Metagenomic insights into taxonomic diversity and metabolic potential of bacterial communities associated with tannery waste-contaminated soils

2021 ◽  
Author(s):  
T. Lukhele ◽  
H. J. O. Ogola ◽  
R. Selvarajan ◽  
R. O. Oruko ◽  
H. Nyoni ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Bacterial Communities ◽  
Taxonomic Diversity ◽  
Metabolic Potential ◽  
Tannery Waste

Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

2017 ◽  
Vol 63 (6) ◽  
pp. 502-515 ◽  
Author(s):  
Natalie P. Blain ◽  
Bobbi L. Helgason ◽  
James J. Germida
Keyword(s):  
Plant Species ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Growth Promotion ◽  
Plant Root ◽  
Gene Copy ◽  
Sampling Location ◽  
Historic Site ◽  
Copy Numbers

The Bitumount Provincial Historic site is the location of 2 of the world’s first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil)−1, plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarbon-contaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.

scholarly journals Prospects for The Use of Thermotolerant Microorganisms for Remediation of Oil-Contaminated Soils

2020 ◽  
Author(s):  
S.A. Aitkeldiyeva ◽  
E.R. Faizulina ◽  
L.G. Tatarkina ◽  
A.V. Alimbetova ◽  
O.N. Auezova ◽  
...  
Keyword(s):  
High Temperatures ◽  
Contaminated Soils ◽  
Soil Cover ◽  
Molecular Genetic ◽  
Taxonomic Diversity ◽  
Oil Fields ◽  
Vital Activity ◽  
Genetic Characteristics ◽  
Low Humidity ◽  
Oil And Oil Products

Most of the world's oil fields are concentrated in geographic areas with high temperature conditions. One of the main problems of remediation of territories in hot climates is the fact that high temperatures reduce the viscosity of oil and, thus, accelerate its diffusion into the soil. This greatly complicates the processes of soil cover restoration using conventional methods. An alternative can be bioremediation using the oil-oxidizing microorganisms that are resistant to high temperatures and low humidity. The presented review is devoted to the analysis of studies of thermotolerant microorganisms by scientists from different countries with the aim of using them in the remediation of contaminated soils from oil and oil products. The data on the influence of the main environmental factors, such as temperature, oxygen, pH, salinity, aeration, the presence of nutrients, etc., on the viability and vital activity of thermotolerant hydrocarbon-oxidizing microorganisms are presented. Examples of biochemical and molecular genetic characteristics of thermotolerant microorganisms are given. Their taxonomic diversity is shown, and examples of the degradation of individual oil components by active strains are given.

Интенсификация биоремедиации нефтезагрязненных почв с использованием природного консорциума микроорганизмов

2021 ◽  
pp. 582-589
Author(s):  
Kalamkas B. Oralbayeva ◽  
Aliya K. Yernazarova ◽  
Medet E. Kundybayev ◽  
Spandiar A. Seitkulov ◽  
Aida S. Kistaubayeva
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Climatic Conditions ◽  
Mineral Fertilizers ◽  
Pseudomonas Sp ◽  
Bacterial Strains ◽  
Biological Product ◽  
Metabolic Potential ◽  
Alcaligenes Denitrificans

Currently biological methods of cleaning oily soils significantly developed as the most accessible and effective. In their basis – the use of hydrocarbon-oxidizing microorganisms (HOM) metabolic potential. At the same time, as practice shows, existing preparations containing HOM are not effective enough in extreme soil-climatic conditions, in this connection the search for indigenous strains of oil-oxidizing bacteria and the development of new biological preparations are of current interest. The aim of this work is to study the effectiveness of HOM strains for restoring the biological activity of oil-contaminated soil. A study of the microflora of unpolluted and oil-contaminated soil taken from the experimental site of the “Shymkent” oil pumping station of “KazTransOil” JSC was carried out: the total number of microorganisms was 210·106cells/g and 130·106 cells/g, respectively. From 16 НOM strains isolated from oil-contaminated soil, 3 bacterial strains were selected to create an association and use as a biological product-oil destructor – P12, P16, A8. Based on the results of genotyping, strains P12 and P16 correspond to the species Pseudomonas aeruginosa, strain A8 belongs to the species Alcaligenes denitrificans. The associations of Pseudomonas sp. P16, Pseudomonas sp. P12 and Alcaligenes sp. A8 showed better growth in comparison with monocultures on a nutrient medium with hydrocarbons. Bioremediation of artificially oil polluted site process, which carried out for 120 days using a biological product created on the basis of the association of strains P12, P16 and A8, decreased the content of hydrocarbons 3.4 times, and with additional application of mineral fertilizers (ammophos) – 4.6 times. Thus, proved the expediency of using HOM strains P12, P16, A8 for the purpose of bioremediation of oil-contaminated soils. The results of the study can be used to improve economical and environmental efficiency of work when carrying out measures to eliminate the consequences of oil spills on the ground. Биологические методы очистки нефтесодержащих почв в настоящее время имеют существенное развитие как наиболее доступные и эффективные. В их основе – использование метаболического потенциала углеводородокисляющих микроорганизмов (УОМ). При этом, как показывает практика, существующие препараты, содержащие УОМ, недостаточно эффективны в экстремальных почвенно-климатических условиях, в связи с чем актуальными являются вопросы поиска аборигенных штаммов нефтеокисляющих бактерий и разработка новых биопрепаратов. Цель работы – исследование эффективности штаммов УОМ для восстановления биологической активности нефтезагрязненного почвогрунта. Проведено изучение микрофлоры незагрязненной и нефтезагрязненной почвы, отобранной с экспериментального участка ГНПС «Шымкент» АО «КазТрансОйл»: общее количество микроорганизмов составило 210·106 кл/г и 130·106кл/г, соответственно. Из выделенных из нефтезагрязненной почвы 16 штаммов УОМ были отобраны три штамма бактерий для создания ассоциации и применения в качестве биопрепарата-нефтедеструктора – Р12, Р16, А8. По итогам генотипирования установлено, что штаммы Р12 и Р16 соответствуют виду Pseudomonas aeruginosa, штамм А8 относится к виду Alcaligenes denitrificans. Установлено, что в составе ассоциаций штаммы Pseudomonas sp. P16, Pseudomonas sp. P12 и Alcaligenes sp. A8. показали лучший по сравнению с монокультурами рост на питательной среде с углеводородами. В процессе биоремедиации участка с искусственным нефтезагрязнением, проводимой в течение 120 суток с использованием биопрепарата, созданного на основе ассоциации штаммов P12, P16 и A8, содержание углеводородов снизилось в 3,4 раза, а при дополнительном внесении минеральных удобрений (аммофоса) – в 4,6 раза. Таким образом, доказана целесообразность использования штаммов УОМ Р12, Р16, А8 с целью биоремедиации нефтезагрязненных почв. Результаты исследования могут быть использованы для повышения экономической и экологической эффективности работ при проведении мероприятий по ликвидации последствий разливов нефти на почве.

