bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benthic Bacterial and Fungal Productivity and Carbon Turnover in a Freshwater Marsh
Authors: Buesing Nanna , Gessner Mark O. 
Published: January 2006

ABSTRACT

Heterotrophic bacteria and fungi are widely recognized as crucial mediators of carbon, nutrient, and energy flow in ecosystems, yet information on their total annual production in benthic habitats is lacking. To assess the significance of annual microbial production in a structurally complex system, we measured production rates of bacteria and fungi over an annual cycle in four aerobic habitats of a littoral freshwater marsh. Production rates of fungi in plant litter were substantial (0.2 to 2.4 mg C g
−1
C) but were clearly outweighed by those of bacteria (2.6 to 18.8 mg C g
−1
C) throughout the year. This indicates that bacteria represent the most actively growing microorganisms on marsh plant litter in submerged conditions, a finding that contrasts strikingly with results from both standing dead shoots of marsh plants and submerged plant litter decaying in streams. Concomitant measurements of microbial respiration (1.5 to 15.3 mg C-CO
2
g
−1
of plant litter C day
−1
) point to high microbial growth efficiencies on the plant litter, averaging 45.5%. The submerged plant litter layer together with the thin aerobic sediment layer underneath (average depth of 5 mm) contributed the bulk of microbial production per square meter of marsh surface (99%), whereas bacterial production in the marsh water column and epiphytic biofilms was negligible. The magnitude of the combined production in these compartments (∼1,490 g C m
−2
year
−1
) highlights the importance of carbon flows through microbial biomass, to the extent that even massive primary productivity of the marsh plants (603 g C m
−2
year
−1
) and subsidiary carbon sources (∼330 g C m
−2
year
−1
) were insufficient to meet the microbial carbon demand. These findings suggest that littoral freshwater marshes are genuine hot spots of aerobic microbial carbon transformations, which may act as net organic carbon importers from adjacent systems and, in turn, emit large amounts of CO
2
(here, ∼870 g C m
−2
year
−1
) into the atmosphere.
Prevalence and Transmission of Honeybee Viruses
Authors: Chen Y. P. , Pettis J. S. , Collins A. , Feldlaufer M. F. 
Published: January 2006

ABSTRACT
Transmission mechanisms of six honeybee viruses, including acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Kashmir bee virus (KBV), and sacbrood bee virus (SBV), in honey bee colonies were investigated by reverse transcription-PCR (RT-PCR) methods. The virus status of individual queens was evaluated by examining the presence of viruses in the queens' feces and tissues, including hemolymph, gut, ovaries, spermatheca, head, and eviscerated body. Except for head tissue, all five tissues as well as queen feces were found to be positive for virus infections. When queens in bee colonies were identified as positive for BQCV, DWV, CBPV, KBV, and SBV, the same viruses were detected in their offspring, including eggs, larvae, and adult workers. On the other hand, when queens were found positive for only two viruses, BQCV and DWV, only these two viruses were detected in their offspring. The presence of viruses in the tissue of ovaries and the detection of the same viruses in queens' eggs and young larvae suggest vertical transmission of viruses from queens to offspring. To our knowledge, this is the first evidence of vertical transmission of viruses in honeybee colonies.
Slow-Release Inoculation Allows Sustained Biodegradation of γ-Hexachlorocyclohexane
Authors: Mertens Birgit , Boon Nico , Verstraete Willy 
Published: January 2006

