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A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘ Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov. A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, the authors isolate a member of the ubiquitous, yet-to-be-cultivated bacterial phylum ‘ Candidatus Atribacteria’ that has an intracytoplasmic membrane apparently surrounding the nucleoid.

Background Excessive application of chemical fertilizer has exerted a great threat to soil quality and the environment. The inoculation of plants with plant-growth-promoting rhizobacteria (PGPR) has emerged as a great prospect for ecosystem recovery. The aim of this work to isolate PGPRs and highlights the effect of bacterial inoculants on available N/P/K content in soil and on the growth of wheat under conditions of reduced fertilizer application. Results Thirty-nine PGPRs were isolated and tested for their growth-promoting potential. Thirteen isolates had nitrogen fixation ability, of which N9 ( Azotobacter chroococcum ) had the highest acetylene reduction activity of 156.26 nmol/gh. Eleven isolates had efficient phosphate solubilizing ability, of which P5 ( Klebsiella variicola ) released the most available phosphorus in liquid medium (231.68 mg/L). Fifteen isolates had efficient potassium solubilizing ability, of which K13 ( Rhizobium larrymoorei ) released the most available potassium in liquid medium (224.66 mg/L). In culture medium supplemented with tryptophan, P9 ( Klebsiella pneumoniae ) produced the greatest amount of IAA. Inoculation with the bacterial combination K14 + 176 + P9 + N8 + P5 increased the alkali-hydrolysed nitrogen, available phosphorus and available potassium in the soil by 49.46, 99.51 and 19.38%, respectively, and enhanced the N, P, and K content of wheat by 97.7, 96.4 and 42.1%, respectively. Moreover, reducing fertilizer application by 25% did not decrease the available nitrogen, phosphorus, and potassium in the soil and N/P/K content, plant height, and dry weight of wheat. Conclusions The bacterial combination K14 + 176 + P9 + N8 + P5 is superior candidates for biofertilizers that may reduce chemical fertilizer application without influencing the normal growth of wheat.

Vegetable cultivation is a promising economic activity, and vegetable consumption is important for human health due to the high nutritional content of vegetables. Vegetables are rich in vitamins, minerals, dietary fiber, and several phytochemical compounds. However, the production of vegetables is insufficient to meet the demand of the ever-increasing population. Plant-growth-promoting rhizobacteria (PGPR) facilitate the growth and production of vegetable crops by acquiring nutrients, producing phytohormones, and protecting them from various detrimental effects. In this review, we highlight well-developed and cutting-edge findings focusing on the role of a PGPR-based bioinoculant formulation in enhancing vegetable crop production. We also discuss the role of PGPR in promoting vegetable crop growth and resisting the adverse effects arising from various abiotic (drought, salinity, heat, heavy metals) and biotic (fungi, bacteria, nematodes, and insect pests) stresses.

Citrus greening disease, also known as huanglongbing (HLB), is caused by the gram-negative α-proteobacteria Candidatus Liberibacter species. This disease poses a significant threat to citrus production worldwide, including in Nepal. This study aimed to perform the diagnosis and phylogenetic analysis of the citrus greening pathogen in Nepal using both conventional PCR and computational methods. A total of 1,026 citrus leaf samples were collected from thirteen districts across six provinces in the country. PCR-based diagnosis was performed using the primer set Las606/LSS, which targets the 16S rRNA gene of Candidatus Liberibacter asiaticus. The reliability of the PCR was validated by including previously confirmed positive and negative controls in every run. Furthermore, each assay was performed in triplicate to ensure consistency and reproducibility of results. Additionally, 16S rRNA gene sequencing was performed using Sanger sequencing for five samples. The obtained sequences were deposited in GenBank and a phylogenetic tree was constructed based on these sequences. Among the 1,026 samples tested, 255 were positive, indicating the widespread distribution of HLB across Nepal. All consensus sequences from Nepal showed strong evolutionary relatedness within the Ca. L. asiaticus cluster, with over 99% genetic similarity to reference sequences from various parts of the world. Phylogenetic analysis revealed that the Nepalese sequences were closely related to Ca. L. asiaticus sequences from India (Punjab and Meerut) and sequences obtained from different regions of Nepal clustered closely together. The molecular findings from this study reveal a high prevalence of citrus greening disease across Nepal and underscore the urgent need for integrated management policies, including the use of certified clean planting material and vector (psyllid) control programs. The generated sequence data serves as a vital resource for developing regional diagnostic tools and guiding future surveillance strategies to mitigate HLB's impact on the world's citrus industry.

