no production of NFB inoculum in the coffee. Therefore, our objective was to evaluate the diversity of potential nitrogen-fixing bacteria (PNFB) in the rhizosphere of C. arabica and C. canephora. The microbial DNA of the soil was extracted, amplified through PCR, and sequenced at the Illumina Miseq. platform. The PNFB prediction was performed using the program PICRUSt2. Three hundred and thirty-seven amplicon sequence variants (ASVs) were identified as PNFB in two coffee species. Xanthobacteraceae, Rhizobium multhospitiium, Rhizobium mesosinicum, and Bradyrhizobium sp. were detected in all samples and main components of the core microbiota of the coffee plant rhizosphere. Some ASVs are exclusive from one of the coffee farms, showing that the coffee specie cultivated may influence the PNFB communities. However, edaphoclimatic factors and soil chemical attributes can also influence the distribution of ASVs in coffee soil. In the C. canephora, the PNFB diversity was influenced by the altitude and the soil chemical attributes, while the altitude and the phosphorus content influenced the PNFB population in C. arabica. Our results are important to the understanding of the PNFB dynamic in coffee soil and for the agricultural inputs bioprospecting to coffee.

Improving soil phosphorus availability in saline areas by marine bacterium Bacillus paramycoides

The utilization of phosphate-solubilizing bacteria (PSB) in agriculture has long been proposed as an eco-friendly method to enhance soil phosphorus (P) availability, thereby reducing reliance on chemical P fertilizers. However, their application in saline soils is challenged by salt-induced stress on common PSB strains. In this study, we sourced bacterial strains from marine environments, aiming to identify robust PSB strains adaptable to saline conditions and assess their potential as P bio-fertilizers through a microcosm experiment. Our findings indicate that the inoculation of a selected marine PSB, Bacillus paramycoides 3-1a, increased soil available P content by 12.5% when applied alone and by 61.2% when combined with organic amendments. This enhancement results from improved inorganic P solubilization and organic P mineralization in soils. Additionally, these treatments raised soil nitrogen levels, reshaped microbial community structures, and significantly enhanced wheat (Triticum aestivum L.) growth, with P accumulation increasing by 24.2-40.9%. Our results underscore the potential of marine PSB in conjunction with organic amendments for the amelioration of saline agricultural soils.

Improved phyllosphere microbiome composition of tea plant with the application of small peptides in combination with rhamnolipid

BACKGROUND

Small peptides play a crucial role in plant growth and adaptation to the environment. Exogenous small peptides are often applied together with surfactants as foliar fertilizers, but the impact of small peptides and surfactants on the tea phyllosphere microbiome remains unknown.

RESULTS

In this study, we investigated the effects of small peptides and different surfactants on the tea phyllosphere microbiome using 16S and ITS sequencing. Our results showed that the use of small peptides reduced the bacterial diversity of the tea phyllosphere microbiome and increased the fungal diversity, while the use of surfactants influenced the diversity of bacteria and fungi. Furthermore, the addition of rhamnolipid to small peptides significantly improved the tea phyllosphere microbiome community structure, making beneficial microorganisms such as Pseudomonas, Chryseobacterium, Meyerozyma, and Vishniacozyma dominant populations.

CONCLUSION

Our study suggests that the combined use of small peptides and surfactants can significantly modify the tea phyllosphere microbiome community structure, particularly for beneficial microorganisms closely related to tea plant health. Thus, this preliminary study offers initial insights that could guide the application of small peptides and surfactants in agricultural production, particularly with respect to their potential for modulating the phyllosphere microbiome community in tea plant management.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Heavy metal-resistant rhizobacteria fosters to alleviate the cadmium toxicity in Arabidopsis by upregulating the plant physiological responses

