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Summary: Potato is the third most important food crop worldwide. Potato production suffers from severe diseases caused by multiple detrimental plant pathogens, and broad‐spectrum disease resistance genes are rarely identified in potato. Here we identified the potato non‐specific lipid transfer protein StLTPa, which enhances species none‐specific disease resistance against various pathogens, such as the oomycete pathogen Phytophthora infestans, the fungal pathogens Botrytis cinerea and Verticillium dahliae, and the bacterial pathogens Pectobacterium carotovorum and Ralstonia solanacearum. The StLTPa overexpression potato lines do not show growth penalty. Furthermore, we provide evidence that StLTPa binds to lipids present in the plasma membrane (PM) of the hyphal cells of P. infestans, leading to an increased permeability of the PM. Adding of PI(3,5)P2 and PI(3)P could compete the binding of StLTPa to pathogen PM and reduce the inhibition effect of StLTPa. The lipid‐binding activity of StLTPa is essential for its role in pathogen inhibition and promotion of potato disease resistance. We propose that StLTPa enhances potato broad‐spectrum disease resistance by binding to, and thereby promoting the permeability of the PM of the cells of various pathogens. Overall, our discovery illustrates that increasing the expression of a single gene in potato enhances potato disease resistance against different pathogens without growth penalty. [ABSTRACT FROM AUTHOR]

Aims: N2O emitted by agricultural ecosystems has a great impact on global warming and climate change. The use of controlled-release fertilizers (CRF) can decrease greenhouse gas emissions. However, the general patterns and variability of nitrogen functional genes in response to CRF associated with N2O emission have not been synthesized under climate change. Methods: We investigated the effects of CRF, elevated CO2 concentration (EC), elevated temperature (ET), and their combination on N2O emission, enzyme activities and gene abundances. Results: We found that the cumulative N2O emissions was in the range of 0.39–1.65 kg·ha−1 in the wheat-growing season, accounting for 0.54%–2.29% of the total nitrogen input. N2O emissions were considerably positively correlated with ammonia-oxidizing bacteria (AOB) at elongation stage. CRF inputs significantly decreased N2O emissions by 29 − 66% compared with urea due to decreased AOB abundance and inhibited nitrite reductase activities at elongation stage. EC significantly decreased N2O emissions by 30 − 50% likely resulting from the inhibition in nitrifying and denitrifying community compared with ambient CO2 concentration. ET significantly increased N2O emissions by increasing N mineralization in wheat soil under CRF due to higher NH4+-N and NO3−-N concentration in wheat soil at elongation stage. In addition, ECET had antagonistic effect on N2O emissions. CRF had no significant effect on wheat yield under climate change scenarios. Conclusions: CRF decreased the cumulative N2O emissions under climate change scenarios. This is critical for understanding the responses of N2O emissions from wheat soil under CRF to future CO2 enrichment and warming for the establishment of mitigation and adaptation policies. [ABSTRACT FROM AUTHOR]

The gray mold caused by the phytopathogen Botrytis cinerea presents a threat to global food security. For the biological regulation of several plant diseases, Bacillus species have been extensively studied. In this work, we explore the ability of a bacterial strain, Bacillus cabrialesii BH5, that was isolated from tomato rhizosphere soil, to control the fungal pathogen B. cinerea. Strain B. cabrialesii BH5 showed a strong antifungal activity against B. cinerea. A compound was isolated and identified as a cyclic lipopeptide of the fengycin family by high-performance liquid chromatography and tandem mass spectrometry (ESI-MS/MS) that we named fengycin H. The fengycin H-treated hyphae of B. cinerea displayed stronger red fluorescence than the control, which is clearly indicating that fengycin H triggered the hyphal cell membrane defects. Moreover, root inoculation of tomato seedlings with BH5 effectively promoted the growth of tomato plants. Transcription analysis revealed that both BH5 and fengycin H stimulate induced systemic resistance of tomato plants via the jasmonic acid signaling pathway and provide a strong biocontrol effect in vivo. Therefore, the strain BH5 and fengycin H are very promising candidates for biological control of B. cinerea and the associated gray mold. [ABSTRACT FROM AUTHOR]

Summary: The development of sustainable agriculture and the increasing antibiotic resistance of human pathogens call for novel antimicrobial compounds. Here, we describe the extraction and characterization of a class of cationic circular lipopeptides, for which we propose the name relacidines, from the soil bacterium Brevibacillus laterosporus MG64. Relacidines are composed of a fatty acid side chain (4‐methylhexanoic acid) and 13 amino acid residues. A lactone ring is formed by the last five amino acid residues and three positively charged ornithines are located in the linear fragment. Relacidines selectively combat Gram‐negative pathogens, including phytopathogens and human pathogens. Further investigation of the mode of action revealed that relacidine B binds to the lipopolysaccharides but does not form pores in the cell membrane. We also provide proof to show that relacidine B does not affect the biosynthesis of the cell wall and RNA. Instead, it affects the oxidative phosphorylation process of cells and diminishes the biosynthesis of ATP. Transcription of relacidines is induced by plant pathogens, which strengthens the potential of B. laterosporus MG64 to be used as a biocontrol agent. Thus, we identified a new group of potent antibiotic compounds for combating Gram‐negative pathogens of plants or animals. [ABSTRACT FROM AUTHOR]