ABSTRACT

This study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (γ-hexachlorocyclohexane [γ-HCH]). Slow-release inoculation of
Sphingomonas
sp. γ 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. The capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluated in comparison with inoculation of free-living cells. Encapsulation of cells in tubes caused the removal of lindane by adsorption to the silicone tubes but also ensured prolonged biodegradation activity. Lindane degradation persisted 2.2 and 1.4 times longer for liquid and soil slurry microcosms, respectively, than that for inoculation with free cells. While inoculation of free-living cells led to a loss in lindane-degrading activity in limited time intervals, encapsulation in tubes allowed for a more stable actively degrading community. The loss in degrading activity was linked to the loss of the
linA
gene, encoding γ-HCH dehydrochlorinase (LinA), which is involved in the initial steps of the lindane degradation pathway. This work shows that a slow-release inoculation approach using a catabolic strain encapsulated in open-ended tubes is a promising bioaugmentation tool for contaminated sites, as it can enhance pollutant removal and can prolong the degrading activity in comparison with traditional inoculation strategies.
Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms
Authors: Kourtev Peter S. , Nakatsu Cindy H. , Konopka Allan 
Published: January 2006

ABSTRACT

Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO
2
) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the
Geobacteraceae
family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO
2
production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as
Pantoea
,
Pseudomonas
, and
Enterobacter
species.
Geobacteraceae
were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.
Distinguishing Nitrous Oxide Production from Nitrification and Denitrification on the Basis of Isotopomer Abundances
Authors: Sutka R. L. , Ostrom N. E. , Ostrom P. H. , Breznak J. A. , Gandhi H. , Pitt A. J. , Li F. 
Published: January 2006

ABSTRACT

The intramolecular distribution of nitrogen isotopes in N
2
O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N
2
O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N
2
O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 ± 1.2‰, 32.5 ± 0.6‰, and 35.6 ± 1.4‰ for
Nitrosomonas europaea
,
Nitrosospira multiformis
, and
Methylosinus trichosporium
, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N
2
O from ammonia oxidation by
N. europaea
(31.4 ± 4.2‰) was similar to that produced during hydroxylamine oxidation (33.5 ± 1.2‰) and distinct from that produced during nitrifier denitrification by
N. multiformis
(0.1 ± 1.7‰), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N
2
O produced during nitrite reduction by the denitrifiers
Pseudomonas chlororaphis
and
Pseudomonas aureofaciens
(−0.6 ± 1.9‰ and −0.5 ± 1.9‰, respectively) were similar to those during nitrate reduction (−0.5 ± 1.9‰ and −0.5 ± 0.6‰, respectively), indicating no influence of either substrate on site preference. Site preferences of ∼33‰ and ∼0‰ are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N
2
O.
Sources of
Campylobacter
spp. Colonizing Housed Broiler Flocks during Rearing
Authors: Bull S. A. , Allen V. M. , Domingue G. , Jørgensen F. , Frost J. A. , Ure R. , Whyte R. , Tinker D. , Corry J. E. L. , Gillard-King J. , Humphrey T. J. 
Published: January 2006

ABSTRACT

The study aimed to identify sources of campylobacter in 10 housed broiler flocks from three United Kingdom poultry companies. Samples from (i) the breeder flocks, which supplied the broilers, (ii) cleaned and disinfected houses prior to chick placement, (iii) the chickens, and (iv) the environments inside and outside the broiler houses during rearing were examined. Samples were collected at frequent intervals and examined for
Campylobacter
spp. Characterization of the isolates using multilocus sequence typing (MLST), serotyping, phage typing, and
flaA
restriction fragment length polymorphism typing was performed. Seven flocks became colonized during the growing period.
Campylobacter
spp. were detected in the environment surrounding the broiler house, prior to as well as during flock colonization, for six of these flocks. On two occasions, isolates detected in a puddle just prior to the birds being placed were indistinguishable from those colonizing the birds. Once flocks were colonized, indistinguishable strains of campylobacter were found in the feed and water and in the air of the broiler house.
Campylobacter
spp. were also detected in the air up to 30 m downstream of the broiler house, which raises the issue of the role of airborne transmission in the spread of campylobacter. At any time during rearing, broiler flocks were colonized by only one or two types determined by MLST but these changed, with some strains superseding others. In conclusion, the study provided strong evidence for the environment as a source of campylobacters colonizing housed broiler flocks. It also demonstrated colonization by successive campylobacter types determined by MLST during the life of a flock.
Prevalence and Virulence Factors ofEscherichia coliSerogroups O26, O103, O111, and O145 Shed by Cattle in Scotland
Authors: Pearce M. C. , Evans J. , McKendrick I. J. , Smith A. W. , Knight H. I. , Mellor D. J. , Woolhouse M. E. J. , Gunn G. J. , Low J. C. 
Published: January 2006