This study was designed to investigate the role of Morganella morganii strains in alleviating Cd stress in Arabidopsis seedlings under controlled conditions. Both M. morganii strains ABT3 (ON316873) and ABT9 (ON316874) strains isolated from salt-affected areas showed higher resistance against Cd and possess plant growth-promoting traits such as nitrogen fixation, indole-acetic acid production, ammonia production, phosphate solubilization, and, catalase, gelatinase and protease enzyme production. Plant inoculation assay showed that varying concentration of Cd (1.5 mM and 2.5 mM) significantly reduced Arabidopsis growth, quantum yield (56.70%-66.49%), and chlorophyll content (31.90%-42.70%). Cd toxicity also triggered different associations between lipid peroxidation (43.61%-69.77%) and enzymatic antioxidant mechanisms. However, when both strains were applied to the Arabidopsis seedlings, the shoot and root length and fresh and dry weights were improved in the control and Cd-stressed plants. Moreover, both strains enhanced the resistance against Cd stress by increasing antioxidant enzyme activities [catalase (19.47%-27.39%) and peroxidase (37.50%-48.07%)]that ultimately cause a substantial reduction in lipid peroxidation (27.71%-41.90%). Both strains particularly ABT3 also showed positive results in improving quantum yield (73.84%-98.64%) and chlorophyll content (41.13%-48.63%), thus increasing the growth of Arabidopsis seedlings. The study suggests that PGPR can protect plants from Cd toxicity, and Cd-tolerant rhizobacterial strains can remediate heavy metal polluted sites and improve plant growth.

Crosstalk between in situ root exudates and rhizobacteria to promote rice growth by selenium nanomaterials

Maximizing the potential of plant-microbe systems offers great opportunities to confront sustainability issues in agroecosystems. However, the dialog between root exudates and rhizobacteria remains largely unknown. As a novel nanofertilizer, nanomaterials (NMs) have significant potential to improve agricultural productivity due to their unique properties. Here, soil amendment with 0.1 mg·kg^-1 selenium (Se) NMs (30-50 nm) significantly promoted rice seedling growth. Differences in root exudates and rhizobacteria were evident. At an earlier time point (3^rd week), Se NMs increased the relative content of malic and citric acid by 15.4- and 8.1-fold, respectively. Meanwhile, the relative abundances of Streptomyces and Sphingomonas were increased by 164.6 % and 38.3 %, respectively. As the exposure time increased, succinic acid (40.5-fold) at the 4^th week and salicylic acid (4.7-fold) and indole-3-acetic (7.0-fold) at the 5^th week were enhanced, while Pseudomonas and Bacillus increased at the 4^th (112.3 % and 50.2 %) and 5^th weeks (190.8 % and 53.1 %), respectively. Further analysis indicated that (1) Se NMs directly enhanced the synthesis and secretion of malic and citric acids by upregulating their biosynthesis and transporter genes and then recruited Bacillus and Pseudomonas; (2) Se NMs upregulated the chemotaxis and flagellar genes of Sphingomonas for more interaction with rice plants, thereby promoting rice growth and stimulating root exudate secretion. This crosstalk of root exudates and rhizobacteria enhanced nutrient uptake, resulting in promoted rice growth. Our study offers insights into the crosstalk between root exudates and rhizobacteria by NMs and provides new insights into rhizosphere regulation in nano-enabled agriculture.

The Zoige pioneer plant Leymus secalinus has different endophytic bacterial community structures to adapt to environmental conditions

Background

Leymus secalinus is a pioneer plant grown in the Zoige desertified alpine grassland and it is also one of the dominant plant species used for environmental remediation. L. secalinus plays a large role in vegetation reconstruction in sandy land, but the abundance and diversity of its endophytes have not yet been investigated.

Objectives

This study was performed to investigate the changes in the endophytic bacterial community structure of L. secalinus under different ecological environments and to analyze the effects of environmental changes and different plant tissues on the L. secalinus endophytic bacteria.

Methods

Leaf, stem, and root tissue samples of L. secalinus were collected from Zoige Glassland (Alpine sandy land) and an open field nursery (Control). DNA was extracted and the 16S ribosomal DNA was amplified. The sequence library was sequenced on an Illumina MiSeq platform and clustered by operational taxonomic units (OTUs). α-diversity and β-diversity analyses, species diversity analyses, functional prediction, and redundancy (RDA) analyses for the soil physicochemical properties were conducted.

Results

α-diversity and β-diversity analyses showed that the endophytic bacteria in L. secalinus varied in different areas and tissues. The abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, which is related to nitrogen fixation, increased significantly in the L. secalinus found in the Zoige Grassland.Moreover, the abundance of nutrition metabolism and anti-stress abilities increased in functional prediction in the desert samples. The soil physicochemical properties had an insignificant influence on bacterial diversity.

Conclusion

The changes in the endophytic bacterial community structure in L. secalinus were significant and were caused by environmental alterations and plant choice. The endophytic bacteria in L. secalinus grown in alpine sandy land may have greater anti-stress properties and the ability to fix nitrogen, which has potential value in environmental remediation and agricultural production.

Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment

The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.

Diversity of the Bacterial Community Associated with Hindgut, Malpighian Tubules, and Foam of Nymphs of Two Spittlebug Species (Hemiptera: Aphrophoridae)

Spittlebugs are xylem-sap feeding insects that can exploit a nutrient-poor diet, thanks to mutualistic endosymbionts residing in various organs of their body. Although obligate symbioses in some spittlebug species have been quite well studied, little is known about their facultative endosymbionts, especially those inhabiting the gut. Recently, the role played by spittlebugs as vectors of the phytopathogenetic bacterium Xylella fastidiosa aroused attention to this insect group, boosting investigations aimed at developing effective yet sustainable control strategies. Since spittlebug nymphs are currently the main target of applied control, the composition of gut bacterial community of the juveniles of Philaenus spumarius and Lepyronia coleoptrata was investigated using molecular techniques. Moreover, bacteria associated with their froth, sampled from different host plants, were studied. Results revealed that Sodalis and Rickettsia bacteria are the predominant taxa in the gut of P. spumarius and L. coleoptrata nymphs, respectively, while Rhodococcus was found in both species. Our investigations also highlighted the presence of recurring bacteria in the froth. Furthermore, the foam hosted several bacterial species depending on the host plant, the insect species, or on soil contaminant. Overall, first findings showed that nymphs harbor a large and diverse bacterial community in their gut and froth, providing new accounts to the knowledge on facultative symbionts of spittlebugs.

A shallow constructed wetland combining porous filter material and Rotala rotundifolia for advanced treatment of municipal sewage at low HRT

Water scarcity is a worldwide problem. Recycled municipal wastewater is considered a useful alternative to the conventional types of water resources. In this study, a shallow constructed wetland (SCW) with porous filter material and Rotala rotundifolia was used for advanced municipal sewage treatment. The wetland without plant was set as the control (SCW-C). The pollutant removal performance of the system at different hydraulic retention times (HRTs) was investigated. The diversity of the microbial community was analyzed, and the fate of nutrients, mainly N and P, in the system was discussed. Results showed that SCW was efficient in pollutant removal. Effluent concentrations of chemical oxygen demand (COD), total phosphorus (TP), and ammonium nitrogen (NH₄⁺-N) were 15.0-23.6, 0.19-0.28, and 0.83-1.16 mg/L, separately, with average removal efficiencies of 61.2%, 46.3%, and 88.1% at HRT 18 h, which met the requirements of type [Formula: see text] water set by the environmental quality standards for surface water in China. The richness and evenness of the bacterial community were significantly higher in the plant-rooted SCW. They increased along with the system. The dominant genera in the system were phosphate-solubilizing bacteria, nitrifying bacteria, and denitrifying bacteria. The P in the influent mainly flowed to the substrate and plant. At the same time, most N was removed by nitrification and denitrification. These findings suggested that the SCW could remove pollutants from the municipal sewage effluent and meet the standard requirement at low HRT.

New insights into engineered plant-microbe interactions for pesticide removal

Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.

Sex-based metabolic and microbiota differences in roots and rhizosphere soils of dioecious papaya (Carica papaya L.)

Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brevundimonas and Microvirga were enriched in the male papaya roots or rhizosphere soils. While Candidatus Solibacter and Tumebacillus, which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Inoculation With Azospirillum spp. Acts as the Liming Source for Improving Growth and Nitrogen Use Efficiency of Potato

Nitrogen (N) is one of the limiting factors for plant growth, and it is mainly supplied exogenously by fertilizer application. It is well documented that diazotrophic rhizobacteria improve plant growth by fixing atmospheric N in the soil. The present study investigates the nitrogen-fixing potential of two Azospirillum spp. strains using the 15N isotope-dilution method. The two diazotrophic strains (TN03 and TN09) native to the rhizosphere of potato belong to the genus Azospirillum (16S rRNA gene accession numbers LN833443 and LN833448, respectively). Both strains were able to grow on an N-free medium with N-fixation potential (138-143 nmol mg-1 protein h-1) and contained the nifH gene. Strain TN03 showed highest indole acetic acid (IAA) production (30.43 μg/mL), while TN09 showed highest phosphate solubilization activity (249.38 μg/mL) while both diazotrophs showed the production of organic acids. A 15N dilution experiment was conducted with different fertilizer inputs to evaluate the N-fixing potential of both diazotrophs in pots. The results showed that plant growth parameters and N contents increased significantly by the inoculations. Moreover, reduced 15N enrichment was found compared to uninoculated controls that received similar N fertilizer levels. This validates the occurrence of N-fixation through isotopic dilution. Strain TN09 showed higher N-fixing potential than TN03 and the uninoculated controls. Inoculation with either strain also showed a remarkable increase in plant growth under field conditions. Thus, there were remarkable increases in N use efficiency, N uptake and N utilization levels. Confocal laser scanning and transmission electron microscopy showed that TN03 is an ectophyte, i.e., present outside root cells or within the grooves of root hairs, while TN09 is an endophyte, i.e., present within root cells, forming a strong association withroot it. This study confirms that diazotrophic Azospirillum spp. added to potato systems can improve plant growth and N use efficiency, opening avenues for improvement of potato crop growth with reduced input of N fertilizer.

Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions

Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Identification of heavy metals tolerant Brevundimonas sp. from rhizospheric zone of Saccharum munja L. and their efficacy in in-situ phytoremediation

Heavy metals phytoremediation from pulp and paper industry (PPI) sludge was conducted by employing root-associated Brevundimonas sp (PS-4 MN238722.1) in rhizospheric zone of Saccharum munja L. for its detoxification. The study was aimed to investigate the efficiency of Saccharum munja L. for the removal of heavy metals along with physico-chemical parameters through bacterial interactions. Physico-chemical examination of PPI sludge showed biochemical oxygen demand (8357 ± 94 mg kg^-1), electrical conductivity (2264 ± 49 μmhoscm^-1), total phenol (521 ± 24 mg kg^-1), total dissolve solid (1547 ± 23 mg kg^-1), total nitrogen (264 ± 2.13 mg kg^-1), pH (8.2 ± 0.11), chemical oxygen demand (34756 ± 214 mg kg^-1), color (2434 ± 45 Co-Pt), total suspended solid (76 ± 0.67 mg kg^-1), sulphate (2462 ± 13 mg kg^-1), chlorolignin (597 ± 13.01 mg kg^-1), K⁺ (21.04 ± 0.26 mg kg^-1), total solid (1740 ± 54 mg kg^-1), phosphorous, Cl^-, and Na⁺. Heavy metals, such as Fe followed by Zn, Mn, Cd, Cu, Ni, Pb, As, Cr and Hg were above the permissible limit. Root and shoot of Saccharum munja L. revealed highest concentrations of Cd followed by Mn, Ni, Fe, Zn, Cu, As, Cr, Hg, and Pb. Tested metals (Fe, Mn, Pb, Cd, Cr, Cu, Zn, Ni, As, and Hg) bioaccumulation and translocation factors were also revealed to be < 1 and >1, respectively, demonstrating that these plants have considerable absorption and translocation abilities. Plant growth-promoting activity, such as ligninolytic enzymes, hydrolytic enzymes, indole acetic acid, and siderophore production activity of Brevundimonas sp. (PS-4 MN238722.1) were also noted to be higher. These findings support the use of Brevundimonas sp (PS-4 MN238722.1) in combination with Saccharum munja L. plant as interdisciplinary management of industrial sludge at polluted areas for the prevention of soils near the industrial site.

Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere

PM_2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM_2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.

Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production

BACKGROUND

Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha^-1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria.

METHODS

We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL^-1 h^-1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed.

RESULTS

The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL^-1h^-1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri)

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Diazotrophic Behaviour in a Non-Sterile Bioreactor: The Effect of O2-Availability

The behaviour of a locally isolated diazotrophic consortium was investigated with the prospect of agricultural applications. A repeatable culture was obtained in a non-sterile bioreactor. Metagenomic analysis indicated Chryseobacterium ssp. and Flavobacterium ssp. were the dominant species, making up approximately 50% of the microbial community. The oxygen supply was varied and mass-transfer limited growth was attained under all experimental conditions. Negligible amounts of aqueous metabolites were formed, indicating a high selectivity towards biomass production. High oxygen availability resulted in decreased growth efficiencies i.e., the specific energy requirements for biomass synthesis. This was attributed to reduced electron transport chain efficiencies and nitrogenase protection mechanisms. Mass and energy balances indicated that sessile biomass with a high C:N served as a carbon sink. The most efficient growth was measured at an aeration feed composition of 21% oxygen and 79% nitrogen. The study presents one of the only known investigations of operational conditions on diazotrophic growth in a non-sterile bioreactor. In addition, it provides a strong foundation for the development of a Biological Nitrogen Fixation process with scaling potential.

