Microbial Ecology最新文献

Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.

Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.

South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.

Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.

Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other’s transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.

A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.

Graphical Abstract

Three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects.

Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.

It is increasingly recognized that different genetic variants of hosts can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for their microbial associations to change during invasion as a result. We asked whether host genotype (G), microbial environment (E), or their interaction (G × E) affected the composition and diversity of host-associated microbiomes in Centaurea solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes and phenotypes and to have altered microbial interactions, in its severe invasion of CA, USA. We conducted an experiment in which native and invading plant genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that native and invading plant genotypes accumulated different microbial associations at the family level in each soil community, often counter to differences in family abundance between soil communities. Root associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range field soil and accumulated on invading genotypes. We also found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Thus variation in microbial associations of invaders was driven by the interaction of plant G and microbial E, and rhizosphere microbial communities appear to change in composition in response to host evolution during invasion.