scholarly journals Characteristics of planktonic and sediment bacterial communities in a heavily polluted urban river

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10866
Author(s):  
Heqing Huang ◽  
Jianhui Liu ◽  
Fanghui Zhang ◽  
Kangwen Zhu ◽  
Chunhua Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Urban River ◽  
Urban Rivers ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Sediment Bacterial Communities ◽  
Water And Sediment Samples

Urban rivers represent a unique ecosystem in which pollution occurs regularly, altering the biogeochemical characteristics of waterbodies and sediments. However, little is presently known about the spatiotemporal patterns of planktonic and sediment bacterial community diversities and compositions in urban rivers. Herein, Illumina MiSeq high-throughput sequencing was performed to reveal the spatiotemporal dynamics of bacterial populations in Liangtan River, a heavily polluted urban river in Chongqing City (China). The results showed the richness and diversity of sediment bacteria were significantly higher than those of planktonic bacteria, whereas a strong overlap (46.7%) in OTUs was identified between water and sediment samples. Bacterial community composition remarkably differed in waters and sediments. Planktonic bacterial communities were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria and Actinobacteria, while sediment bacterial communities mainly included Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Additionally, several taxonomic groups of potential bacterial pathogens showed an increasing trend in water and sediment samples from residential and industrial areas (RI). Variation partition analysis (VPA) indicated that temperature and nutrient were identified as the main drivers determining the planktonic and sediment bacterial assemblages. These results highlight that bacterial communities in the polluted urban river exhibit spatiotemporal variation due to the combined influence of environmental factors associated with sewage discharge and hydropower dams.

scholarly journals Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds

2020 ◽  
Vol 8 (2) ◽  
pp. 311
Author(s):  
Xin Tai ◽  
Rui Li ◽  
Bao Zhang ◽  
Hao Yu ◽  
Xiao Kong ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sediment Samples ◽  
Pollution Levels ◽  
Water And Sediment

Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.

scholarly journals Local domestication of microbes via cassava beer fermentation

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.

scholarly journals Local domestication of microbes via cassava beer fermentation

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.

scholarly journals Dynamics of the Fermentation Products, Residual Non-structural Carbohydrates, and Bacterial Communities of Wilted and Non-wilted Alfalfa Silage With and Without Lactobacillus plantarum Inoculation

2022 ◽  
Vol 12 ◽  
Author(s):  
Fengyuan Yang ◽  
Yanping Wang ◽  
Shanshan Zhao ◽  
Changsong Feng ◽  
Xiaomiao Fan
Keyword(s):  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Water Soluble ◽  
Soluble Carbohydrates ◽  
Fermentation Products ◽  
Fermentation Quality ◽  
Alfalfa Silage

The aim of this study was to investigate effects of wilting and Lactobacillus plantarum inoculation on the dynamics of the fermentation products, residual non-structural carbohydrates, and bacterial communities in alfalfa silage. Fresh and wilted alfalfa were ensiled with and without L. plantarum for 10, 30, 60, and 90 days. A high-throughput sequencing method for absolute quantification of 16S rRNA was adopted to determine the bacterial community composition at different ensiling periods. For the wilted silage, the bacterial community, pH value, and ammonia nitrogen concentration remained stable in the silage at 30 days. L. plantarum inoculation accelerated lactic acid fermentation and altered the predominant genus in the wilted silage as compared with the non-inoculated group. For the non-wilted group, fast consumption of water-soluble carbohydrates (WSCs) was observed at 10 days in the non-inoculated silage along with rapid growth of undesirable Hafnia. L. plantarum inoculation inhibited growth of Hafnia at 10 days in the non-wilted silage. Clostridia fermentation occurred in the non-wilted silage at 90 days, as indicated by an increased pH, formation of butyric acid (BA), and apparent abundance of genera belonging to Clostridia. L. plantarum inoculation inhibited BA accumulation and growth of Garciella in the non-wilted silage at 90 days as compared with the non-wilted silage without inoculation, but had little effect on the growth of Clostridium sensu stricto. Overall, the high moisture content of the non-wilted alfalfa silage led to rapid consumption of WSCs and growth of harmful microorganisms at the early stage of ensiling, resulting in poor fermentation quality. Wilting and L. plantarum inoculation both improved fermentation quality and inhibited the growth of spoilage microorganisms in alfalfa silage, while L. plantarum inoculation alone failed to achieve optimum fermentation quality of non-wilted alfalfa silage.

scholarly journals Spatial Variations of the Bacterial Diversity in an Alkaline Lake

