Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Effects of root inoculation of entomopathogenic fungi on olfactory-mediated behavior and life-history traits of the parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae)

BACKGROUND

Although most biological control programs use multiple biological agents to manage pest species, to date only a few programs have combined the use of agents from different guilds. Using sweet pepper (Capsicum annuum L.), the entomopathogenic fungus Akanthomyces muscarius ARSEF 5128, the tobacco peach aphid Myzus persicae var. nicotianae and the aphid parasitoid Aphidius ervi as the experimental model, we explored whether root inoculation with an entomopathogenic fungus is compatible with parasitoid wasps for enhanced biocontrol of aphids.

RESULTS

In dual-choice behavior experiments, A. ervi was significantly attracted to the odor of M. persicae-infested C. annuum plants that had been inoculated with A. muscarius, compared to noninoculated infested plants. There was no significant difference in attraction to the odor of uninfested plants. Myzus persicae-infested plants inoculated with A. muscarius emitted significantly higher amounts of indole, (E)-nerolidol, (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene and one unidentified terpene compared to noninoculated infested plants. Coupled gas chromatography-electroantennography, using the antennae of A. ervi, confirmed the physiological activity of these elevated compounds. Inoculation of plants with A. muscarius did not affect parasitism rate nor parasitoid longevity, but significantly increased the speed of mummy formation in parasitized aphids on fungus-inoculated plants.

CONCLUSION

Our data suggest that root inoculation of C. annuum with A. muscarius ARSEF 5128 alters the olfactory-mediated behavior of parasitoids, but has little effect on parasitism efficiency or life-history parameters. However, increased attraction of parasitoids towards M. persicae-infested plants when inoculated by entomopathogenic fungi can accelerate host localization and hence improve biocontrol efficacy. © 2023 Society of Chemical Industry.

Floral nectar and honeydew microbial diversity and their role in biocontrol of insect pests and pollination

Sugar-rich plant-related secretions, such as floral nectar and honeydew, that are commonly used as nutrient sources by insects and other animals, are also the ecological niche for diverse microbial communities. Recent research has highlighted the great potential of nectar and honeydew microbiomes in biological pest control and improved pollination, but the exploitation of these microbiomes requires a deep understanding of their community dynamics and plant-microbe-insect interactions. Additionally, the successful application of microbes in crop fields is conditioned by diverse ecological, legal, and ethical challenges that should be taken into account. In this article, we provide an overview of the nectar and honeydew microbiomes and discuss their potential applications in sustainable agricultural practices.

Limited effects of plant-beneficial fungi on plant volatile composition and host-choice behavior of Nesidiocoris tenuis

Biological control using plant-beneficial fungi has gained considerable interest as a sustainable method for pest management, by priming the plant for enhanced defense against pathogens and insect herbivores. However, despite promising outcomes, little is known about how different fungal strains mediate these beneficial effects. In this study, we evaluated whether inoculation of tomato seeds with the plant-beneficial fungi Beauveria bassiana ARSEF 3097, Metarhizium brunneum ARSEF 1095 and Trichoderma harzianum T22 affected the plant's volatile organic compound (VOC) profile and the host-choice behavior of Nesidiocoris tenuis, an emerging pest species in NW-European tomato cultivation, and the related zoophytophagous biocontrol agent Macrolophus pygmaeus. Results indicated that fungal inoculation did not significantly alter the VOC composition of tomato plants. However, in a two-choice cage assay where female insects were given the option to select between control plants and fungus-inoculated plants, N. tenuis preferred control plants over M. brunneum-inoculated plants. Nearly 72% of all N. tenuis individuals tested chose the control treatment. In all other combinations tested, no significant differences were found for none of the insects. We conclude that inoculation of tomato with plant-beneficial fungi had limited effects on plant volatile composition and host-choice behavior of insects. However, the observation that N. tenuis was deterred from the crop when inoculated with M. brunneum and attracted to non-inoculated plants may provide new opportunities for future biocontrol based on a push-pull strategy.