The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘ Candidatus Liberibacter asiaticus’ (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘ Ca . L. asiaticus’ infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in ‘ Ca . L. asiaticus’-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of ‘ Ca . L. asiaticus’ infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the ‘ Ca . L. asiaticus’-infected citrus rhizosphere. Our results showed that the microbial community of the ‘ Ca . L. asiaticus’-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by ‘ Ca . L. asiaticus’ infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability of citrus-producing agro-ecosystems.

Over the last century, repeated emergence events within the Candidatus Liberibacter taxon have produced pathogens with devastating effects. Presently, our knowledge of Ca . Liberibacter diversity, host associations, and interactions with vectors is limited due to a focus on studying this taxon within crops. But to understand traits associated with pathogen emergence it is essential to study pathogen diversity in wild vegetation as well. Here, we explore historical native host plant associations and diversity of the cosmopolitan species, Ca . L. psyllaurous, also known as Ca . L. solanacearum, which is associated with psyllid yellows disease and zebra chip disease, especially in potato. We screened tissue from herbarium samples of three native solanaceous plants collected near potato-growing regions throughout Southern California over the last century. This screening revealed a new haplotype of Ca . L. psyllaurous (G), which, based on our sampling, has been present in the U.S. since at least 1970. Phylogenetic analysis of this new haplotype suggests that it may be closely related to a newly emerged North American haplotype (F) associated with zebra chip disease in potatoes. Our results demonstrate the value of herbarium sampling for discovering novel Ca . Liberibacter haplotypes not previously associated with disease in crops.

Elongation of many rod-shaped bacteria occurs by peptidoglycan synthesis at discrete foci along the sidewall of the cells. However, within the Rhizobiales, there are many budding bacteria, in which new cell growth is constrained to a specific region. The phylogeny of the Rhizobiales indicates that this mode of zonal growth may be ancestral. We demonstrate that the rod-shaped bacterium Agrobacterium tumefaciens grows unidirectionally from the new pole generated after cell division and has an atypical peptidoglycan composition. Polar growth occurs under all conditions tested, including when cells are attached to a plant root and under conditions that induce virulence. Finally, we show that polar growth also occurs in the closely related bacteria Sinorhizobium meliloti, Bruceila abortus, and Ochrobactrum anthropi. We find that unipolar growth is an ancestral and conserved trait among the Rhizobiales, which includes important mutualists and pathogens of plants and animals.

This study investigates the combined effect of locally adopted plant growth promoting rhizobacteria (PGPR), biochar, and synthetic fertilizer on the wheat crop for the production and economic returns. A total of 20 PGPR strains were isolated from three different ecological zones of Pakistan and were evaluated. Of them, three isolates were selected for further studies. The treatments included (i) control with a full dose of the recommended fertilizer, (ii) control with half a dose of the fertilizer, (iii) PGPR consortia with half a dose of the fertilizer, (iv) biochar with half a dose of the fertilizer, and (v) PGPR + biochar with half a dose of the fertilizer. The study was repeated at three different locations. The data collected for leaf area index (LAI), grain yield, biological yield, straw yield, and harvest index (HI) revealed significant differences ( P  ≤ 0.05) for the locations and treatments, but the interaction of location and treatments was not significant. Based on the productivity and economic returns, the treatment with PGPR + biochar with half a dose of the fertilizer proved to be the best. Thus, the use of the PGPR consortia and biochar can improve the yield and profit of wheat crop with reduced synthetic fertilization. Graphical abstract ᅟ

