Anatomy & Physiology
1st Edition
ISBN:9781938168130
Author:Kelly A. Young, James A. Wise, Peter DeSaix, Dean H. Kruse, Brandon Poe, Eddie Johnson, Jody E. Johnson, Oksana Korol, J. Gordon Betts, Mark Womble
Publisher:Kelly A. Young, James A. Wise, Peter DeSaix, Dean H. Kruse, Brandon Poe, Eddie Johnson, Jody E. Johnson, Oksana Korol, J. Gordon Betts, Mark Womble
Chapter3: The Cellular Level Of Organization
Section: Chapter Questions
Problem 42CTQ: Which of the following structures could be found within the nucleolus?
Related questions
Concept explainers
Bacterial Genomics
The study of the morphological, physiological, and evolutionary aspects of the bacterial genome is referred to as bacterial genomics. This subdisciplinary field aids in understanding how genes are assembled into genomes. Further, bacterial or microbial genomics has helped researchers in understanding the pathogenicity of bacteria and other microbes.
Transformation Experiment in Bacteria
In the discovery of genetic material, the experiment conducted by Frederick Griffith on Streptococcus pneumonia proved to be a stepping stone.
Plasmids and Vectors
The DNA molecule that exists in a circular shape and is smaller in size which is capable of its replication is called Plasmids. In other words, it is called extra-chromosomal plasmid DNA. Vectors are the molecule which is capable of carrying genetic material which can be transferred into another cell and further carry out replication and expression. Plasmids can act as vectors.
Question
Why would the researchers look for transposase genes when the transposase protein itself does not confer antibiotic resistance?
please prephrase and find the answer in the article
Transcribed Image Text:A
B
C
Transposase
Fold Increase
Total Transposases
105
104
103
10²
10¹
10⁰
105
104
10³
10²
10¹
10⁰
10-1
300
250
200
150
100
50
0
0
58
TH
L
9
III
·
Manure
O
● Transposase
O
10
43
35
13
zÅÏžÃÖ¤
54
■
56
P
Compost Soil+Compost.
104
3438 www.pnas.org/cgi/doi/10.1073/pnas.1222743110
10³
10²
10¹
10-1
200 400 600 800 1000 1200 1400
Total Antibiotic Resistance
10⁰
17
Oxytetracycline (µg kg-¹)
10³
10²
101
10⁰
10-1
Copper (mg kg-¹)
Oxytetracycline
Copper
Fig. 3. Abundance of resistance genes and transposases. In the box plots, the
symbols indicate the following: box, 25th to 75th percentile; horizontal line,
median; whiskers, 10th and 90th percentile; and square, maximum value. The
y
axis is a log scale of fold increase: farm manure compared with the control
manure, and farm compost or soil compared with the control soil. (A) Only
statistically enriched resistance genes are represented. The number above
each site indicates the number of primer sets that yielded statistically signifi-
cant results. (B) Summary of all nine primer sets used to target different
transposase alleles (in B, top whisker represents the maximum value). (C)
Correlation of total resistance and transposase abundances, oxytetracycline
concentration, and copper concentration. Total antibiotic resistance and total
transposases values are the sum of AAC, values of all assays of that type in
each sample. The sample identifiers below B apply to both A and B.
were broadly enriched (Table S6). It seems that genes with specific
mechanisms of resistance were preferably enriched in these high-
selection-pressure environments. The diversity of resistance genes
enriched and coenriched at the farm level is concerning because
this broad set of ARGs or a subset thereof could be (co)enriched
or transferred to pathogens under future selection conditions.
Swine farms are known hotspots for pervasive and abundant
antibiotic resistance both in antibiotic-free animals (19, 37) and,
especially, in antibiotic-treated animals (26, 38). The level of
enrichment of individual resistance genes is on par with previous
field-scale studies. Tetracycline resistance genes were enriched
10² to 10-fold in cattle waste lagoons (39), and the median
enrichment of ARGs in this manure was about 10-fold. Of bac-
terial isolates from swine and chicken manure, 92% and >80%,
respectively, were found resistant to at least one antibiotic (26,
31). We estimate about 43% of bacteria possess at least the
aphA3 gene; hence, it is feasible that upward of 90% of the
entire community would carry one of the other 148 resistance
genes detected. Considering all antibiotic resistance genes com-
bined in the manure or compost samples, we estimate a total of
50,000-fold enrichment (Table S3). Although enrichment of in-
dividual resistance genes is similar to that found in previous
studies, we were able to capture a more complete picture of the
total level of the antibiotic resistance reservoir.