Microbe-mediated alterations in floral nectar: consequences for insect parasitoids

Floral nectar is frequently colonized by microbes among which bacteria and yeasts are the most abundant. These microbes have the ability to alter nectar characteristics with consequences for the whole community of flower-visiting insects. Recent research carried out on natural enemies of insect herbivores has shown that microbe-mediated changes in nectar traits can influence the foraging behavior and life history traits of parasitoids. The production of microbial volatile organic compounds can affect the attraction of parasitoids to nectar, while changes in sugar and amino acid composition can impact their longevity. Future research should focus on understanding the effects of nectar microbial colonization on parasitoid reproduction, with a specific emphasis on the interactions among different microbial taxa known to co-occur in floral nectar. Overall, this review highlights the importance of considering the role of nectar-inhabiting microbes in shaping the interactions between parasitoids and their food resources.

Bacterial biota composition in gut regions of black soldier fly larvae reared on industrial residual streams: revealing community dynamics along its intestinal tract

Some insect species have gained attention as efficient bioconverters of low-value organic substrates (i.e., residual streams) into high-value biomass. Black soldier fly (BSF) (Hermetia illucens) larvae are particularly interesting for bioconversion due to their ability to grow on a wide range of substrates, including low-value industrial residual streams. This is in part due to the plasticity of the gut microbiota of polyphagous insects, like BSF. Gut microbiota composition varies depending on rearing substrates, via a mechanism that might support the recruitment of microorganisms that facilitate digestion of a specific substrate. At the same time, specific microbial genera do persist on different substrates via unknown mechanisms. This study aimed to offer insights on this microbial plasticity by investigating how the composition of the bacterial community present in the gut of BSF larvae responds to two industrial residual streams: swill (a mixture of catering and supermarket leftovers) and distiller's dried grains with solubles. The bacterial biota composition of substrates, whole larvae at the beginning of the rearing period and at harvest, rearing residues, and larval gut regions were investigated through 16S rRNA gene sequencing. It was observed that both substrate and insect development influenced the bacterial composition of the whole larvae. Zooming in on the gut regions, there was a clear shift in community composition from a higher to a lower diversity between the anterior/middle midgut and the posterior midgut/hindgut, indicating a selective pressure occurring in the middle midgut region. Additionally, the abundance of the bacterial biota was always high in the hindgut, while its diversity was relatively low. Even more, the bacterial community in the hindgut was found to be relatively more conserved over the different substrates, harboring members of the BSF core microbiota. We postulate a potential role of the hindgut as a reservoir for insect-associated microbes. This warrants further research on that underexplored region of the intestinal tract. Overall, these findings contribute to our understanding of the bacterial biota structure and dynamics along the intestinal tract, which can aid microbiome engineering efforts to enhance larval performance on (industrial) residual streams.

Bacterial volatiles elicit differential olfactory responses in insect species from the same and different trophic levels

Insect communities consist of species from several trophic levels that have to forage for suitable resources among and within larger patches of nonresources. To locate their resources, insects use diverse stimuli, including olfactory, visual, acoustic, tactile and gustatory cues. While most research has focused on cues derived from plants and other insects, there is mounting evidence that insects also respond to volatile organic compounds (VOCs) emitted by microorganisms. However, to date little is known about how the olfactory response of insects within and across different trophic levels is affected by bacterial VOCs. In this study, we used Y-tube bioassays and chemical analysis of VOCs to assess how VOCs emitted by bacteria affect the olfactory response of insects of the same and different trophic levels. Experiments were performed using two aphid species (Amphorophora idaei Börner and Myzus persicae var. nicotianae Blackman), three primary parasitoid species (Aphidius colemani Viereck, A. ervi Haliday, and A. matricariae Viereck), and two hyperparasitoid species (Asaphes suspensus Nees and Dendrocerus aphidum Rondani). Olfactory responses were evaluated for three bacterial strains (Bacillus pumilus ST18.16/133, Curtobacterium sp. ST18.16/085, and Staphylococcus saprophyticus ST18.16/160) that were isolated from the habitat of the insects. Results revealed that insects from all trophic levels responded to bacterial volatiles, but olfactory responses varied between and within trophic levels. All bacteria produced the same set of volatile compounds, but often in different relative concentrations. For 11 of these volatiles we found contrasting correlations between their concentration and the behavior of the primary parasitoids and hyperparasitoids. Furthermore, olfactometer experiments on three of these compounds confirmed the contrasting olfactory responses of primary parasitoids and hyperparasitoids. The potential of these findings for the development of novel semiochemical-based strategies to improve biological aphid control has been discussed.

