In-field rates of decomposition and microbial communities colonizing residues vary by depth of residue placement and plant part, but not by crop genotype for residues from two Cry1AB Bt corn hybrids and their non-transgenic isolines.

The adoption of Bt corn has been largely overshadowed by concerns about their unintended effects on human health and the environment. Residues of transgenic Bt crops decomposed more slowly than their non-transgenic isolines in one laboratory study, although no mechanism to explain these observations was proposed. If Bt crop residues were to decompose more slowly in field soils, changes in carbon cycling and nutrient availability could result. We compared the in-field decomposition rates and diversity of decomposers colonizing residues of two Cry1Ab Bt corn hybrids, active against the European corn borer, with their non-transgenic isolines in litterbags placed in a Nebraska field. After five months, we found no significant differences in either the rates of residue mass loss or in the bacterial, fungal or microarthropod communities colonizing the transgenic versus the non-transgenic residues. Instead, both residue mass loss and detritivore colonizers were significantly affected by residue placement (surface versus buried) and plant part, demonstrating that environmental factors and residue quality, not the presence of the Cry1Ab protein, were the key drivers of residue decomposition and detritivore colonization in this study

The influence of vegetation in riparian filterstrips on coliform bacteria: II. Survival in soils

Survival of total and fecal coliform bacteria was measured in the 0 to 5, 5 to 15, and 15 to 30 cm soil depths at 1, 3, 7, 14, and 90 to 120 d after swine (Sus scrofa) wastewater application to riparian filterstrips in southern Georgia during each season of the year. Vegetative treatments evaluated were: (i) 20 m grass-10 m forest, (ii) 10 m grass-20 m forest, and (iii) 10 m grass-20 m maidencane (Panicum hemitomon Schult.). During winter, spring, and summer vegetation type in riparian filterstrips did not affect survival of total and fecal coliform bacteria. Total and fecal coliform bacterial numbers were usually higher in the top 0 to 5 cm of soil than in the 5 to 15 and 15 to 30 cm soil depths in all treatments. Total and fecal coliform numbers in the 0 to 5, 5 to 15, and 15 to 30 cm depths declined approximately 10-fold every 7 to 14 d after waste application in all seasons of the year. At 90 to 120 d after waste application, total and fecal coliform numbers in the three soil depths did not differ from riparian filterstrips that did not have animal waste applied. Total coliform bacteria in the O to 5, 5 to 15, and 15 to 30 cm soil depths correlated with temperature and moisture in a curvilinear relationship (r2 = 0.80 , 0.77, and 0.64, respectively). Fecal coliform bacteria in 0 to 5, 6 to 15, and 16 to 30 cm of soil also correlated with temperature and moisture in a curvilinear relationship (r 2 = 0.56 , 0.53, and 0.53, respectively)

The influence of vegetation in riparian filterstrips on coliform bacteria: I. Movement and survival in water

Swine (Sus scrofa) wastewater was applied to three separate 4 m wide x 30 m long riparian filterstrips consisting of 20 m grass and 10 m forest, 10 m grass and 20 m forest, and 10 m grass and 20 m maidencane (Panicum hemitomon Schult.) in Southern Georgia during each season. Total and fecal coliform numbers in the applied wastewater pulse did not decline as water moved downslope regardless of vegetation type or season. The pulse of applied wastewater did not move beyond 15 m in any treatment in autumn or summer (dry seasons) and only moved beyond 7.5 m in the 20 m grass-10 m forest treatment in the summer. Total and fecal coliform numbers in soil water and shallow ground water declined by approximately 10-fold every 7 d for the first 14 d regardless of vegetative treatment or season. Soil temperature and soil moisture correlated with total coliform bacteria in both 13 m wells (r2 = 0.89) and 2.0 m wells (r2 = 0.89), and with fecal coliform bacteria in 1.5 (r2 = 0.82) and 2.0 m (r2 = 0.76) wells. Animal production operations may need to locate in warm–dry climates so animal waste can be applied to lands to help ensure enteric bacteria input to surface and ground water will not occur

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments

Modeling ecological determinants of the symbiotic performance of introduced rhizobia in tropical soils

