scholarly journals Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

2019 ◽  
Vol 7 (10) ◽  
pp. 416 ◽  
Author(s):  
Dyda ◽  
Pyzik ◽  
Wilkojc ◽  
Kwiatkowska-Kopka ◽  
Sklodowska
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Extreme Environment ◽  
Microbial Colonization ◽  
Marker Genes ◽  
Lime Mortar ◽  
Preventive Actions ◽  
Important Challenge ◽  
Cultural Heritage Objects

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e. g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

scholarly journals Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes

2016 ◽  
Vol 92 (2) ◽  
pp. fiw004 ◽  
Author(s):  
Sebastian Liebe ◽  
Daniel Wibberg ◽  
Anika Winkler ◽  
Alfred Pühler ◽  
Andreas Schlüter ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Marker Genes ◽  
Sugar Beets ◽  
Taxonomic Analysis

scholarly journals Analysis of Microbial Diversity and Variation Law During Xiaoqu Baijiu Fermentation using High-throughput Sequencing Technology

2021 ◽  
Author(s):  
Qing Wang ◽  
Xiaoqing Xiang ◽  
PengFei Wu ◽  
Guoqiang Han
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Sequencing Technology ◽  
Theoretical Support ◽  
Brewing Process ◽  
Dominant Bacteria ◽  
Brewing Time

Abstract In this study, high-throughput sequencing (HTS) was used to compare and analyze the microbial diversity and variation law during the brewing process of xiaoqu Baijiu. The results showed that 34 phyla, 378 genera of bacteria and 4 phyla, 32 genera of fungi were detected. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Ascomycota and Bacteroidetes were the dominant groups. During the brewing process of xiaoqu Baijiu, the dominant bacteria were Weissella and unidentified Rickettsiales 2 days before brewing and Lactobacillus 3 days after brewing until the end of brewing. The dominant fungi were Rhizopus, Saccharomyces and Issatchenkia. The relative abundance of Rhizopus decreased with the extension of brewing time, while the relative abundance of Saccharomyces increased and became the dominant bacteria after the second day of brewing. This study revealed the diversity and variation of microbial community in the brewing process of xiaoqu Baijiu, and provide theoretical support and lay the foundation for future study on the contribution of microbial metabolism during brewing of xiaoqu Baijiu, thereby promote the development of xiaoqu baijiu industry.

scholarly journals Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Danyang Zheng ◽  
Yujiao Sun ◽  
Huijuan Li ◽  
Sidan Lu ◽  
Mingjun Shan ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Activated Sludge ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Public Health Issue ◽  
Activated Sludge Process ◽  
Degrading Bacteria

In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

scholarly journals Sugarcane-Legume Intercropping Can Enrich the Soil Microbiome and Plant Growth

2021 ◽  
Vol 5 ◽  
Author(s):  
Mukesh Kumar Malviya ◽  
Manoj Kumar Solanki ◽  
Chang-Ning Li ◽  
Zhen Wang ◽  
Yuan Zeng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Soil Microbes ◽  
Negative Impact ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Sugarcane Plant

Soil microbes have a direct impact on plant metabolism and health. The current study investigates the comparative rhizobiome between sugarcane monoculture and sugarcane–soybean intercropping. A greenhouse experiment was performed with two treatments: (1) sugarcane monoculture and (2) sugarcane–soybean intercropped. We used a high-throughput sequencing (HTS) platform to analyze the microbial community. We used the 16S rRNA gene and internal transcribed spacer region primers to identify the microbial diversity. HTS results revealed that a total of 2,979 and 124 bacterial and fungal operational taxonomic units (OTUs) were observed, respectively. Microbial diversity results concluded that the intercropping system has a beneficial impact on soil microbes. The highest numbers of bacterial and fungal OTUs were found in the intercropping system, and these results also collaborated with quantitative PCR results. Additionally, intercropped sugarcane plants showed a higher weight of above- and below-ground parts than the monoculture. Soil chemical analysis results also complemented that the intercropping system nourished organic carbon, total nitrogen, and soil enzyme activities. Correlation analysis of the diversity index and abundance concluded that soil nutrient content positively influenced the microbial abundance that improves plant growth. The present study frames out the profound insights of microbial community interaction under the sugarcane–soybean intercropping system. This information could help improve or increase the sugarcane crop production without causing any negative impact on sugarcane plant growth and development.

scholarly journals Coastal Hypoxia Drives Microbial Diversity: Elucidation through 16S rRNA Amplicon Sequencing

2021 ◽  
Author(s):  
Vruti V Naik ◽  
Samir R Damare ◽  
Shruti S Shah ◽  
Damodar M Shenoy ◽  
Amara Begum Mulla
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Nitrogen Loss ◽  
Amplicon Sequencing ◽  
Southwest Monsoon ◽  
16S Rrna Amplicon Sequencing ◽  
Community Shift ◽  
Different Seasons ◽  
Nitrate And Nitrite

