Multiple toxins and a protease contribute to the aphid-killing ability of Pseudomonas fluorescens PpR24.

Aphids are globally important pests causing damage to a broad range of crops. Due to insecticide resistance, there is an urgent need to develop alternative control strategies. In our previous work, we found Pseudomonas fluorescens PpR24 can orally infect and kill the insecticide-resistant green-peach aphid (Myzus persicae). However, the genetic basis of the insecticidal capability of PpR24 remains unclear. Genome sequencing of PpR24 confirmed the presence of various insecticidal toxins such as Tc (toxin complexes), Rhs (rearrangement hotspot) elements, and other insect-killing proteases. Upon aphids infection with PpR24, RNA-Seq analysis revealed 193 aphid genes were differentially expressed with down-regulation of 16 detoxification genes. In addition, 1325 PpR24 genes (542 were upregulated and 783 downregulated) were subject to differential expression, including genes responsible for secondary metabolite biosynthesis, the iron-restriction response, oxidative stress resistance, and virulence factors. Single and double deletion of candidate virulence genes encoding a secreted protease (AprX) and four toxin components (two TcA-like; one TcB-like; one TcC-like insecticidal toxins) showed that all five genes contribute significantly to aphid killing, particularly AprX. This comprehensive host-pathogen transcriptomic analysis provides novel insight into the molecular basis of bacteria-mediated aphid mortality and the potential of PpR24 as an effective biocontrol agent.

Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.

Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.

Is there sufficient Ensifer and Rhizobium species diversity in UK farmland soils to support red clover (Trifolium pratense), white clover (T. repens), lucerne (Medicago sativa) and black medic (M. lupulina)?

Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial partners. For black medic (Medicago lupulina) and lucerne (Medicago sativa) little is known about the natural prevalence of their rhizobial partner Ensifer meliloti in UK soils, so that the need for inoculating them is unclear. We analysed the site-dependence of rhizobial seed inoculation effects on the subsequent ability of rhizobial communities to form symbioses with four legume species (Medicago lupulina, M. sativa, Trifolium repens and T. pratense). At ten organic farms across the UK, a species-diverse legume based mixture (LBM) which included these four species was grown. The LBM seed was inoculated with a mix of commercial inocula specific for clover and lucerne. At each site, soil from the LBM treatment was compared to the soil sampled prior to the sowing of the LBM (the control). From each site and each of the two treatments, a suspension of soils was applied to seedlings of the four legume species and grown in axenic conditions for six weeks. Root nodules were counted and their rhizobia isolated. PCR and sequencing of a fragment of the gyrB gene from rhizobial isolates allowed identification of strains. The number of nodules on each of the four legume species was significantly increased when inoculated with soil from the LBM treatment compared to the control. Both the proportion of plants forming nodules and the number of nodules formed varied significantly by site, with sites significantly affecting the Medicago species but not the Trifolium species. These differences in nodulation were broadly reflected in plant biomass where site and treatment interacted; at some sites there was a significant advantage from inoculation with the commercial inoculum but not at others. In particular, this study has demonstrated the commercial merit of inoculation of lucerne with compatible rhizobia.

The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition.

Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met.

Identification and genomic analysis of a thermophilic bacterial strain that reduces ammonia loss from composting.

Ammonia loss is the most severe during the high-temperature stage (>50°C) of aerobic composting. Regulating ammonia volatilization during this period via thermophilic microbes can significantly improve the nitrogen content of compost and reduce air pollution due to ammonia loss. In this study, an ammonia-assimilating bacterial strain named LL-8 was screened out as having the strongest ammonia nitrogen conversion rate (32.7%) at high temperatures (50°C); it is able to significantly reduce 42.9% ammonia volatile loss in chicken manure composting when applied at a high-temperature stage. Phylogenetic analysis revealed that LL-8 was highly similar (>98%) with Priestia aryabhattai B8W22T and identified as Priestia aryabhatta. Genomic analyses indicated that the complete genome of LL-8 comprised 5,060,316 base pairs with a GC content of 32.7% and encoded 5,346 genes. Genes, such as gudB, rocG, glnA, gltA, and gltB, that enable bacteria to assimilate ammonium nitrogen were annotated in the LL-8 genome based on the comparison to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results implied that the application of thermophilic ammonia-assimilating strain P. aryabhatta LL-8 would be a promising solution to reduce ammonia loss and mitigate air pollution of aerobic composting.IMPORTANCEAerobic composting is one of the essential ways to recycle organic waste, but its ammonia volatilization is severe and results in significant nitrogen loss, especially during the high-temperature period, which is also harmful to the environment. The application of thermophilic bacteria that can use ammonia as a nitrogen source at high temperatures is helpful to reduce the ammonia volatilization loss of composting. In this study, we screened and identified a bacteria strain called LL-8 with high temperature (50°C) resistance and strong ammonia-assimilating ability. It also revealed significant effects on decreasing ammonia volatile loss in composting. The whole-genome analysis revealed that LL-8 could utilize ammonium nitrogen by assimilation to decrease ammonia volatilization. Our work provides a theoretical basis for the application of this functional bacteria in aerobic composting to control nitrogen loss from ammonia volatilization.

Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat.

The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea.

We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production.

Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.

BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research.

Plant microbiomes are the microbial communities essential to the functioning of the phytobiome-the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure. The UK Crop Microbiome Cryobank (UKCMC) project is developing a unique, integrated and open-access resource to enable the development of solutions to improve soil and crop health. Six economically important crops (Barley, Fava Bean, Oats, Oil Seed Rape, Sugar Beet and Wheat) are targeted, and the methods as well as data outputs will underpin research activity both in the UK and internationally. This manuscript describes the approaches being taken, from characterisation, cryopreservation and analysis of the crop microbiome through to potential applications. We believe that the model research framework proposed is transferable to different crop and soil systems, acting not only as a mechanism to conserve biodiversity, but as a potential facilitator of sustainable agriculture systems.

