scholarly journals Grazing effects on microbial community composition, growth and nutrient cycling in salt marsh and sand dune grasslands

2012 ◽  
Vol 49 (1) ◽  
pp. 89-98 ◽  
Author(s):  
H. Ford ◽  
J. Rousk ◽  
A. Garbutt ◽  
L. Jones ◽  
D. L. Jones
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Nutrient Cycling ◽  
Community Composition ◽  
Sand Dune ◽  
Microbial Community Composition ◽  
Grazing Effects

scholarly journals Microbial Community Composition and Denitrifying Enzyme Activities in Salt Marsh Sediments

2008 ◽  
Vol 74 (24) ◽  
pp. 7585-7595 ◽  
Author(s):  
Yiping Cao ◽  
Peter G. Green ◽  
Patricia A. Holden
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Carbon Content ◽  
Community Composition ◽  
Enzyme Activities ◽  
Nutrient Loading ◽  
Microbial Community Composition ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
And Function

ABSTRACT Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

Changes in soil microbial biomass and community composition along vegetation zonation in a coastal sand dune

Soil Research ◽  
2008 ◽  
Vol 46 (4) ◽  
pp. 390 ◽  
Author(s):  
Shinpei Yoshitake ◽  
Takayuki Nakatsubo
Keyword(s):  
Microbial Community ◽  
Microbial Biomass ◽  
Community Composition ◽  
Sand Dune ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Coastal Sand Dune ◽  
Vegetation Zonation ◽  
Soil Microbial ◽  
Coastal Sand

We used phospholipid fatty acid (PLFA) analysis to examine the relation of microbial biomass and community composition to vegetation zonation on a coastal sand dune. Soil samples were collected along 3 line transects established from the shoreline to the inland bush. Total PLFA content and PLFA composition of soils were used as indices of total microbial biomass and community composition, respectively. The microbial biomass was much higher in the inland Vitex rotundifolia zone than in the seaside plots. The microbial community composition also differed among the vegetation zones, with a higher contribution of fungal biomarkers in the inland plots. The microbial biomass increased significantly with increasing soil organic matter (SOM) content, but was not correlated with soil salinity. These results suggest that microbial biomass in the coastal sand dune was controlled primarily by the accumulation of SOM. The microbial community composition also changed with SOM content in the seaside plots, but SOM had little effect in the inland plots. These results suggest that the factors limiting the microbial community composition differed with location on the dune.

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.

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