scholarly journals Effects of an Eco-Friendly Sanitizing Wash on Spinach Leaf Bacterial Community Structure and Diversity

2020 ◽  
Vol 10 (8) ◽  
pp. 2986
Author(s):  
Sangay Tenzin ◽  
Abiodun D. Ogunniyi ◽  
Sergio Ferro ◽  
Permal Deo ◽  
Darren J. Trott
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Foodborne Pathogens ◽  
Tap Water ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Minimally Processed ◽  
16S Rrna Pyrosequencing ◽  
Significant Difference ◽  
Spinach Leaf

Ready-to-eat (RTE) spinach is considered a high-risk food, susceptible to colonization by foodborne pathogens; however, other microbial populations present on the vegetable surface may interact with foodborne pathogens by inhibiting/inactivating their growth. In addition, sanitizers applied to minimally processed salad leaves should not disrupt this autochthonous barrier and should be maintained throughout the shelf life of the product. This investigation aimed at comparing the effects of a pH neutral electrochemically activated solution (ECAS), a peroxyacetic acid (PAA)-based commercial sanitizer (Ecolab Tsunami® 100), and tap water wash on the minimally processed spinach leaf microbiome profile for 10 days after washing. The bacterial microbiota composition on spinach samples was assessed by 16S rRNA pyrosequencing and downstream analyses. Predominant phyla observed in decreasing order of abundance were Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes corresponding with the dominant families Micrococcaceae, Clostridiales Family XII, Flavobacteriaceae, Pseudomonadaceae, and Burkholderiaceae. Bacterial species richness and evenness (alpha diversity) and bacterial community composition among all wash types were not significantly different. However, a significant difference was apparent between sampling days, corresponding to a loss of overall heterogeneity over time. Analysis of composition of microbiome (ANCOM) did not identify any amplicon sequence variants (ASVs) or families having significantly different abundance in wash types; however, differences (17 ASVs and five families) were found depending on sampling day. This was the first bacterial microbiome composition study focused on ECAS and PAA-based wash solutions. These wash alternatives do not significantly alter microbial community composition of RTE spinach leaves; however, storage at refrigerated temperature reduces bacterial species heterogeneity.

scholarly journals Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Nan Jiang ◽  
Yinghua Juan ◽  
Lulu Tian ◽  
Xiaodong Chen ◽  
Wentao Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Water ◽  
Community Composition ◽  
Bacterial Communities ◽  
N Mineralization ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
N Immobilization ◽  
Freeze Thaw ◽  
Dissolved Nitrogen

Background. Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities. Method. In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO3--N, NH4+-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH4+-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO3--N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman’s correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.

scholarly journals Bacteria associated with jellyfish during bloom and post-bloom periods

2018 ◽  
Author(s):  
Maja Kos Kramar ◽  
Tinkara Tinta ◽  
Davor Lučić ◽  
Alenka Malej ◽  
Valentina Turk
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Body Part ◽  
Body Parts ◽  
Population Peak ◽  
Significant Difference ◽  
Jellyfish Population

AbstractThis study is the first to investigate bacterial community associated with live medusaAurelia sp. in the Gulf of Trieste (northern Adriatic Sea) using both culture independent and culture-based methods. We have analysed bacterial community composition of different body parts of medusa: exumbrella surface, oral arms (‘outer’ body parts) and of gastric cavity (‘inner’ body part) and investigated possible differences in medusa associated bacterial community structure at the time of jellyfish population peak and during senescent phase at the end of bloom, when jellyfish start to decay. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we demonstrated significant difference between bacterial community associated withAureliaand the ambient seawater bacterial assemblage. Comparing bacterial community composition between differentAureliamedusa body parts, communities differed significantly, especially the one within the gastral cavity. The pronounced difference is dominance ofBetaproteobacteria(Burkholderia, CupriavidusandAchromobacter) in gastral cavity of medusa andAlpha- (Phaeobacter, Ruegeria) andGamma-proteobacteria(Stenotrophomonas, Alteromonas, PseudoalteromonasandVibrio) on ‘outer’ body parts. This suggests that body-part specific bacterial association might have an important functional roles for the host. The results of bacterial isolates showed the dominance ofGammaproeteobacteria, especiallyVibrioandPseudoalteromonasin all body parts. Finally, comparison of medusa associated bacterial community structure, at the time of jellyfish population peak and during senescent phase at the end of bloom showed increased abundance ofGammaproteobacteria, especiallyVibrio. Our results suggest members ofVibriogroup are possible commensal opportunistic visitors, later becoming consumer of moribund jellyfish biomass and that the structure of jellyfish bacterial community might be affected by anthropogenic pollution in the marine environment.