Fungal strain and crop cultivar affect growth of sweet pepper plants after root inoculation with entomopathogenic fungi

As endophytes, entomopathogenic fungi can protect plants against biotic and abiotic stresses and at the same time promote plant growth and plant health. To date, most studies have investigated whether Beauveria bassiana can enhance plant growth and plant health, while only little is known about other entomopathogenic fungi. In this study, we evaluated whether root inoculation of the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128, B. bassiana ARSEF 3097 and Cordyceps fumosorosea ARSEF 3682 can promote plant growth of sweet pepper (Capsicum annuum L.), and whether effects are cultivar-dependent. Plant height, stem diameter, number of leaves, canopy area, and plant weight were assessed four weeks following inoculation in two independent experiments using two cultivars of sweet pepper (cv. 'IDS RZ F1' and cv. 'Maduro'). Results showed that the three entomopathogenic fungi were able to enhance plant growth, particularly canopy area and plant weight. Further, results showed that effects significantly depended on cultivar and fungal strain, with the strongest fungal effects obtained for cv. 'IDS RZ F1', especially when inoculated with C. fumosorosea. We conclude that inoculation of sweet pepper roots with entomopathogenic fungi can stimulate plant growth, but effects depend on fungal strain and crop cultivar.

Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid

Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.

Phylogenomic analysis of the genus Rosenbergiella and description of Rosenbergiella gaditana sp. nov., Rosenbergiella metrosideri sp. nov., Rosenbergiella epipactidis subsp. epipactidis subsp. nov., Rosenbergiella epipactidis subsp. californiensis subsp. nov., Rosenbergiella epipactidis subsp. japonicus subsp. nov., Rosenbergiella nectarea subsp. nectarea subsp. nov. and Rosenbergiella nectarea subsp. apis subsp. nov., isolated from floral nectar and insects

The genus Rosenbergiella is one of the most frequent bacterial inhabitants of flowers and a usual member of the insect microbiota worldwide. To date, there is only one publicly available Rosenbergiella genome, corresponding to the type strain of Rosenbergiella nectarea (8N4^T), which precludes a detailed analysis of intra-genus phylogenetic relationships. In this study, we obtained draft genomes of the type strains of the other Rosenbergiella species validly published to date (R. australiborealis, R. collisarenosi and R. epipactidis) and 23 additional isolates of flower and insect origin. Isolate S61^T, retrieved from the nectar of an Antirrhinum sp. flower collected in southern Spain, displayed low average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values when compared with other Rosenbergiella members (≤86.5 and ≤29.8 %, respectively). Similarly, isolate JB07^T, which was obtained from the floral nectar of Metrosideros polymorpha plants in Hawaii (USA) had ≤95.7 % ANI and ≤64.1 % isDDH with other Rosenbergiella isolates. Therefore, our results support the description of two new Rosenbergiella species for which we propose the names Rosenbergiella gaditana sp. nov. (type strain: S61^T=NCCB 100789^T=DSM 111181^T) and Rosenbergiella metrosideri sp. nov. (JB07^T=NCCB 100888^T=LMG 32616^T). Additionally, some R. epipactidis and R. nectarea isolates showed isDDH values<79 % with other conspecific isolates, which suggests that these species include subspecies for which we propose the names Rosenbergiella epipactidis subsp. epipactidis subsp. nov. (S256^T=CECT 8502^T=LMG 27956^T), Rosenbergiella epipactidis subsp. californiensis subsp. nov. (FR72^T=NCCB 100898^T=LMG 32786^T), Rosenbergiella epipactidis subsp. japonicus subsp. nov. (K24^T=NCCB 100924^T=LMG 32785^T), Rosenbergiella nectarea subsp. nectarea subsp. nov. (8N4^T = DSM 24150^T = LMG 26121^T) and Rosenbergiella nectarea subsp. apis subsp. nov. (B1A^T=NCCB 100810^T= DSM 111763^T), respectively. Finally, we present the first phylogenomic analysis of the genus Rosenbergiella and update the formal description of the species R. australiborealis, R. collisarenosi, R. epipactidis and R. nectarea based on new genomic and phenotypic information.