ABSTRACTA national survey was conducted to determine the prevalence ofEscherichia coliO26, O103, O111, and O145 in feces of Scottish cattle. In total, 6,086 fecal pats from 338 farms were tested. The weighted mean percentages of farms on which shedding was detected were 23% forE. coliO26, 22% forE. coliO103, and 10% forE. coliO145. The weighted mean prevalences in fecal pats were 4.6% forE. coliO26, 2.7% forE. coliO103, and 0.7% forE. coliO145. NoE. coliO111 was detected. Farms with cattle sheddingE. coliserogroup O26, O103, or O145 were widely dispersed across Scotland and were identified most often in summer and autumn. However, on individual farms, fecal shedding ofE. coliO26, O103, or O145 was frequently undetectable or the numbers of pats testing positive were small. For serogroup O26 or O103 there was clustering of positive pats within management groups, and the presence of an animal shedding one of these serogroups was a positive predictor for shedding by others, suggesting local transmission of infection. Carriage ofvtxwas rare inE. coliO103 and O145 isolates, but 49.0% ofE. coliO26 isolates possessedvtx, invariablyvtx1alone orvtx1andvtx2together. The carriage ofeaeandehxAgenes was highly associated in all three serogroups. AmongE. coliserogroup O26 isolates, 28.9% carriedvtx,eae, andehxA—a profile consistent withE. coliO26 strains known to cause human disease.
Quantification of
Campylobacter
Species Cross-Contamination during Handling of Contaminated Fresh Chicken Parts in Kitchens
Authors: Luber Petra , Brynestad Sigrid , Topsch Daniela , Scherer Kathrin , Bartelt Edda 
Published: January 2006

ABSTRACT

Numerous outbreak investigations and case-control studies for campylobacteriosis have provided evidence that handling
Campylobacter
-contaminated chicken products is a risk factor for infection and illness. There is currently extremely limited quantitative data on the levels of
Campylobacter
cross-contamination in the kitchen, hindering risk assessments for the pathogen commodity combination of
Campylobacter
and chicken meat. An exposure assessment needs to quantify the transfer of the bacteria from chicken to hands and the kitchen environment and from there onto ready-to-eat foods. We simulated some typical situations in kitchens and quantified the
Campylobacter
transfer from naturally contaminated chicken parts most commonly used in Germany. One scenario simulated the seasoning of five chicken legs and the reuse of the same plate for cooked meat. In another, five chicken breast filets were cut into small slices on a wooden board where, without intermediate cleaning, a cucumber was sliced. We also investigated the transfer of the pathogen from chicken via hands to a bread roll. The numbers of
Campylobacter
present on the surfaces of the chicken parts, hands, utensils, and ready-to-eat foods were detected by using Preston enrichment and colony counting after surface plating on Karmali agar. The mean transfer rates from legs and filets to hands were 2.9 and 3.8%. The transfer from legs to the plate (0.3%) was significantly smaller (
P
< 0.01) than the percentage transferred from filets to the cutting board and knife (1.1%). Average transfer rates from hands or kitchen utensils to ready-to-eat foods ranged from 2.9 to 27.5%.
Protective Effects of Organic Acids on Survival of
Escherichia coli
O157:H7 in Acidic Environments
Authors: Bjornsdottir K. , Breidt F. , McFeeters R. F. 
Published: January 2006

