Bioremediation of oil shale chemical industry solid wastes using phytoremedition and bioaugmentation

Although the production of oil shale energy and oil has decreased steadily during the last years with a corresponding decrease in wastes, the semi-coke mounds constitute one of the major adverse environmental challenges in Estonia The processed oil shale (semicoke) contains several organic and inorganic compounds (oil fractions, sulphides, phenolic compounds, polycyclic aromatic hydrocarbons). Laboratory and field experiments were carried out in order to test the effect of phytoremediation and bioaugmentation for remediation of pollutants in semi-coke. Four pilot test plots (50 m2 ) were established at semi-coke depository in July 2001. For bioaugmentation experiment the set of bacteria consisting of three biodegradative strains isolated from nearby area was selected. Several molecular microbiological methods were used to assess and compare the microbial community structure and diversity as well as the presence and diversity of biodegradative genes in collected samples. The dominant bacterial species based on 16S rDNA sequences in semi-coke samples were also identified. These analyses revealed that semi-coke microbial community is characterized by few dominant populations and possesses low diversity. The phytoremediation increased the number of bacteria and diversity of microbial community in semi-coke. Within a one and half year period starting from establishment of test plots, the concentration of phenolic compounds decreased up to 50% and oil products up to three times at plots with vegetation compared to control. Bioaugmentation experiment, performed in summer 2002 increased biodegradation intensity of oil products up to 50% compared to untreated planted controls. The plots, which were supplemented with laboratory-selected bacteria, were characterized by higher microbial activity and showed changes in microbial community structure. Our findings also indicate that plant growth; particularly rooting depth and belowground biomass could be enhanced by adding mixture of selected bacterial strains to semi-coke.

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Effects of tobacco–peanut relay intercropping on soil bacteria community structure

Annals of Microbiology ◽

10.1007/s13213-019-01537-9 ◽

2019 ◽

Vol 69 (13) ◽

pp. 1531-1536 ◽

Cited By ~ 1

Author(s):

Lin Gao ◽

Xin-min Liu ◽

Yong-mei Du ◽

Hao Zong ◽

Guo-ming Shen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Soil Bacteria ◽

Pathogenic Bacteria ◽

Bacterial Species ◽

Continuous Cropping ◽

Soil Microbial ◽

Relay Intercropping ◽

Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

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Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis

Scientific Reports ◽

10.1038/s41598-021-82709-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Qian Wang ◽

Xuelan Chen ◽

Huan Hu ◽

Xiaoyuan Wei ◽

Xiaofan Wang ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Structural Changes ◽

Dental Fluorosis ◽

Bacterial Species ◽

Fusobacterium Nucleatum ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Diseases

AbstractDental fluorosis is a very prevalent endemic disease. Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome. To this end, we investigated the changes in oral microbial community structure and identified bacterial species associated with moderate and severe dental fluorosis. Salivary samples of 42 individuals, assigned into Healthy (N = 9), Mild (N = 14) and Moderate/Severe (M&S, N = 19), were investigated using the V4 region of 16S rRNA gene. The oral microbial community structure based on Bray Curtis and Weighted Unifrac were significantly changed in the M&S group compared with both of Healthy and Mild. As the predominant phyla, Firmicutes and Bacteroidetes showed variation in the relative abundance among groups. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the M&S group. LEfSe analysis was used to identify differentially represented taxa at the species level. Several genera such as Streptococcus mitis, Gemella parahaemolysans, Lactococcus lactis, and Fusobacterium nucleatum, were significantly more abundant in patients with moderate/severe dental fluorosis, while Prevotella melaninogenica and Schaalia odontolytica were enriched in the Healthy group. In conclusion, our study indicates oral microbiome shift in patients with moderate/severe dental fluorosis. We identified several differentially represented bacterial species enriched in moderate and severe fluorosis. Findings from this study suggests that the roles of these bacteria in oral health and related diseases warrant more consideration in patients with moderate and severe fluorosis.

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Microbial biomass, enzyme activities and microbial community structure in two European long-term field experiments

Agriculture Ecosystems & Environment ◽

10.1016/j.agee.2005.01.017 ◽

2005 ◽

Vol 109 (1-2) ◽

pp. 141-152 ◽

Cited By ~ 194

Author(s):

Livia Böhme ◽

Uwe Langer ◽

Frank Böhme

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Biomass ◽

Microbial Community Structure ◽

Enzyme Activities ◽

Field Experiments ◽

Term Field

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Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events

Frontiers in Microbiology ◽

10.3389/fmicb.2021.632935 ◽

2021 ◽

Vol 12 ◽

Author(s):

Benjamin Zwirzitz ◽

Stefanie U. Wetzels ◽

Emmanuel D. Dixon ◽

Svenja Fleischmann ◽

Evelyne Selberherr ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Meat Products ◽

