Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization

BACKGROUND

Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis.

RESULTS

Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization.

CONCLUSIONS

Our results highlight that AM fungi do not function in  isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.

Devosia lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic Microcystis

A novel alphaproteobacterial strain JXJ CY 41T was isolated from a culture mass of Microcystis, collected from Lake Dianchi, south-west, China. Strain JXJ CY 41T was gram-strain-negative, aerobic, motile, with rod-shaped cells (0.4-1.0 × 1.7-3.5 μm). It was positive for catalase and starch hydrolysis, negative for oxidase and hydrolysis of Tweens (20, 40, and 80). Growth occurred at 10-44 °C, pH 5.0-10.0, and 0-5.0% (w/v) NaCl. Major fatty acids included C16:0 (28.1%), 11-methyl C18:1 ω7c (36.7%) and C18:1 ω7c (20.8%). Q10 was the sole ubiquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, and an unidentified lipid. The DNA G + C content was 63.1%. Its 16S rRNA gene sequence showed high similarities with Devosia oryziradicis G19T (99.5%; not validly published), D. yakushimensis Yak96BT (98.3%) and D. ginsengisoli Gsoil 520T (98.1%), and less than 98.1% similarities with other members of the genus Devosia. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain JXJ CY 41T and its 5 closest similar strains were 19.9-24.1% and 75.7-80.5%, respectively. Based on the data above, strain JXJ CY 41T was identified as a novel species of the genus Devosia, for which the epithet Devosia lacusdianchii sp. nov. was proposed. The type strain is JXJ CY 41T (= KCTC 72812T = CGMCC 1.17502T). Strain JXJ CY 41T exhibited different interactions with Microcystis aeruginosa FACHB-905 (Maf) under different conditions, and Maf could control the bacterial cellular density by secreting unknown specific chemical compounds according to its nutritional requirements.

Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment

The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.

Insight into the plant-associated bacterial interactions: Role for plant arsenic extraction and carbon fixation

This study investigated the interactions between rhizosphere and endosphere bacteria during phytoextraction and how the interactions affect arsenic (As) extraction and carbon (C) fixation of plants. Pot experiments, high-throughput sequencing, metabonomics, and network analysis were integrated. Results showed that positive correlations dominated the interconnections within modules (>95 %), among modules (100 %), and among keystone taxa (>72 %) in the bacterial networks of plant rhizosphere, root endosphere, and shoot endosphere. This confirmed that cooperative interactions occurred between bacteria in the rhizosphere and endosphere during phytoextraction. Modules and keystone taxa positively correlating with plant As extraction and C fixation were identified, indicating that modules and keystone taxa promoted plant As extraction and C fixation simultaneously. This is mainly because modules and keystone taxa in plant rhizosphere, root endosphere, and shoot endosphere carried arsenate reduction and C fixation genes. Meanwhile, they up-regulated the significant metabolites related to plant As tolerance. Additionally, shoot C fixation increased peroxidase activity and biomass thereby facilitating plant As extraction was confirmed. This study revealed the mechanisms of plant-associated bacterial interactions contributing to plant As extraction and C fixation. More importantly, this study provided a new angle of view that phytoextraction can be applied to achieve multiple environmental goals, such as simultaneous soil remediation and C neutrality.

Neoroseomonas alba sp. nov., Neoroseomonas nitratireducens sp. nov., Paraoseomonas indoligenes sp. nov and Paraoseomonas baculiformis sp. nov., isolated from the rhizosphere of paddy soil