ABSTRACT

Outbreaks of disease due to acid-tolerant bacterial pathogens in apple cider and orange juice have raised questions about the safety of acidified foods. Using gluconic acid as a noninhibitory low-pH buffer, we investigated the killing of
Escherichia coli
O157:H7 strains in the presence or absence of selected organic acids (pH of 3.2), with ionic strength adjusted to 0.60 to 0.68. During a 6-h exposure period in buffered solution (pH 3.2), we found that a population of acid-adapted
E. coli
O157:H7 strains was reduced by 4 log cycles in the absence of added organic acids. Surprisingly, reduced lethality for
E. coli
O157:H7 was observed when low concentrations (5 mM) of fully protonated acetic, malic, or
l
-lactic acid were added. Only a 2- to 3-log reduction in cell counts was observed, instead of the 4-log reduction attributed to pH effects in the buffered solution. Higher concentrations of these acids at the same pH aided in the killing of the
E. coli
cells, resulting in a 6-log or greater reduction in cell numbers. No protective effect was observed when citric acid was added to the
E. coli
cells.
d
-Lactic acid had a greater protective effect than other acids at concentrations of 1 to 20 mM. Less than a 1-log decrease in cell numbers occurred during the 6-h exposure to pH 3.2. To our knowledge, this is the first report of the protective effect of organic acids on the survival of
E. coli
O15:H7 under low-pH conditions.
Leaching of Phage from Class B Biosolids and Potential Transport through Soil
Authors: Chetochine Alexandra S. , Brusseau Mark L. , Gerba Charles P. , Pepper Ian L. 
Published: January 2006

ABSTRACT

The objective of this study was to investigate leaching and transport of viruses, specifically those of an indigenous coliphage host specific to
Escherichia coli
ATTC 15597 (i.e., MS-2), from a biosolid-soil matrix. Serial extractions of 2% and 7% (solids) class B biosolid matrices were performed to determine the number of phage present in the biosolids and to evaluate their general leaching potential. Significant concentrations of coliphage were removed from the biosolids for each sequential extraction, indicating that many phage remained associated with the solid phase. The fact that phage was associated with or attached to solid particles appeared to influence the potential for release and subsequent transport of phage under saturated-flow conditions, which was examined in a series of column experiments. The results indicated that less than 8% of the indigenous coliphage initially present in the biosolids leached out of the biosolid-soil matrix. A fraction of this was subsequently transported through the sandy porous medium with minimal retention. The minimal retention observed for the indigenous phage, once released from the biosolids, was consistent with the results of control experiments conducted to examine MS-2 transport through the porous medium.
Impact of Inoculum Preparation and Storage Conditions on the Response of
Escherichia coli
O157:H7 Populations to Undercooking and Simulated Exposure to Gastric Fluid
Authors: Stopforth Jarret D. , Skandamis Panagiotis N. , Ashton Laura V. , Geornaras Ifigenia , Kendall Patricia A. , Belk Keith E. , Scanga John A. , Smith Gary C. , Sofos John N. 
Published: January 2006

ABSTRACT

This study evaluated the impact of inoculum preparation and storage conditions on the response of
Escherichia coli
O157:H7 exposed to consumer-induced stresses simulating undercooking and digestion. Lean beef tissue samples were inoculated with
E. coli
O157:H7 cultures prepared in tryptic soy broth or meat decontamination runoff fluids (WASH) or detached from moist biofilms or dried biofilms formed on stainless steel coupons immersed in inoculated WASH. After inoculation, the samples were left untreated or dipped for 30 s each in hot (75°C) water followed by lactic acid (2%, 55°C), vacuum packaged, stored at 4 (28 days) or 12°C (16 days), and periodically transferred to aerobic storage (7°C for 5 days). During storage, samples were exposed to sequential heat (55°C; 20 min) and simulated gastric fluid (adjusted to pH 1.0 with HCl; 90 min) stresses simulating consumption of undercooked beef. Under the conditions of this study, cells originating from inocula of planktonic cells were, in general, more resistant to heat and acid than cells from cultures grown as biofilms and detached prior to meat inoculation. Heat and acid tolerance of cells on meat stored at 4°C was lower than that of cells on nondecontaminated meat stored at 12°C, where growth occurred during storage. Decontamination of fresh beef resulted in injury that inhibited subsequent growth of surviving cells at 12°C, as well as in decreases in resistance to subsequent heat and acid stresses. The shift of pathogen cells on beef stored under vacuum at 4°C to aerobic storage did not affect cell populations or subsequent survival after sequential exposure to heat and simulated gastric fluid. However, the transfer of meat stored under vacuum at 12°C to aerobic storage resulted in reduction in pathogen counts during aerobic storage and sensitization of survivors to the effects of sequential heat and acid exposure.
Ochratoxin A Production and Amplified Fragment Length Polymorphism Analysis of
Aspergillus carbonarius
,
Aspergillus tubingensis
, and
Aspergillus niger
Strains Isolated from Grapes in Italy
Authors: Perrone Giancarlo , Mulè Giuseppina , Susca Antonia , Battilani Paola , Pietri Amedeo , Logrieco Antonio 
Published: January 2006