Diversity and composition of the microbiome associated with eggs of the Southern green stinkbug, Nezara viridula (Hemiptera: Pentatomidae)

Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug Nezara viridula (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A Pantoea-like symbiont previously found in the midgut of N. viridula was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a Sodalis symbiont, which has previously been found in the abdomen of several insects, but so far not in N. viridula populations. We conclude that the egg-associated bacterial microbiome of N. viridula is species-poor and dominated by a few symbionts, particularly the species-specific obligate Pantoea-like symbiont.

Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia

Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.

Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing

Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae

Entomopathogenic fungi can adopt an endophytic lifestyle and provide protection against insect herbivores and plant pathogens. So far, most studies have focused on Beauveria bassiana to increase plant resistance against abiotic and biotic stresses, while only little is known for other entomopathogenic fungi. In this study, we investigated whether root inoculation of sweet pepper (Capsicum annuum L.) by the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128 and B. bassiana ARSEF 3097 can improve resistance against the tobacco peach aphid Myzus persicae var. nicotianae. First, dual-choice experiments were performed to test the hypothesis that the fungi deter aphids via modifying plant volatile profiles. Next, we tested the hypothesis that endophytic colonization negatively affects aphid life history traits, such as fecundity, development and mortality rate. Aphids were significantly attracted to the odor of plants inoculated with A. muscarius over non-inoculated plants. Plants inoculated with A. muscarius emitted significantly higher amounts of β-pinene than non-inoculated plants, and significantly higher amounts of indole than B. bassiana-inoculated and non-inoculated plants. Inoculation with the fungal strains also caused significantly higher emission of terpinolene. Further, both aphid longevity and fecundity were significantly reduced by 18% and 10%, respectively, when feeding on plants inoculated with A. muscarius, although intrinsic rate of population increase did not differ between inoculated and non-inoculated plants. Sweet pepper plants inoculated with B. bassiana ARSEF 3097 did not elicit a significant behavioral response nor affected the investigated life history traits. We conclude that endophytic colonization by entomopathogenic fungi has the potential to alter olfactory behavior and performance of M. persicae var. nicotianae, but effects are small and depend on the fungal strain used.

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.

Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar

The floral nectar of angiosperms harbors a variety of microorganisms that depend predominantly on animal visitors for their dispersal. Although some members of the genus Acinetobacter and all currently known species of Rosenbergiella are thought to be adapted to thrive in nectar, there is limited information about the response of these bacteria to variation in the chemical characteristics of floral nectar. We investigated the growth performance of a diverse collection of Acinetobacter (n = 43) and Rosenbergiella (n = 45) isolates obtained from floral nectar and the digestive tract of flower-visiting bees in a set of 12 artificial nectars differing in sugar content (15% w/v or 50% w/v), nitrogen content (3.48/1.67 ppm or 348/167 ppm of total nitrogen/amino nitrogen), and sugar composition (only sucrose, 1/3 sucrose + 1/3 glucose + 1/3 fructose, or 1/2 glucose + 1/2 fructose). Growth was only observed in four of the 12 artificial nectars. Those containing elevated sugar concentration (50% w/v) and low nitrogen content (3.48/1.67 ppm) were limiting for bacterial growth. Furthermore, phylogenetic analyses revealed that the ability of the bacteria to grow in different types of nectar is highly conserved between closely related isolates and genotypes, but this conservatism rapidly vanishes deeper in phylogeny. Overall, these results demonstrate that the ability of Acinetobacter spp. and Rosenbergiella spp. to grow in floral nectar largely depends on nectar chemistry and bacterial phylogeny.

Nectar-Inhabiting Bacteria Affect Olfactory Responses of an Insect Parasitoid by Altering Nectar Odors

