scholarly journals Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

2014 ◽  
Vol 81 (4) ◽  
pp. 1530-1539 ◽  
Author(s):  
Merete Wiken Dees ◽  
Erik Lysøe ◽  
Berit Nordskog ◽  
May Bente Brurberg
Keyword(s):  
Bacterial Community ◽  
Pathogenic Bacteria ◽  
Bacterial Colonization ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Human Pathogens ◽  
Content Type ◽  
Leaf Maturity ◽  
Leafy Greens ◽  
Over Time

ABSTRACTThe phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of theL. sativasamples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied betweenD. tenuifoliaandL. sativaat harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.

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.

scholarly journals Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

2012 ◽  
Vol 78 (7) ◽  
pp. 2359-2366 ◽  
Author(s):  
Merritt G. Gillilland ◽  
John R. Erb-Downward ◽  
Christine M. Bassis ◽  
Michael C. Shen ◽  
Galen B. Toews ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Structural Heterogeneity ◽  
Ecological Succession ◽  
Rrna Gene ◽  
Gi Tract ◽  
Content Type ◽  
Germ Free ◽  
Over Time

ABSTRACTLittle is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by eitherEscherichiaorBacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a “pioneering” community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

scholarly journals Analysis of rhizosphere bacterial diversity of Angelica dahurica var. formosana based on different experimental sites and varieties (strains)

2021 ◽  
Author(s):  
Meiyan Jiang ◽  
Fei Yao ◽  
Yunshu Yang ◽  
Yang Zhou ◽  
Kai Hou ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Growth Promotion ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Fertilizer Application ◽  
Angelica Dahurica ◽  
Soil Environment ◽  
Yield And Quality

Only with good producing areas and good germplasm can good medicinal materials be produced. In this study, in order to explore the effects of soil environment and germplasm on yield and quality of Angelica dahurica var. formosana from microorganism level, Illumina MiSeq was used to study the rhizosphere bacterial diversity of A. dahurica var. formosana based on different origin and varieties (strains). The results showed that the bacterial community of A. dahurica var. formosana was stable and conserved to a certain extent, and the bacteria of Proteobacteria and Firmicutes might play an important role in improving the yield and quality of A. dahurica var. formosana. Soil variables were the key factors affecting the rhizosphere bacterial community composition of A. dahurica var. formosana. These results are of great significance for further understanding the growth promotion mechanism of beneficial rhizosphere bacteria, reducing fertilizer application, expanding planting area, improving soil environment, and improving yield and quality.

scholarly journals Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hannah E. Pilch ◽  
Andrew J. Steinberger ◽  
Donald C. Sockett ◽  
Nicole Aulik ◽  
Garret Suen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Pathogenic Bacteria ◽  
Bacterial Community Composition ◽  
Dairy Farm ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Recycling System ◽  
Core Microbiota ◽  
Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie and tropical ecosystems

2020 ◽  
Author(s):  
Xun Qian ◽  
Santosh Gunturu ◽  
Jiarong Guo ◽  
Benli Chai ◽  
James R. Cole ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Bacterial Community Composition ◽  
Amazon Rainforest ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequence Information ◽  
Human Pathogens ◽  
Soil Dna

Abstract Background Soil is likely the largest reservoir of antibiotic resistance genes (ARGs), but their distribution across soil resistomes of different ecosystems is unknown. We used a metagenomic approach to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. Results High diversity (242 ARG subtypes) and abundance (0.184–0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance genes and efflux pump the dominant class and mechanism. We identified 55 “background ARGs” which were shared by all 26 soil metagenomes of all three ecosystems, which accounted for more than 81% of resistome abundance. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. Conversion of Amazon rainforest to pasture significantly increased soil ARG diversity, with eight ARGs significantly enriched. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. There was also wide co-occurrence among ARGs in all samples. Conclusions Our results define common background ARGs, quantify resistance classes, provide sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future.

scholarly journals Sample Dilution and Bacterial Community Composition Influence Empirical Leucine-to-Carbon Conversion Factors in Surface Waters of the World's Oceans

2015 ◽  
Vol 81 (23) ◽  
pp. 8224-8232 ◽  
Author(s):  
Eva Teira ◽  
Víctor Hernando-Morales ◽  
Francisco M. Cornejo-Castillo ◽  
Laura Alonso-Sáez ◽  
Hugo Sarmento ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Nucleic Acid Content ◽  
Carbon Conversion ◽  
Production Rates ◽  
Conversion Factors ◽  
Content Type ◽  
Carbon Production ◽  
The Impact

ABSTRACTThe transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu−1and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyllaconcentration, picocyanobacterial abundance (mostlyProchlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that bothProchlorococcusand HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean.

scholarly journals Livestock Origin for a Human Pandemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Laura E. Spoor ◽  
Paul R. McAdam ◽  
Lucy A. Weinert ◽  
Andrew Rambaut ◽  
Henrik Hasman ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Pathogenic Bacteria ◽  
Control Measures ◽  
Human Populations ◽  
Epidemic Spread ◽  
Human Pathogens ◽  
Methicillin Resistant ◽  
Content Type ◽  
Evolutionary Origins ◽  
Healthy Humans

ABSTRACTThe importance of livestock as a source of bacterial pathogens with the potential for epidemic spread in human populations is unclear. In recent years, there has been a global increase in community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) infections of healthy humans, but an understanding of the different evolutionary origins of CA-MRSA clones and the basis for their recent expansion is lacking. Here, using a high-resolution phylogenetic approach, we report the discovery of two emergent clones of human epidemic CA-MRSA which resulted from independent livestock-to-human host jumps by the major bovineS. aureuscomplex, CC97. Of note, one of the new clones was isolated from human infections on four continents, demonstrating its global dissemination since the host jump occurred over 40 years ago. The emergence of both humanS. aureusclones coincided with the independent acquisition of mobile genetic elements encoding antimicrobial resistance and human-specific mediators of immune evasion, consistent with an important role for these genetic events in the capacity to survive and transmit among human populations. In conclusion, we provide evidence that livestock represent a reservoir for the emergence of new human-pathogenicS. aureusclones with the capacity for pandemic spread. These findings have major public health implications highlighting the importance of surveillance for early identification of emergent clones and improved transmission control measures at the human-livestock interface.IMPORTANCEAnimals are the major source of new pathogens affecting humans. However, the potential for pathogenic bacteria that originally were found in animals to switch hosts and become widely established in human populations is not clear. Here, we report the discovery of emergent clones of methicillin-resistantStaphylococcus aureus(MRSA) that originated in livestock and switched to humans, followed by host-adaptive evolution and epidemic spread in global human populations. Our findings demonstrate that livestock can act as a reservoir for the emergence of new human bacterial clones with potential for pandemic spread, highlighting the potential role of surveillance and biosecurity measures in the agricultural setting for preventing the emergence of new human pathogens.

scholarly journals Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

2015 ◽  
Vol 81 (14) ◽  
pp. 4697-4710 ◽  
Author(s):  
Kelsea A. Jewell ◽  
Caroline A. McCormick ◽  
Christine L. Odt ◽  
Paul J. Weimer ◽  
Garret Suen
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Milk Production ◽  
Feed Efficiency ◽  
Production Efficiency ◽  
Bacterial Community Composition ◽  
Feed Consumption ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Microbiota

ABSTRACTFourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows wereBacteroidetes(49.42%),Firmicutes(39.32%),Proteobacteria(5.67%), andTenericutes(2.17%), and the most abundant genera includedPrevotella(40.15%),Butyrivibrio(2.38%),Ruminococcus(2.35%),Coprococcus(2.29%), andSucciniclasticum(2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

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