Summary: Soil‐dwelling entomopathogenic nematodes (EPNs) kill arthropod hosts by injecting their symbiotic bacteria into the host hemolymph and feed on the bacteria and the tissue of the dying host for several generations cycles until the arthropod cadaver is completely depleted. The EPN–bacteria–arthropod cadaver complex represents a rich energy source for the surrounding opportunistic soil fungal biota and other competitors. We hypothesized that EPNs need to protect their food source until depletion and that the EPN symbiotic bacteria produce volatile and non‐volatile exudations that deter different soil fungal groups in the soil. We isolated the symbiotic bacteria species (Alcaligenes faecalis) from the EPN Oscheius spp. and ran infectivity bioassays against entomopathogenic fungi (EPF) as well as against plant pathogenic fungi (PPF). We found that both volatile and non‐volatile symbiotic bacterial exudations had negative effects on both EPF and PPF. Such deterrent function on functionally different fungal strains suggests a common mode of action of A. faecalis bacterial exudates, which has the potential to influence the structure of soil microbial communities, and could be integrated into pest management programs for increasing crop protection against fungal pathogens. [ABSTRACT FROM AUTHOR]

Summary: Bacillus subtilis HS3 and Bacillus mycoides EC18 are two rhizosphere‐associated bacteria with plant growth‐promoting activity. The CRISPR‐Cas9 system was implemented to study various aspects of plant‐microbe interaction mechanisms of these two environmental isolates. The results show that fengycin and surfactin are involved in the antifungal activity of B. subtilis HS3. Moreover, this strain emits several other volatile organic compounds than 2,3‐butanediol, contributing to plant growth promotion. Confocal laser scanning microscopy observations of the GFP‐labelled strain showed that HS3 selectively colonizes root hairs of grass (Lolium perenne) in a hydroponic system. For B. mycoides EC18, we found that the wild‐type EC18 strain and a ΔasbA (petropectin‐deficient) mutant, but not the ΔdhbB (bacillibactin‐deficient) and ADKO (asbA and dhbB double knockout) mutants, can increase the plant biomass and total chlorophyll. All the mutant strains have a reduced colonization capability on Chinese cabbage (Brassica rapa) roots, at the root tip and root hair region compared with the wild‐type strain. These results indicate that the siderophore, bacillibactin, is involved in the plant growth promoting activity and could affect the root colonization of B. mycoides. Collectively, the CRISPR‐Cas9 system we developed for environmental isolates is broadly applicable and will facilitate deciphering the mechanisms of Bacillus‐plant interactions. © 2018 The Authors. [ABSTRACT FROM AUTHOR]

Swarming motility is a flagella-driven multicellular behaviour that allows bacteria to colonize new niches and escape competition. Here, we investigated the evolution of specific mutations in the GacS/GacA two-component regulatory system in swarming colonies of Pseudomonas protegens Pf-5. Experimental evolution assays showed that repeated rounds of swarming by wildtype Pf-5 drives the accumulation of gacS/gacA spontaneous mutants on the swarming edge. These mutants cannot swarm on their own because they lack production of the biosurfactant orfamide A, but they do co-swarm with orfamide-producing wildtype Pf-5. These co-swarming assays further demonstrated that Δ gacA mutant cells indeed predominate on the edge and that initial Δ gacA:wildtype Pf-5 ratios of at least 2:1 lead to a collapse of the swarming colony. Subsequent whole-genome transcriptome analyses revealed that genes associated with motility, resource acquisition, chemotaxis and efflux were significantly upregulated in Δ gacA mutant on swarming medium. Moreover, transmission electron microscopy showed that Δ gacA mutant cells were longer and more flagellated than wildtype cells, which may explain their predominance on the swarming edge. We postulate that adaptive evolution through point mutations is a common feature of range-expanding microbial populations and that the putative fitness benefits of these mutations during dispersal of bacteria into new territories are frequency-dependent. [ABSTRACT FROM AUTHOR]

The rhizobacterium P seudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome-wide search for sRNAs and performed transcriptomic analyses to identify genes associated with the Rsm ( repressor of secondary metabolites) regulon. In silico analysis led to the identification of 16 putative sRNAs in the SS101 genome. In frame deletion of the sRNAs rsmY and rsmZ showed that the Rsm system regulates the biosynthesis of the lipopeptide massetolide A and involves the two repressor proteins RsmA and RsmE, with the LuxR-type transcriptional regulator MassAR as their most likely target. Transcriptome analyses of the rsmYZ mutant further revealed that genes associated with iron acquisition, motility and chemotaxis were significantly upregulated, whereas genes of the type VI secretion system were downregulated. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/ RsmZ are also controlled by the GacS/ GacA two-component system. We conclude that the Rsm regulon of P. fluorescens SS101 plays a critical role in the regulation of lipopeptide biosynthesis and controls the expression of other genes involved in motility, competition and survival in the plant rhizosphere. [ABSTRACT FROM AUTHOR]

