Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach.

AIMS: The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources. METHOD AND RESULTS: Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH4 -N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful. CONCLUSIONS: Dairy-based composts are less likely to support E. coli survival than poultry-based composts. SIGNIFICANCE AND IMPACT OF THE STUDY: Results aid in risk assessment of the use of different types of manure-based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.

Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest.

Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum-likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated 'species' richness ranged from 464 to 502 within the four 40 x 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil-dwelling plant-parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.

Response of soil invertebrates to disturbance across three resource regions in North Carolina.

We evaluated the potential of soil microarthropods and enchytraeid worms to be useful as bioindicators of soil condition in forest, wetland, and agricultural ecosystems over a range of ecoregions. Selected mesofauna and soil characteristics in soil and litter in relatively undisturbed and disturbed examples of each of three ecosystems within each of three land resource regions were monitored over two years. Optimal times of year to sample these organisms as indicators of disturbance were April, May, July and September. No single measure reflected disturbance across all three ecosystems. Among forest sites, Simpson's diversity index, evenness, abundance of ants, and proportion of enchytraeids in the mesofauna differed between soils of different disturbance levels. Among agricultural sites, richness, evenness, abundance of mites, and proportions of collembolans and of enchytraeids in the mesofauna differed between disturbance levels. Among wetland sites, Shannon's and Simpson's diversity indices, richness based on the total mesofauna, and abundances of mites, diplurans, ants, and isotomid and onychiurid collembolans differed between disturbance levels. Covariates most frequently associated with abundance and diversity of the measured mesofauna were soil electrical conductivity, available N, organic matter, and pH. Canonical correspondence analysis provided information somewhat different to bivariate analysis. Using both approaches to examine soil and litter taxa that have distinctive responses to disturbance may help to identify candidate groups applicable for use in large-scale environmental monitoring programs.

Third position codon composition suggests two classes of genes within the Cauliflower mosaic virus genome.

The translation of viral mRNAs by host ribosomes is essential for infection. Hence, codon usage of virus genes may influence efficiency of infection. In addition, composition of nucleotides in the third position within codons of genes can reflect evolutionary relationships. In this study, third position codon composition was examined for the seven genes of eight Cauliflower mosaic virus isolates. Genes IV-VII had similar codon composition values and were termed Class 1 genes. Genes I-III possessed corresponding codon composition values and were termed Class 2 genes. The codon composition values of Class 1 and genes differed significantly. Neither Class 1 nor Class 2 genes had codon composition values identical to that of the host plant, Arabidopsis thaliana. However, Class 1 genes possessed codon composition values closer to those of the host than Class 2 genes. Examination of the genomes of three Rous sarcoma virus isolates indicated that codon composition values were similar for the gag, pol, and env genes but these genes differed significantly from the src genes. Since codon composition values for Rous sarcoma virus distinguished a "foreign" gene from the rest of the viral genome, it is possible that the Cauliflower mosaic virus genome is composed of genes from two different sources. Others have suggested that Cauliflower mosaic virus evolved in this manner and our data provide support for this hypothesis.

Role of nematodes in soil health and their use as indicators.

The composition of nematode communities (plant-parasitic and free-living) may be used as bioindicators of soil health or condition because composition correlates well with nitrogen cycling and decomposition, two critical ecological processes in soil. Maturity and trophic diversity indices withstand statistical rigor better than do abundances, proportions, or ratios of trophic groups. Maturity indices respond to a variety of land-management practices, based largely on inferred life history characteristics of families. Similarity indices may be more useful than diversity indices because they reflect taxon composition. Improving existing indices or developing alternative indices refined by a greater understanding of the biology of key taxa may enhance the utility of nematodes as bioindicators.

Nematode communities in organically and conventionally managed agricultural soils.

Interpretation of nematode community indices requires a reference to a relatively undisturbed community. Maturity and trophic diversity index values were compared for five pairs of certified organically and conventionally managed soils in the Piedmont region of North Carolina. Available nitrogen (nitrate, ammonium) was estimated at various lag periods relative to times of sampling for nematode communities to determine the strength of correlative relationship between nematode communities and nitrogen availability. Soils were sampled six times yearly in 1993 and 1994 to determine the best time of year to sample. Maturity values for plant parasites were greater in organically than conventionally managed soils, and differences between management systems were greater in fall than spring months. However, other maturity and diversity indices did not differ between the two management practices. Differences in crop species grown in the two systems accounted for most differences observed in the community of plant-parasitic nematodes. Indices of free-living nematodes were correlated negatively with concentrations of ammonium, whereas indices of plant-parasitic nematodes were correlated positively with concentrations of nitrate. Due to the similarity of index values between the two systems, organically managed soils are not suitable reference sites for monitoring and assessing the biological aspects of soil quality for annually harvested crops.

Sampling for regional monitoring of nematode communities in agricultural soils.

Regional assessment of nematode communities to monitor the condition or ecological health of agricultural soils requires sampling programs with measures of known reliability and the ability to detect differences over time. Numbers of fields sampled in a region, samples taken per field, and subsamples assayed per sample must be balanced with cost to provide the best sampling scheme. We used components of variance from statewide surveys in North Carolina (1992) and Nebraska (1993) to estimate number of (i) fields to be sampled; (ii) 20-core, composite soil samples to be obtained for each field; and (iii) subsamples to be assayed for each composite sample to detect a specified amount of change in index values within a geographic region. Variances for these three components were used to estimate the degree of reliability for five ecologically based indices (four measures of maturity and one of diversity) of nematode communities. Total variance for maturity and diversity indices, based upon communities of free-living nematodes, was greater in North Carolina than in Nebraska; the opposite was true for indices based strictly upon maturity of communities of plant-parasitic nematodes or of all nematodes in soil. Variability within samples was greater in North Carolina than in Nebraska, especially for maturity indices based only upon free-living nematodes. We identified two possible sampling strategies for a regional survey: Option 1, with two independent samples per field and a single subsample assayed per sample, which would provide a reliability ratio value >/=0.6 for most indices; and Option 2, with three independent samples per field and two subsamples assayed per sample, which would provide a reliability ratio value >/=0.7 for several indices. When cost was considered, Option 1 was the better strategy. Number of fields to be sampled within a region or state varied with the index chosen; with specific indices, however, a 10% change in mean index value could be detected with a sample of 50 to 100 fields.

Influence of age structure of plant populations on damping-off epidemics.

Germination synchrony may facilitate damping-off epidemics by creating a high density of uniformly susceptible individuals. We tested the hypothesis that synchronous germination causes increased seed and seedling mortality from damping-off in two legume species attacked by the fungal pathogen, Pythium aphanidermatum. Glycine max exhibited rapid, synchronous germination compared to its progenitor, G. soja, and suffered greater mortality from both pre-and postemergent damping-off in controlled environment experiments. However, when mixed-aged populations of G. max were created experimentally by staggering planting times, a significant increase in damping-off mortality occurred. In G. soja, which typically has mixed-aged populations due to asynchronous germination, experimental populations with an even-aged distribution also suffered increased damping-off mortality. Hence, the relationship between population age structure and damping-off mortality was species-specific. We propose that species differences in the duration of individual seedling susceptibility to disbase interact with population age structure to control the cutcome of damping-off epidemics.