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.

scholarly journals 16S rRNA Amplicon Sequencing of Sediment Bacterial Communities in an Oyster Farm in Rhode Island

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Joshua T. E. Stevens ◽  
Robinson W. Fulweiler ◽  
Priyanka Roy Chowdhury
Keyword(s):  
16S Rrna ◽  
Rhode Island ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Oyster Farm ◽  
Rrna Gene Sequencing ◽  
The Impact

Little is known about the impact of oyster farming on sediment microbial communities. Here, we use 16S rRNA gene sequencing to identify bacterial communities in 24 sediment samples collected from an oyster farm in Ninigret Pond, RI. A total of 13,147 unique operational taxonomic units (OTUs) were assigned, with Proteobacteria being the dominant phyla across all samples.

scholarly journals From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

2020 ◽  
Author(s):  
Pedro E. Romero ◽  
Erika Calla-Quispe ◽  
Camila Castillo-Vilcahuaman ◽  
Mateo Yokoo ◽  
Hammerly Lino Fuentes-Rivera ◽  
...  
Keyword(s):  
Metropolitan Area ◽  
Bacterial Communities ◽  
Geographical Location ◽  
Microbiological Quality ◽  
Amplicon Sequencing ◽  
Urban Sewage ◽  
16S Rrna Amplicon Sequencing ◽  
The Andes ◽  
Metabolic Functions ◽  
Quality Assessments

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

scholarly journals Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

2020 ◽  
Author(s):  
Saeed Keshani Langroodi ◽  
Yemin Lan ◽  
Ben Stenuit ◽  
Gail Rosen ◽  
Joseph B Hughes ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Military Conflict ◽  
Nitro Explosives ◽  
And Function ◽  
Aerobic And Anaerobic

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented.

scholarly journals Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

Foods ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1247
Author(s):  
Emiel Van Reckem ◽  
Christina Charmpi ◽  
David Van der Veken ◽  
Wim Borremans ◽  
Luc De Vuyst ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Bacterial Communities ◽  
Geographical Origin ◽  
Salt Content ◽  
Amplicon Sequencing ◽  
Taxonomic Resolution ◽  
Future Application ◽  
Processing Conditions ◽  
The Impact

Insight into the microbial species diversity of fermented meats is not only paramount to gain control over quality development, but also to better understand the link with processing technology and geographical origin. To study the composition of the microbial communities, the use of culture-independent methods is increasingly popular but often still suffers from drawbacks, such as a limited taxonomic resolution. This study aimed to apply a previously developed high-throughput amplicon sequencing (HTS) method targeting the 16S rRNA and tuf genes to characterize the bacterial communities in European fermented meats in greater detail. The data obtained broadened the view on the microbial communities that were associated with the various products examined, revealing the presence of previously underreported subdominant species. Moreover, the composition of these communities could be linked to the specificities of individual products, in particular pH, salt content, and geographical origin. In contrast, no clear links were found between the volatile organic compound profiles of the different products and the country of origin, distinct processing conditions, or microbial communities. Future application of the HTS method offers the potential to further unravel complex microbial communities in fermented meats, as well as to assess the impact of different processing conditions on microbial consortia.

Bacterial communities of the rhizosphere and endorhiza associated with field-grown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative

1997 ◽  
Vol 43 (4) ◽  
pp. 344-353 ◽  
Author(s):  
W. F. Mahaffee ◽  
J. W. Kloepper
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Genetically Modified ◽  
Acid Methyl Ester ◽  
Wild Type ◽  
Natural Ecosystems ◽  
Genus Level ◽  
Plant Growth Promoting ◽  
The Impact

The future use of genetically modified microorganisms in the environment will be dependent on the ability to assess potential or theoretical risks associated with their introduction into natural ecosystems. To assess potential risks, several ecological parameters must be examined, including the impact of the introduced genetically modified organism on the microbial communities associated with the environment into which the introduction will occur. A 2-year field study was established to examine whether the indigenous bacterial communities of the rhizosphere and endorhiza (internal root tissues) were affected differently by the introduction of an unaltered wild type and its genetically modified derivative. Treatments consisted of the wild-type strain Pseudomonas fluorescens 89B-27 and a bioluminescent derivative GEM-8 (89B-27::Tn4431). Cucumber root or seed samples were taken 0, 7, 14, 21, 35, and 70 days after planting (DAP) in 1994 and 0, 7, 14, 28, 42, and 70 DAP in 1995. Samples were processed to examine the bacterial communities of both the rhizosphere and endorhiza. Over 7200 bacterial colonies were isolated from the rhizosphere and endorhiza and identified using the Sherlock System (Microbial ID, Inc.) for fatty acid methyl ester analysis. Community structure at the genus level was assessed using genera richness and Hill's diversity numbers, N1 and N2. The aerobic–heterotrophic bacterial community structure at the genus level did not significantly vary between treatments but did differ temporally. The data indicate that the introduction of the genetically modified derivative of 89B-27 did not pose a greater environmental risk than its unaltered wild type with respect to aerobic–heterotrophic bacterial community structure.Key words: diversity, ecology, PGPR, Pseudomonas, root colonizaton, GEM.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

scholarly journals Increase in Bacterial Community Diversity in Subsurface Aquifers Receiving Livestock Wastewater Input

2000 ◽  
Vol 66 (3) ◽  
pp. 956-965 ◽  
Author(s):  
Jang-Cheon Cho ◽  
Sang-Jong Kim
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Community Diversity ◽  
Similarity Coefficients ◽  
Livestock Wastewater ◽  
Contaminated Aquifer ◽  
Bacterial Community Diversity ◽  
Rdna Sequences ◽  
Wastewater Samples ◽  
The Impact

ABSTRACT Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the Cytophaga-Flexibacter-Bacteroidesand low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.

scholarly journals Deciphering the Influence of Multiple Anthropogenic Inputs on Taxonomic and Functional Profiles of the Microbial Communities in Yitong River, Northeast China

2021 ◽  
Author(s):  
Ying Zhang ◽  
Yang Huo ◽  
Zhiruo Zhang ◽  
Suiyi Zhu ◽  
Wei Fan ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Northeast China ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Amplicon Sequencing ◽  
Fecal Indicator ◽  
16S Rrna Amplicon Sequencing ◽  
Anthropogenic Inputs ◽  
Wwtp Effluent ◽  
The Impact

Abstract We conducted physicochemical parameters analysis, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nutrients were significantly declined at the reservoir outlet, and WWTP effluent discharge caused changes in the river microbial community. NH3-N and NO3--N were the main environmental factors that drive the shift of the bacteria community, and rare taxa played a more important role in the response to environmental changes compared with the abundant ones. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.

scholarly journals Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities

2017 ◽  
Author(s):  
Kruttika Phalnikar ◽  
Krushnamegh Kunte ◽  
Deepa Agashe
Keyword(s):  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Butterfly Species ◽  
Species Identity ◽  
Active Selection ◽  
Key Factor ◽  
Host Diet ◽  
Taxonomic Groups ◽  
The Impact

ABSTRACTBacterial communities associated with insects can substantially influence host ecology, evolution and behavior. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analyzed bacterial communities of 12 butterfly species across different development stages, using 16S rDNA amplicon sequencing. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, very few species showed significant developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species identity and dietary variation across species. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbor distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities.

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