FEMS microbiology ecology最新文献

Increased usage of nanotechnological applications inevitably leads to exposure of hosts and their associated microbiomes to metallic nanoparticles. Various bacteria within the microbiome harbour mechanisms to protect themselves against metal-related toxicity. These mechanisms have been broadly described in the absence of a host. Here, we studied how silver ion-resistant bacteria isolated from the Daphnia magna microbiome shape the host's exposure to silver nanoparticles. With germfree and mono-associated neonates, the effects of these microbes on the sensitivity of D. magna to silver nanoparticles were studied. By using this approach, a core member of the D. magna microbiome Sphingomonas yanoikuyae was identified to be silver-resistant. Neonates mono-associated with S. yanoikuyae were as sensitive to silver nanoparticles as naturally colonized neonates, whereas mono-association with Microbacterium and germfree neonates had increased sensitivity. Silver ions are the major attribution to toxicity in germfree and Microbacterium-associated neonates, whereas particles contribute more to the toxicity for the naturally- and Sphingomonas-colonized neonates. Sphingomonas accumulated in vivo more silver ions from its local environment than the other D. magna bacterial isolates. The current study shows that bacteria can play a vital role in shaping the speciation of nanomaterials and thereby modifying the toxicity to hosts.

Microbes play a critical role in regulating tri-trophic interactions among plants, herbivores, and their natural enemies, influencing key ecological and evolutionary processes. To fully understand these interactions through the food chain, a well-defined tri-trophic system is required. We investigated microbial dynamics involving plants (beans, cucumbers, and eggplants), spider mites (Tetranychus urticae), and predatory mites (Phytoseiulus persimilis) through 16S rRNA gene sequencing. The results revealed significant variations in microbiota across different trophic levels. Source tracking analysis indicated that microbiota at each trophic level were rarely inherited from the previous one, and deterministic processes played a key role in shaping the endosphere communities of these levels. Most shared zero-radius operational taxonomic units across each trophic level belonged to Pseudomonas, Bacillus, and Staphylococcus. Leaf microbiota differed among plants, while spider mites harbored similar microbiota. Notably, the microbiota of predatory mites on eggplants differed significantly from those on the other two plants. Biomarker selection and correlation analyses revealed that the abundance of Methylobacterium and Stenotrophomonas was strongly correlated with the improved fitness of predatory mites across different plants. Our study highlights the complex and dynamic nature of microbial communities across different trophic levels in a well-defined plant-herbivore-predator system.

Positive relationships between plant diversity, microbial diversity, and ecosystem functioning have widely been observed in experimental grasslands. However, the impact of cover crop (CC) species diversification on soil microbial diversity and function in croplands remains underexplored. This study investigated how increasing the diversity of undersown CCs affected seasonal properties of soil microbiomes and whether these changes resulted in legacy effects on next-year crops. In barley fields undersown with functionally diverse CCs, soil samples were collected throughout the year to assess microbial properties. To evaluate legacy effects on the following year's barley, soil microorganisms were sequenced from spring samples collected before CC termination. Additionally, a pot experiment using flax was conducted to study how CC diversity influenced arbuscular mycorrhizal (AM) fungal colonization in roots. Results showed that vegetation presence and higher CC richness increased microbial biomass carbon and decreased the microbial metabolic quotient. Legumes' presence reduced microbial respiration. Fungal and AM fungal diversity also increased with CC richness, while legumes helped suppress fungal pathogens. In the pot experiment, presence of both vegetation and legumes positively influenced AM fungal root colonization. Overall, undersowing diverse CCs, particularly legumes, can increase soil microbial diversity and soil health, benefiting both the current and next-year crops.

Even decades after being banned in Europe, atrazine and its main metabolites can still be found in soils. While bioaugmentation using pesticide-degrading bacteria is already employed for remediating polluted soils, there is a need to improve its efficiency. Investigating the use of carrier materials to deliver pesticide-degrading microorganisms in situ emerges as a promising approach. Here, we generated atrazine-degrading biocomposites by cultivating either a bacterial strain or a four-species consortium on zeolite as the carrier material. Using a microcosm approach, we evaluated their efficiency to mineralize 14C-atrazine in soil compared to free-living cells, and assessed their side effects on the native soil bacterial community using 16S rRNA metabarcoding. We showed that, right after inoculation, atrazine mineralization potential of the free-living cells was higher than that of the biocomposites. However, microcosms inoculated with the biocomposites displayed significantly higher atrazine mineralization potential after 15 and 45 days of incubation, indicating a higher efficiency but also a better stability in soil. Inoculation of free-living cells and biocomposites differently influenced the diversity and composition of the native microbial community, their impacts being modulated by the atrazine contamination scenario. Altogether, our results provide a thorough evaluation of the efficiency and the ecological impact of atrazine-degrading biocomposites in soil.

Changes in organic matter accumulation in wetlands are critical for climate dynamics. Different nitrogen (N) inputs in Sphagnum-dominated peat bogs can lead to varying rates of carbon (C) and N accumulation, influencing greenhouse gas emissions. We investigated how contrasting N deposition shapes microbial communities in two Czech peat bogs, focusing on biological N2 fixation (BNF) as a key N input in pristine wetlands. Higher N deposition resulted in a more active microbial community with increased enzyme activity and C acquisition, potentially accelerating decomposition and reducing C storage. Enhanced denitrification, indicated by active nosZ Clade I genes, suggests that higher N inputs may increase N losses through denitrification. In contrast, the lower N site showed a less active microbial community with slower decomposition, beneficial for C sequestration, though potentially less adaptable to future N increases. Experimental BNF rates were 70 times higher at the high N site, consistent with elevated diazotroph activity indicated by active nifH gene. Phosphorus (P) availability and NH4+/NO3- ratios appeared to drive BNF differences, emphasizing the need for managed N inputs to maintain peatland ecological functions.