Four novel Gram-stain negative bacteria, designated as HAJ6T, PWR1T, SG15T and SSH11T, were isolated from the soil sample of paddy fields from Goyang in the Republic of Korea. The isolated strains were aerobic, short-rod or rod shaped, non-sporulating. They grew optimally at 30 °C, pH 7 and without additional NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that they belong to the genus of Neoroseomonas and Pararoseomonas and closely relate to Neoroseomonas terrae DS-48T (97.5%; HJA6T), Neoroseomonas rubea MO17T (99.4%; PWR1T), Pararoseomonas pecuniae N75T (97.3%; SG15T) and Pararoseomonas rosea 173-96T (97.8%; SSH11T). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the isolates with the most closely related strains were 72.9-90.9% and 19.1-42.5%, respectively. The major fatty acids in the isolates were C16:0, C19:0 cyclo ω8c, C18:1 2-OH and summed feature 8 (composed of C18:1 ω7c and/or C18:1 ω6c), and the predominant quinone was ubiquinone 10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and other unidentified polar lipids. Based on the draft genome sequences, the genomic DNA G + C content of HAJ6T, PWR1T, SG15T and SSH11T were 69.5%, 72.0%, 70.8% and 69.7%, respectively. All isolates produced indole-3-acetic acid (IAA), a type of plant growth hormone in the presence of L-tryptophan. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that the isolates were novel species belonging to the genus Neoroseomonas and Pararoseomonas. Their proposed names were as follows: Neoroseomonas alba sp. nov. for strain HJA6T (= KACC 21545T = NBRC 114316T), Neoroseomonas nitratireducens sp. nov. for strain PWR1T (= KCTC 82687T = NBRC 114490T), Pararoseomonas indoligenes sp. nov. for strain SG15T (= KCTC 82686T = NBRC 114481T) and Paraoseomonas baculiformis sp. nov. for strain SSH11T (= KCTC 82685T = NBRC 11482T).

Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant

A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.

Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings

BACKGROUND

The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota.

RESULTS

The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant.

CONCLUSIONS

Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.

Effects of different cultivation media on root bacterial community characteristics of greenhouse tomatoes

Tomato, as a typical greenhouse crop, is commonly first planted as seedlings in a variety of substrates before being transplanted into soil. However, there is rare research on the characteristics of the bacterial community in tomato roots under this planting mode. In this study, tomatoes were planted in pots containing three different cultivation media, including soil and two types of substrates in a greenhouse, followed by a transplanting treatment. After collecting tomato root samples, high-throughput sequencing and bioinformatic analysis were used to compare the differences in bacterial diversity and functions between tomato roots before and after transplanting in different cultivation media. In total, 702776 sequences were obtained, and the OTUs were belonging to 109 genera, 58 families, 41 orders, 14 classes, and 12 phyla. Among the three cultivation media, the β-diversity was significant, and there was a slight difference in bacterial species diversity along with a large difference in their abundance at the genus level. Soil and both substrates had 79 bacterial genera in common, these genera accounted for 68.70%, 76.70%, and 71.17% of the total genera found in the soil, substrate 1, and substrate 2, respectively. After being transplanted from the two substrates to the soil, the bacterial community structure and abundance exhibited similarities with those found in the soil. Furthermore, based on microbial function prediction, the microbial communities in the two-substrate environment demonstrated a greater potential for promoting growth, while the microbial communities in the soil exhibited a greater tendency to exert their antibacterial potential. Our findings offer theoretical support for the creation of artificially reconstructed microbial communities in greenhouse cultivation.

Cooperative Action of Fulvic Acid and Bacillus paralicheniformis Ferment in Regulating Soil Microbiota and Improving Soil Fertility and Plant Resistance to Bacterial Wilt Disease