Potential for Horizontal Gene Transfer of ARGs. This study high-
lights that ARGs in swine farms are not only diverse but are
also remarkably abundant, which together offers a higher sta-
tistical probability of dispersal, further selection, and/or hori-
zontal transfer in the environment. The emergence and spread of
ARGs are closely associated with mobile genetic elements such as
plasmids, integrases, and transposases (20, 40, 41). The high de-
gree of transposase enrichment and correlation with abundance
of ARGs suggests that horizontal gene transfer may have aided
the enrichment of ARGs. The transposases detected most fre-
quently belong to the IS6 family of insertion sequences, which
are typically found flanking an array of genes, often resistance
genes (42). The most abundant member of the IS6 family in these
samples, IS26, has been isolated, along with integrons in multi-
drug-resistant plasmids in enterobacteria (43). Integrons most
commonly contain resistance cassettes encoding aadA genes (44),
as well as qacE^I and sul2, which were among the most enriched
genes in this study. The Putian farm ARGs that are more
enriched in the compost than in the manure (Fig. 2, D boxes and
Table S6) are predominately aadA and other aminoglycoside
resistance genes and their enrichment may be due to their pres-
ence in integrons that also hold a resistance gene cassette relevant
to the drugs used on the farm (34, 45). Additionally, the combi-
nation of antibiotics and metals may provide a stronger selection
for realized horizontal gene transfer within the microbial com-
munity than either alone (9, 23, 34, 46). It appears that a number
of factors in swine farms could contribute to elevated rates of
horizontal gene transfer, including elevated concentrations of
antibiotics, metals, ARGs, and mobile genetic elements, making
subsequent dispersal, (co)enrichment, or horizontal transfer, in-
cluding to human-associated bacteria, more probable.
Role of Manure Management in Controlling ARGs. The long-term
goal of manure management is to remove environmental con-
taminants while disposing of this high-volume waste product and
capturing its value to improve soil fertility. The goal in the case of
ARGs is to identify practices that decrease their concentration to
a greater degree than by simple dilution (47). Manure composting
decreased the abundance of ARGs at Beijing, but abundance
remained nearly the same in the Jiaxing manure, while at Putian
composting actually increased the abundance of ARGs. Com-
posting concentrated sulfonamides (Fig. S1), sulfonamide resistance
genes, and some metals (Fig. S2), consistent with the observation
that sulfonamide resistance genes are more recalcitrant than tet-
racycline genes (22, 48, 49). The common practice of spreading
compost on soil was not sufficient to reduce abundance of ARGS
to background levels, and the Putian soil showed up to 3,000-fold
enrichment. However, the practice decreased concentrations of
ARGs substantially below compost levels. The relatively high en-
richment of ARGs in Putian soil may be due to a higher manure/
soil ratio and/or shorter time before sampling after amendment
compared with other farms. These observations highlight the need
to determine adequate composting time to reduce resistance levels
before release to the more uncontrolled environment (50), as well
Zhu et al.
![quantitative PCR (qPCR) (19) with 313 validated primer sets,
which target 244 ARGs (Table S1) from all major classes of ARGS,
to extensively sample the antibiotic resistance reservoir. We sam-
pled three large-scale commercial swine farms, each from a differ-
ent region of China, at three stages of manure management:
manure, manure compost, and soil receiving manure compost.
Manure from pigs never fed antibiotics and soil from a pristine
forest in Putian, China were used as experimental controls.
Results
-1
Antibiotics and Metal Concentrations. Antibiotics and their use as
reported by the farmers are listed in Table S2. Total tetracycline
concentrations in these manure and soil samples were as high as
15.2 mg kg-¹ and 0.78 mg.kg¹, respectively, as was determined
previously (15). Of the sulfonamides analyzed in this study, sul-
famethoxazole had the highest concentrations for all samples,
ranging from 1.08 to 3.02 µg-kg-¹ (Fig. S1). Sulfadiazine was also
detected in all samples in a range of 0.50-4.81 µg-kg-¹. Of the
fluoroquinolones analyzed in this study, only ofloxacin and
enrofloxacin were observed in most samples. The highest mean
concentration of ofloxacin (335 µg-kg-¹) and enrofloxacin (96.0
ug.kg ¹) were observed in Putian compost and soil samples, re-
spectively (Fig. S1). Zinc, copper, and arsenic, used as feed
additives, were also elevated above background concentrations.