Floral nectar is ubiquitously colonized by a variety of microorganisms among which yeasts and bacteria are the most common. Microorganisms inhabiting floral nectar can alter several nectar traits, including nectar odor by producing microbial volatile organic compounds (mVOCs). Evidence showing that mVOCs can affect the foraging behavior of insect pollinators is increasing in the literature, whereas the role of mVOCs in altering the foraging behavior of third-trophic level organisms such as insect parasitoids is largely overlooked. Parasitoids are frequent visitors of flowers and are well known to feed on nectar. In this study, we isolated bacteria inhabiting floral nectar of buckwheat, Fagopyrum esculentum (Polygonales: Polygonaceae), to test the hypothesis that nectar bacteria affect the foraging behavior of the egg parasitoid Trissolcus basalis (Hymenoptera: Scelionidae) via changes in odors of nectar. In behavioral assays, we found that T. basalis wasps are attracted toward nectar fermented by 4 out of the 14 bacterial strains isolated, which belong to Staphylococcus epidermidis, Terrabacillus saccharophilus (both Firmicutes), Pantoea sp. (Proteobacteria), and Curtobacterium sp. (Actinobacteria). Results of chemical investigations revealed significant differences in the volatile blend composition of nectars fermented by the bacterial isolates. Our results indicate that nectar-inhabiting bacteria play an important role in the interactions between flowering plants and foraging parasitoids. These results are also relevant from an applied perspective as flowering resources, such as buckwheat, are largely used in agriculture to promote conservation biological control of insect pests.

Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease

The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.

Parasitism by endoparasitoid wasps alters the internal but not the external microbiome in host caterpillars

BACKGROUND

The microbiome of many insects consists of a diverse community of microorganisms that can play critical roles in the functioning and overall health of their hosts. Although the microbial communities of insects have been studied thoroughly over the past decade, little is still known about how biotic interactions affect the microbial community structure in and on the bodies of insects. In insects that are attacked by parasites or parasitoids, it can be expected that the microbiome of the host insect is affected by the presence of these parasitic organisms that develop in close association with their host. In this study, we used high-throughput amplicon sequencing targeting both bacteria and fungi to test the hypothesis that parasitism by the endoparasitoid Cotesia glomerata affected the microbiome of its host Pieris brassicae. Healthy and parasitized caterpillars were collected from both natural populations and a laboratory culture.

RESULTS

Significant differences in bacterial community structure were found between field-collected caterpillars and laboratory-reared caterpillars, and between the external and the internal microbiome of the caterpillars. Parasitism significantly altered the internal microbiome of caterpillars, but not the external microbiome. The internal microbiome of all parasitized caterpillars and of the parasitoid larvae in the caterpillar hosts was dominated by a Wolbachia strain, which was completely absent in healthy caterpillars, suggesting that the strain was transferred to the caterpillars during oviposition by the parasitoids.

CONCLUSION

We conclude that biotic interactions such as parasitism have pronounced effects on the microbiome of an insect host and possibly affect interactions with higher-order insects.

The Pupal Parasitoid Trichopria drosophilae Is Attracted to the Same Yeast Volatiles as Its Adult Host

There is increasing evidence that microorganisms, particularly fungi and bacteria, emit volatile compounds that mediate the foraging behaviour of insects and therefore have the potential to affect key ecological relationships. However, to what extent microbial volatiles affect the olfactory response of insects across different trophic levels remains unclear. Adult parasitoids use a variety of chemical stimuli to locate potential hosts, including those emitted by the host's habitat, the host itself, and microorganisms associated with the host. Given the great capacity of parasitoids to utilize and learn odours to increase foraging success, parasitoids of eggs, larvae, or pupae may respond to the same volatiles the adult stage of their hosts use when locating their resources, but compelling evidence is still scarce. In this study, using Saccharomyces cerevisiae we show that Trichopria drosophilae, a pupal parasitoid of Drosophila species, is attracted to the same yeast volatiles as their hosts in the adult stage, i.e. acetate esters. Parasitoids significantly preferred the odour of S. cerevisiae over the blank medium in a Y-tube olfactometer. Deletion of the yeast ATF1 gene, encoding a key acetate ester synthase, decreased attraction of T. drosophilae, while the addition of synthetic acetate esters to the fermentation medium restored parasitoid attraction. Bioassays with individual compounds revealed that the esters alone were not as attractive as the volatile blend of S. cerevisiae, suggesting that other volatile compounds also contribute to the attraction of T. drosophilae. Altogether, our results indicate that pupal parasitoids respond to the same volatiles as the adult stage of their hosts, which may aid them in locating oviposition sites.

Microbial profile during fermentation and aerobic stability of ensiled mixtures of maize stover and banana pseudostem in South Ethiopia

AIMS

This study evaluated pH reduction and microbial growth during fermentation of maize stover (MS) mixed with banana pseudostem (BPS) under South Ethiopian conditions.

