Legume tasters: symbiotic rhizobia host preference and smart inoculant formulations

Mutualistic interactions have great importance in ecology, with genetic information that takes shape through interactions within the symbiotic partners and between the partners and the environment. It is known that variation of the host-associated microbiome contributes to buffer adaptation challenges of the host’s physiology when facing varying environmental conditions. In agriculture, pivotal examples are symbiotic nitrogen-fixing rhizobia, known to contribute greatly to host (legume plants) adaptation and host productivity. A holistic view of increasing crop yield and resistance to biotic and abiotic stresses is that of microbiome engineering, the exploitation of a host-associated microbiome through its rationally designed manipulation with synthetic microbial communities. However, several studies highlighted that the expression of the desired phenotype in the host resides in species-specific, even genotype-specific interactions between the symbiotic partners. Consequently, there is a need to dissect such an intimate level of interaction, aiming to identify the main genetic components in both partners playing a role in symbiotic differences/host preferences. In the present paper, while briefly reviewing the knowledge and the challenges in plant–microbe interaction and rhizobial studies, we aim to promote research on genotype x genotype interaction between rhizobia and host plants for a rational design of synthetic symbiotic nitrogen-fixing microbial communities to be used for sustainably improving leguminous plants yield.This work was supported by the grant MICRO4Legumes (“Il microbioma vegetale simbionte come strumento per il miglioramento delle leguminose foraggere. Acronimo”), D.M.n.89267 (Italian Ministry of Agriculture)

Role and regulation of ACC deaminase gene in Sinorhizobium meliloti: is it a symbiotic, rhizospheric or endophytic gene?

Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR). acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental adaptations and/or niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological niches and an overall reprogramming following niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated niche adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes

Effect of bioactive compounds released from Brassicaceae defatted seed meals on bacterial load in pig manure.

Animal manure application to soils is considered to be one of the main cause of antibiotic and bacterial pathogen spread in the environment. Pig livestock, which is the source of one of the most used fertilizer for cultivated land, is also a hotspot for antibiotics and antibiotic-resistant bacteria. Besides harsh chemical and physical sanitization treatments for the abatement of antibiotics and bacterial load in livestock waste, more sustainable and environmentally friendly strategies need to be considered. In this context, the use of natural substances which are proved useful for pest and disease control is currently under exploration for their role in the reduction of bacterial pathogen population. Among these, plants and derived products from the Brassicaceae family, characterized by the presence of a defensive glucosinolate-myrosinase enzymatic system, have been successfully exploited for years in agriculture using the so-called biofumigation technique against crop diseases. Although the application of biofumigation to suppress a range of soil borne pests has been well documented, no studies have been examined to reduce bacterial population in animal waste. In the present study, the release and the antibacterial activity of bioactive compounds deriving from different Brassicaceae defatted seed meals against pathogens and bacterial population in pig manure is addressed. Rapistrum rugosum and Brassica nigra defatted seed meals were found to be the most active products against tested pathogens and able to significantly reduce the bacterial load in the manure

Taxonomical and functional composition of strawberry microbiome is genotype-dependent

Introduction: Specific microbial communities are associated to host plants, influencing their phenotype and fitness. Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. Objectives: This work provides the first comprehensive description of the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organs of three commercially important strawberry genotypes under cultural conditions. Methods: Strawberry-associated fungal and bacterial microbiomes were characterised by NextGeneration Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. Results: Results showed that the strawberry core microbiome included 24 bacteria and 15 fungal operational taxonomic units (OTUs). However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highest tolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonas fluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhiza Rhizophagus irregularis. Conclusion: This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop productio

I Like the Way You Eat It: Lemur (Indri indri) Gut Mycobiome and Geophagy

Here, we investigated the possible linkages among geophagy, soil characteristics, and gut mycobiome of indri (Indri indri), an endangered lemur species able to survive only in wild conditions. The soil eaten by indri resulted in enriched secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Besides, we found that soil subject to geophagy and indris’ faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) commonly associated with soil and plant material were found in both geophagic soil and indri samples. On the contrary, some taxa with pathogenic potentials, such as Cryptococcus, were only found in indri samples. Further, many saprotrophs and plant-associated fungal taxa were detected in the indri faeces. These fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. In conclusion, we found an intimate connection between gut mycobiome and soil, highlighting, once again, the potential consequent impacts on the wider habitat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-020-01677-5

Multifunctional nanoassemblies target bacterial lipopolysaccharides for enhanced antimicrobial DNA delivery

The development of new therapeutic strategies against multidrug resistant Gram-negative bacteria is a major challenge for pharmaceutical research. In this respect, it is increasingly recognized that an efficient treatment for resistant bacterial infections should combine antimicrobial and anti-inflammatory effects. Here, we explore the multifunctional therapeutic potential of nanostructured self-assemblies from a cationic bolaamphiphile, which target bacterial lipopolysaccharides (LPSs) and associates with an anti-bacterial nucleic acid to form nanoplexes with therapeutic efficacy against Gram-negative bacteria. To understand the mechanistic details of these multifunctional antimicrobial-anti-inflammatory properties, we performed a fundamental study, comparing the interaction of these nanostructured therapeutics with synthetic biomimetic bacterial membranes and live bacterial cells. Combining a wide range of experimental techniques (Confocal Microscopy, Fluorescence Correlation Spectroscopy, Microfluidics, NMR, LPS binding assays), we demonstrate that the LPS targeting capacity of the bolaamphiphile self-assemblies, comparable to that exerted by Polymixin B, is a key feature of these nanoplexes and one that permits entry of therapeutic nucleic acids in Gram-negative bacteria. These findings enable a new approach to the design of efficient multifunctional therapeutics with combined antimicrobial and anti-inflammatory effects and have therefore the potential to broadly impact fundamental and applied research on self-assembled nano-sized antibacterials for antibiotic resistant infections

Disentangling the Possible Drivers of Indri indri Microbiome: A Threatened Lemur Species of Madagascar

Research on the gut microbiome may help with increasing our understanding of primate health with species’ ecology, evolution, and behavior. In particular, microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar. This species is classified as “critically endangered” by the IUCN Red List of Threatened Species, representing one of the world’s 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Indris have never been successfully bred under human care, suggesting that some behavioral and/or ecological factors are still not considered from the ex situ conservation protocols. Here, we explored gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, Synergistetes 16.7 ± 4.5%, and Firmicutes 11.1 ± 1.9%. Further, our results revealed that bacterial alpha and beta diversity were influenced by indri family group and sex. In addition, we investigated the chemical composition of geophagic soil to explore the possible ecological value of soil as a nutrient supply. The quite acidic pH and high levels of secondary oxide-hydroxides of the soils could play a role in the folivorous diet’s gut detoxification activity. In addition, the high contents of iron and manganese found the soils could act as micronutrients in the indris’ diet. Nevertheless, the concentration of a few elements (i.e., calcium, sulfur, boron, nickel, sodium, and chromium) was higher in non-geophagic than in geophagic soils. In conclusion, the data presented herein provide a baseline for outlining some possible drivers responsible for the gut microbiome diversity in indris, thus laying the foundations for developing further strategies involved in indris’ conservation

A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists

Making use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data