Pyomelanin-Producing Brevundimonas vitisensis sp. nov., Isolated From Grape (Vitis vinifera L.)

A novel endophytic bacterial strain, designated GR-TSA-9^T, was isolated from surface-sterilized grape (Vitis vinifera L.). 16S rRNA gene sequence analyses showed that the isolate was grouped within the genus Brevundimonas, displaying the highest similarity with Brevundimonas lenta DS-18^T (97.9%) and Brevundimonas kwangchunensis KSL-102^T (97.8%) and less than 97.5% similarity with other members of Brevundimonas. The strain GR-TSA-9^T was a gram negative, rod shaped, facultatively anaerobic, catalase and oxidase positive, and motile bacterium. Its growth occurred at 10–37°C (optimally 25–30°C), at pH 7.0–8.0, and in NaCl 0–1% (optimally 0%). It contained ubiquinone-10 as a respiratory quinone, and the major cellular fatty acids (>10% of the total) were C_16:0 (14.2%) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c, 65.6%). The polar lipids present in the strain were phosphoglycolipids, phosphatidylglycerol, 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol, and unidentified lipids (L1, L2, and L4). The strain had one 2,976,716bp circular chromosome with a G+C content of 66.4%. The digital DNA–DNA hybridization value between strain GR-TSA-9^T and B. lenta DS-18^T was 20.9%, while the average nucleotide identity value was 76.7%. In addition, the dDDH and ANI values to other members in this genus, whose genome sequences are available, are less than 21.1 and 77.6%. Genome annotation predicted the presence of some gene clusters related to tyrosine degradation and pyomelanin formation. Strain GR-TSA-9^T produced a brown melanin-like pigment in the presence of L-tyrosine-containing media. The highest pigment production (0.19g/L) was observed in tryptic soy broth with 1.0mg/ml L-tyrosine at 25°C for 6days of culture. Biophysical characterization by ultraviolet (UV)–visible spectroscopy, Fourier-transform infrared spectroscopy, and electrospray ionization mass spectrometry confirmed that the pigment was pyomelanin. Additionally, melanized GR-TSA-9^T cells could protect the cells against UVC exposure. The phylogenetic, genomic, phenotypic, and chemotaxonomic features indicated that strain GR-TSA-9^T represents a novel melanin-producing species of Brevundimonas. The type strain was GR-TSA-9^T (KCTC 82386^T=CGMCC 1.18820^T).

Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states

The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.

Prospecting Endophytic Bacteria Endowed With Plant Growth Promoting Potential Isolated From Camellia sinensis

Endophytes are well-acknowledged inoculants to promote plant growth, and extensive research has been done in different plants. However, there is a lacuna about the endophytes associated with tea clones and their benefit to promote plant growth. The present study focuses on isolating and characterizing the beneficial endophytic bacteria (EnB) prevalent in commercially important tea clones cultivated in North Eastern India as plant growth promoters. Diversity of culturable EnB microbiome, in vitro traits for plant growth promotion (PGP), and applicability of potent isolates as bioinoculant for in vivo PGP abilities have been assessed in the present study. A total of 106 EnB identified as members of phyla Proteobacteria, Firmicutes, and Actinobacteria were related to 22 different genera and six major clusters. Regarding PGP traits, the percentage of isolates positive for the production of indole acetic acid, phosphate solubilization, nitrogen fixation siderophore, ammonia, and 1-aminocyclopropane-1-carboxylic acid deaminase production were 86.8, 28.3, 78.3, 30.2, 95.3, and 87.7, respectively. In total, 34.0, 52.8, and 17.0% of EnB showed notable production of hydrolytic enzymes like cellulase, protease, and amylase, respectively. Additionally, based on the bonitur score, the top two isolates K96 identified as Stenotrophomonas sp. and M45 identified as Pseudomonas sp. were evaluated for biofilm formation, motility, and in vivo plant growth promoting activity. Results suggested strong biofilm formation and motility in K96 and M45 which may attribute to the colonization of the strains in the plants. Further in vivo plant growth promotion experiment suggested sturdy efficacy of the K96 and M45 as plant growth promoters in nursery condition in commercial tea clones Tocklai vegetative (TV) TV22 and TV26. Thus, this study emphasizes the opportunity of commercialization of the selected isolates for sustainable development of tea and other crops.