Patterns in utilization of carbon sources in soil microbial communities contaminated with mine solid wastes from San Luis Potosi, Mexico

ABSTRACT Sole-carbon-source tests (Biolog), designed to identify bacteria, have become very popular for metabolically fingerprinting soil microbial communities, despite disadvantages associated with the use of carbon source profiles that primarily select for fast-growing bacteria. In this paper we describe the use of an alternative method that combines the advantages of the Biolog community-level physiological profile (CLPP) method, in which microtiter-based detection plates are used, with the ability to measure carbon dioxide evolution from whole soil. This method facilitates measurement over short periods of time (4 to 6 h) and does not require the extraction and culturing of organisms. Deep-well microtiter plates are used as test wells into which soil is placed. The apparatus to fill the deep-well plates and interface it with a second removable detection plate is described. Two detection systems, a simple colorimetric reaction in absorbent alkali and scintillation counting with radioactive carbon sources, are described. The methods were compared to the Biolog-CLPP system by using soils under different vegetation types and soil treated with wastewater sludge. We aimed to test the hypothesis that using whole soil would have specific advantages over using extracts in that more immediate responses to substrates could be obtained that would reflect activity rather than growth. The whole-soil method was more rapid and gave earlier detection of C source use. Also, the metabolic fingerprints obtained could discriminate between sludge treatments.

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Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-Laden Minerals with Different Carbon Sources

Environmental Science & Technology ◽

10.1021/acs.est.9b03467 ◽

2019 ◽

Vol 53 (21) ◽

pp. 12398-12406 ◽

Cited By ~ 2

Author(s):

Shigeki Yamamura ◽

Hibiki Kurasawa ◽

Yuta Kashiwabara ◽

Tomoyuki Hori ◽

Tomo Aoyagi ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Reductive Dissolution ◽

Soil Microbial

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Microbial communities and their predictive functional profiles in the arid soil of Saudi Arabia

SOIL ◽

10.5194/soil-6-513-2020 ◽

2020 ◽

Vol 6 (2) ◽

pp. 513-521

Author(s):

Munawwar A. Khan ◽

Shams T. Khan

Keyword(s):

Saudi Arabia ◽

Microbial Communities ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Survival Strategies ◽

Semiarid Region ◽

Ammonia Oxidizers ◽

Arid Soil ◽

Soil Microbial ◽

Nitrogen Fixers

Abstract. Saudi Arabia has the world's fifth-largest desert and is the biggest importer of food and agricultural products. Understanding soil microbial communities is key to improving the agricultural potential of the region. Therefore, soil microbial communities of the semiarid region of Abha, known for agriculture, and arid regions of Hafar Al Batin and Muzahmiya were studied using Illumina sequencing. The results show that the microbial communities of the Saudi desert were characterized by the presence of high numbers of Actinobacteria, Proteobacteria, and Firmicutes. In addition to Sahara desert signature phyla like Gemmatimonadetes, biogeochemically important microorganisms like primary producers, nitrogen fixers and ammonia oxidizers were also present. The composition of the microbial community varied greatly among the sites sampled. The highest diversity was found in the rhizospheric soil of Muzahmiya followed by Abha. Firmicutes, Proteobacteria and Actinobacteria were the three main phyla detected in all the samples. Soils from the agricultural region of Abha were significantly different from other samples in containing only 1 % Firmicutes and 3–6 times higher population of Actinobacteria and Bacteroidetes, respectively. The presence of photosynthetic bacteria, ammonia oxidizers, and nitrogen fixers along with bacteria capable of surviving on simple and unlikely carbon sources like dimethylformamide was indicative of their survival strategies under harsh environmental conditions in the arid soil. Functional inference using PICRUSt analysis shows an abundance of genes involved in photosynthesis and nitrogen fixation.