The highest mean concentrations of copper, zinc, and arsenic
were detected in Putian manure, Jiaxing compost, and Beijing
manure, respectively, with copper up to 1,700 mg kg-¹ manure
(Fig. S2). The concentration of copper, zinc, and arsenic were
much higher in manure than in compost and soil samples, with
the exception of the Jiaxing compost, in which copper and zinc
had the highest concentrations of all of the samples.
Diversity of Antibiotic Resistance Genes. We detected 149 unique
ARGS among all of the samples, which is three times more types
of ARGs than were found in the control samples (Fig. 14). The
ARGS detected in these farms encompass the three major re-
sistance mechanisms-efflux pumps, antibiotic deactivation, and
cellular protection (Fig. 1B) and potentially confer resistance to
most major classes of antibiotics (Fig. 1C). Resistance gene pro-
files indicate the patterns and degrees of enrichment of ARGs for
each site (Fig. 2) and that manure samples cluster separately from
the other samples with the exception of the Putian compost. The
compost and soil samples also cluster separately with the excep-
tion of one of the Beijing compost replicates, which grouped with
the soil samples. Furthermore, Shannon diversity (indicating
richness and abundance) of ARGs from farm samples was sig-
nificantly higher than that of the control samples (Fig. S3).
Abundance of Antibiotic Resistance Genes. ARGs were highly
enriched in the farm samples. We used the sum of the enrichment
of all unique ARGs in a sample to approximate total enrichment
in the farms. Maximum enrichment occurred in the manure
samples at Beijing (121,000-fold) and Jiaxing (39,000-fold) farms,
and in the compost at the Putian farm (57,000-fold enrichment),
demonstrating the large expansion of the antibiotic resistance
reservoir in these farms, including the enrichment of up to 19
unique tet genes in a single site (Table S3 gives enrichment details
for all genes). A total of 63 unique ARGs were significantly
enriched in at least one sample compared with controls at an
overall median enrichment of 192-fold for all samples. The max-
imum enrichment of a single ARG was over 28,000-fold in the
Beijing manure (Fig. 3A). In terms of absolute abundance, an
aminoglycoside phosphorylation gene aphA3 is found 43% as
frequently as the 16S rRNA gene in the manure samples, based on
a 0.58 average value of the delta threshold cycle (ACT) values
(Table S4), meaning this single gene would be found in nearly one
in every second bacterium, assuming a single copy of each gene
in single genomes. In general, enrichment of individual ARGS
3436 www.pnas.org/cgi/doi/10.1073/pnas.1222743110
A
B
اساس ال
100
60
Antibiotic deactivation
□ Efflux pump
Cellular protection
Other/ unknown
Aminoglycoside
Beta Lactam
OFCA
OMLSB
Tetracycline
Vancomycin
Other/ efflux
Fig. 1. Antibiotic resistance gene detection statistics. Sample names are
abbreviated with two letters representing location and sample type: first
C, B, J, and P (control, Beijing, Jiaxing, and Putian, respectively) and second
M, C, and S [manure, compost, and soil (with compost amendment), re-
spectively]. Because many resistance genes were targeted with multiple
primers, if multiple primer sets detected the same gene, this was only
counted as detection of a single unique resistance gene. (A) Average number
of unique resistance genes detected in each sample. Error bars represent
SEM of four field replicates. The resistance genes detected in all samples
were classified based on (B) the mechanism of resistance, and (C) the anti-
biotic to which they confer resistance. FCA, fluoroquinolone, quinolone,
florfenicol, chloramphenicol, and amphenicol resistance genes; MLSB,
Macrolide-Lincosamide-Streptogramin B resistance.
decreases in soil samples but is still elevated, with average en-
richment of nearly 100-fold, and some genes were enriched over
1,000-fold compared with the soil control. The Putian soil had
more unique resistance genes enriched at a higher level than the
other two farm soils. When combining the data from all farms, 56,
44, and 17 unique ARGs were statistically elevated in the manure,
compost, and soil samples, respectively.
Transposase Enrichment. Transposases, in parallel to ARGs, were
highly enriched (Fig. 3B). Transposases were found in all sam-
ples (Fig. 2, subgroups A and B) and were enriched up to 90,000-
fold in the manure samples and up to 1,000-fold in the soil
samples. The abundance of ARGs is highly correlated to the
levels of transposases in these farm samples (Fig. 3C) (e.g., as
high as 0.970 for correlation between the abundance of tetra-
cycline resistance genes and transposase genes) (Table S5).