Glaciers are retreating, altering alpine ecosystems and creating new proglacial lakes. Compared to lakes fed by snowpack, glacial lakes are often enriched in nutrients and suspended solids that decrease light penetration. However, the microorganisms and biogeochemical conditions within these newly formed lakes are not well characterized. We describe the microbial communities in 14 glacial lakes in Glacier National Park, MT, USA using 16S rRNA gene amplicon sequencing and measurements of nutrient concentrations, water clarity, and other environmental properties. Microbial communities were distinct between lakes, including those connected to the same glacier, indicating the importance of site-specific biogeochemical and physical dynamics on these systems. Microbial community composition correlated with lake age (formation before or after the Little Ice Age) and conductivity but not with whether a lake was connected to a contemporaneous glacier > 0.1 km2. Heterotrophic lineages found in other glacial systems were abundant and widespread, while cyanobacteria only reached appreciable abundances in shallow lakes where light reached the benthos. Relative abundances of ammonia and nitrite oxidizers correlated with concentrations of nitrate and nitrite, suggesting nitrification may help control nitrogen forms and concentrations in glacial lakes. We show that as glaciers recede, unique glacial lake microbial communities will be formed and lost with them.

Coffee leaf rust (CLR) caused by Hemileia vastatrix, has emerged as a growing threat to coffee production in China. This study focused on the identification and characterization of the hyperparasitic fungus Acremonium persicinum using integrated plant pathology and molecular biology approaches. The spore suspension of the fungal strain HY85 exhibited a 91.18% inhibition rate against the germination of H. vastatrix urediniospores. Inoculation of coffee leaf discs with H. vastatrix urediniospores resulted in the development of visible chlorotic lesions after 16 days. However, other inoculation methods did not yield early chlorotic lesions, indicating an absence of H. vastatrix infection. Quantitative PCR analysis revealed that the copy numbers of H. vastatrix DNA after 16 days postinoculation were 1.41 × 108, 7.59 × 108, and 1.66 × 108, respectively. Notably, H. vastatrix DNA was undetectable in leaf discs coinoculated with H. vastatrix urediniospores and the hyperparasitic strain HY85, suggesting complete suppression of the pathogen. In vitro lesion control experiments demonstrated that 96 h after inoculation with HY85, the characteristic yellow urediniospore masses on the lesions were entirely replaced by the white mycelium of the hyperparasitic fungus. The control efficacy of strain HY85 against coffee rust fungus was 66.67%. Scanning electron microscopy revealed that strain HY85 caused significant morphological alterations in the urediniospores, including indentation and collapse, leading to severe structural damage. These findings underscore the capability of A. persicinum to disrupt the life cycle of H. vastatrix and its potential as an effective biocontrol agent strain for CLR management.

Roots are essential plant organs for anchorage in soil, uptake of water with nutrients, storage of photosynthates, and microbial interactions. More knowledge on microorganisms stimulating root growth is needed to control root development of cultured plants. A marker-assisted approach would facilitate vast screenings of microbes for eventual effects on root development. It was aimed to select for transcripts that report on root growth stimulation at the early tomato plant growth stage upon microbial treatments. Microbially treated tomato (Solanum lycopersicum) plants were cultivated in stone wool slabs and screened for genes that increased or decreased in differential expression upon increased root growth, by RNAseq. Expression of 21 selected genes was measured by quantitative polymerase chain reaction (qPCR) in relation with stimulated root growth, recorded by X-ray microtomography, of microbially treated tomato plants cultivated in stone wool blocks. Two genes were identified of which expression significantly correlated with high measured root length, and for one also with high measured shoot wet and dry weight. The translated products, both involved in modulation of Rubisco activity, were a chloroplast-localized acetyltransferase (SlSNAT2) and a Rubisco activase (Rca). Transcripts whose translated products modulate Rubisco activity can serve as candidates for reporting on early root development upon microbial inoculation.

Previous studies have highlighted the widespread presence of thermophilic bacterial genera in upper soil layers, their role in biogeochemical cycles, and their potential application in soil fertilization. However, the mechanisms by which these thermophiles maintain cell viability in temperate soils remain largely unknown. The isolation of thermophilic bacteria from rhizospheric soils has been reported, hence it may be hypothesized that the rhizosphere environment plays a role in their survival. In this study, we developed a hydroponic system to introduce the thermophilic bacterium Parageobacillus thermoglucosidasius into the rhizosphere of tomato plants, demonstrating that this environment increased bacterial survival rates at 20°C-25°C by over 23-fold. The rhizosphere exudates contributed to this increase, as their addition boosted bacterial survival in pure cultures at 25°C by up to twofold. We propose that the rhizosphere and its exudates, characterized through targeted metabolomics, support the persistence of thermophilic bacteria in temperate soils during colder periods, ensuring viable cells that contribute to soil fertilization during warmer seasons.