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Unravelling the Functional Diversity of the Soil Microbial Community of Chinese Fir Plantations of Different Densities

Forests ◽

10.3390/f9090532 ◽

2018 ◽

Vol 9 (9) ◽

pp. 532 ◽

Cited By ~ 6

Author(s):

Chaoqun Wang ◽

Lin Xue ◽

Yuhong Dong ◽

Yihui Wei ◽

Ruzhen Jiao

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Functional Diversity ◽

Soil Microbial Community ◽

Diversity Index ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Stand Density ◽

Chinese Fir ◽

Soil Microbial

The structure and function of forest ecosystems are directly or indirectly affected by their stand density. However, what effect the density of Chinese fir plantations has on the functional diversity of the soil microbial community remains unclear. The microbial metabolic functional diversity of soils sampled at the topsoil (0–20 cm) of 35-year-old Chinese fir plantations of five initial densities (D1: 1667 stems∙hm−2, D2: 3333 stems∙hm−2, D3: 5000 stems∙hm−2, D4: 6667 stems∙hm−2, and D5: 10,000 stems∙hm−2) was studied by using Biolog ECO technology. The results showed that the soil pH, oxidizable organic carbon (SOOC), available N (AN), available P (AP), and available K (AK) contents all showed a gradual increase from D1 to D4 and a decrease from D4 to D5, while the number of culturable bacteria and total microorganisms, the average well color development (AWCD) values for the single carbon substrate and six types of carbon sources used by the microbial community, as well as the Shannon-Wiener diversity index (H’), Pielou evenness index (J), and McIntosh Diversity Index (U), were the opposite, suggesting that low-densities favored C and N mineralization and the nutrient cycle. The density of Chinese fir plantations had a significant effect on the use of carbohydrates, amino acids, carboxylic acids, and phenolic acids by the soil microbial community, but it had no significant effect on the use of polymers (p < 0.05). Principal component analysis (PCA) revealed that carbohydrates, polymers, and phenolic acids were sensitive carbon sources that caused differences in the metabolic functions of soil microbial communities in Chinese fir plantations. Redundancy analysis (RDA) showed that physicochemical factors have a significant influence on the metabolic function of soil microbial communities (RDA1 and RDA2 explained >85% variance). The changes in density affected the soil physicochemical properties, the composition, and the metabolic functional diversity of microbial communities in Chinese fir plantations, which is certainly useful for the stand density regulation of Chinese fir plantations.

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Denaturing gradient gel electrophoresis and multi-SIR profiles of soil microbial communities from a karst doline at Aggtelek National Park, Hungary

Folia Microbiologica ◽

10.1007/s12223-020-00828-y ◽

2020 ◽

Author(s):

Márton Mucsi ◽

Gergely Krett ◽

Tibor Szili-Kovács ◽

János Móga ◽

Andrea K. Borsodi

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Vegetation Type ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Rrna Gene ◽

Soil Microbial ◽

Gradient Gel Electrophoresis

Abstract Soils play an important role in the ecosystem of karstic landscapes both as a buffer zone and as a source of acidity to belowground water. Although the microbiota of karstic soils is known to have a great effect on karstification processes, the activity and composition of these communities are largely unknown. This study gives a comparative analysis of soil microbial profiles from different parts of a doline located at Aggtelek, Hungary. The aim was to reveal the relationships between the vegetation type and genetic fingerprints and substrate utilisation (multi-SIR) profiles of the soil microbiota. Soil samples were collected in early and late springs along a transect in a doline covered with different types of vegetation. Genetic fingerprints of bacterial communities were examined by denaturing gradient gel electrophoresis (DGGE) based on the 16S rRNA gene, along with multi-SIR profiles of the microbial communities measured by the MicroResp method using 15 different carbon sources. Genetic fingerprinting indicated that vegetation cover had a strong effect on the composition of soil bacterial communities. Procrustean analysis showed only a weak connection between DGGE and multi-SIR profiles, probably due to the high functional redundancy of the communities. Seasonality had a significant effect on substrate usage, which can be an important factor to consider in future studies.

