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  • 11
    Publication Date: 2016-12-07
    Description: The Agricultural Act of 2014 replaced dairy product price supports and countercyclical income support payments with the Margin Protection Program for Dairy Producers. Using farm-level data, producer decisions and aggregate policy costs under a variety of risk environments and policy design alternatives are simulated. Fixed premium rates may result in budget outlays that are substantially higher than for equivalent variable-rate insurance subsidized at levels observed in revenue-based crop insurance policies. Due to the absence of adjusted gross income or production eligibility constraints, a significant portion of benefits may accrue to a small share of large dairy farms.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 12
    Publication Date: 2016-11-17
    Description: Clostridium difficile is both a hospital and community-acquired pathogen. The current study determined if C. difficile could be cultured from clinical laundry facility surfaces. A total of 240 surface samples were collected from dirty areas ( n = 120), which handle soiled clinical linens, and from clean areas ( n = 120), which process and fold the clean linens, within the University of Washington Consolidated Laundry facility in 2015. Sampling was done four times over the course of 1 year. The dirty area was significantly more contaminated than the clean area (21% vs 2%, P 〈 0.001). Clostridium difficile isolates were genetically characterized using multilocus sequence typing and PCR for the detection of genes encoding toxin A and toxin B. The MLST types 1, 2, 3, 15, 26, 34, 35, 39, 42, 43, 44, 53, 63 and 284 were identified and have previously been found in both clinical and community settings. Toxin positive isolates were identified in both the dirty ( n = 16/25) and clean areas ( n = 2/2). Seasonal variation was observed with 40% of the 27 isolates cultured in April 2015. The study suggests that soiled clinical linens may be a source of C. difficile surface contamination.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 13
    Publication Date: 2016-11-17
    Description: Polyploidy is a well-described trait in some prokaryotic organisms; however, it is unusual in marine microbes from oligotrophic environments, which typically display a tendency towards genome streamlining. The biogeochemically significant diazotrophic cyanobacterium Trichodesmium is a potential exception. With a relatively large genome and a comparatively high proportion of non-protein-coding DNA, Trichodesmium appears to allocate relatively more resources to genetic material than closely related organisms and microbes within the same environment. Through simultaneous analysis of gene abundance and direct cell counts, we show for the first time that Trichodesmium spp. can also be highly polyploid, containing as many as 100 genome copies per cell in field-collected samples and 〉600 copies per cell in laboratory cultures. These findings have implications for the widespread use of the abundance of the nifH gene (encoding a subunit of the N 2 -fixing enzyme nitrogenase) as an approach for quantifying the abundance and distribution of marine diazotrophs. Moreover, polyploidy may combine with the unusual genomic characteristics of this genus both in reflecting evolutionary dynamics and influencing phenotypic plasticity and ecological resilience.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 14
    Publication Date: 2016-11-17
    Description: Members of subdivision 1 of the phylum Acidobacteria were grown at different pH values in a new medium formulation named PSYL 5, which includes sucrose as a carbon source and other compounds (such as KH 2 PO 4 and MgSO 4 .7H 2 O). Growth rate was nearly constant at pH 5.0 and declined at pH 3–4 and 6–7. However, it was found that effects involving good carbon/nitrogen ratios and pH on the growth of the members of Acidobacteria subdivision 1 were significant, and the strongest effect of these conditions was at pH 5.0. In addition, incubation time of 48, 72, 96 and 120 h was shorter than that described previously for members of Acidobacteria subdivision 1 on solid laboratory media.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 15
    Publication Date: 2016-10-30
    Description: Plant-growth-promoting bacteria belonging to Azospirillum and Pseudomonas genera are major inhabitants of the rhizosphere. Both are increasingly commercialized as crops inoculants. Interspecific interaction in the rhizosphere is critical for inoculants aptness. The objective of this work was to evaluate Azospirillum and Pseudomonas interaction in mixed biofilms by co-cultivation of the model strains Azospirillum brasilense Sp245 and Pseudomonas protegens CHA0. The results revealed enhanced growth of both strains when co-cultured in static conditions. Moreover, Sp245 biofilm formed in plastic surfaces was increased 2-fold in the presence of CHA0. Confocal microscopy revealed highly structured mixed biofilms showing Sp245 mainly on the bottom and CHA0 towards the biofilm surface. In addition, A. brasilense biofilm was thicker and denser when co-cultured with P. protegens. In a colony–colony interaction assay, Sp245 changed nearby CHA0 producing small colony phenotype, which accounts for a diffusible metabolite mediator; though CHA0 spent medium did not affect Sp245 colony phenotype. Altogether, these results point to a cooperative interaction between A. brasilense Sp245 and P. protegens CHA0 in which both strains increase their static growth and produce structured mixed biofilms with a strain-specific distribution.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 16
    Publication Date: 2016-10-30
