Leaching of Mycobacterium avium Subsp paratuberculosis in Soil under In Vitro Conditions

Mycobacterium avium subsp paratuberculosis (Map), the causative agent of Johne's disease, has a robust ability to survive in the environment. However, the ability of Map to migrate through soil to drainage tiles or ground water, leave the farm, and leak into local watersheds is inadequately documented. In order to assess the ability of Map to leach through soil, two laboratory experiments were conducted. In the first study, 8 columns (30 cm long each) of a sandy loam soil were treated with pure cultures of Map. Two soil moisture levels and two Map concentrations were used. The columns were leached with 500 mL of water once a week for three weeks, the leachate was collected, and detection analysis was conducted. In the second experiment, manure from Map negative cows (control) and Map high shedder cows (treatment) were deposited on 8 similar columns and the columns were leached with 500 mL of water once a week for four weeks. Map detection and numeration in leachate samples were done with RT-PCR and culture techniques, respectively. Using RT-PCR, Map could be detected in the leachates in both experiments for several weeks but could only be recovered using culture techniques in experiment one. Combined, these experiments indicate the potential for Map to move through soil as a result of rainfall or irrigation following application

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Mycobacterium avium subsp paratuberculosis (Map), the causative agent of Johne's disease, has a robust ability to survive in the environment. However, the ability of Map to migrate through soil to drainage tiles or ground water, leave the farm, and leak into local watersheds is inadequately documented. In order to assess the ability of Map to leach through soil, two laboratory experiments were conducted. In the first study, 8 columns (30 cm long each) of a sandy loam soil were treated with pure cultures of Map. Two soil moisture levels and two Map concentrations were used. The columns were leached with 500 mL of water once a week for three weeks, the leachate was collected, and detection analysis was conducted. In the second experiment, manure from Map negative cows (control) and Map high shedder cows (treatment) were deposited on 8 similar columns and the columns were leached with 500 mL of water once a week for four weeks. Map detection and numeration in leachate samples were done with RT-PCR and culture techniques, respectively. Using RT-PCR, Map could be detected in the leachates in both experiments for several weeks but could only be recovered using culture techniques in experiment one. Combined, these experiments indicate the potential for Map to move through soil as a result of rainfall or irrigation following application

Longitudinal river zonation in the tropics: examples of fish and caddisflies from endorheic Awash river, Ethiopia

Primary Research PaperSpecific concepts of fluvial ecology are well studied in riverine ecosystems of the temperate zone but poorly investigated in the Afrotropical region. Hence, we examined the longitudinal zonation of fish and adult caddisfly (Trichoptera) assemblages in the endorheic Awash River (1,250 km in length), Ethiopia. We expected that species assemblages are structured along environmental gradients, reflecting the pattern of large-scale freshwater ecoregions. We applied multivariate statistical methods to test for differences in spatial species assemblage structure and identified characteristic taxa of the observed biocoenoses by indicator species analyses. Fish and caddisfly assemblages were clustered into highland and lowland communities, following the freshwater ecoregions, but separated by an ecotone with highest biodiversity. Moreover, the caddisfly results suggest separating the heterogeneous highlands into a forested and a deforested zone. Surprisingly, the Awash drainage is rather species-poor: only 11 fish (1 endemic, 2 introduced) and 28 caddisfly species (8 new records for Ethiopia) were recorded from the mainstem and its major tributaries. Nevertheless, specialized species characterize the highland forests, whereas the lowlands primarily host geographically widely distributed species. This study showed that a combined approach of fish and caddisflies is a suitable method for assessing regional characteristics of fluvial ecosystems in the tropicsinfo:eu-repo/semantics/publishedVersio

Survival of Escherichia coli in the environment: fundamental and public health aspects

In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health. The ISME Journal (2011) 5, 173-183; doi:10.1038/ismej.2010.80; published online 24 June 2010NATO [ESP.EAP.CLG 981785]; The Soil Biotechnology Foundationinfo:eu-repo/semantics/publishedVersio

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha(-1) over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 10(7), 2.5 × 10(7), and 2.1 × 10(7)copies g(-1) soil, respectively) than in the control (8.1 × 10(6) copies g(-1) soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 10(7) copies g(-1) soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA

The impact of on-site wastewater treatment systems on the nitrogen load and baseflow in urbanizing watersheds of Metropolitan Atlanta, Georgia

Proceedings of the 2013 Georgia Water Resources Conference, April 10-11, 2013, Athens, Georgia.On-site wastewater treatment systems (OWTSs) are widely used in the Southeastern United States for municipal wastewater treatment. As urban and suburban populations increase, the use of OWTSs is expected to further increase. This region heavily depends on surface waters for its water supply, therefore, the impact of OWTSs on surface water quality and quantity must be investigated. Conventional OWTSs can be potential sources of N pollution for groundwater and streams that can cause human health concerns and stimulate algal growth resulting in eutrophication. The overall goal of this project is to determine the impact of OWTSs on the N load and baseflow in urbanizing watersheds of Ocmulgee and Oconee River basins in Georgia. This paper presents preliminary results of the differences in the N load and baseflow as well as other water quality indicators such as electrical conductivity (EC) and chloride (Cl-) in streams of watersheds impacted by high (HD) and low density (LD) OWTSs. Synoptic samples and discharge measurements of 24 watersheds were taken 3 times per year in fall, spring, and summer under baseflow conditions. EC and Cl- concentrations were significantly higher in HD OWTS watersheds for all three sampling events. N concentrations were not statistically different between HD and LD watersheds for all three sampling events. Baseflow measurements in the fall and spring were not statistically different between HD and LD watersheds, but summer measurements were significantly higher in the HD watersheds. The results indicate the presence of OWTS effluent in streams of watersheds with HD OWTSs, while N analysis indicates a reduction in concentration through dilution and denitrification. However, increased baseflow in watersheds impacted by HD OWTSs results in an increase in total N load. Further analysis is needed to accurately determine and quantify the impact of OWTSs on water quality and quantity at the watershed-scale.Sponsored by: Georgia Environmental Protection Division; U.S. Department of Agriculture, Natural Resources Conservation Service; Georgia Institute of Technology, Georgia Water Resources Institute; The University of Georgia, Water Resources Faculty.This book was published by Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, Georgia 30602-2152. The views and statements advanced in this publication are solely those of the authors and do not represent official views or policies of The University of Georgia, the Georgia Water Research Institute as authorized by the Water Research Institutes Authorization Act of 1990 (P.L. 101-307) or the other conference sponsors