Browsing by Subject "BACTERIAL COMMUNITY"

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  • Pacwa-Plociniczak, Magdalena; Plociniczak, Tomasz; Yu, Dan; Kurola, Jukka Mikael; Sinkkonen, Aki Tapio; Piotrowska-Seget, Zofia; Romantschuk, Martin L. (2018)
    In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.
  • Säde, Elina; Johansson, Per; Heinonen, Tytti; Hultman, Jenni; Björkroth, Johanna (2020)
    Lactobacillus algidus is a meat spoilage bacterium often dominating the bacterial communities on chilled, packaged meat. Yet, L. algidus strains are rarely recovered from meat, and only few studies have focused on this species. The main reason limiting detailed studies on L. algidus is related to its poor growth on the media routinely used for culturing food spoilage bacteria. Thus, our study sought to develop reliable culture media for L. algidus to enable its recovery from meat, and to allow subculturing and phenotypic analyses of the strains. We assessed the growth of meat-derived L. algidus strains on common culture media and their modifications, and explored the suitability of potential media for the recovery of L. algidus from meat. Moreover, we determined whether 12 meat-derived L. algidus strains selected from our culture collection produce biogenic amines that may compromise safety or quality of meat, and finally, sequenced de novo and annotated the genomes of two meat-derived L. algidus strains to uncover genes and metabolic pathways relevant for phenotypic traits observed. MRS agar supplemented with complex substances (peptone, meat and yeast extract, liver digest) supported the growth of L. algidus, and allowed the recovery of new L. algidus isolates from meat. However, most strains grew poorly on standard MRS agar and on general-purpose media. In MRS broth, most strains grew well but a subset of strains required supplementation of MRS broth with additional cysteine. Supplementation of MRS broth with catalase allowed growth in aerated cultures suggesting that the strains produced hydrogen peroxide when grown aerobically. The strains tested (n = 12) produced ornithine from arginine and putrescine from agmatine, and two strains produced tyramine from tyrosine. Our findings reveal that L. algidus populations are underestimated if routine culture protocols are applied, and prompt concerns that L. algidus may generate tyramine or putrescine in meat or fermented meat products.
  • Liu, Xinxin; Hui, Nan; Kontro, Merja H. (2020)
    The triazine herbicide atrazine easily leaches with water through soil layers into groundwater, where it is persistent. Its behavior during short-term transport is poorly understood, and there is no in situ remediation method for it. The aim of this study was to investigate whether water circulation, or circulation combined with bioaugmentation (Pseudomonassp. ADP, or four isolates from atrazine-contaminated sediments) alone or with biostimulation (Na-citrate), could enhance atrazine dissipation in subsurface sediment-water systems. Atrazine concentrations (100 mg L-1) in the liquid phase of sediment slurries and in the circulating water of sediment columns were followed for 10 days. Atrazine was rapidly degraded to 53-64 mg L(-1)in the slurries, and further to 10-18 mg L(-1)in the circulating water, by the inherent microbes of sediments collected from 13.6 m in an atrazine-contaminated aquifer. Bioaugmentation without or with biostimulation had minor effects on atrazine degradation. The microbial number simultaneously increased in the slurries from 1.0 x 10(3)to 0.8-1.0 x 10(8)cfu mL(-1), and in the circulating water from 0.1-1.0 x 10(2)to 0.24-8.8 x 10(4)cfu mL(-1). In sediments without added atrazine, the cultivable microbial numbers remained low at 0.82-8.0 x 10(4)cfu mL(-1)in the slurries, and at 0.1-2.8 x 10(3)cfu mL(-1)in the circulating water. The cultivated microorganisms belonged to the nine generaAcinetobacter,Burkholderia,Methylobacterium,Pseudomonas,Rhodococcus,Sphingomonas,Streptomyces,VariovoraxandWilliamsia; i.e., biodiversity was low. Water flow through the sediments released adsorbed and complex-bound atrazine for microbial degradation, though the residual concentration of 10-64 mg L(-1)was high and could contaminate large groundwater volumes from a point source, e.g., during heavy rain or flooding.
  • Legay, Nicolas; Clément, Jean-Christophe; Grassein, Fabrice; Lavorel, Sandra; Lemauviel-Lavenant, S; Personeni, Eleanor; Poly, Frank; Pommier, T; Robson, Thomas Matthew; Mouhamadou, B; Binet, M-N (2020)
    Relationships between plants and nitrogen-related microbes may vary with plant growth. We investigated these dynamic relationships over three months by analyzing plant functional traits (PFT), arbuscular mycorrhizal fungal (AMF) colonization, potential N mineralization (PNM), potential nitrification (PNA) and denitrification activities (PDA) in Dactylis glomerata cultures. D. glomerata recruited AMF during early growth, and thereafter maintained a constant root colonization intensity. This may have permitted high enough plant nutrient acquisition over the three months as to offset reduced soil inorganic N. PFT changed with plant age and declining soil fertility, resulting in higher allocation to root biomass and higher root C:N ratio. Additional to root AMF presence, PR' changes may have favored denitrification over mineralization through changes in soil properties, particularly increasing the quality of the labile carbon soil fraction. Other PFT changes, such as N uptake, modified the plants' ability to compete with bacterial groups involved in N cycling. (C) 2020 Elsevier Ltd and British Mycological Society. All rights reserved.