Abstract One main approach to computational analysis of microbiome sequences is first align against a reference database annotated protein (NCBI‐nr) and then perform taxonomic functional binning the based on resulting alignments. For both short long reads (or assembled contigs), alignment performed using DIAMOND, whereas binning, followed by inter‐ active exploration analysis, MEGAN. We provide two step‐by‐step descriptions this approach: © 2021 The Authors. This article was corrected 20...

ABSTRACT Plant-beneficial microorganisms are gaining importance for sustainable plant production and phytosanitary practices. Yet there is a lack of computational approaches targeting bacterial traits associated with growth-promotion (PGP), which hinders the in-silico identification, comparison, selection phytostimulatory strains. To address this problem, we have developed new web resource PLaBAse (v1.01, http://plabase.informatik.uni-tuebingen.de/pb/plabase.php ), provides number services,...

In a recent publication, we introduce the PGPT ontology and PGPT-db of bacterial plant growth-promotion traits associated database protein sequences, provide several tools for genome analysis on PLaBAse server. Here, extend scope to perform metagenomic datasets. First, mgPGPT-db, an extended 39, 582, 183 sequences obtained computationally by including proteins from AnnoTree. With this, have integrated into our metagenome tool MEGAN mapping files identify PGPT-related genes using results...

Exploiting native plant growth-promoting rhizobacteria (PGPR) in Cameroonian agro-ecosystems provides a means to improve plant–microbe interactions that may enhance ecosystem sustainability and agricultural productivity an environmentally eco-friendly way. Consequently, we aimed investigate the community structure functional PGPR diversity of maize grown Cameroon. Native bacteria isolated from Cameroon rhizosphere soil were identified by partial 16S rRNA gene sequencing screened for traits...

The global market for biosupplements is expected to grow by 14 percent between 2014 and 2019 as a consequence of the proven benefits on crop yields, soil fertility, fertilizer efficiency. One important segment plant growth-promoting bacteria (PGPB). Although many potential PGPB have been discovered, suitable biotechnological processing shelf-life stability are challenges overcome their successful use biosupplements. Here, Gram-negative strain Kosakonia radicincitans DSM<mml:math...

The recent worldwide discovery of plant growth-promoting (PGP) Kosakonia radicincitans in a large variety crop plants suggests that this species confers significant influence on plants, both terms yield increase and product quality improvement. We provide comparative genome analysis which helps to unravel the genetic basis for K. radicincitans' motility, competitiveness capacities. discovered carries multiple copies complex gene clusters, among them two flagellar systems three type VI...

Despite the great interest in using halophyte Salicornia europaea L. as a crop extreme saline habitats, little is known about role played by associated endophytic bacteria increasing tolerance of host-plant to nutrient deficiency. Main objectives this study were investigate community composition diazotrophic endophytes S. grown under natural conditions, and determine proportion plant-growth promoting bacterial strains able fix N2. To quantify abundance stems roots europaea, nifH gene 16S...

Salinity and phosphorus (P) deficiency are among the most serious soil factors constraining crop productivity. A proposed strategy for alleviating these stresses is supporting plants by inoculation with growth-promoting rhizobacteria (PGPR). Here, a comparison of ability two maize composite F1 hybrid varieties to tolerate P in either saline or non-saline environment showed that uptake nutrients all four entries was significantly reduced imposition both salinity deficiency, their growth...

Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here, we propose two new Rhizobiales species isolated from root common sainfoin (Onobrychis viciifolia), as shown core-gene phylogeny, overall genome relatedness indices, and pan-genome analysis. Mesorhizobium onobrychidis sp. nov. actively induces achieves atmospheric nitrogen carbon dioxide fixation. This appears to be depleted in motility genes is enriched for direct effects on plant growth...

Plants are often challenged by multiple abiotic stresses simultaneously. The inoculation of beneficial bacteria is known to enhance plant growth under these stresses, such as phosphorus starvation or salt stress. Here, for the first time, we assessed efficiency selected bacterial strains in improving tomato better cope with double salty and P-deficient soil conditions. Six Arthrobacter Bacillus different reservoirs growth-promoting traits were tested vitro their abilities tolerate 2–16%...