MATERIALS AND RESULTS

The MS and BPS were chopped and mixed into six treatments (T): 80% BPS plus 20% DMS (T1), 70% BPS plus 30% DMS (T2), 40% BPS plus 60% FMS (fresh MS) (T3), 20% BPS plus 80% FMS (T4), 100% FMS (T5), and 95% BPS plus 5% molasses (T6). At 0, 7, 14, 30, 60, and 90 days, pH and dry matter were determined. Microbiological quality was assessed using plate counts and Illumina MiSeq sequencing. On day 60 and 90, aerobic stability was investigated. The results showed a significant reduction in pH in all mixtures, except in T1 and T2. Lactic acid bacteria counts reached a maximum in all treatments within 14 days. Sequencing showed marked changes in dominant bacteria, such as Buttiauxella and Acinetobacter to Lactobacillus and Bifidobacterium.

CONCLUSIONS

The fresh MS and BPS mixtures and fresh maize showed significant pH reduction and dominance of desirable microbial groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study enables year-round livestock feed supplementation to boost milk and meat production in South Ethiopia.

Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov., isolated from floral nectar and honey bees

A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter. Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis, Acinetobacter boissieri and Acinetobacter nectaris, previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477^T (=TSD-214^T=LMG 31655^T), B10A^T (=TSD-213^T=LMG 31702^T) and EC24^T (=TSD-215^T=LMG 31703^T=DSM 111781^T).

Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters

Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.

Inoculation of pear flowers with Metschnikowia reukaufii and Acinetobacter nectaris enhances attraction of honeybees and hoverflies, but does not increase fruit and seed set

Currently, one of the most important challenges is to provide sufficient and affordable food and energy for a fast-growing world population, alongside preserving natural habitats and maintaining biodiversity. About 35% of the global food production depends on animals for pollination. In recent years, an alarming worldwide decline in pollinators has been reported, putting our food production under additional pressure. Therefore, there is an urgent need to find sustainable ways to ensure this crucial ecosystem service. Recent studies have shown that floral nectar is generally colonized by microorganisms, specifically yeasts and bacteria, which may alter nectar chemistry and enhance attraction of pollinators. In this study, we investigated changes in pollinator foraging behavior and pollination success in European pear (Pyrus communis L.) cultivars 'Regal Red' and 'Sweet Sensation' (red sports of 'Doyenné de Comice') after flower inoculation with the typical nectar-inhabiting microorganisms Metschnikowia reukaufii and Acinetobacter nectaris, and a combination of both. Pollination success was monitored by measuring the number of flower visits, fruit set and seed set in two consecutive years, 2019 and 2020. Results revealed that application of a mixture of M. reukaufii and A. nectaris resulted in significantly higher visitation rates of honeybees and hoverflies. By contrast, no effects on flower visits were found when yeasts and bacteria were applied separately. Fruit set and seed set were not significantly affected by any of the inoculation treatments. The only factors affecting fruit set were initial number of flower clusters on the trees and the year. The absence of treatment effects can most likely be attributed to the fact that pollination was not a limiting factor for fruit set in our experiments. Altogether, our results show that inoculation of flowers with nectar microbes can modify pollinator foraging patterns, but did not lead to increased pollination success under the conditions tested.

Yeast-nectar interactions: metacommunities and effects on pollinators

About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and, as a result, on bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.

Identification and application of bacterial volatiles to attract a generalist aphid parasitoid: from laboratory to greenhouse assays

BACKGROUND

Recent studies have shown that microorganisms emit volatile compounds that affect insect behaviour. However, it remains largely unclear whether microbes can be exploited as a source of attractants to improve biological control of insect pests. In this study, we used a combination of coupled gas chromatography-electroantennography (GC-EAG) and Y-tube olfactometer bioassays to identify attractive compounds in the volatile extracts of three bacterial strains that are associated with the habitat of the generalist aphid parasitoid Aphidius colemani, and to create mixtures of synthetic compounds to find attractive blends for A. colemani. Subsequently, the most attractive blend was evaluated in two-choice cage experiments under greenhouse conditions.

