FEMS microbiology ecology最新文献

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.

Pooling individual samples could be an efficient approach for large-scale population-based microbiome studies. However, it is unknown whether pooled samples accurately reflect the microbiome composition and diversity obtained from individual samples. This study investigated the impact of various pooling methods on the observed fecal microbiome of preweaned piglets. Individual fecal samples were collected from 10 litters of day-old piglets (N = 137) and 10 litters of 20-day-old piglets (N = 121), as well as pen-floor samples from the same litters. The individually collected samples were processed individually and also used to create pools of both raw feces and extracted DNA. Individual samples, raw feces pools, DNA pools, and pen-floor samples were subjected to 16S rRNA gene sequencing. The microbial profile in pen-floor samples from litters of preweaned piglets was very different from individual piglet samples within the pen; thus, they may not be suitable for litter-level piglet microbiome studies. However, overall microbial diversity and composition from DNA and feces pools were comparable to individual samples, despite potentially underestimating some low-abundance or low-prevalence taxa. These results suggest that pooling can be used as an efficient and cost-effective approach to characterize litter-level microbial profiles for current and future population-level microbiome research in preweaned piglet populations.

Chronic inflammation creates an oxidative environment, altering the gut microbiota. However, the mechanisms underlying oxidative stress-induced community changes remain poorly understood, owing to the complexity of the host environment, high inter-individual variability, and a lack of comparative data on stress tolerance across intestinal taxa. To address this, we developed an in vitro cultivation approach to assess the effects of oxidative stress, induced by 12 concentrations each of hydrogen peroxide (H₂O₂) and oxygen (O₂), on 41 intestinal strains and seven adults' fecal microbiota. Fusicatenibacter saccharivorans and Lachnospira eligens emerged as particularly sensitive taxa in both pure cultures and complex communities. Oxidative stress also reduced butyrate-producing taxa, like Agathobacter and Anaerostipes, along with total butyrate levels. In contrast, facultative anaerobes, like Escherichia-Shigella and Enterococcus, were largely unaffected, and Bacteroides showed high resilience. Notably, the impact of oxidative stress varied among individuals, with numerous genera showing taxon-specific changes depending on the host microbiota composition. These findings underscore the importance of considering individual microbiota backgrounds when assessing oxidative stress effects on microbial communities. Our study provides a tolerance profile of gut microbes to oxidative stress, reveals overlooked taxa involved in community restructuring, and introduces a screening tool to characterize individual microbial and metabolic responses.

Plant-soil feedback and soil microbial legacies play crucial roles in replanting success of apple. This study investigated how different soil amendment strategies influence these factors in replant disease-affected soil. Two approaches were tested: (i) the preculture and amendment of catch crops-either a single species, Tagetes patula, or a diverse catch crop mixture (CCM), and (ii) the inoculation of plant-beneficial microbes-bacteria, arbuscular mycorrhizal fungi, or their combination (SynC). Apple rootstock M.26 was grown for seven weeks in a greenhouse, and plant growth, soil nutrients, root phytoalexins, and microbial communities in rhizosphere and root-affected soil were analyzed. Catch crop amendments but not microbial inoculations, significantly altered soil nutrients. Root length increased significantly under CCM, and in tendency in Tagetes and SynC. Phytoalexin contents were lowest in Tagetes and highest in CCM, both differing from the control in specific compounds. Microbiome analysis revealed that catch crops strongly modulated fungal communities in rhizosphere and root-affected soil, favoring potentially beneficial Linnemannia and Mortierella, while microbial inoculations predominantly modulated bacterial/archaeal rhizosphere communities. Our results suggest that catch crops and microbial inoculants induced distinct shifts in soil-plant-microbe interactions under replanting conditions.