Typescript.Thesis (Ph. D.)--University of Hawaii at Manoa, 1990.Includes bibliographical references (leaves 164-173)Microfiche.xi, 173 leaves, bound ill. 29 cmDespite selection of inoculant strains for improved nitrogen fixation capacity and competitive ability, rhizobial inoculation frequently fails to improve crop yield. The natural diversity in rhizobial population size, soils, and climates present at five sites on Maui, Hawaii, was used to examine, under field conditions, the role that indigenous rhizobia and other environmental factors play in determining the symbiotic performance of inoculant strains. Eight inoculation trials were conducted using 2-4 legumes from among 9 species which yielded 29 legume/site observations. Uninoculated, inoculated, and fertilizer N treatments evaluated the impact of indigenous rhizobial populations and soil N availability on inoculation response and yield potential. Inoculation increased yield by 62% on average. A significant inoculation response was obtained in 38% of the trials and varied by both legume species and site. Significant responses to N application, significant increases in nodule parameters, and greater than 50% nodule occupancy by inoculant rhizobia did not necessarily coincide with significant inoculation responses. Size of indigenous rhizobial populations and soil N status had the greatest influence on inoculation response. As few as 54 rhizobia g-1 soil prevented a significant response to inoculation. Inoculation response and competitive success of inoculant rhizobia were inversely related to numbers of indigenous rhizobia. Hyperbolic and log-linear equations, respectively, were most useful in quantifying these relationships. Combining indices of soil N with hyperbolic-response models yielded useful equations for determining the need to inoculate and predicting success of inoculant strains introduced into new environments. Rhizobial interstrain competition studies identified both highly and poorly competitive inoculant strains across diverse environments. Symbiotic crops attained, on average, only 88% of maximum yield as defined by the fertilizer N treatment. Nitrogen source also significantly affected crop development. Crops supplied with urea had higher rates of vegetative growth, but, delayed reproductive maturity compared with crops relying on soil N and nitrogen fixation. Results of 4 soybean trials were compared with output from an existing soybean crop model. Difficulty in accurately simulating field results was encountered, indicating the need to address both source and supply of N when predicting legume yield and inoculation success

Characterisation of dry and mucoid colonies isolated from Australian rhizobial inoculant strains for Medicago species

The presence of dry and mucoid colonies in cultures of rhizobial strains used in the production of commercial Australian inoculants is of concern for quality assurance because of the possibility of altered capacity for nodulation and nitrogen fixation by the different colony types. In this study, single colony isolates obtained from dry and mucoid colonies present in commercial cultures of Sinorhizobium meliloti were investigated to identify stability in culture, genetic identity and changes in exopolysaccharide (EPS) production, nodulation and nitrogen fixation. The 2 strains studied were WSM688 and WSM826 (Australian inoculant strains for annual and perennial medics, respectively), both of which produced only mucoid colonies on agar media when originally isolated from nodules. Dry and mucoid single colony isolates from the ‘mother cultures’ of the 2 strains exhibited stable colony phenotypes during successive subculturing in our laboratory and were shown to be most closely related to S. meliloti using 16S rRNA partial sequencing. All isolates produced at least 1 of 3 exopolysaccharides (succinoglycan, EPS II and K antigen) that are required for successful nodulation of Medicago species by S. meliloti strains, as indicated by nodulation of host legumes. Strain WSM826 isolates probably produce succinoglycan, as shown by similarity to the succinoglycan-producing strain Rm1021 in a calcofluor binding assay. In contrast to published work, there was no evidence that loss of mucoidy in dry colony isolates of either strain was associated with the presence of an insertion sequence element in the expR gene that inhibits EPS II production. For strain WSM688, dry and mucoid isolates were identical by PCR fingerprinting and showed a similar capacity to nodulate and fix nitrogen with the target host legume M. truncatula in glasshouse tests. In contrast, strain WSM826 mucoid isolates produced PCR fingerprints that were different from each other and from the WSM826 dry colony isolates. Dry and mucoid colonies may have arisen from substantial genetic change or through contamination of cultures by other S. meliloti strains. One WSM826 mucoid isolate (826-3) produced significantly lower shoot dry weight when inoculated onto both the target host M. sativa and non-target host M. truncatula, even though the capacity to nodulate both hosts was retained. This suggests that this isolate was affected in its nitrogen fixation capacity. Further research is required to identify the origin and extent of colony variation in commercial S. meliloti cultures

Effects of Participation in Organic Markets and Farmer-based Organizations on the Adoption of Soil Conservation Practices among Small-scale Farmers in Honduras

Conservation agriculture is often perceived to provide “win-win” outcomes for farmers leading to reduced erosion and off-site sedimentation, as well as improved soil fertility and productivity. However, adoption rates for conservation agriculture in many regions of the world remain below expected levels. This paper looks at the effect of organic markets in providing incentives for farmers to adopt soil conservation practices. Farmer-based organizations may link farmers to these markets by helping them overcome information deficiencies with respect to production standards and consumer preferences. Based on original survey data from 241 small-scale farm households in Honduras, we find that both participation in organic markets and farmer-based groups have positive effects on the number of soil conservation practices adopted on the farm. The results indicate that besides supply-oriented policy measures, such as the provision of technical assistance and extension, demand-related factors are likely to play an important role in sustainable soil management. Demand-oriented policy measures can include support for labeling initiatives and consumer education to facilitate value-added product differentiation and market segmentation