Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

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Bacterial community evolution along full-scale municipal wastewater treatment processes

Journal of Water and Health ◽

10.2166/wh.2020.092 ◽

2020 ◽

Vol 18 (5) ◽

pp. 665-680

Author(s):

Lei Zhang ◽

Yanan Cheng ◽

Chang Qian ◽

Wenxuan Lu

Keyword(s):

Wastewater Treatment ◽

Bacterial Community ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Municipal Wastewater ◽

Wastewater Treatment Plants ◽

Oxygen Demand ◽

Illumina Miseq ◽

Municipal Wastewater Treatment ◽

Bacterial Assemblage

Abstract Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.

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Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture

BioMed Research International ◽

10.1155/2019/4943150 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Xiaoning Gao ◽

Zilin Wu ◽

Rui Liu ◽

Jiayun Wu ◽

Qiaoying Zeng ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Illumina Miseq ◽

Miseq Sequencing ◽

Community Characteristics ◽

Dynamic Changes ◽

Operational Taxonomic Units ◽

Total Bacterial Community ◽

Rhizosphere Bacterial Community ◽

Rhizosphere Bacterial Communities

To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.

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Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China

Transactions of Tianjin University ◽

10.1007/s12209-019-00226-7 ◽

2019 ◽

Vol 26 (1) ◽

pp. 22-32 ◽

Cited By ~ 2

Author(s):

Xueke Feng ◽

Zhen Liu ◽

Xiaoqiang Jia ◽

Wenyu Lu

Keyword(s):

Bacterial Community ◽

Contaminated Soil ◽

Contaminated Soils ◽

Bacterial Communities ◽

Petroleum Hydrocarbon ◽

High Throughput Sequencing ◽

Environmental Parameters ◽

Significant Difference ◽

Petroleum Contaminated Soil ◽

Different Depths

AbstractDiversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient (0–0.4043 g/g) in surface (5–10 cm) and subsurface (35–40 cm) petroleum-contaminated soil samples from the Dagang Oilfield, China. Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods, the bacterial diversity of the soil was studied. Subsequently, the environmental parameters were measured to analyze its relationship with the community variation. Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils, but no differences were observed in different depths of petroleum-contaminated soil. Meanwhile, many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties. Total petroleum hydrocarbon, total organic carbon, and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils. Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.

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Evaluation of bacterial diversity during fermentation process: a comparison between handmade and machine-made high-temperature Daqu of Maotai-flavor liquor

Annals of Microbiology ◽

10.1186/s13213-020-01598-1 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Qiancheng Zuo ◽

Yongguang Huang ◽

MinGuo

Keyword(s):

High Temperature ◽

Bacterial Diversity ◽

Relative Abundance ◽

Fermentation Process ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Functional Bacteria ◽

Significant Difference ◽

Fermentation Technology ◽

Molding Methods

Abstract Purpose High-temperature Daqu is a traditional fermentation starter that is used for Chinese Maotai-flavor Baijiu production. Although the bacteria in high-temperature Daqu are known to be responsible for developing the quality and flavor of Baijiu during the fermentation process, there is little information on the properties of the bacteria during the fermentation of high-temperature Daqu, especially machine-made high-temperature Daqu. This has limited the development of the Maotai-flavor Baijiu industry, particularly with regard to the mechanized production of Maotai-flavor Baijiu. Methods Illumina MiSeq high-throughput sequencing was applied to study bacterial compositions during the fermentation of handmade and machine-made high temperatures. Results The results show that bacterial diversity in machine-made Daqu was similar but higher than that in handmade Daqu at the end of fermentation, and there was no significant difference between the methods with regard to the dominant genera and their dynamic changes during fermentation. Rhizobium, Bacillus, Thermoactinomyces, Weissella, Lactobacillus, and Saccharopolyspora were the dominant genera during the fermentation of both Daqus, although the relative abundance of these dominant genera differed between the two methods. Interestingly, the machine-made Daqu contained a higher relative abundance of Bacillus than handmade Daqu at all fermentation times. Bacillus is the most important functional bacteria in the fermentation of Maotai-flavor Baijiu, suggesting that mechanical-molding methods could be applied to industrial Maotai-flavor Daqu production. Conclusion These results suggest that mechanical-molding methods could be applied to industrial Maotai-flavor Daqu production, which could be helpful for industrial Maotai-flavor Baijiu production and the development of fermentation technology.

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Analysis of the effects of nanosilver on bacterial community in the intestinal fluid of silkworms using high-throughput sequencing

Bulletin of Entomological Research ◽

10.1017/s0007485319000634 ◽

2019 ◽

Vol 110 (3) ◽

pp. 309-320

Author(s):

Chen Lin ◽

Zhou Wei ◽

Zhou Yi ◽

Tan Tingting ◽

Du Huamao ◽

...