2021 ◽  
Vol 4 ◽  
Author(s):  
E. Gozde Ozbayram ◽  
Latife Koker ◽  
Reyhan Akçaalan ◽  
Fatih Aydın ◽  
Meriç Albay
Keyword(s):  
Surface Water ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Water Samples ◽  
Bacterial Communities ◽  
Sediment Samples ◽  
Diversity Patterns ◽  
Water And Sediment ◽  
Alkaline Lake ◽  
Community Profile

Lake Iznik is one of the largest lake of Turkey covering 308 km2 surface area with 65 m max. depth. The lake has alkaline characteristics (Akcaalan et al. 2014). It is a mesotrophic lake that becomes stratified between June-September and well mixed between October-April. Although there are almost 200 lakes in Turkey, there is very little published research focused on the bacterial diversity structures (Ozbayram et al. 2020.) The specific objective of this study was to evaluate the bacterial community profile in the surface water and sediment of the alkaline lake during the winter turnover. For this purpose, the samples were collected from 6 stations (5 on the shore and 1 in the middle of the lake) in February 2020 when the lake was completely mixed. In addition to the surface water and sediment samples, a sample was also collected from the depth of 40 m from the station located in the mid-lake. The water samples were filtered from a 0.22 µm filter and the sediment samples were taken into sterile plastic containers. The total DNAs were extracted using the NucleoSpin® Soil Kit (Macherey-Nagel, Germany) following the manufacturer’s instructions. Bacterial community profiles of the samples were analyzed by 16S rRNA gene-targeted sequencing using Illumina® MiSeq™. Physicochemical parameters were measured as explained by Ozbayram et al. 2020. The pH was between 8.29-8.67 and the Electrical Conductivity (EC) was in the range of 734-996 µS/cm (Suppl. material 1 -Table S1). Whereas the Dissolved Oxygen (DO) levels were measured as 10.12-11.65 mg/L in the surface waters, it was 9.72 mg/L in the 40 m. Among all samples, the highest value of the Shannon and Pielou's evenness indices were calculated for the surface water sample collected from station 2 indicated a more evenly distributed and diverse bacterial community (Suppl. material 1-Table S2). Bacterial diversity patterns of the samples were presented at the phylum level in Figure 1. In compliance with the literature on freshwaters (Zhang et al. 2014), the community was dominated by Proteobacteria species, and higher abundances were determined in the sediment samples (ranged 40.4-50.0 %). Especially, Gammaproteobacteria, Deltaproteobacteria were the major classes of this phylum in the sediment. On the other hand, the composition of bacterial communities in water samples showed a difference in which Actinobacteria and Bacteroidetes (in particular, the order: Flavobacteriales) were also predominated the communities. However, the community profile slightly differed with depth (station 6). At the genus level, most of the reads were not assigned any genera. Ilumatobacter, Fluviicola, and Flavobacterium were represented 3.4-7.1% of the bacterial community of water samples. Fig. 1 Overall, due to the complete mixing conditions in the lake, there was a homogenization of the bacterial communities and the diversity patterns were quite similar in the water samples. In further studies, samples will be collected during the stratification and the community structures will be compared.

scholarly journals Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Meltwater Runoff ◽  
Glacial Runoff ◽  
Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

scholarly journals Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

2018 ◽  
Vol 84 (12) ◽  
pp. e02797-17 ◽  
Author(s):  
Dandi Hou ◽  
Zhi Lin ◽  
Runze Wang ◽  
Jun Ge ◽  
Shuai Wei ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sedum Alfredii ◽  
Cd Stress ◽  
Metal Hyperaccumulation ◽  
Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

scholarly journals Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

2019 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Bacterial Community Composition ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress influences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: OJ was more shade-tolerant than LP. Shifts in rhizosphere soil bacterial community structure play a vital role in shade-tolerance of OJ plants.

scholarly journals Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc

2020 ◽  
Vol 8 (5) ◽  
pp. 642 ◽  
Author(s):  
María Gómez-Brandón ◽  
Manuel Aira ◽  
Natielo Santana ◽  
Marcos Pérez-Losada ◽  
Jorge Domínguez
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Bacterial Community Composition ◽  
Active Phase ◽  
Acid Synthesis ◽  
Pilot Scale ◽  
Functional Changes ◽  
Grape Marc

Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants.

scholarly journals Composition and Functional Characteristics and Influencing Factors of Bacterioplankton Community in the Huangshui River, China

2021 ◽  
Vol 9 (11) ◽  
pp. 2260
Author(s):  
Qianqian Zhang ◽  
Zhenbing Wu ◽  
Juan Zhao ◽  
Guojie Wang ◽  
Jingwen Hao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Loess Plateau ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
The Arctic ◽  
Valuable Insight ◽  
Potential Health ◽  
Bacterioplankton Community ◽  
Principal Coordinates

Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.

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