Pfge Type ◽

Rrna Gene ◽

Meat Processing ◽

Pfge Typing ◽

Microbiological Methods ◽

Meat Samples

A large part of foodborne outbreaks related to Listeria monocytogenes are linked to meat and meat products. Especially, recontamination of meat products and deli-meat during slicing, packaging, and repackaging is in the focus of food authorities. In that regard, L. monocytogenes persistence in multi-species biofilms is one major issue, since they survive elaborate cleaning and disinfection measures. Here, we analyzed the microbial community structure throughout a meat processing facility using a combination of high-throughput full-length 16S ribosomal RNA (rRNA) gene sequencing and traditional microbiological methods. Samples were taken at different stages during meat cutting as well as from multiple sites throughout the facility environment to capture the product and the environmental associated microbiota co-occurring with Listeria spp. and L. monocytogenes. The listeria testing revealed a widely disseminated contamination (50%; 88 of 176 samples were positive for Listeria spp. and 13.6%; 24 of 176 samples were positive for L. monocytogenes). The pulsed-field gel electrophoresis (PFGE) typing evidenced 14 heterogeneous L. monocytogenes profiles with PCR-serogroup 1/2a, 3a as most dominant. PFGE type MA3-17 contributed to the resilient microbiota of the facility environment and was related to environmental persistence. The core in-house microbiota consisted mainly of the genera Acinetobacter, Pseudomonas, Psychrobacter (Proteobacteria), Anaerobacillus, Bacillus (Firmicutes), and Chryseobacterium (Bacteroidota). While the overall microbial community structure clearly differed between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria spp. in both sample groups. Specifically, our longitudinal analysis revealed association of Listeria spp. with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the built environment microbiome in the meat processing context and promoted more effective options for targeted disinfection in the analyzed facility.

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Horizontal and Vertical Transfer of Oral Microbial Dysbiosis and Periodontal Disease

Journal of Dental Research ◽

10.1177/0022034519877150 ◽

2019 ◽

Vol 98 (13) ◽

pp. 1503-1510 ◽

Cited By ~ 7

Author(s):

M.A. Payne ◽

A. Hashim ◽

A. Alsam ◽

S. Joseph ◽

J. Aduse-Opoku ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Periodontal Disease ◽

Microbial Community Structure ◽

Bacterial Species ◽

Oral Microbiome ◽

Vertical Transfer ◽

Microbial Dysbiosis ◽

Disease Agent

One of the hallmark features of destructive periodontal disease, well documented over the last 50 y, is a change to the quantitative and qualitative composition of the associated microbiology. These alterations are now generally viewed as transformational shifts of the microbial populations associated with health leading to the emergence of bacterial species, which are only present in low abundance in health and a proportionate decrease in the abundance of others. The role of this dysbiosis of the health associated microbiota in the development of disease remains controversial: is this altered microbiology the driving agent of disease or merely a consequence of the altered environmental conditions that invariably accompany destructive disease? In this work, we aimed to address this controversy through controlled transmission experiments in the mouse in which a dysbiotic oral microbiome was transferred either horizontally or vertically into healthy recipient mice. The results of these murine studies demonstrate conclusively that natural transfer of the dysbiotic oral microbiome from a periodontally diseased individual into a healthy individual will lead to establishment of the dysbiotic community in the recipient and concomitant transmission of the disease phenotype. The inherent resilience of the dysbiotic microbial community structure in diseased animals was further demonstrated by analysis of the effects of antibiotic therapy on periodontally diseased mice. Although antibiotic treatment led to a reversal of dysbiosis of the oral microbiome, in terms of both microbial load and community structure, dysbiosis of the microbiome was reestablished following cessation of therapy. Collectively, these data suggest that an oral dysbiotic microbial community structure is stable to transfer and can act in a similar manner to a conventional transmissible infectious disease agent with concomitant effects on pathology. These findings have implications to our understanding of the role of microbial dysbiosis in the development and progression of human periodontal disease.

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Alkylphenols and Chlorophenols Remediation in Vertical Flow Constructed Wetlands: Removal Efficiency and Microbial Community Response

Water ◽

10.3390/w13050715 ◽

2021 ◽

Vol 13 (5) ◽

pp. 715

Author(s):

Inês P. F. M. Montenegro ◽

Ana P. Mucha ◽

Maria Paola Tomasino ◽

Carlos Rocha Gomes ◽

Cristina Marisa R. Almeida

Keyword(s):

Organic Matter ◽

Community Structure ◽

Microbial Community ◽

Phenolic Compounds ◽

Removal Efficiency ◽

Constructed Wetlands ◽

Microbial Community Structure ◽

Community Response ◽

Urban Stream ◽

Vertical Flow

This study aims to investigate the effect of two different groups of phenolic compounds (the alkylphenols nonylphenol (NP) and octylphenol (OP), and the chlorophenol pentachlorophenol (PCP)) on constructed wetlands (CWs) performance, including on organic matter, nutrients and contaminants removal efficiency, and on microbial community structure in the plant bed substrate. CWs were assembled at lab scale simulating a vertical flow configuration and irrigated along eight weeks with Ribeira de Joane (an urban stream) water not doped (control) or doped with a mixture of NP and OP or with PCP (at a 100 μg·L−1 concentration each). The presence of the phenolic contaminants did not interfere in the removal of organic matter or nutrients in CWs in the long term. Removals of NP and OP were >99%, whereas PCP removals varied between 87% and 98%, mainly due to biodegradation. Microbial richness, diversity and dominance in CWs substrate were generally not affected by phenolic compounds, with only PCP decreasing diversity. Microbial community structure, however, showed that there was an adaptation of the microbial community to the presence of each contaminant, with several specialist genera being enriched following exposure. The three more abundant specialist genera were Methylotenera and Methylophilus (methylophilaceae family) and Hyphomicrobium (hyphomicrobiaceae family) when the systems were exposed to a mixture of NP and OP. When exposed to PCP, the three more abundant genera were Denitromonas (Rhodocyclaceae family), Xenococcus_PCC_7305 (Xenococcaceae family) and Rhodocyclaceae_uncultured (Rhodocyclaceae family). To increase CWs efficiency in the elimination of phenolic compounds, namely PCP which was not totally removed, strategies to stimulate (namely biostimulation) or increase (namely bioaugmentation) the presence of these bacteria should be explore. This study clearly shows the potential of vertical flow CWs for the removal of phenolic compounds, a still little explored subject, contributing to promote the use of CWs as nature-based solutions to remediate water contaminated with different families of persistent and/or emergent contaminants.

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