ABSTRACT

Ochratoxin A is a potent nephrotoxin and a possible human carcinogen that can contaminate various agricultural products, including grapes and wine. The capabilities of species other than
Aspergillus carbonarius
within
Aspergillus
section
Nigri
to produce ochratoxin A from grapes are uncertain, since strain identification is based primarily on morphological traits. We used amplified fragment length polymorphisms (AFLPs) and genomic DNA sequences (rRNA, calmodulin, and β-tubulin genes) to identify 77 black aspergilli isolated from grape berries collected in a 2-year survey in 16 vineyards throughout Italy. Four main clusters were distinguished, and they shared an AFLP similarity of <25%. Twenty-two of 23 strains of
A. carbonarius
produced ochratoxin A (6 to 7,500 μg/liter), 5 of 20 strains of
A. tubingensis
produced ochratoxin A (4 to 130 μg/liter), 3 of 15 strains of
A. niger
produced ochratoxin A (250 to 360 μg/liter), and none of the 19 strains of
Aspergillus
“uniseriate” produced ochratoxin A above the level of detection (4 μg/liter). These findings indicate that
A. tubingensis
is able to produce ochratoxin and that, together with
A. carbonarius
and
A. niger
, it may be responsible for the ochratoxin contamination of wine in Italy.
Anaerobic Nitrate-Dependent Iron(II) Bio-Oxidation by a Novel Lithoautotrophic Betaproteobacterium, Strain 2002
Authors: Weber Karrie A. , Pollock Jarrod , Cole Kimberly A. , O'Connor Susan M. , Achenbach Laurie A. , Coates John D. 
Published: January 2006

ABSTRACT

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)-oxidizing microbial community (2.4 × 10
3
to 1.5 × 10
4
cells g
−1
wet sediment) from which a novel anaerobic, lithoautotrophic, Fe(II)-oxidizing bacterium, strain 2002, was isolated. Analysis of the complete 16S rRNA gene sequence revealed that strain 2002 was a member of the beta subclass of the proteobacteria with 94.8% similarity to
Chromobacterium violaceum
, a bacterium not previously recognized for the ability to oxidize nitrate-dependent Fe(II). Under nongrowth conditions, both strain 2002 and
C. violaceum
incompletely reduced nitrate to nitrite with Fe(II) as the electron donor, while under growth conditions nitrate was reduced to gaseous end products (N
2
and N
2
O). Lithoautotrophic metabolism under nitrate-dependent Fe(II)-oxidizing conditions was verified by the requirement of CO
2
for growth as well as the assimilation of
14
C-labeled CO
2
into biomass. The isolation of strain 2002 represents the first example of an anaerobic, mesophilic, neutrophilic Fe(II)-oxidizing lithoautotroph isolated from freshwater samples. Our studies further demonstrate the abundance of nitrate-dependent Fe(II) oxidizers in freshwater lake sediments and provide further evidence for the potential of microbially mediated Fe(II) oxidation in anoxic environments.