Discussion
Feed Additive Use. These swine farms use a complex mixture of
growth-promoting chemicals, including antibiotics and metals.
However, the individual dosage of each chemical, when considered
alone, on these farms is not excessive compared with other farms
Zhu et al.](/v2/_next/image?url=https%3A%2F%2Fcontent.bartleby.com%2Fqna-images%2Fquestion%2Fa535256e-0857-4f61-a16c-a16363561f95%2Fecf1a0fb-bcf5-4f0e-a7dc-4e0c9f19809d%2Fo5ditga_processed.png&w=3840&q=75)
Transcribed Image Text:quantitative PCR (qPCR) (19) with 313 validated primer sets,
which target 244 ARGs (Table S1) from all major classes of ARGS,
to extensively sample the antibiotic resistance reservoir. We sam-
pled three large-scale commercial swine farms, each from a differ-
ent region of China, at three stages of manure management:
manure, manure compost, and soil receiving manure compost.
Manure from pigs never fed antibiotics and soil from a pristine
forest in Putian, China were used as experimental controls.
Results
-1
Antibiotics and Metal Concentrations. Antibiotics and their use as
reported by the farmers are listed in Table S2. Total tetracycline
concentrations in these manure and soil samples were as high as
15.2 mg kg-¹ and 0.78 mg.kg¹, respectively, as was determined
previously (15). Of the sulfonamides analyzed in this study, sul-
famethoxazole had the highest concentrations for all samples,
ranging from 1.08 to 3.02 µg-kg-¹ (Fig. S1). Sulfadiazine was also
detected in all samples in a range of 0.50-4.81 µg-kg-¹. Of the
fluoroquinolones analyzed in this study, only ofloxacin and
enrofloxacin were observed in most samples. The highest mean
concentration of ofloxacin (335 µg-kg-¹) and enrofloxacin (96.0
ug.kg ¹) were observed in Putian compost and soil samples, re-
spectively (Fig. S1). Zinc, copper, and arsenic, used as feed
additives, were also elevated above background concentrations.
The highest mean concentrations of copper, zinc, and arsenic
were detected in Putian manure, Jiaxing compost, and Beijing
manure, respectively, with copper up to 1,700 mg kg-¹ manure
(Fig. S2). The concentration of copper, zinc, and arsenic were
much higher in manure than in compost and soil samples, with
the exception of the Jiaxing compost, in which copper and zinc
had the highest concentrations of all of the samples.
Diversity of Antibiotic Resistance Genes. We detected 149 unique
ARGS among all of the samples, which is three times more types
of ARGs than were found in the control samples (Fig. 14). The
ARGS detected in these farms encompass the three major re-
sistance mechanisms-efflux pumps, antibiotic deactivation, and
cellular protection (Fig. 1B) and potentially confer resistance to
most major classes of antibiotics (Fig. 1C). Resistance gene pro-
files indicate the patterns and degrees of enrichment of ARGs for
each site (Fig. 2) and that manure samples cluster separately from
the other samples with the exception of the Putian compost. The
compost and soil samples also cluster separately with the excep-
tion of one of the Beijing compost replicates, which grouped with
the soil samples. Furthermore, Shannon diversity (indicating
richness and abundance) of ARGs from farm samples was sig-
nificantly higher than that of the control samples (Fig. S3).