Formation and Immobilization of Cr(VI) Species in Long-Term Tannery Waste Contaminated Soils

2020 ◽  
Vol 54 (12) ◽  
pp. 7226-7235 ◽  
Author(s):  
Jingjing Shi ◽  
William B. McGill ◽  
Ning Chen ◽  
P. Michael Rutherford ◽  
Todd W. Whitcombe ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Tannery Waste

scholarly journals Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms

2006 ◽  
Vol 72 (1) ◽  
pp. 628-637 ◽  
Author(s):  
Peter S. Kourtev ◽  
Cindy H. Nakatsu ◽  
Allan Konopka
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Community Change ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Organic C ◽  
Iron Reducing Bacteria ◽  
Chromium Vi ◽  
Reducing Bacteria

ABSTRACT Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO2) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO2 production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.

scholarly journals Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types

2021 ◽  
Vol 9 (8) ◽  
pp. 1673
Author(s):  
Andrea K. Borsodi ◽  
Márton Mucsi ◽  
Gergely Krett ◽  
Attila Szabó ◽  
Tamás Felföldi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Vegetation Types ◽  
Metabolic Potential ◽  
Sodic Soils ◽  
Sodic Soil ◽  
Strain Collection

In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.

scholarly journals Shifts in Bacterial Community Associated with Green Manure Soybean Intercropping and Edaphic Properties in a Tea Plantation

2021 ◽  
Vol 13 (20) ◽  
pp. 11478
Author(s):  
Fo-Ting Shen ◽  
Shih-Han Lin
Keyword(s):  
Organic Matter ◽  
Bacterial Communities ◽  
Green Manure ◽  
Biological Properties ◽  
Population Diversity ◽  
Plant Growth Promoting Bacteria ◽  
Plant Interactions ◽  
Metabolic Potential ◽  
Tea Plantation ◽  
Edaphic Properties

The continuous cultivation with excessive application of agrochemicals has led to the deterioration of soils. Incorporating leguminous green manure (GM) was found to improve the physicochemical and biological properties of soils. However, the influence of GM soybean intercropping on the temporal distribution of bacterial communities in strongly acidic soils is less explored. In this study, a nine-month field trial of soybean intercropping was conducted in a deteriorated tea plantation. This was used to test the hypothesis that GM treatment ameliorates tea-cultivated environments through changing bacterial communities as well as edaphic properties. GM treatment was demonstrated to increase both functional and population diversity during all the months that were considered. An alteration of life strategies exhibited by bacterial communities in GM treatment was observed, which shifted from oligotrophy (Acidobacteria, Chloroflexi, and the candidate phylum WPS-2) to copiotrophy (Bacteroidetes and Proteobacteria). This also contributed to the remarkable increase in metabolic potential of bacterial communities toward all six carbon source categories. The potentially versatile organic matter decomposers and/or plant growth-promoting bacteria, such as Burkholderiaceae, Chitinophagaceae, Sphingobacteriaceae, and Sphingomonadaceae bacteria, were identified as the most effective biomarkers in GM treatment. These bacterial groups showed strong correlation with soil pH; organic matter; and available K, Ca, and Mg. The increased diversity, metabolic potential, and copiotrophic taxa provided insight into the benefits brought by soybean intercropping, with enhanced community stability, facilitated nutrient cycling, and microbe–plant interactions in the strongly acidic tea plantation.

scholarly journals Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10302
Author(s):  
Li Song ◽  
Zhenzhi Pan ◽  
Yi Dai ◽  
Lin Chen ◽  
Li Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Cadmium Concentration ◽  
Normal Growth ◽  
Amplicon Sequencing ◽  
Negative Influence ◽  
Cadmium Pollution ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

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