Identification of novel aphid-killing bacteria to protect plants.

Aphids, including the peach-potato aphid, Myzus persicae, are major insect pests of agriculture and horticulture, and aphid control measures are limited. There is therefore an urgent need to develop alternative and more sustainable means of control. Recent studies have shown that environmental microbes have varying abilities to kill insects. We screened a range of environmental bacteria isolates for their abilities to kill target aphid species. Tests demonstrated the killing aptitude of these bacteria against six aphid genera (including Myzus persicae). No single bacterial strain was identified that was consistently toxic to insecticide-resistant aphid clones than susceptible clones, suggesting resistance to chemicals is not strongly correlated with bacterial challenge. Pseudomonas fluorescens PpR24 proved the most toxic to almost all aphid clones whilst exhibiting the ability to survive for over three weeks on three plant species at populations of 5-6 log CFU cm-2 leaf. Application of PpR24 to plants immediately prior to introducing aphids onto the plants led to a 68%, 57% and 69% reduction in aphid populations, after 21 days, on Capsicum annuum, Arabidopsis thaliana and Beta vulgaris respectively. Together, these findings provide new insights into aphid susceptibility to bacterial infection with the aim of utilizing bacteria as effective biocontrol agents.

Identification of new single nucleotide polymorphism-based markers for inter- and intraspecies discrimination of obligate bacterial parasites (Pasteuria spp.) of invertebrates.

Protein-encoding and 16S rRNA genes of Pasteuria penetrans populations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of "cryptic" SNPs which were not present in the consensus sequences of any P. penetrans population. Additionally, hierarchical cluster analysis separated P. penetrans 16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among three Pasteuria species, namely, P. penetrans, P. hartismeri, and P. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination of Pasteuria at both the inter- and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.

Defining the wheat microbiome: Towards microbiome-facilitated crop production.

Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.

Culture-based Methods for Studying the Bacterial Root Microbiome of Wheat.

Beneficial plant-microbe interactions are important and desirable for sustainable intensification of agriculture. Here, we describe methods to isolate microbes from the roots of field-grown wheat plants. This includes the rhizosphere and rhizoplane soil, as well as the root endosphere. We also describe a method to test for endosphere competence of putative endophytes.

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria.

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A "PGPR" database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.

Land Management Legacy Affects Abundance and Function of the acdS Gene in Wheat Root Associated Pseudomonads.

Land management practices can vastly influence belowground plant traits due to chemical, physical, and biological alteration of soil properties. Beneficial Pseudomonas spp. are agriculturally relevant bacteria with a plethora of plant growth promoting (PGP) qualities, including the potential to alter plant physiology by modulating plant produced ethylene via the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS). This study evaluated the impact of land management legacy on the selection and function of wheat root associated culturable pseudomonad isolates. Three distinct previous land uses prior to wheat culture (grassland, arable, and bare fallow) were tested and culturable pseudomonad abundance, phylogeny (gyrB and acdS genes), function (ACC deaminase activity), and the co-selection of acdS with other PGP genes examined. The pseudomonad community could to some extent be discriminated based on previous land use. The isolates from rhizosphere and root compartments of wheat had a higher acdS gene frequency than the bulk soil, particularly in plants grown in soil from the bare fallow treatment which is known to have degraded soil properties such as low nutrient availability. Additionally, other genes of interest to agriculture encoding anti-fungal metabolites, siderophores, and genes involved in nitrogen metabolism were highly positively associated with the presence of the acdS gene in the long-term arable treatment in the genomes of these isolates. In contrast, genes involved in antibiotic resistance and type VI secretion systems along with nitrogen cycling genes were highly positively correlated with the acdS gene in bare fallow isolated pseudomonad. This highlights that the three land managements prior to wheat culture present different selection pressures that can shape culturable pseudomonad community structure and function either directly or indirectly via the influence of wheat roots.

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale.

BACKGROUND: The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK's third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers' fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. RESULTS: We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition. CONCLUSIONS: We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield. Video abstract.

Wheat dwarfing influences selection of the rhizosphere microbiome.

The development of dwarf wheat cultivars combined with high levels of agrochemical inputs during the green revolution resulted in high yielding cropping systems. However, changes in wheat cultivars were made without considering impacts on plant and soil microbe interactions. We studied the effect of these changes on root traits and on the assembly of rhizosphere bacterial communities by comparing eight wheat cultivars ranging from tall to semi-dwarf plants grown under field conditions. Wheat breeding influenced root diameter and specific root length (SRL). Rhizosphere bacterial communities from tall cultivars were distinct from those associated with semi-dwarf cultivars, with higher differential abundance of Actinobacteria, Bacteroidetes and Proteobacteria in tall cultivars, compared with a higher differential abundance of Verrucomicrobia, Planctomycetes and Acidobacteria in semi-dwarf cultivars. Predicted microbial functions were also impacted and network analysis revealed a greater level of connectedness between microbial communities in the tall cultivars relative to semi-dwarf cultivars. Taken together, results suggest that the development of semi-dwarf plants might have affected the ability of plants to recruit and sustain a complex bacterial community network in the rhizosphere.

Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists.

Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.

Correction to: Microbiome definition re-visited: old concepts and new challenges.

An amendment to this paper has been published and can be accessed via the original article.

Microbiome definition re-visited: old concepts and new challenges.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.