Bacterial Communities Associated with Retail Alfalfa Sprouts

2008 ◽  
Vol 71 (1) ◽  
pp. 200-204 ◽  
Author(s):  
CINDY LOUI ◽  
GRIGOR GRIGORYAN ◽  
HAOHAO HUANG ◽  
LEE W. RILEY ◽  
SANGWEI LU
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Fresh Produce ◽  
Growth Conditions ◽  
Human Pathogens ◽  
Culture Independent ◽  
Foodborne Outbreaks ◽  
Total Bacterial Community ◽  
Alfalfa Sprouts ◽  
Alfalfa Sprout

Fresh produce, including salad, is increasingly implicated in foodborne outbreaks. Although studies have been carried out to detect specific human pathogens from fresh produce, the total bacterial community associated with fresh produce is poorly understood. In this study, we characterized the bacterial community associated with alfalfa sprouts, using a culture-independent method. Four retail-purchased alfalfa sprout samples were obtained from different producers, and the bacterial community associated with each sample was determined by 16S rDNA profiling. Our results indicate that alfalfa sprouts sampled in our study shared significant similarities in their bacterial communities. Proteobacteria was the dominant phylum detected from all alfalfa sprout samples, with Enterobacteriaceae, Oxalobacteraceae, Moraxellaceae, and Sphingomonadaceae as the most frequently detected families. These results indicate that growth conditions of alfalfa sprouts should be taken into consideration to prevent the proliferation of pathogenic proteobacteria such as Escherichia coli O157 and Salmonella.

Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Tong-tong Liu ◽  
Hong Yang
Keyword(s):  
Bacterial Community ◽  
Surface Sediment ◽  
Bacterial Communities ◽  
Surface Sediments ◽  
Lake Taihu ◽  
Dynamic Changes ◽  
Dna And Rna ◽  
Close Relationship ◽  
Total Bacterial Community ◽  
Quantitative Results

ABSTRACT Bacterial communities play crucial roles in the biogeochemical cycle of the surface sediments of freshwater lakes, but previous studies on bacterial community changes in this habitat have mostly been based on the total bacterial community (DNA level), while an exploration of the active microbiota at the RNA level has been lacking. Herein, we analysed the bacterial communities in the surface sediments of Lake Taihu at the DNA and RNA levels. Using MiSeq sequencing and real-time quantification, we found that the sequencing and quantitative results obtained at the RNA level compared with the DNA level were more accurate in responding to the spatiotemporal dynamic changes of the bacterial community. Although both sequencing methods indicated that Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Bacteroidetes and Actinobacteria were the dominant phyla, the co-occurrence network at the RNA level could better reflect the close relationship between microorganisms in the surface sediment. Additionally, further analysis showed that Prochlorococcus and Microcystis were the most relevant and dominant genera of Cyanobacteria in the total and active bacterial communities, respectively; our results also demonstrated that the analysis of Cyanobacteria-related groups at the RNA level was more ‘informative’.

scholarly journals Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

2009 ◽  
Vol 75 (11) ◽  
pp. 3407-3418 ◽  
Author(s):  
Jorge Alonso-Gutiérrez ◽  
Antonio Figueras ◽  
Joan Albaigés ◽  
Núria Jiménez ◽  
Marc Viñas ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Oil Spill ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Mycolic Acids ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Northwestern Spain

ABSTRACT The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

scholarly journals Effective Recovery of Bacterial DNA and Percent-Guanine-Plus-Cytosine-Based Analysis of Community Structure in the Gastrointestinal Tract of Broiler Chickens

1998 ◽  
Vol 64 (10) ◽  
pp. 4084-4088 ◽  
Author(s):  
Juha H. A. Apajalahti ◽  
Laura K. Särkilahti ◽  
Brita R. E. Mäki ◽  
J. Pekka Heikkinen ◽  
Päivi H. Nurminen ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Broiler Chickens ◽  
Direct Method ◽  
Gi Tract ◽  
Bacterial Dna ◽  
Initial Characterization ◽  
Total Bacterial Community

ABSTRACT A DNA-based, direct method for initial characterization of the total bacterial community in ileum and cecum of the chicken gastrointestinal (GI) tract was developed. The efficiencies of bacterial extraction and lysis were >95 and >99%, respectively, and therefore the DNA recovered should accurately reflect the bacterial communities of the ileal and cecal digesta. Total bacterial DNA samples were fractionated according to their percent G+C content. The profiles reflecting the composition of the bacterial community were reproducible within each compartment, but different between the compartments of the GI tract. This approach is independent of the culturability of the bacteria in the consortium and can be used to improve our understanding of how diet and other variables modulate the microbial communities of the GI tracts of animals.

scholarly journals Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer

2021 ◽  
Vol 9 (6) ◽  
pp. 1326
Author(s):  
Thijs Van Gerrewey ◽  
Christophe El-Nakhel ◽  
Stefania De Pascale ◽  
Jolien De Paepe ◽  
Peter Clauwaert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Growth Conditions ◽  
Plant Performance ◽  
Shoot Biomass ◽  
Sustainable Food ◽  
High Performing ◽  
Nutrient Environment ◽  
Hydroponically Grown ◽  
The Impact

Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3-/NH4+ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.