Keyword(s):

Bacterial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Intestinal Bacteria ◽

Illumina Miseq ◽

The Body ◽

Dependent Manner ◽

Negative Effects ◽

Silkworm Larvae ◽

Intestinal Bacterial Community

AbstractNanosilver is an environment-friendly, harmless alternative of traditional disinfectants which can be potentially applied in the sericulture industry. However, the effects of nanosilver on the intestinal bacterial community of the silkworms (Bombyx mori L.) are unclear. In this study, Illumina MiSeq high-throughput sequencing technology was used to assess the intestinal bacterial community in both male and female silkworms while treated with different concentrations of nanosilver. We found that nanosilver significantly influenced the composition of silkworm intestinal bacterial community on the different taxonomic levels. Most conspicuously, the abundance of Firmicutes was increased by the treatment of 20 mg L−1 nanosilver but decreased by that of 100 mg L−1 nanosilver at the phylum level. The same trend was observed in Bacilli at the class level and in Enterococcus at the genus level. In some extreme cases, application of nanosilver eliminated the bacterium, e.g., Brevibacillus, but increased the population of several other bacteria in the host intestine, such as Blautia, Terrisporobacter, Faecalibacterium, and some bacteria could only be found in nanosilver treatment groups, e.g., Dialister. In addition, although nanosilver generally showed negative effects on the cocooning rate in a dose-dependent manner, we found that 20 mg L−1 nanosilver treatment significantly increased the body weight of silkworms and did not show negative effects on the survival rate. These results indicated that the intestinal bacteria community of silkworm larvae was significantly changed after nanosilver treatment which might consequently influence host growth and development.

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Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

Biomolecules ◽

10.3390/biom9050187 ◽

2019 ◽

Vol 9 (5) ◽

pp. 187 ◽

Cited By ~ 1

Author(s):

Gaozhong Pu ◽

Yanna Lv ◽

Lina Dong ◽

Longwu Zhou ◽

Kechao Huang ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Soil Microorganisms ◽

Operational Taxonomic Unit ◽

Soil Characteristics ◽

Soil Samples ◽

Controlling Factors ◽

Bacterial Composition ◽

Microbial Distribution ◽

Significant Difference

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

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The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

Gut ◽

10.1136/gutjnl-2016-312904 ◽

2016 ◽

Vol 67 (2) ◽

pp. 216-225 ◽

Cited By ~ 48

Author(s):

Christian Schulz ◽

Kerstin Schütte ◽

Nadine Koch ◽

Ramiro Vilchez-Vargas ◽

Melissa L Wos-Oxley ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Illumina Miseq ◽

Gi Tract ◽

Upper Gi ◽

Miseq Platform ◽

H Pylori ◽

Bacterial Assemblages ◽

First Time ◽

Upper Gi Tract

ObjectivePatients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.DesignSaliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1–V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.ResultsOverall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.ConclusionsThe detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.

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Local domestication of microbes via cassava beer fermentation

10.7287/peerj.preprints.233 ◽

2014 ◽

Author(s):

Alese Colehour ◽

James F Meadow ◽

Tara J Cepon-Robins ◽

Theresa E Gildner ◽

Melissa A Liebert ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Manihot Esculenta ◽

Nutritional Quality ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Ribosomal Gene ◽

Ecuadorian Amazon ◽

Traditional Fermentation

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) improves nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes beneficial to human health, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples, demonstrating that chicha is a source of organisms related to known probiotics. Significantly greater taxonomic similarity was observed between communities in chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human preference, may be responsible for creating locally adapted and regionally resilient ferments. Our results suggest that traditional fermentation may be a form of domestication that provides endemic beneficial inocula for consumers.

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Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649981 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wen Tian ◽

Xing Xiang ◽

Hongmei Wang

Keyword(s):

Amino Acids ◽

Bacterial Community ◽

Pore Water ◽

Water Table ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Acid Methyl Ester ◽

Central China ◽

Utilization Rate ◽

Carbon Utilization

The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (August and November in 2017 and May 2018) with a gradient of water table changes and temperatures at the Dajiuhu peatland, Central China. The samples were analyzed with 16S rRNA high-throughput sequencing and Biolog EcoMicroplates. Bacterial communities varied in the relative abundances of dominant taxa and harbored exclusive indicator operational taxonomic units across the different months. Despite these differences, bacterial communities showed high similarities in carbon utilization, with preferences for esters (pyruvic acid methyl ester, Tween 40, Tween 80, and D-galactonic acid γ-lactone), amino acids (L-arginine and L-threonine), and amines (phenylethylamine and putrescine). However, rates of carbon utilization (as indicated by average well-color development) and metabolic diversity (McIntosh and Shannon index) in May and August were higher than those in November. Redundancy analysis revealed that the seasonal variations in bacterial communities were significantly impacted by the level of the water table, whereas the temperature had a fundamental role in bacterial carbon utilization rate. Co-occurrence analysis identified Sphingomonas, Mucilaginibacter, Novosphingobium, Lacunisphaera, Herminiimonas, and Bradyrhizobium as keystone species, which may involve in the utilization of organic compounds such as amino acids, phenols, and others. Our findings suggest that bacterial community functions were more stable than their compositions in the context of water table changes. These findings significantly expand our current understanding of the variations of bacterial community structures and metabolic functions in peatland ecosystems in the context of global warming and fluctuation of the water table.

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