Journal: FEMS Microbiology Ecology

Abbreviation

FEMS microbiol. ecol.

Publisher

Oxford University Press

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ISSN

0168-6496
1574-6941

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Publications1 - 10 of 48
  • Aeolian dispersal of bacteria in southwest Greenland: Their sources, abundance, diversity and physiological states
    Item type: Journal Article
    Šantl-Temkiv, Tina; Gosewinkel, Ulrich; Starnawski, Piotr; et al. (2018)
    FEMS Microbiology Ecology
    The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×10³ ± 1.0×10³ cells m⁻³, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell⁻¹), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.
  • Calystegine degradation capacities of microbial rhizosphere communities of Zea mays (calystegine-negative) and Calystegia sepium (calystegine-positive)
    Item type: Journal Article
    Guntli, Daniel; Burgos, Stéphane; Moënne-Loccoz, Yvan; et al. (1999)
    FEMS Microbiology Ecology
  • Colonization of Cutibacterium avidum during infant gut microbiota establishment
    Item type: Journal Article
    Rocha Martin, Vanesa N.; Schwab, Clarissa; Krych, Lukasz; et al. (2019)
    FEMS Microbiology Ecology
    Abstract Establishment of the infant gut microbiota affects gut maturation and influences long-term health. Cutibacterium (formerly Propionibacterium) have been identified as early colonizers, but little is known about their function. Using a cultivation-dependent and -independent approach, we determined Cutibacterium prevalence, diversity and functional potential. In feces from a Swiss infant cohort (n = 38), prevalence of Propionibacterium/Cutibacterium decreased from 84% at 2 weeks, to 65% at 4 weeks, 47% at 8 weeks and 41% at 12 weeks of age. Abundance varied among individuals, and persistence depended on the colonization levels at 2 weeks. Cutibacterium isolates (n = 87) were obtained from 10 infants from a smaller cohort (n = 12); restriction fragment length polymorphism clustered isolates in four groups, and all identified as Cutibacterium avidum. Colonization potential and metabolic effects of C. avidum addition were tested in an in vitro continuous intestinal fermentation model mimicking infant proximal colon conditions. Cutibacterium avidum spiked daily at 10⁸ or 10⁹ cells mL-¹ colonized, decreased formate and persisted during the washout period. Significant correlations were observed between Propionibacterium/Cutibacterium and lactate-producers and protein-degraders in both reactors and infant feces. Our findings highlight the natural presence of C. avidum and its role as a lactate-consumer and propionate-producer in infants younger than 3 months.
  • Assessing effects of the entomopathogenic fungus Metarhizium brunneum on soil microbial communities in Agriotes spp. biological pest control
    Item type: Journal Article
    Mayerhofer, Johanna; Eckard, Sonja; Hartmann, Martin; et al. (2017)
    FEMS Microbiology Ecology
    The release of large quantities of microorganisms to soil for purposes such as pest control or plant growth promotion may affect the indigenous soil microbial communities. In our study, we investigated potential effects of Metarhizium brunneum ART2825 on soil fungi and prokaryota in bulk soil using high-throughput sequencing of ribosomal markers. Different formulations of this strain, and combinations of the fungus with garlic as efficacy-enhancing agent, were tested over 4 months in a pot and a field experiment carried out for biological control of Agriotes spp. in potatoes. A biocontrol effect was observed only in the pot experiment, i.e. the application of FCBK resulted in 77% efficacy. Colony counts combined with genotyping and marker sequence abundance confirmed the successful establishment of the applied strain. Only the formulated applied strain caused small shifts in fungal communities in the pot experiment. Treatment effects were in the same range as the effects caused by barley kernels, the carrier of the FCBK formulation and temporal effects. Garlic treatments and time affected prokaryotic communities. In the field experiment, only spatial differences affected fungal and prokaryotic communities. Our findings suggest that M. brunneum may not adversely affect soil microbial communities.
  • Natural variation of gliding motility in a centimetre-scale population of Myxococcus xanthus
    Item type: Journal Article
    Vos, Michiel; Velicer, Gregory J. (2008)
    FEMS Microbiology Ecology
  • Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota
    Item type: Journal Article
    Grouzdev, Denis; Gaisin, Vasil; Lunina, Olga; et al. (2022)
    FEMS Microbiology Ecology
    Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.
  • Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop
    Item type: Journal Article
    Ramoneda, Josep; Le Roux, Johannes J.; Frossard, Emmanuel; et al. (2020)
    FEMS Microbiology Ecology
    Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.
  • Soil microbial communities are sensitive to differences in fertilization intensity in organic and conventional farming systems
    Item type: Journal Article
    Lori, Martina; Hartmann, Martin; Kundel, Dominika; et al. (2023)
    FEMS Microbiology Ecology
    Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic and integrated farming, can provide numerous benefits for soil quality but also compromise the environment by polluting soils and producing greenhouse gases through animal husbandry. The need for reduced stocking density is inevitably accompanied by lower FYM inputs, but little research is available on the impact of these effects on the soil microbiome. We collected soil samples from winter wheat plots of a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities and measured soil quality parameters and microbial community diversity through DNA metabarcoding. High-input fertilization, corresponding to 1.4 livestock units (LU) improved the soil's nutritional status and increased soil microbial biomass and respiration when compared to low-input at 0.7 LU. Bacterial and fungal alpha-diversity was largely unaffected by fertilization intensity, whereas their community structure changed consistently, accompanied by an increase in the bacterial copiotroph-to-oligotroph ratio in high-input systems and by more copiotrophic indicator OTUs associated with high than low-input. This study shows that reduced nutrient availability under low-input selects oligotrophic microbes efficiently obtaining nutrients from various carbon sources; a potentially beneficial trait considering future agroecosystems.
  • Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance
    Item type: Journal Article
    Dennert, Francesca; Imperiali, Nicola; Staub, Cornelia; et al. (2018)
    FEMS Microbiology Ecology
    Conservation tillage and organic farming are strategies used worldwide to preserve the stability and fertility of soils. While positive effects on soil structure have been extensively reported, the effects on specific root- and soil-associated microorganisms are less known. The aim of this study was to investigate how conservation tillage and organic farming influence the frequency and activity of plant-beneficial pseudomonads. Amplicon sequencing using the 16S rRNA gene revealed that Pseudomonas is among the most abundant bacterial taxa in the root microbiome of field-grown wheat, independent of agronomical practices. However, pseudomonads carrying genes required for the biosynthesis of specific antimicrobial compounds were enriched in samples from conventionally farmed plots without tillage. In contrast, disease resistance tests indicated that soil from conventional no tillage plots is less resistant to the soilborne pathogen Pythium ultimum compared to soil from organic reduced tillage plots, which exhibited the highest resistance of all compared cropping systems. Reporter strain-based gene expression assays did not reveal any differences in Pseudomonas antimicrobial gene expression between soils from different cropping systems. Our results suggest that plant-beneficial pseudomonads can be favoured by certain soil cropping systems, but soil resistance against plant diseases is likely determined by a multitude of biotic factors in addition to Pseudomonas.
Publications1 - 10 of 48