RESULTS

GC-EAG analysis revealed 20 compounds that were linked to behaviourally attractive bacterial strains. A mixture of two EAG-active compounds, styrene and benzaldehyde applied at a respective dose of 1 μg and 10 ng, was more attractive than the single compounds or the culture medium of the bacteria in Y-tube olfactometer bioassays. Application of this synthetic mixture under greenhouse conditions resulted in significant attraction of the parasitoids, and outperformed application of the bacterial culture medium.

CONCLUSION

Compounds isolated from bacterial blends were capable of attracting parasitoids both in laboratory and greenhouse assays, indicating that microbial cultures are an effective source of insect attractants. This opens new opportunities to attract and retain natural enemies of pest species and to enhance biological pest control.

Silage making of maize stover and banana pseudostem under South Ethiopian conditions: evolution of pH, dry matter and microbiological profile

The study was conducted to evaluate the microbial dynamics during silage of maize stover and banana pseudostem in the environmental conditions of southern Ethiopia. To meet this objective, microsilos containing either maize stover or banana pseudostem, both with and without molasses, were prepared. Subsequently, samples were analysed on day 0, 7, 14, 30, 60 and 90 of the fermentation process. As a result, on day 7, all treatments except banana pseudostem without molasses showed a significant reduction in pH. It was also this silage type that supported the growth of Enterobacteriaceae longer than three other silage types, i.e. until 30 days. The yeasts and moulds and the Clostridum endospore counts also showed a reducing trend in early fermentation and afterwards remained constant until day 90. Illumina MiSeq sequencing revealed that Leuconostoc, Buttiauxella species and Enterobacteriaceae were the most abundant bacteria in the initial phases of the fermentation. Later on, Buttiauxella, Lactobacillus, Weissella and Bifidobacterium species were found to be dominant. In conclusion, silage of the two crop by-products is possible under South Ethiopian conditions. For banana pseudostem, the addition of molasses is crucial for a fast fermentation, in contrast to maize. Upscaling needs to be investigated for the two by-products.

Identification of bacterial endospores and targeted detection of foodborne viruses in industrially reared insects for food

With edible insects being increasingly produced, food safety authorities have called for the determination of microbiological challenges posed to human health. Here, we find that the bacterial endospore fraction in industrially reared mealworm and cricket samples is largely comprised of Bacillus cereus group members that can pose insect or human health risks. Hepatitis A virus, hepatitis E virus and norovirus genogroup II were not detected in the sample collection, indicating a low food safety risk from these viral pathogens.

Towards a better understanding of the role of nectar-inhabiting yeasts in plant-animal interactions

Flowers offer a wide variety of substrates suitable for fungal growth. However, the mycological study of flowers has only recently begun to be systematically addressed from an ecological point of view. Most research on the topic carried out during the last decade has focused on studying the prevalence and diversity of flower-inhabiting yeasts, describing new species retrieved from floral parts and animal pollinators, and the use of select nectar yeasts as model systems to test ecological hypotheses. In this primer article, we summarize the current state of the art in floral nectar mycology and provide an overview of some research areas that, in our view, still require further attention, such as the influence of fungal volatile organic compounds on the foraging behavior of pollinators and other floral visitors, the analysis of the direct and indirect effects of nectar-inhabiting fungi on the fitness of plants and animals, and the nature and consequences of fungal-bacterial interactions taking place within flowers.

Microbial communities of the house fly Musca domestica vary with geographical location and habitat

House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.

Variation in arbuscular mycorrhizal fungal communities associated with lowland rice (Oryza sativa) along a gradient of soil salinity and arsenic contamination in Bangladesh

Rice is an essential food crop that nourishes >50% of the world population. In many regions of Bangladesh rice production is constrained by high soil salinity and heavy metal contamination due to irrigation practices. Plants may naturally overcome such stress through mutualistic interactions with arbuscular mycorrhizal fungi (AMF). Yet, little is known regarding the diversity and composition of AMF communities in rice fields with high saline and arsenic concentration. Here we used high throughput Illumina sequencing to characterize AMF communities in rice roots from 45 Bangladeshi rice fields, along a large geographical gradient of soil salinity and arsenic contamination. We obtained 77 operational taxonomic units (OTUs, based on a sequence similarity threshold of 97%) from eight AMF families, and showed that high soil salinity and arsenic concentration are significantly associated with low AMF diversity in rice roots. Soil salinity and arsenic concentration also explained a large part of the variation in AMF community composition, but also soil pH, moisture, organic matter content and plant available soil phosphorus played an important role. Overall, our study showed that even at very high salinity and arsenic levels, some AMF OTUs are present in rice roots. Their potential role in mediating a reduction of rice stress and arsenic uptake remains to be investigated.