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

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
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.

scholarly journals Comparison of Soil Bacterial Communities in Rhizospheres of Three Plant Species and the Interspaces in an Arid Grassland

2002 ◽  
Vol 68 (4) ◽  
pp. 1854-1863 ◽  
Author(s):  
Cheryl R. Kuske ◽  
Lawrence O. Ticknor ◽  
Mark E. Miller ◽  
John M. Dunbar ◽  
Jody A. Davis ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Species ◽  
Environmental Conditions ◽  
Bacterial Communities ◽  
Soil Depth ◽  
Plant Cover ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Dna ◽  
Total Bacterial Community

ABSTRACT Soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. In parallel studies, the composition of the total bacterial community and of members of the Acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (TRF, also known as T-RFLP) analysis of 16S rRNA genes amplified from soil DNA. Bacterial communities associated with the rhizospheres of the native bunchgrasses Stipa hymenoides and Hilaria jamesii, the invading annual grass Bromus tectorum, and the interspaces colonized by cyanobacterial soil crusts were compared at three depths. When used in a replicated field-scale study, TRF analysis was useful for identifying broad-scale, consistent differences in the bacterial communities in different soil locations, over the natural microscale heterogeneity of the soil. The compositions of the total bacterial community and Acidobacterium division in the soil crust interspaces were significantly different from those of the plant rhizospheres. Major differences were also observed in the rhizospheres of the three plant species and were most apparent with analysis of the Acidobacterium division. The total bacterial community and the Acidobacterium division bacteria were affected by soil depth in both the interspaces and plant rhizospheres. This study provides a baseline for monitoring bacterial community structure and dynamics with changes in plant cover and environmental conditions in the arid grasslands.

scholarly journals   Long-term agrichemical use leads to alterations in bacterial community diversity

2012 ◽  
Vol 58 (No. 10) ◽  
pp. 452-458 ◽  
Author(s):  
H. Tan ◽  
M. Barret ◽  
O. Rice ◽  
D.N. Dowling ◽  
J. Burke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Spring Barley ◽  
Community Diversity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Culture Independent ◽  
Concomitant Reduction ◽  
Soil Bacterial

  Bacterial communities are key drivers of soil fertility and agriculture productivity. Understanding how soil bacterial communities change in response to different conditions is an important aspect in the development of sustainable agriculture. There is a desire to reduce the current reliance on high inputs of chemicals and fertilisers in agriculture, but limited data are available on how this might impact soil bacterial communities. This study investigated the bacterial communities in a spring barley monoculture site subjected to two different input regimes for over 12 years: a conventional chemical/fertiliser regime, and a reduced input regime. A culture independent approach was performed to compare the bacterial communities through 16S rRNA gene PCR-DGGE. PCO analysis revealed that the rhizosphere has a strong structuring effect on the bacterial community. Moreover, high inputs of agrichemicals lead to an increase of phosphorus level in the soil and a concomitant reduction of the bacterial diversity. These results may help to evaluate the environmental risks associated with agrichemical usage.  

scholarly journals Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches

2021 ◽  
Author(s):  
Sameh H. Youseif ◽  
Fayrouz H. Abd El-Megeed ◽  
Ethan A. Humm ◽  
Maskit Maymon ◽  
Akram H. Mohamed ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bacterial Community ◽  
Plant Growth ◽  
Soil Health ◽  
Natural Environments ◽  
Beneficial Effects ◽  
Wheat Rhizosphere ◽  
Culture Independent ◽  
Total Bacterial Community ◽  
Culture Dependent

Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored.

scholarly journals Tolerance of soil bacterial community to tetracycline antibiotics induced by As, Cd, Zn, Cu, Ni, Cr and Pb pollution

2021 ◽  
Author(s):  
Vanesa Santás-Miguel ◽  
Avelino Núñez-Delgado ◽  
Esperanza Álvarez-Rodríguez ◽  
Montserrat Díaz-Raviña ◽  
Manuel Arias-Estévez ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Samples ◽  
Leucine Incorporation ◽  
Human Pathogens ◽  
High Concentration ◽  
Tetracycline Antibiotics ◽  
Co Tolerance

Abstract. The widespread use of both heavy metals and antibiotics in livestock farming and their subsequent arrival on agricultural soils through manure/slurry spreading has become a problem of vital importance for human health and the environment. In the current research, a laboratory experiment was carried out for 42 days to study co-selection for tolerance of three tetracycline antibiotics (tetracycline, TC; oxytetracycline, OTC; chlortetracycline, CTC) in soils polluted with heavy metals (As, Cd, Zn, Cu, Ni, Cr and Pb) at high concentration levels (1000 mg kg−1 of each one, separately). Pollution Induced Community Tolerance (PICT) of the bacterial community was estimated using the leucine incorporation technique. The Log IC50 (logarithm of the concentration causing 50 % inhibition in bacterial community growth) values obtained in uncontaminated soil samples for all the heavy metals tested showed the following toxicity sequence: Cu > As > Cr ≥ Pb ≥ Cd > Zn > Ni. However, in polluted soil samples the toxicity sequence was: Cu > Pb ≥ As ≥ Cd ≥ Cr ≥ Ni ≥ Zn. Moreover, at high metal concentrations the bacterial communities show tolerance to the metal itself, this taking place for all the metals tested in the long term. The bacterial communities of the soil polluted with heavy metals showed also long-term co-tolerance to TC, OTC, and CTC. This kind of studies, focusing on the eventual increases of tolerance and co-tolerance of bacterial communities in agricultural soil, favored by the presence of other pollutants, is of crucial importance, mostly bearing in mind that the appearance of antibiotic resistance genes in soil bacteria could be transmitted to human pathogens.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

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