Excessive continuous cropping and soil degradation, such as acidification, hardening, fertility decline, and the degradation of microbial community, lead to the epidemic of soilborne diseases and cause great loss in agriculture production. Application of fulvic acid can improve the growth and yield of various crops and effectively suppress soilborne plant diseases. Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid is used to remove the organic acid that can cause soil acidification and increase the fertilizer effect of fulvic acid and the effect of improving soil quality and inhibiting soilborne disease. In field experiments, the application of fulvic acid and Bacillus paralicheniformis ferment effectively reduced the incidence of bacterial wilt disease and improved soil fertility. Both fulvic acid powder and B. paralicheniformis ferment improved soil microbial diversity and increased the complexity and stability of the microbial network. For B. paralicheniformis ferment, the molecular weight of poly-gamma-glutamic acid became smaller after heating, which could better improve the soil microbial community and network structure. In fulvic acid and B. paralicheniformis ferment-treated soils, the synergistic interaction between microorganisms increased and the number of keystone microorganisms increased, which included antagonistic bacteria and plant growth-promoting bacteria. Changes in the microbial community and network structure were the main reason for the reduced incidence of bacterial wilt disease. Application of fulvic acid and Bacillus paralicheniformis ferment improved soil physicochemical properties and effectively controlled bacterial wilt disease by changing microbial community and network structure and enriching antagonistic and beneficial bacteria. IMPORTANCE Continuous cropping tobacco has led to soil degradation and caused soilborne bacterial wilt disease. Fulvic acid as a biostimulator was applied to restore soil and control bacterial wilt disease. For improving its effect, fulvic acid was fermented with Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid. Fulvic acid and B. paralicheniformis ferment inhibited bacterial wilt disease, improved soil quality, enriched beneficial bacteria, and increased microbial diversity and microbial network complexity. Some keystone microorganisms in fulvic acid and B. paralicheniformis ferment-treated soils had potential antimicrobial activity and plant growth-promoting attributes. Fulvic acid and B. paralicheniformis 285-3 ferment could be used to restore soil quality and microbiota and control bacterial wilt disease. This study found new biomaterial to control soilborne bacterial disease by combining fulvic acid and poly-gamma-glutamic acid application.

Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter

A Gram-stain-negative, halotolerant bacterium designated as PTR5^T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5^T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C_16:0, C_18:1 ω7c 11-methyl and summed feature 8 (comprising C_18:1 ω7c/C_18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5^T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5^T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5^T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5^T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5^T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5^T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5^T (KCTC 82691^T = TBRC 15163^T) is proposed.

Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community

The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.

Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan

To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.

Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato)

A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36^T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02^T (99.0%) and Paraburkholderia sacchari IPT101^T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36^T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36^T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C_16:0, C_17:0 cyclo, C_19:0 cyclo ω8c, and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c). Strain RG36^T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36^T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36^T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36^T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36^T (=KACC 22685^T = TBRC 15696^T).

Plant growth promoting bacteria drive food security

The essence of food security centers on ensuring availability and accessibility of foods in adequate amounts and quality for all populations at all times for an active and healthy life. Microorganisms are tiny bioreactors, which represent sustainable resources and promising approaches to bridging the gap between food production and consumption globally via various biotechnological applications. This review focuses on plant-growth promoting bacteria (PGPB) which exert their potential impacts on increasing soil fertility, plant growth, and productivity through a variety of processes, including direct, indirect, and synergistic mechanisms. PGPB plays a substantial role in accelerating nutrients' availability such as (N, P), producing phytohormones such as gibberellins, IAA, and bioactive compounds against biotic and abiotic stressors. Recent advances in PGPB will be addressed as a sustainable approach to satisfy global food demand.

Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils

Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4^T, JC52^T and PR3^T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4^T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201^T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80^T (97.2/-/18.2±1.2 %). Values for JC52^T with Paenibacillus validus NBRC 15382^T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352^T were 96.1, 72.1 and 19.3 %. Values for PR3^T with Paenibacillus ginsengiterrae DCY89^T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1^T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729^T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C_15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4^T, JC52^T and PR3^T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717^T=JCM 32775^T), Paenibacillus cremeus sp. nov. (=KACC 21221^T=NBRC 113867^T) and Paenibacillus terricola sp. nov. (=KACC 21455^T=NBRC 114385^T), respectively.

Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants

Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.

International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021

Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.