Apibacter muscae sp. nov., a novel bacterial species isolated from house flies

We describe the isolation and characterization of three bacterial isolates from the common house fly, Musca domestica, caught in Londerzeel, Belgium and Huye District, Rwanda. Although isolated from distinct geographical locations, the strains show >99 % identical 16S rRNA gene sequences and are <95 % identical to type strains of Apibacter species. Whole-genome sequences were obtained for all three strains. The genomes are 2.4-2.5 Mb with a G+C content of ~30.3 mol%. Bacteriological and biochemical analysis of the strains demonstrate distinctly different characteristics compared to known Apibacter species. Particularly, the three strains investigated in this study can be distinguished from the known Apibacter species (Apibacter mensalisand Apibacter adventoris) through urease and β-glucosidase activities. Whole-cell fatty acid methyl ester analysis shows that the fatty acid composition of the novel strains is also unique. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify these isolates as representatives of a novel species of the genus Apibacter, Apibacter muscae sp. nov., in reference to its prevalence in house flies, with strain G8^T (=LMG 30898^T=DSM 107922^T) as the type strain.

Temporal and spatial variation in bacterial communities of "Jonagold" apple (Malus x domestica Borkh.) and "Conference" pear (Pyrus communis L.) floral nectar

Production of many agricultural crops and fruits strongly depends on pollinators. For instance, pome fruits such as apple and pear are highly dependent on pollination for fruit set, fruit quality, and yield. Nectar is often inhabited by microbes, most often yeasts and bacteria, which may change nectar quality and therefore also affect plant–pollinator interactions. Here, we used high‐throughput 16S ribosomal RNA gene amplicon sequencing to investigate the temporal and spatial variation in bacterial communities in floral nectar of apple and pear. We sampled 15 apple (Malus x domestica Borkh.) and 15 pear (Pyrus communis L.) orchards distributed over the eastern part of Belgium over a timespan of seven days. Nectar bacterial community composition differed strongly among fruit species. Nectar of pear was dominated by Actinobacteria, followed by Proteobacteria and Firmicutes. Apple nectar was strongly enriched in Bacteroidetes, a phylum which until now has been found to be rarely associated with floral nectar. Nectar was dominated by only a few bacterial species, with Brevibacterium (Actinobacteria) and Undibacterium (Proteobacteria) as the most abundant bacteria in pear and apple nectar, respectively. Bacterial richness and diversity were found to fluctuate during flowering, likely due to changing environmental conditions. Additionally, spatial structure in nectar bacterial community composition was found in apple orchards, while this was not the case for pear. Differences in nectar bacterial communities between apple and pear nectar may differently affect the chemical and nutritional composition of the nectar, influencing pollinator attraction and visitation, and thus pollination efficacy in general.

Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group

The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402^T, had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas

Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here, we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.

Yeast-Bacterium Interactions: The Next Frontier in Nectar Research

Beyond its role as a reward for pollinators, floral nectar also provides a habitat for specialized and opportunistic yeasts and bacteria. These microbes modify nectar chemistry, often altering mutualistic relationships between plants and pollinators in ways that we are only beginning to understand. Many studies on this multi-partite system have focused on either yeasts or bacteria without consideration of yeast-bacterium interactions, but recent evidence suggests that such interactions drive the assembly of nectar microbial communities and its consequences for pollination. Unexplored potential mechanisms of yeast-bacterium interactions include the formation of physical complexes, nutritional interactions, antibiosis, signaling-based interactions, and horizontal gene transfer. We argue that studying these mechanisms can elucidate how nectar microbial communities are established and affect plant fitness via pollinators.

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale

This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.

Effect of fermentation system on the physicochemical and microbial community dynamics during enset (Ensete ventricosum) fermentation

AIMS

The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho.

METHODS AND RESULTS

Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated.

CONCLUSIONS

The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a sauerkraut jar.