Abundance of Antibiotic Resistance Genes. ARGs were highly
enriched in the farm samples. We used the sum of the enrichment
of all unique ARGs in a sample to approximate total enrichment
in the farms. Maximum enrichment occurred in the manure
samples at Beijing (121,000-fold) and Jiaxing (39,000-fold) farms,
and in the compost at the Putian farm (57,000-fold enrichment),
demonstrating the large expansion of the antibiotic resistance
reservoir in these farms, including the enrichment of up to 19
unique tet genes in a single site (Table S3 gives enrichment details
for all genes). A total of 63 unique ARGs were significantly
enriched in at least one sample compared with controls at an
overall median enrichment of 192-fold for all samples. The max-
imum enrichment of a single ARG was over 28,000-fold in the
Beijing manure (Fig. 3A). In terms of absolute abundance, an
aminoglycoside phosphorylation gene aphA3 is found 43% as
frequently as the 16S rRNA gene in the manure samples, based on
a 0.58 average value of the delta threshold cycle (ACT) values
(Table S4), meaning this single gene would be found in nearly one
in every second bacterium, assuming a single copy of each gene
in single genomes. In general, enrichment of individual ARGS
3436 www.pnas.org/cgi/doi/10.1073/pnas.1222743110
A
B
اساس ال
100
60
Antibiotic deactivation
□ Efflux pump
Cellular protection
Other/ unknown
Aminoglycoside
Beta Lactam
OFCA
OMLSB
Tetracycline
Vancomycin
Other/ efflux
Fig. 1. Antibiotic resistance gene detection statistics. Sample names are
abbreviated with two letters representing location and sample type: first
C, B, J, and P (control, Beijing, Jiaxing, and Putian, respectively) and second
M, C, and S [manure, compost, and soil (with compost amendment), re-
spectively]. Because many resistance genes were targeted with multiple
primers, if multiple primer sets detected the same gene, this was only
counted as detection of a single unique resistance gene. (A) Average number
of unique resistance genes detected in each sample. Error bars represent
SEM of four field replicates. The resistance genes detected in all samples
were classified based on (B) the mechanism of resistance, and (C) the anti-
biotic to which they confer resistance. FCA, fluoroquinolone, quinolone,
florfenicol, chloramphenicol, and amphenicol resistance genes; MLSB,
Macrolide-Lincosamide-Streptogramin B resistance.
decreases in soil samples but is still elevated, with average en-
richment of nearly 100-fold, and some genes were enriched over
1,000-fold compared with the soil control. The Putian soil had
more unique resistance genes enriched at a higher level than the
other two farm soils. When combining the data from all farms, 56,
44, and 17 unique ARGs were statistically elevated in the manure,
compost, and soil samples, respectively.
Transposase Enrichment. Transposases, in parallel to ARGs, were
highly enriched (Fig. 3B). Transposases were found in all sam-
ples (Fig. 2, subgroups A and B) and were enriched up to 90,000-
fold in the manure samples and up to 1,000-fold in the soil
samples. The abundance of ARGs is highly correlated to the
levels of transposases in these farm samples (Fig. 3C) (e.g., as
high as 0.970 for correlation between the abundance of tetra-
cycline resistance genes and transposase genes) (Table S5).
Discussion
Feed Additive Use. These swine farms use a complex mixture of
growth-promoting chemicals, including antibiotics and metals.
However, the individual dosage of each chemical, when considered
alone, on these farms is not excessive compared with other farms
Zhu et al.
Expert Solution
This question has been solved!
Explore an expertly crafted, step-by-step solution for a thorough understanding of key concepts.
Step by step
Solved in 2 steps
Knowledge Booster
Learn more about
Need a deep-dive on the concept behind this application? Look no further. Learn more about this topic, biology and related others by exploring similar questions and additional content below.Recommended textbooks for you
Anatomy & Physiology
Biology
ISBN:
9781938168130
Author:
Kelly A. Young, James A. Wise, Peter DeSaix, Dean H. Kruse, Brandon Poe, Eddie Johnson, Jody E. Johnson, Oksana Korol, J. Gordon Betts, Mark Womble
Publisher:
OpenStax College
Essentials of Pharmacology for Health Professions
Nursing
ISBN:
9781305441620
Author:
WOODROW
Publisher:
Cengage
Biology 2e
Biology
ISBN:
9781947172517
Author:
Matthew Douglas, Jung Choi, Mary Ann Clark
Publisher:
OpenStax
Anatomy & Physiology
Biology
ISBN:
9781938168130
Author:
Kelly A. Young, James A. Wise, Peter DeSaix, Dean H. Kruse, Brandon Poe, Eddie Johnson, Jody E. Johnson, Oksana Korol, J. Gordon Betts, Mark Womble
Publisher:
OpenStax College
Essentials of Pharmacology for Health Professions
Nursing
ISBN:
9781305441620
Author:
WOODROW
Publisher:
Cengage
Biology 2e
Biology
ISBN:
9781947172517
Author:
Matthew Douglas, Jung Choi, Mary Ann Clark
Publisher:
OpenStax
Essentials Health Info Management Principles/Prac…
Health & Nutrition
ISBN:
9780357191651
Author:
Bowie
Publisher:
Cengage
Biochemistry
Biochemistry
ISBN:
9781305577206
Author:
Reginald H. Garrett, Charles M. Grisham
Publisher:
Cengage Learning