    Description: Phosphorus (P) is a critical, non-renewable nutrient; yet excess discharges can lead to eutrophication and deterioration of water quality. Thus, P removal from water must be coupled with P recovery to achieve sustainable P management. P-specific proteins provide a novel, promising approach to recover P from water. Bacterial phosphate-binding proteins (PBPs) are able to effectively remove phosphate, achieving extremely low levels in water (i.e. 0.015 mg-P L –1 ). A prerequisite of using PBP for P recovery, however, is not only removal, but also controlled P release, which has not yet been reported. Phosphate release using recombinant PBP-expressing Escherichia coli was explored in this study. Escherichia coli was genetically modified to overexpress PBP in the periplasmic space. The impacts of ionic strength, temperature and pH on phosphate release were assessed. PBP-expressed E. coli demonstrated consistently superior ability to adsorb more phosphate from liquid and release more phosphate under controlled conditions relative to negative controls (unexpressed PBP E. coli and E. coli K12). Lower pH (3.8), higher temperature (35ºC) and higher ionic strength (100 mM KCl) facilitated increased phosphate release, providing a maximum of 2.1% P recovery within 3 h. This study provides proof of concept of the feasibility of using PBP to recover P.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 17
    Publication Date: 2016-10-26
    Description: Knowledge about the factors shaping the rumen microbiota in wild animals is limited. Therefore, the aim of this study was to compare the microbiota from the three cervid species moose ( Alces alces , n = 5), red deer ( Cervus elaphus , n = 4) and roe deer ( Capreolus capreolus , n = 12), sharing the same habitat. Using deep 16S rRNA gene sequencing, we found that the largest species moose had the highest number of unique operational taxonomic units. Furthermore, red deer and moose shared more of the microbiota, compared with the smallest species, roe deer, with Firmicutes and Euryarchaeota being significantly overrepresented for the shared microbiota. These differences could not be explained by diet or range. The animals largely shared the same range, and there are no systematic differences in diet. We therefore believe rumen physiology can be one of the main contributing factors to the observed distribution of the rumen microbiota in cervid species.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 18
    Publication Date: 2016-10-12
    Description: Mesorhizobium loti MAFF303099 has a functional Type III secretion system (T3SS) that is involved in the determination of competitiveness for legume nodulation. Here we demonstrate that the transcriptional factor TtsI, which positively regulates T3SS genes expression, is involved in a negative regulation of M. loti swimming motility in soft-agar. Conditions that induce T3SS expression affect flagella production. The same conditions also affect promoter activity of M. loti visN gene, a homolog to the positive regulator of flagellar genes that has been described in other rhizobia. Defects in T3SS complex assembly at membranes limited the negative regulation of motility by the expression of TtsI.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 19
    Publication Date: 2016-10-12
    Description: Carbonyl sulfide (COS) is an atmospheric trace gas and one of the sources of stratospheric aerosol contributing to climate change. Although one of the major sinks of COS is soil, the distribution of COS degradation ability among bacteria remains unclear. Seventeen out of 20 named bacteria belonging to Actinomycetales had COS degradation activity at mole fractions of 30 parts per million by volume (ppmv) COS. Dietzia maris NBRC 15801 T and Mycobacterium sp. THI405 had the activity comparable to a chemolithoautotroph Thiobacillus thioparus THI115 that degrade COS by COS hydrolase for energy production. Among 12 bacteria manifesting rapid degradation at 30 ppmv COS, D. maris NBRC 15801 T and Streptomyces ambofaciens NBRC 12836 T degraded ambient COS (~500 parts per trillion by volume). Geodermatophilus obscurus NBRC 13315 T and Amycolatopsis orientalis NBRC 12806 T increased COS concentrations. Moreover, six of eight COS-degrading bacteria isolated from soils had partial nucleotide sequences similar to that of the gene encoding clade D of β-class carbonic anhydrase, which included COS hydrolase. These results indicate the potential importance of Actinomycetes in the role of soils as sinks of atmospheric COS.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 20
    Publication Date: 2016-09-17
    Description: A composite transposon is a mobile genetic element consisting of two insertion sequences (ISs) flanking a segment of cargo DNA often containing antibiotic resistance (AR) genes. Composite transposons can move as a discreet unit. There have been recently several reports on a novel mechanism of movement of an IS 26 -based composite transposon through the formation of a translocatable unit (TU), carrying the internal DNA segment of a composite transposon and one copy of a flanking IS. In this study, we determined the presence of composite transposons and TUs in human oral metagenomic DNA using PCR primers from common IS elements. Analysis of resulting amplicons showed four different IS 1216 composite transposons and one IS 257 composite transposon in our metagenomic sample. As our PCR strategy would also detect TUs, PCR was carried out to detect circular TUs predicted to originate from these composite transposons. We confirmed the presence of two novel TUs, one containing an experimentally proven antiseptic resistance gene and another containing a putative universal stress response protein (UspA) encoding gene. This is the first report of a PCR strategy to amplify the DNA segment on composite transposons and TUs in metagenomic DNA. This can be used to identify AR genes associated with a variety of mobile genetic elements from metagenomes.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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