scholarly journals Microbial community composition of translocated ancient woodland soil: a case study

2021 ◽  
Author(s):  
Nicolas Borchers ◽  
Jacqueline Hannam ◽  
Mark Pawlett
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Ancient Woodland

Microbial community composition of translocated ancient woodland soil: a case study

2021 ◽  
Author(s):  
Nicolas Borchers ◽  
Jacqueline Hannam ◽  
Mark Pawlett
Keyword(s):  
Fatty Acid ◽  
Microbial Community ◽  
Community Composition ◽  
Soil Ph ◽  
Soil Chemistry ◽  
Donor Site ◽  
Microbial Community Composition ◽  
Receptor Site ◽  
Ancient Woodland ◽  
Soil Translocation

Soil translocation is an ecological habitat restoration technique which consists of moving the entire topsoil from a donor site to a chosen receptor site. We investigated changes in soil chemistry and microbiology three years following the salvage of semi-ancient woodland soil and materials (0.94 ha) to a nearby receptor pasture due to road widening works (Kent, UK). We sampled i) intact woodland soils adjacent to the area of soils that was translocated to represent the lost donor site, ii) the soil three years after it had been translocated, and iii) grassland soils adjacent to the translocated soil to represent the original receptor site. The intention was to ascertain if shifts in soil chemistry and microbial community composition (Phospholipid Fatty-acid analysis: PLFA) occurred due to soil translocation. PLFA signature biomarkers demonstrated the overall microbial community profile of the translocated and woodland soils were similar; however, salvaged soils had a 40% increase in the Arbuscular Mycorrhizal Fungi (AMF) bioindicator fatty acid 16:1ω5, a 10% decrease in the Gram-positive bacterial fatty acids, and increased pH (5.01-5.77) compared to the original donor woodland soil. The AMF bioindicator and the first Principal Component (PC1) of the PCA of PLFA data positively correlated with soil pH (r2=0.94 and r2=0.88 respectively) across all three experimental groups. Considering that soil pH increases with depth in this location, it is likely that mixing of soil horizons during translocation increased the topsoil pH causing changes in the soil microbial communities. We concluded that after three years, the chemical and microbial properties of the salvaged soil were characteristic of a woodland soil but showed signs of disturbance.

Microbial Community Composition During Artificial Frosting of Dried Persimmon Fruits

LWT ◽  
2021 ◽  
pp. 111694
Author(s):  
Xiaoxi Chen ◽  
Qin Chen ◽  
Yaxin Liu ◽  
Bin Liu ◽  
Xubo Zhao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition

scholarly journals Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raiza Hasrat ◽  
Jolanda Kool ◽  
Wouter A. A. de Steenhuijsen Piters ◽  
Mei Ling J. N. Chu ◽  
Sjoerd Kuiling ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Positive Control ◽  
Rrna Gene ◽  
Elution Buffer ◽  
Community Profile ◽  
Microbial Community Profile ◽  
Microbial Dna ◽  
Pcr Conditions

AbstractThe low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.

scholarly journals Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?

2021 ◽  
Author(s):  
Tamara J. H. M. van Bergen ◽  
Ana B. Rios-Miguel ◽  
Tom M. Nolte ◽  
Ad M. J. Ragas ◽  
Rosalie van Zelm ◽  
...  
Keyword(s):  
Microbial Community ◽  
Activated Sludge ◽  
Community Composition ◽  
Rate Constants ◽  
Wastewater Treatment Plants ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Initial Concentration ◽  
Different Seasons

Abstract Pharmaceuticals find their way to the aquatic environment via wastewater treatment plants (WWTPs). Biotransformation plays an important role in mitigating environmental risks; however, a mechanistic understanding of involved processes is limited. The aim of this study was to evaluate potential relationships between first-order biotransformation rate constants (kb) of nine pharmaceuticals and initial concentration of the selected compounds, and sampling season of the used activated sludge inocula. Four-day bottle experiments were performed with activated sludge from WWTP Groesbeek (The Netherlands) of two different seasons, summer and winter, spiked with two environmentally relevant concentrations (3 and 30 nM) of pharmaceuticals. Concentrations of the compounds were measured by LC–MS/MS, microbial community composition was assessed by 16S rRNA gene amplicon sequencing, and kb values were calculated. The biodegradable pharmaceuticals were acetaminophen, metformin, metoprolol, terbutaline, and phenazone (ranked from high to low biotransformation rates). Carbamazepine, diatrizoic acid, diclofenac, and fluoxetine were not converted. Summer and winter inocula did not show significant differences in microbial community composition, but resulted in a slightly different kb for some pharmaceuticals. Likely microbial activity was responsible instead of community composition. In the same inoculum, different kb values were measured, depending on initial concentration. In general, biodegradable compounds had a higher kb when the initial concentration was higher. This demonstrates that Michealis-Menten kinetic theory has shortcomings for some pharmaceuticals at low, environmentally relevant concentrations and that the pharmaceutical concentration should be taken into account when measuring the kb in order to reliably predict the fate of pharmaceuticals in the WWTP. Key points • Biotransformation and sorption of pharmaceuticals were assessed in activated sludge. • Higher initial concentrations resulted in higher biotransformation rate constants for biodegradable pharmaceuticals. • Summer and winter inocula produced slightly different biotransformation rate constants although microbial community composition did not significantly change. Graphical abstract

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