The use of microbial gene abundance in the development of fuel remediation guidelines in polar soils

2014 ◽  
Vol 11 (2) ◽  
pp. 235-241 ◽  
Author(s):  
Elizabeth L Richardson ◽  
Catherine K King ◽  
Shane M Powell
Keyword(s):  
2021 ◽  
Vol 9 (7) ◽  
pp. 1352
Author(s):  
Lynn E. Ferro ◽  
Kameron Y. Sugino ◽  
Vanja Klepac-Ceraj ◽  
Sarah S. Comstock

Herein, we report the abundance and prevalence of HMO-metabolizing genes, specifically those of Bifidobacterium infantis, in fecal samples from human infants. Forty dyads were enrolled, and each mother collected a fecal sample from her infant at six months of age. Genomic DNA was extracted, and quantitative real-time PCR was used to determine gene abundance. The mode of delivery was not associated with gene abundance. Several gene regions, Sia (a sialidase), B. inf (16S), and GH750 (a glycoside hydrolase), were more abundant in the feces of human milk-fed infants (p < 0.05). Others, Sia and HC bin (16S), tended to be less abundant when a larger percentage of an infant’s diet consisted of solids (p < 0.10). When accounting for solid food intake, human milk exposure was positively associated with Sia and B. inf (p < 0.05) and tended to be related to the abundance of the GH750 and HC bin (p < 0.10) gene regions. With further development and validation in additional populations of infants, these assays could be used to group samples by dietary exposure even where no record of dietary intake exists. Thus, these assays would provide a method by which infant human milk intake can be assessed quickly in any well-equipped molecular biology laboratory.


2019 ◽  
Author(s):  
Meghan R. Perry ◽  
Bram van Bunnik ◽  
Luke McNally ◽  
Bryan Wee ◽  
Patrick Munk ◽  
...  

ABSTRACTIntroductionHospital wastewater is a potential major source of antimicrobial resistance (AMR). This study uses metagenomics to ask how abundances of AMR genes in hospital wastewater are related to clinical activity.MethodsSewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. AMR gene abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates.FindingsMicrobiota and AMR gene composition varied between each collection point and overall AMR gene abundance was higher in hospital wastewater than in community influent. The composition of AMR genes correlated with microbiota composition (Procrustes analysis, p=0.002). Increased antimicrobial consumption at a class level was associated with higher AMR gene abundance within that class in wastewater (incidence rate ratio 2.80, C.I. 1.2-6.5, p=0.016). Prolonged average patient length of stay was associated with higher total AMR gene abundance in wastewater (incidence rate ratio 2.05, C.I. 1.39-3.01, p=0.0003). AMR gene abundance at a class level within hospital wastewater did not reflect resistance patterns in the 181 clinical isolates grown from hospital inpatients over the time of wastewater sampling.ConclusionsHospital antimicrobial consumption and patient length of stay are important drivers of AMR gene outflow into the environment. Using metagenomics to identify the full range of AMR genes in hospital wastewater could represent a useful surveillance tool to monitor hospital AMR gene outflow and guide environmental policy on AMR.


2021 ◽  
Author(s):  
Jie Luo ◽  
Lukas Beule ◽  
Guodong Shao ◽  
Edzo Veldkamp ◽  
Marife D. Corre

&lt;p&gt;Monoculture croplands are considered as major sources of the greenhouse gas, nitrous oxide (N&lt;sub&gt;2&lt;/sub&gt;O). The conversion of monoculture croplands to agroforestry systems, e.g., integrating trees within croplands, is an essential climate-smart management system through extra C sequestration and can potentially mitigate N&lt;sub&gt;2&lt;/sub&gt;O emissions. So far, no study has systematically compared gross rates of N&lt;sub&gt;2&lt;/sub&gt;O emission and uptake between cropland agroforestry and monoculture. In this study, we used an in-situ &lt;sup&gt;15&lt;/sup&gt;N&lt;sub&gt;2&lt;/sub&gt;O pool dilution technique to simultaneously measure gross N&lt;sub&gt;2&lt;/sub&gt;O emission and uptake over two consecutive growing seasons (2018 - 2019) at three sites in Germany: two sites were on Phaeozem and Cambisol soils with each site having a pair of cropland agroforestry and monoculture systems, and an additional site with only monoculture on an Arenosol soil prone to high nitrate leaching. Our results showed that cropland agroforestry had lower gross N&lt;sub&gt;2&lt;/sub&gt;O emissions and higher gross N&lt;sub&gt;2&lt;/sub&gt;O uptake than in monoculture at the site with Phaeozem soil (P &amp;#8804; 0.018 &amp;#8211; 0.025) and did not differ in gross N&lt;sub&gt;2&lt;/sub&gt;O emissions and uptake with cropland monoculture at the site with Cambisol soil (P &amp;#8805; 0.36). Gross N&lt;sub&gt;2&lt;/sub&gt;O emissions were positively correlated with soil mineral N and heterotrophic respiration which, in turn, were correlated with soil temperature, and with water-filled pore space (WFPS) (r = 0.24 &amp;#8210; 0.54, P &lt; 0.01). Gross N&lt;sub&gt;2&lt;/sub&gt;O emissions were also negatively correlated with nosZ clade I gene abundance (involved in N&lt;sub&gt;2&lt;/sub&gt;O-to-N&lt;sub&gt;2&lt;/sub&gt; reduction, r = -0.20, P &lt; 0.05). These findings showed that across sites and management systems changes in gross N&lt;sub&gt;2&lt;/sub&gt;O emissions were driven by changes in substrate availability and aeration condition (i.e., soil mineral N, C availability, and WFPS), which also influenced denitrification gene abundance. The strong regression values between gross N&lt;sub&gt;2&lt;/sub&gt;O emissions and net N&lt;sub&gt;2&lt;/sub&gt;O emissions (R&lt;sup&gt;2 &lt;/sup&gt;&amp;#8805; 0.96, P &lt; 0.001) indicated that gross N&lt;sub&gt;2&lt;/sub&gt;O emissions largely drove net soil N&lt;sub&gt;2&lt;/sub&gt;O emissions. Across sites and management systems, annual soil gross N&lt;sub&gt;2&lt;/sub&gt;O emissions and uptake were controlled by clay contents which, in turn, correlated with indices of soil fertility (i.e., effective cation exchange capacity, total N, and C/N ratio) (Spearman rank&amp;#8217;s rho = -0.76 &amp;#8211; 0.86, P &amp;#8804; 0.05). The lower gross N&lt;sub&gt;2&lt;/sub&gt;O emissions from the agroforestry tree rows at two sites indicated the potential of agroforestry in reducing soil N&lt;sub&gt;2&lt;/sub&gt;O emissions, supporting the need for temperate cropland agroforestry to be considered in greenhouse gas mitigation policies.&lt;/p&gt;


2019 ◽  
Vol 20 (1) ◽  
pp. 99-108 ◽  
Author(s):  
Yuzhen Luo ◽  
Weiwei Zhang ◽  
Yaying Li ◽  
Yongjie Wang ◽  
Huaiying Yao ◽  
...  

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