Abstract The formation of oxygen-depleted zones in the bottom waters is one of the most widespread phenomena in coastal areas. Upwelling episodes occurring along the west coast of India due to the southwest monsoon lead to an increase in biological productivity which further lowers the dissolved oxygen in the upwelled waters, which intensifies annually between June and October. Here, we have determined the changes in the microbial community in response to the varying oxygen levels and other physicochemical parameters at the Candolim Time Series Station using high-throughput sequencing. Amplicon Sequence Variants across all the samples collected in different seasons were mostly affiliated to the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Firmicutes and Planctomycetes, with the most dominant being Proteobacteria (21-41%). Statistical analysis revealed that microbial diversity differed significantly with changing DO, ammonia, nitrate and nitrite concentrations during different seasons. The microbial community shift due to seasonal hypoxia results in the differential biogeochemical cycling of essential nutrients with certain years seeing redox conditions up to sulphate reduction, while certain years seeing only nitrogen loss. Future scenario of global warming will serve as a big challenge for understanding the role of microbial diversity and its implications in the cycling of natural elements.

scholarly journals The Rhizosphere Microbial Community of Tobacco and Its Relationship With The Properties of Leaves and Rhizosphere Soils

2021 ◽  
Author(s):  
Yingying Jiang ◽  
Xiaomin Wei ◽  
Xiaofen Yu ◽  
Xin Liu ◽  
Xiaodong Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Physicochemical Characteristics ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tobacco Leaf ◽  
Leaf Properties ◽  
Soil Physicochemical Characteristics ◽  
Rhizosphere Microbial Community

Abstract BackgroundRhizosphere microbes possess important effects on plant growth and quality. Here we collected tobacco roots and leaf samples from ten places in Yunnan province to investigate the interaction of the rhizosphere microbes, the soil physicochemical characteristics, and the tobacco leaf properties. ResultsA high-throughput sequencing method was used to sequence the V3–V4 region of 16S rRNA genes, and the operational taxonomic units (OTUs) were clustered using QIIME under 97% identity. A total of 4571 OTUs were obtained from the 30 tobacco root samples, and the top three phyla were Proteobacteria, Acidobacteria, and Actinobacteria, while the top three annotated genera were Gp6, Gemmatimonas, and Gp4. Redundancy analysis (RDA) showed that most of the soil physicochemical properties (10 out of 17) had a significant influence on the rhizosphere microbial community. Both correlation analysis and RDA analysis revealed that quick potassium (K) and Acidobacteria_Gp3 had a significant correlation with the tobacco leaf properties. The variance partitioning analysis showed that rhizosphere microbes had a bigger influence on the tobacco leaf properties. ConclusionsOur results showed great differences in the rhizosphere microbial diversity of tobacco and complex interaction among the microbial diversity, soil physicochemical characteristics, and tobacco leaf properties.

scholarly journals An Active Gelatin Coating Containing Eugenol and Vacuum Delays the Decay of Chinese Seabass (Lateolabrax maculatus) Fillets during Cold Storage: A Microbiome Perspective

Coatings ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 147
Author(s):  
Xuan Ma ◽  
Qianqian Zhou ◽  
Weiqiang Qiu ◽  
Jun Mei ◽  
Jing Xie
Keyword(s):  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Vacuum Treatment ◽  
C Storage ◽  
Basic Nitrogen ◽  
Spoilage Bacteria ◽  
Lateolabrax Maculatus ◽  
Gelatin Coating ◽  
Microbial Enumeration ◽  
Growth And Reproduction

The purpose of this study was to evaluate the effect of an active gelatin coating containing eugenol and vacuum on the microbial diversity of Chinese seabass (Lateolabrax maculatus) during cold (−0.9 °C) storage. The bacterial sequences in Chinese seabass were observed using a high-throughput sequencing technique targeting the V3–V4 region of the 16S Ribosomal DNA (rDNA) on 0, 12th, and 24th day, which showed a more comprehensive estimate of the microbial diversity in seabass samples compared with microbial enumeration. The results revealed that the species diversity of fresh seabass was rich, mainly including Carnobacterium, Glutamicibacter, and Pseudomonas, with abundance ratios of 0.286, 0.160, and 0.130, respectively. Pseudomonas and Shewanella were the primary contaminants in the spoiled control samples, where the abundance ratios increased from 0.220 and 0.174 on the 12th day to 0.802 and 0.163 on the 24th day, respectively. Vacuum treatment could inhibit the growth of Pseudomonas and Shewanella such that when stored on the 12th day, Brochothrix became the superior genus. However, Pseudomonas and Shewanella dominated the storage until the 24th day, where their abundance ratios were 0.343 and 0.279, respectively. The inhibition of Pseudomonas and Carnobacterium was gradually enhanced with increasing concentrations of eugenol. Furthermore, an active gelatin coating containing eugenol and vacuum treatment was more effective at inhibiting the increase of the total volatile basic nitrogen. This study confirmed that an active gelatin coating containing eugenol and vacuum could reduce the species of bacteria, inhibit the growth and reproduction of the main dominant spoilage bacteria, and delay the spoilage of seabass.

scholarly journals Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Ecosystem Functions ◽  
Microbial Composition ◽  
Wetland Ecosystems ◽  
Soil Microbial ◽  
Geochemical Properties ◽  
Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

scholarly journals Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

2016 ◽  
Vol 82 (15) ◽  
pp. 4757-4766 ◽  
Author(s):  
Caterina R. Giner ◽  
Irene Forn ◽  
Sarah Romac ◽  
Ramiro Logares ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
Ribosomal Dna ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
454 Sequencing ◽  
Epifluorescence Microscopy ◽  
Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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