scholarly journals Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Madangchanok Imchen ◽  
Ranjith Kumavath ◽  
Debmalya Barh ◽  
Vasco Azevedo ◽  
Preetam Ghosh ◽  
...  
2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Madangchanok Imchen ◽  
Ranjith Kumavath ◽  
Debmalya Barh ◽  
Vasco Azevedo ◽  
Preetam Ghosh ◽  
...  

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Juhi Gupta ◽  
Rashmi Rathour ◽  
Madan Kumar ◽  
Indu Shekhar Thakur

ABSTRACT We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.


2016 ◽  
Vol 15 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Sujay Paul ◽  
Yolanda Cortez ◽  
Nadia Vera ◽  
Gretty Villena ◽  
Marcel Gutiérrez-Correa

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sang In Lee ◽  
Jungmin Choi ◽  
Hyunhee Hong ◽  
Jun Haeng Nam ◽  
Bernadine Strik ◽  
...  

AbstractMicrobial communities on soil are fundamental for the long-term sustainability of agriculture ecosystems. Microbiota in soil would impact the yield and quality of blueberries since microbial communities in soil can interact with the rhizosphere of plant. This study was conducted to determine how different mulching treatments induce changes in soil microbial composition, diversity, and functional properties. A total of 150 soil samples were collected from 5 different mulch treatments (sawdust, green weed mat, sawdust topped with green weed mat, black weed mat, and sawdust topped with black weed mat) at 3 different depths (bottom, middle, and top region of 20 cm soil depth) from 2 different months (June and July 2018). A total of 8,583,839 sequencing reads and 480 operational taxonomic units (OTUs) of bacteria were identified at genus level. Eight different plant growth promoting rhizobacteria (PGPR) were detected, and the relative abundances of Bradyrhizobium, Bacillus, and Paenibacillus were more than 0.1% among all soil samples. Sampling depth and month of soil samples impacted the amount of PGPR, while there were no significant differences based on mulch type. Functional properties of bacteria were identified through PICRUSt2, which found that there is no significant difference between mulch treatment, depth, and month. The results indicated that sampling month and depth of soil impacted the relative abundance of PGPR in soil samples, but there were no significant differences of functional properties and beneficial microbial communities based on mulch type.


1999 ◽  
Vol 65 (7) ◽  
pp. 3064-3070 ◽  
Author(s):  
Casey Hubert ◽  
Yin Shen ◽  
Gerrit Voordouw

ABSTRACT Toluene-degrading bacteria were isolated from hydrocarbon-contaminated soil by incubating liquid enrichment cultures and agar plate cultures in desiccators in which the vapor pressure of toluene was controlled by dilution with vacuum pump oil. Incubation in desiccators equilibrated with either 100, 10, or 1% (wt/wt) toluene in vacuum pump oil and testing for genomic cross-hybridization resulted in four genomically distinct strains (standards) capable of growth on toluene (strains Cstd1, Cstd2, Cstd5, and Cstd7). The optimal toluene concentrations for growth of these standards on plating media differed considerably. Cstd1 grew best in an atmosphere equilibrated with 0.1% (wt/wt) toluene, but Cstd5 failed to grow in this atmosphere. Conversely, Cstd5 grew well in the presence of 10% (wt/wt) toluene, which inhibited growth of Cstd1. 16S ribosomal DNA sequencing and cross-hybridization analysis indicated that both Cstd1 and Cstd5 are members of the genus Pseudomonas. An analysis of the microbial communities in soil samples that were incubated with 10% (wt/wt) toluene with reverse sample genome probing indicated thatPseudomonas strain Cstd5 was the dominant community member. However, incubation of soil samples with 0.1% (wt/wt) toluene resulted in a community that was dominated by Pseudomonas strain Q7, a toluene degrader that has been described previously (Y. Shen, L. G. Stehmeier, and G. Voordouw, Appl. Environ. Microbiol. 64:637–645, 1998). Q7 was not able to grow by itself in an atmosphere equilibrated with 0.1% (wt/wt) toluene but grew efficiently in coculture with Cstd1, suggesting that toluene or metabolic derivatives of toluene were transferred from Cstd1 to Q7.


2020 ◽  
Author(s):  
Chupei Shi ◽  
Carolina Urbina Malo ◽  
Ye Tian ◽  
Shasha Zhang ◽  
Marilena Heitger ◽  
...  

<p>Human activities have caused global warming by 0.95 °C since the industrial revolution, and average temperatures in Austria have risen by almost 2 °C since 1880. Increased global mean temperatures have been reported to accelerate carbon (C) cycling, but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, the extent of warming-induced increases in soil C, N and P processes can differ, causing an eventual uncoupling of biogeochemical C, N and P cycles, and leading to altered elemental imbalances between available plant and soil resources and soil microbial communities. The altered dynamics in soil C and nutrient availability caused by increased soil temperature could shift the growth-limiting element for soil microorganisms, with strong repercussions on the decomposition, mineralization and sequestration of organic C and nutrients. The latter relates to the conservative cycling of limiting elements while elements in excess are mineralized and released at greater rates by microbial communities.</p><p>Despite the many laboratory and in situ studies investigating factors that limit soil microbial activity, most of them explored nutrient addition effects on soil respiration or soil enzyme activities. A critical assessment, however, clearly indicated the inappropriateness of these measures to deduce growth-limiting nutrients for soil microbes. Similar to studies of plant nutrient limitation, unequivocal assessment of soil microbial element limitation can only be derived from the response of microbial growth to element amendments. To our knowledge this has not been performed on soils undergoing long-term soil warming.</p><p>In this study, we therefore investigated the effect of long-term soil warming on microbial nutrient limitation based on microbial growth measurements in a temperate calcareous forest soil. Soil samples were taken from two soil depths (0-10, 10-20 cm) in both control and heated plots in the Achenkirch soil warming project (>15 yrs soil warming by + 4 °C). Soil samples were pre-incubated at their corresponding field temperature after sieving and removal of visible roots. The soils were amended with different combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, the nutrients being dissolved in <sup>18</sup>O-water. After 24 hours of incubation, microbial growth was measured based on the <sup>18</sup>O incorporation into genomic DNA. Nutrient (co)limitation was determined by comparing microbial growth responses upon C and nutrient additions relative to unamended controls. Basal respiration was also measured based on the increase in headspace CO<sub>2</sub>, allowing to estimate microbial C use efficiency (CUE). The fate of C and nutrient amendments was finally traced by measurements of inorganic and organic extractable and microbial biomass C, N and P. This study will thereby provide key insights into potential shifts in limiting nutrients for microbial growth under long-term soil warming, and into concomitant effects on soil C and nutrient cycles.</p>


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