scholarly journals Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Dong Yan ◽  
Tao Zhang ◽  
Jing Su ◽  
Li-Li Zhao ◽  
Hao Wang ◽  
...  
Keyword(s):  
Particulate Matter ◽  
Bacterial Community ◽  
Community Composition ◽  
Structural Variation ◽  
Bacterial Community Composition ◽  
Total Suspended Particulate ◽  
Content Type ◽  
Suspended Particulate ◽  
Significant Difference ◽  
Haze Days

ABSTRACTThe structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM2.5[<2.5 μm], PM10[<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions (R= 0.157,P< 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example,Methylobacillus,Tumebacillus, andDesulfurisporaspp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO2concentration, relative humidity, PM10concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM10samples (Dokdonella,Caenimonas,Geminicoccus, andSphingopyxis) and PM2.5samples (CellulomonasandRhizobacter), while a large number of taxa significantly increased in total suspended particulate samples, such asParacoccus,Kocuria, andSphingomonas. Network analysis indicated thatParacoccus,Rubellimicrobium,Kocuria, andArthrobacterwere the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days.IMPORTANCEThe results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such asMethylobacillus,Tumebacillus, andDesulfurispora) increased significantly on heavy-haze days. In addition,Paracoccus,Rubellimicrobium,Kocuria, andArthrobacterwere the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze.

scholarly journals Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 27
Author(s):  
Hyo-Ryeon Kim ◽  
Jae-Hyun Lim ◽  
Ju-Hyoung Kim ◽  
Il-Nam Kim
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Marine Bacteria ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Composition Data ◽  
Decomposition Of Organic Matter ◽  
Class Level ◽  
Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

scholarly journals Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danijela Šantić ◽  
Kasia Piwosz ◽  
Frano Matić ◽  
Ana Vrdoljak Tomaš ◽  
Jasna Arapov ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Analysis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Adriatic Sea ◽  
Bacterial Community Composition ◽  
Environmental Data ◽  
Large Contribution ◽  
Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

scholarly journals One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Qingyao Wang ◽  
Yixiang Zhang ◽  
Qian Yang ◽  
Songzhe Fu ◽  
Baocheng Qu ◽  
...  
Keyword(s):  
Community Composition ◽  
Foodborne Pathogens ◽  
Migratory Birds ◽  
Bacterial Community Composition ◽  
Hypervariable Region ◽  
Shrimp Farming ◽  
Clinical Strain ◽  
Coastal Regions ◽  
Aquatic Animals ◽  
Gut Pathogens

Abstract Background Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp. Results Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella. Conclusions In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.

scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

scholarly journals Longitudinal assessment of the bovine ocular bacterial community dynamics in calves

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Alison C. Bartenslager ◽  
Nirosh D. Althuge ◽  
John Dustin Loy ◽  
Matthew M. Hille ◽  
Matthew L. Spangler ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Clinical Signs ◽  
Sampling Time ◽  
Experimental Population ◽  
Opportunistic Pathogens ◽  
Time Periods ◽  
Over Time

Abstract Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK. Results In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study consisting of 227 calves and evaluated the microbiota composition over time using amplicon sequence variants (ASVs) based on 16S rRNA sequencing data and culture-based approaches. Beef calves on trial consisted of both male (intact) and females. Breeds were composed of purebred Angus and composites with varying percentages of Simmental, Angus, and Red Angus breeds. Average age at the start of the trial was 65 days ±15.02 and all calves remained nursing on their dam until weaning (day 139 of the study). The trial consisted of 139 days with four sampling time points on day 0, 21, 41, and 139. The experimental population received three different vaccination treatments (autogenous, commercial (both inactivated bacteria), and adjuvant placebo), to assess the effectiveness of different vaccines for IBK prevention. A significant change in bacterial community composition was observed across time periods sampled compared to the baseline (p < 0.001). However, no treatment effect of vaccine was detected within the ocular bacterial community. The bacterial community composition with the greatest time span between sampling time periods (98d span) was most similar to the baseline sample collected, suggesting re-establishment of the ocular microbiota to baseline levels over time after perturbation. The effect of IgA levels on the microbial community was investigated in a subset of cattle within the study. However, no significant effect of IgA was observed. Significant changes in the ocular microbiota were identified when comparing communities pre- and post-clinical signs of IBK. Additionally, dynamic changes in opportunistic pathogens Moraxella spp. were observed and confirmed using culture based methods. Conclusions Our results indicate that the bovine ocular microbiota is well represented by opportunistic pathogens such as Moraxella and Mycoplasma. Furthermore, this study characterizes the diversity of the ocular microbiota in calves and demonstrates the plasticity of the ocular microbiota to change. Additionally, we demonstrate the ocular microbiome in calves is similar between the eyes and the perturbation of one eye results in similar changes in the other eye. We also demonstrate the bovine ocular microbiota is slow to recover post perturbation and as a result provide opportunistic pathogens a chance to establish within the eye leading to IBK and other diseases. Characterizing the dynamic nature of the ocular microbiota provides novel opportunities to develop potential probiotic intervention to reduce IBK outbreaks in cattle.

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