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Microbial communities and their predictive functional profiles in arid soil of Saudi Arabia

10.5194/soil-2020-31 ◽

2020 ◽

Author(s):

Munawwar A. Khan ◽

Shams T. Khan

Keyword(s):

Saudi Arabia ◽

Microbial Communities ◽

Microbial Community Composition ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Survival Strategies ◽

Major Constituent ◽

Soil Microbial ◽

Agricultural Potential ◽

Semi Arid Region

Abstract. Saudi Arabia has world's fifth largest desert and is the biggest importer of food and agricultural products. Understanding soil microbial communities is key to improving agricultural potential of the region. Therefore, soil microbial communities of semi-arid region of Abha known for agriculture and arid regions of Hafr Al-Batin and Muzahmiyah were studied using Illumina sequencing. Microbial community composition varied remarkably from other deserts and from one place to another. Highest diversity was found in rhizospheric soil of Muzahmiyah followed by Abha. Firmicutes, Proteobacteria and Actinobacteria were three main phyla detected in all the samples. Unlike other deserts, Bacteroidetes was not a major constituent and population of Firmicutes was quite high. Soils from agricultural region of Abha were significantly different from other samples in containing only 1 % Firmicutes and three to six times higher population of Actinobacteria and Bacteroidetes, respectively. Presence of photosynthetic bacteria, ammonia oxidizers, and nitrogen fixers along with bacteria capable of surviving on simple and unlikely carbon sources like DMF was indicative of their survival strategies under harsh environmental condition. Functional inference using PICRUSt show abundance of genes involved in photosynthesis and nitrogen fixation. Microbial communities show greater similarity with hot Namib desert than with cold Antarctic desert.

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Utilization of carbon sources by the soil microbial communities of four plant functional groups in Songnen Steppe

Acta Ecologica Sinica ◽

10.5846/stxb201311132727 ◽

2015 ◽

Vol 35 (17) ◽

Author(s):

曲同宝 QU Tongbao ◽

王呈玉 WANG Chengyu ◽

庞思娜 PANG Sina ◽

张建峰 ZHANG Jianfeng

Keyword(s):

Microbial Communities ◽

Functional Groups ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Plant Functional Groups ◽

Soil Microbial

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Use of rhizosphere carbon sources in sole carbon source tests to discriminate soil microbial communities

Journal of Microbiological Methods ◽

10.1016/s0167-7012(97)00041-9 ◽

1997 ◽

Vol 30 (1) ◽

pp. 33-41 ◽

Cited By ~ 260

Author(s):

C.D Campbell ◽

S.J Grayston ◽

D.J Hirst

Keyword(s):

Carbon Source ◽

Microbial Communities ◽

Sole Carbon Source ◽

Carbon Sources ◽

Soil Microbial Communities ◽

Soil Microbial

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Percepciones y experiencias de usuarias sobre las limitaciones sanitarias para la promoción de lactancia materna

Revista de Salud Pública ◽

10.15446/rsap.v20n3.62580 ◽

2018 ◽

Vol 20 (3) ◽

pp. 308-313

Author(s):

Yesica Yolanda Rangel-Flores ◽

Ulises Martínez Plascencia ◽

Ma. Estela Rodriguez Martínez

Keyword(s):

San Luis ◽

San Luis Potosi ◽

Investigación Cualitativa ◽

Las Mujeres ◽

San Luis Potosí

Objetivo Comprender las percepciones y experiencias que usuarias de distintos servicios de salud han desarrollado respecto a las limitaciones sanitarias para la promoción de la Lactancia Materna.Metodología Investigación cualitativa con enfoque fenomenológico. Se aplicaron entrevistas en profundidad a 12 madres que habitan en una comunidad clasificada con alto nivel de marginación en San Luis Potosí, México, cuyos partos fueron atendidos en servicios de salud públicos, privados y de seguridad social. Se realizó análisis fenomenológico sobre las entrevistas trascritas en totalidad.Resultados Con independencia del tipo de atención sanitaria, las mujeres reciben poca capacitación para la lactancia durante la etapa prenatal y la mayor parte de esta ocurre de manera impersonal. La mayoría narra experiencias de exigencia y juzgamiento, más que de consejería, por parte del personal de salud.Conclusión La lactancia materna es contemplada como derivada de una decisión personal e individual, en la que no impacta la consejería del personal sanitario. Es necesario impulsar procesos de capacitación y sensibilización dirigidos a fortalecer las habilidades de acompañamiento para la Lactancia Materna en el personal de salud, con el fin de ejercer la función de consejería de manera asertiva.

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