Abstract Background Extreme weather events induced by climate change, particularly droughts, have detrimental consequences for crop yields and food security. Concurrently, these conditions provoke substantial changes in the soil bacterial microbiota affect plant health. Early recognition of affected drought enables farmers to implement appropriate agricultural management practices. In this context, interpretable machine learning holds immense potential stress classification based on marker...

The rapid development of high-throughput techniques and expansion bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate mimic the nutritional matrices roots. herein employed G3 PhyloChip microarray meticulously characterize culture-dependent -independent communities maize root compartments, endo- ecto-rhizospheres. An emphasis was placed on preference growth unculturable divisions/phyla...

Abstract Kosakonia radicincitans is a species within the new genus . Many strains of this have been isolated from plants, but some are assumed to act as facultative human pathogens. In study, an in-depth analysis isolate blood was performed. The strain originally and identified member Enterobacter cloacae complex, exhibiting atypical result in susceptibility testing. Therefore, genetic background examined, including phylogenetic classification screening for virulence factors. Using...

In an effort to axenically culture the previously uncultivable populations of rhizobacteria Lucerne (Medicago sativa L.), we propose plant-only teabags media mimic nutritional matrix available in rhizosphere. Here, show that prepared from powder substantially increased cultivability compared with a standard nutrient agar, where found cultivable significantly by up 60% total bacterial numbers as estimated Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis 16S rDNA...

High-throughput cultivation methods have recently been developed to accelerate the recovery of microorganisms reluctant cultivation. They simulate in situ environmental conditions for isolation microbiota through exchange growth substrates during Here, we introduce leaf-based culture media adopting concept plant being master architect composition its microbial community. Pre-physical treatments sunflower leaves, namely punching, freezing, and/or autoclavation, allowed diffusion electrolytes...

Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation hub taxa. Despite recent advances high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably human microbiome. As a plant-based culturing strategy, we developed culture media based on broth cooked aqueous mixtures host This improved growth representative isolates plant extended situ recovery microbiota....

The plant phyllosphere is colonized by a complex ecosystem of microorganisms. Leaves raw eaten vegetables and herbs are habitats for bacteria important not only to the host plant, but also human health when ingested via meals. aim current study was determine presence putative probiotic in produce. Quantification bifidobacteria showed that leaves Lepidium sativum L., Cichorium endivia Thymus vulgaris L. harbor between 103 106 DNA copies per gram fresh weight. Total cultivable those three...

Plant microbiota have co-evolved with their associated plants in the entire holobiont, and assemblages support diversity productivity on our planet. Of importance is vitro cultivation identification of hub taxa for possible core microbiome modification. Recently, we introduced situ-similis culturing strategy, based use plant leaves as a platform growth microbiota. Here, strategy further extended by exploring organ compatible when grown corresponding leaf/root-based culture media. Pooling...

Biological nitrogen fixation (BNF) is considered one of the key plant-growth-promoting (PGP) factors for diazotrophic organisms. Whether iron and iron–molybdenum nitrogenases Kosakonia radicincitans contribute to its PGP effect yet be proven. Hence, first time, we conducted site-directed mutagenesis in K. knock out anfH (or) nifH as a mean deactivate BNF this strain. We used 15 N 2 -labeled air trace activities ΔanfH, ΔnifH, ΔanfHΔnifH mutants. Assessing bacterial growth, content,...

Bacteria, which establish positive interactions with plant roots, play a key role in agricultural environments and are promising for their potential use sustainable agriculture. Many of these mutualistic bacteria provide benefits to hosts by facilitating soil mineral nutrient uptake, protecting plants from biotic abiotic stresses producing substances that promote growth. The dataset presented here, is related the publication entitled "Community structure growth-promoting cultivable isolated...

Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as

Abstract Background Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive...

Abstract Medium-chain carboxylates are used in various industrial applications. These chemicals typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce medium-chain carboxylates, such as n -caproate (C6) and -caprylate (C8), organic substrates wastes. Even though the production of relatively well-characterized, bacteria metabolic pathways that responsible for not. Here, three 5-L with continuous...