An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth

Rice is a symbol of life and a representation of prosperity in South Korea. However, studies on the diversity of the bacterial communities in the rhizosphere of rice plants are limited. In this study, four bundles of root samples were collected from the same rice field located in Goyang, South Korea. These were systematically analyzed to discover the diversity of culturable bacterial communities through culture-dependent methods. A total of 504 culturable bacteria were isolated and evaluated for their plant growth-promoting abilities in vitro. Among them, Arthrobacter sp. GN70 was selected for inoculation into the rice plants under laboratory and greenhouse conditions. The results showed a significantly positive effect on shoot length, root length, fresh plant weight, and dry plant weight. Moreover, scanning electron microscopic (SEM) images demonstrated the accumulation of bacterial biofilm networks at the junction of the primary roots, confirming the root-colonizing ability of the bacterium. The strain also exhibited a broad spectrum of in vitro antimicrobial activities against bacteria and fungi. Here, we first report the rice plant growth-promoting ability of the Arthrobacter species with the biofilm-producing and antimicrobial activities against plant and human pathogens. Genome analyses revealed features attributable to enhance rice plant growth, including the genes involved in the synthesis of plant hormones, biofilm production, and secondary metabolites. This study revealed that the rhizobacteria isolated from the roots of rice plants have dual potential to be utilized as a plant growth promoter and antimicrobial agent.

Chryseobacterium tagetis sp. nov., a plant growth promoting bacterium with an antimicrobial activity isolated from the roots of medicinal plant (Tagetes patula)

A novel plant growth-promoting and indole acetic acid (IAA) producing strain designated RG1^T was isolated from the roots of Tagetes patula (marigold) collected from Goyang, South Korea. The cells of strain RG1^T is aerobic, yellow, Gram-stain-negative, pleomorphic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RG1^T belongs to the genus Chryseobacterium and is closely related to Chryseobacterium gwangjuense THG-A18^T (98.6%). The strain produced IAA (70.5 µg ml^-1) in the presence of _L-tryptophan and showed antimicrobial activity against Gram-negative bacterium Xanthomonas campestris pv. campestris KACC 10377^T. The isolate had a significant positive effect on rice plant shoot and root growth. The novel strain RG1^T had a draft genome size of 4,430,189 bp, with ten scaffolds and 3969 protein-coding genes. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RG1^T and other closely related members ranged from 21.5 to 36.6% and from 79.2 to 86.6%, respectively. The genomic DNA G + C content was 34.8 mol%. Furthermore, anti-SMASH analysis of the whole genome revealed six putative biosynthetic gene clusters responsible for various secondary metabolites. The major respiratory quinone was MK-6 and the major fatty acids were iso-C_15:0, summed feature 3 (comprising C_16: 1ω7c and/or C_16: 1ω6c) and summed feature 9 (comprising iso-C_17: 1 ω9c and/or 10-methyl C_16:0). The major polar lipid is phosphatidylethanolamine. Based on the genotypic, chemotaxonomic and physiological data, strain RG1^T represents a novel species, for which the name Chryseobacterium tagetis sp. nov. is proposed. The type strain is designated as RG1^T ( = KCTC 82696^T = NBRC 115057^T).

Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features

Abstract Significant food resource shortages are occurring worldwide. Plant growth-promoting rhizobacteria (PGPR) represent an ecofriendly and efficient approach for increasing soil fertility and plant productivity. The current study explored biostimulating traits of PGPR from the rhizosphere of Lotus corniculatus growing in the Al-Ahsa region. A bacterial isolate (LCK121) was obtained, characterized for phenotypic, and identified by 16S rRNA gene sequencing. In addition, its growth-stimulating effects on barley were investigated. The strain identity was confirmed via comparative analysis of the 16S rDNA sequences with Klebsiella oxytoca (99.3% similarity level). LCK121 exhibited multiple plant growth-promoting features, including indole-3-acetic acid (IAA) production (16.34 µg mL-1), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity (1.35±0.02 µmol α-ketobutyrate mg−1 h−1), phosphate solubilization, and nitrogen fixation. Furthermore, in vitro inoculation of barley with LCK121 significantly increased the root and shoot dry weights. The results highlight the potential of LCK121 for developing green fertilizers for sustainable agriculture.