Background Diverse diseases are typically associated with perturbed microbiome homeostasis, across ecosystems such as the gut and root habitats. Clubroot, which is caused by the devastating soil-borne pathogen Plasmodiophora brassicae , is a broad-spectrum disease that infects almost all cruciferous vegetables. However, the microbial ecological and metabolic cues underlying pathogen-driven deleterious disruptions of the microbiome remain enigmatic. Results In this study, changes in the microbiome and metabolome of the rhizosphere and roots in susceptible (diseased and nondiseased) and resistant pakchoi plants infected with  P. brassicae were investigated. Diverse potential beneficial and disease-suppressive microbial families, including Rhizobiaceae and Sphingomonadaceae, were enriched in the healthy group compared with the diseased group. Rhizobiaceae was further characterized as a core driver family between the healthy and diseased groups. Reductionist-based strain validation studies further confirmed that Rhizobium sp. 25F3 showed drastic disease-suppressing activity in soil. The integrated metabolome‒microbiome correlation analysis revealed that phenolic acids were negatively correlated with the relative abundance of Rhizobiaceae . We further confirmed that genes related to phenolic acids were upregulated in diseased roots and that two phenolic acids suppressed beneficial Rhizobiaceae growth and accelerated P. brassicae infection in pakchoi . Conclusions Upon P. brassicae infection, significant differences in the microbiome and metabolome were observed between diseased and healthy plants, as well as between resistant and susceptible varieties. Rhizobiaceae is dominant in the root microbiome and acts as a keystone family affected by P. brassicae infection. P. brassicae -induced phenolic acid metabolites selectively inhibit the growth of beneficial Rhizobium sp. 25F3 while promoting P. brassicae bursts in pakchoi. Our work provides ecological and metabolic explanations for how pathogenesis ultimately triggers a decrease in the relative abundance of beneficial microbes, which can guide future genetic and microbiome-based approaches to control clubroot disease. 1dpYNqtZmQWAziudZeLgS4 Video Abstract

Although microbes influence plant growth, little is known about the impact of microbial diversity on plant fitness trade-offs, intraspecific-interactions, and soil nutrient dynamics in the context of biodiversity-ecosystem functioning (BEF) research. The BEF theory states that higher species richness can enhance ecosystem functioning. Thus, we hypothesize that rhizobacterial species richness will alter sorghum ( Sorghum bicolor L.) growth, soil nutrient dynamics and interactions (antagonism or synergism) in a nutrient-poor greenhouse soil. Using six rhizobacterial species in a BEF experiment, we tested the impact of a species richness gradient (0, 1, 3, 5 or 6 species per community) on plant growth, nutrient assimilation, and soil nutrient dynamics via seed-inoculation. Our experiment included, one un-inoculated control, six rhizobacterial monoculture (Pseudomonas poae, Pseudomonas sp., Bacillus pumilus., Pantoea agglomerance., Microbacterium sp., and Serratia marcescens ) , and their nine mixture treatments in triplicate (48). Rhizobacterial species richness enhanced per pot above- or below-ground dry mass. However, the per plant growth and plant nutrient assimilation declined, most likely, due to microbial-driven competitive interactions among sorghum plants. But nevertheless, some rhizobacterial monoculture and mixture treatments improved per plant (shoot and root) growth and nutrient assimilation as well. Soil nutrient contents were mostly lower at higher plant-associated rhizobacterial diversity; among these, the soil Zn contents decreased significantly across the rhizobacterial diversity gradient. Rhizobacterial diversity promoted synergistic interactions among soil nutrients and improved root–soil interactions. Overall, our results suggest that a higher rhizobacterial diversity may enhance soil–plant interactions and total productivity under resource limited conditions.