Pseudomonas fluorescens SS101 produces the cyclic lipopeptide massetolide with diverse functions in antimicrobial activity, motility, and biofilm formation. To understand how massetolide biosynthesis is genetically regulated in SS101, c. 8000 random plasposon mutants were screened for reduced or loss of massetolide production. Of a total of 58 putative mutants, 45 had a mutation in one of the three massetolide biosynthesis genes massA, massB, or massC. For five mutants, the insertions were located in the known regulatory genes gacS, gacA, and clpP. For the remaining eight mutants, insertions were located in clpA, encoding the ClpP chaperone, in phgdh, encoding D-3-phosphoglycerate dehydrogenase, in the heat shock protein-encoding dnaK, or in the transmembrane regulatory gene prtR. Genetic, chemical, and phenotypic analyses showed that phgdh, dnaK, and prtR are indeed involved in the regulation of massetolide biosynthesis, most likely by transcriptional repression of the LuxR-type regulator genes mass AR and mass BCR. In addition to their role in massetolide biosynthesis, dnaK and prtR were found to affect siderophore and extracellular protease(s) production, respectively. The identification of new regulatory genes substantially extended insights into the signal transduction pathways of lipopeptide biosynthesis in P. fluorescens and into regulation of other traits that may contribute to its life-style in the rhizosphere. [ABSTRACT FROM AUTHOR]

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45--52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2- hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire. [ABSTRACT FROM AUTHOR]

Abstract: Zwittermicin A (ZwA) is a hybrid polyketide–non-ribosomal peptide that is thought to be biosynthesized from five proposed building blocks, including the 2,3-diaminopropionate. Candidate genes for de novo biosynthesis of 2,3-diaminopropionate, zwa5A and zwa5B, have been identified in a previous study. In this research, zwa5A was interrupted and chemically synthesized 2,3-diaminopropionate was used to feed the zwa5A − mutant. Results showed that feeding with 2,3-diaminopropionate restored the ability of the zwa5A − mutant to produce ZwA. Another non-ribosomal peptide synthase gene, designated orf3, was identified. Amino acid dependent PPi release assay showed that the adenylation domain ZWAA2 of ORF3 acyl-adenylated l-2,3-diaminopropionate effectively. Taken together, it can be concluded that l-2,3-diaminopropionate is indeed one of the building blocks for the biosynthesis of Zwittermicin A. [Copyright &y& Elsevier]

• Reciprocal interactions between the microbiome and the plant can shape the foundation of the MicrobiHome. • Soil pore sizes along roots generate differently sized 'rooms' for microbiomes. • Design crops with extended root phenotypes and genotypes to recruit and activate beneficial microbiomes. • Develop new strategies to engineer crops and microbiome with mutual benefits. The plant microbiome comprises a highly diverse community of saprotrophic, mutualistic, and pathogenic microbes that can affect plant growth and plant health. There is substantial interest to exploit beneficial members of plant microbiomes for new sustainable management strategies in crop production. However, poor survival and colonization of plant tissues by introduced microbial isolates as well as lack of expression of the plant growth-promoting or disease-suppressive traits at the right time and place are still major limitations for successful implementation of microbiomes in future agricultural practices and plant breeding programs. Similar to building a home for humans, we discuss different strategies of building a home for beneficial plant microbiomes, here referred to as the 'MicrobiHome'. [ABSTRACT FROM AUTHOR]

Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments. [ABSTRACT FROM AUTHOR]

[Display omitted] • Integration of electric field with electrophilic fungi propels innovative composting. • Microbial electrochemical composting promoted the conversion of lignocellulose to humus. • Electric fields can act as activators of Aspergillus oryzae. • Electric fields increase the catalytic efficiency of lignin oxidases. Achieving satisfactory levels of humification during composting is recognised as a challenge due to the recalcitrance of lignocellulose and the uncertainty of current biofortification techniques. Therefore, a novel microbial electrochemical composting technology was developed from insights into microbiology and electrochemistry in this study to strengthen microorganisms' function promoting the conversion from lignocellulose into humus. Firstly, a fungus (Aspergillus oryzae) was introduced which exhibited a higher propagation rate (29.9%) and secreted more lignocellulose-degrading enzymes (18.9–74.9%) under electric field assistance. Subsequently, an in-situ composting trial was conducted with supplementary electric fields simultaneously combined with Aspergillus oryzae inoculation. The abundance of Aspergillus oryzae increased 3.0–7.8-fold under the influence of electric field, which enabled the production of more extracellular enzymes (by 8.4–149.5%) to promote the conversion of lignocellulose to humus (increased by 7.0–20.2%). The results indicated electric field can act as an activator of Aspergillus oryzae and magnify its function. It provides an innovative and efficient technique for enhancing humification during composting that contributes to the conversion of organic waste into high-quality soil conditioner products. [ABSTRACT FROM AUTHOR]