Cross-Disciplinary Analysis of the On-Farm Transition from Conventional to Organic Vegetable Production

This farm-scale analysis of the three-year transition to organic from conventional vegetable production tracked the changes in crop, soil, pest and management on two ranches (40 and 47 ha) in the Salinas Valley, California. Many small plantings of a diverse set of cash crop and cover crop species were used, as compared to only a few species in large monocultures in conventional production. The general trends with time were: increase in soil biological indicators, low soil nitrate pools, adequate crop nutrients, minor disease and weed problems, and sporadic mild insect damage. Some crops and cultivars consistently produced higher yields than others, relative to the maximum yield for a given crop. Differences in insect and disease damage were also observed. These results support the value of initially using a biodiverse set of taxa to reduce risk, then later choosing the best-suited varieties for optimal production. The grower used some principles of organic farming (e.g., crop diversity, crop rotation, and organic matter management), but also relied on substitution-based management, such as fertigation with soluble nutrients, initially heavy applications of organic pesticides, and use of inputs derived from off-farm sources. The organic transition was conducive to both production goals and environmental quality

Land use and climatic factors structure regional patterns in soil microbialcommunities

Aim Although patterns are emerging for macroorganisms, we have limited under- standing of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeo- graphical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass. Location Great Basin Province, Desert Province and California Floristic Province, California, USA. Methods Using phospholipid fatty acid analysis, we compared microbial com- munities across eight land-use types sampled throughout the State of California, USA (n = 1117). Results The main factor driving composition and microbial biomass was land- use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here. Main conclusions Distinct microbial communities were associated with land- use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and manage- ment factors, such as flooding, tillage and irrigation, suggest that agricultural man- agement can have larger effects on soil microbial communities than elevation and precipitation gradients

Soil microbial community composition as affected by restoration practices in California grassland

Agricultural practices have strong impacts on soil microbes including both the indices related to biomass and activity as well as those related to community composition. In a grassland restoration project in California, where native perennial bunchgrasses were introduced into non-native annual grassland after a period of intensive tillage, weeding, and herbicide use to reduce the annual seed bank, microbial community composition was investigated. Three treatments were compared: annual grassland, bare soil fallow, and restored perennial grassland. Soil profiles down to 80cm in depth were investigated in four separate layers (0–15, 15–30, 30–60, and 60–80cm) using both phospholipid ester-linked fatty acid (PLFAs) and ergosterol as biomarkers in addition to microbial biomass C by fumigation extraction. PLFA fingerprinting showed much stronger differences between the tilled bare fallow treatment vs. grasslands, compared to fewer differences between restored perennial grassland and annual grassland. The presence or absence of plants over several years clearly distinguished microbial communities. Microbial communities in lower soil layers were little affected by management practices. Regardless of treatment, soil depth caused a strong gradient of changing habitat conditions, which was reflected in Canonical Correspondence Analysis of PLFAs. Fungal organisms were associated with the presence of plants and/or litter since the total amount and the relative proportion of fungal markers were reduced in the tilled bare fallow and in lower layers of the grassland treatments. Total PLFA and soil microbial biomass were highly correlated, and fungal PLFA biomarkers showed strong correlations to ergosterol content. In conclusion, microbial communities are resilient to the grassland restoration process, but do not reflect the change in plant species composition that occurred after planting native bunchgrasses

Tomato root transcriptome response to a nitrogen-enriched soil patch

Background: Nitrogen (N), the primary limiting factor for plant growth and yield in agriculture, has a patchy distribution in soils due to fertilizer application or decomposing organic matter. Studies in solution culture oversimplify the complex soil environment where microbial competition and spatial and temporal heterogeneity challenge roots\u27 ability to acquire adequate amounts of nutrients required for plant growth. In this study, various ammonium treatments (as 15N) were applied to a discrete volume of soil containing tomato (Solanum lycopersicum) roots to simulate encounters with a localized enriched patch of soil. Transcriptome analysis was used to identify genes differentially expressed in roots 53 hrs after treatment. Results: The ammonium treatments resulted in significantly higher concentrations of both ammonium and nitrate in the patch soil. The plant roots and shoots exhibited increased levels of 15N over time, indicating a sustained response to the enriched environment. Root transcriptome analysis identified 585 genes differentially regulated 53 hrs after the treatments. Nitrogen metabolism and cell growth genes were induced by the high ammonium (65 μg NH4 +-N g-1 soil), while stress response genes were repressed. The complex regulation of specific transporters following the ammonium pulse reflects a simultaneous and synergistic response to rapidly changing concentrations of both forms of inorganic N in the soil patch. Transcriptional analysis of the phosphate transporters demonstrates cross-talk between N and phosphate uptake pathways and suggests that roots increase phosphate uptake via the arbuscular mycorrhizal symbiosis in response to N. Conclusion: This work enhances our understanding of root function by providing a snapshot of the response of the tomato root transcriptome to a pulse of ammonium in a complex soil environment. This response includes an important role for the mycorrhizal symbiosis in the utilization of an N patch. Additional files attached below

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns.

Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes

How does tillage intensity affect soil organic carbon? A systematic review protocol

Background Soils contain the greatest terrestrial carbon (C) pool on the planet. Since approximately 12% of soil C is held in cultivated soils, management of these agricultural areas has a huge potential to affect global carbon cycling; acting sometimes as a sink but also as a source. Tillage is one of the most important agricultural practices for soil management and has been traditionally undertaken to mechanically prepare soils for seeding and minimize effects of weeds. It has been associated with many negative impacts on soil quality, most notably a reduction in soil organic carbon (SOC), although still a matter of considerable debate, depending on factors such as depth of measurement, soil type, and tillage method. No tillage or reduced intensity tillage are frequently proposed mitigation measures for preservation of SOC and improvement of soil quality, for example for reducing erosion. Whilst several reviews have demonstrated benefits to C conservation of no till agriculture over intensive tillage, the general picture for reduced tillage intensity is unclear. This systematic review proposes to synthesise an extensive body of evidence, previously identified through a systematic map. Methods This systematic review is based on studies concerning tillage collated in a recently completed systematic map on the impact of agricultural management on SOC restricted to the warm temperate climate zone (i.e. boreo-temperate). These 311 studies were identified and selected systematically according to CEE guidelines. An update of the original search will be undertaken to identify newly published academic and grey literature in the time since the original search was performed in September 2013. Studies will be critically appraised for their internal and external validity, followed by full data extraction (meta-data describing study settings and quantitative study results). Where possible, studies will be included in meta-analyses examining the effect of tillage reduction (‘moderate' (i.e. shallow) and no tillage relative to ‘intensive' tillage methods such as mouldboard ploughing, where soil is turned over throughout the soil profile). The implications of the findings will be discussed in terms of policy, practice and research along with a discussion of the nature of the evidence base

Exploring the costs and outcomes of sexually transmitted infection (STI) screening interventions targeting men in football club settings: preliminary cost-consequence analysis of the SPORTSMART pilot randomised controlled trial

Background: The objective of this study was to compare the costs and outcomes of two sexually transmitted infection (STI) screening interventions targeted at men in football club settings in England, including screening promoted by team captains. Methods: A comparison of costs and outcomes was undertaken alongside a pilot cluster randomised control trial involving three trial arms: (1) captain-led and poster STI screening promotion; (2) sexual health advisor-led and poster STI screening promotion and (3) poster-only STI screening promotion (control/comparator). For all study arms, resource use and cost data were collected prospectively. Results: There was considerable variation in uptake rates between clubs, but results were broadly comparable across study arms with 50% of men accepting the screening offer in the captain-led arm, 67% in the sexual health advisor-led arm and 61% in the poster-only control arm. The overall costs associated with the intervention arms were similar. The average cost per player tested was comparable, with the average cost per player tested for the captain-led promotion estimated to be £88.99 compared with £88.33 for the sexual health advisor-led promotion and £81.87 for the poster-only (control) arm. Conclusions: Costs and outcomes were similar across intervention arms. The target sample size was not achieved, and we found a greater than anticipated variability between clubs in the acceptability of screening, which limited our ability to estimate acceptability for intervention arms. Further evidence is needed about the public health benefits associated with screening interventions in non-clinical settings so that their cost-effectiveness can be fully evaluated

Exploring the intangible economic costs of stillbirth

BACKGROUND: Compared to other pregnancy-related events, the full cost of stillbirth remains poorly described. In the UK one in every 200 births ends in stillbirth. As a follow-up to a recent study which explored the direct costs of stillbirth, this study aimed to explore the intangible costs of stillbirth in terms of their duration and economic implication. METHODS: Systematic searches identified relevant papers on the psychological consequences of stillbirth. A narrative review of the quantitative studies was undertaken. This was followed by a qualitative synthesis using meta-ethnography to identify over-arching themes common to the papers. Finally, the themes were used to generate questions proposed for use in a questionnaire to capture the intangible costs of stillbirth. RESULTS: The narrative review revealed a higher level of anxiety and depression in couples with stillbirth compared to those without stillbirth. The qualitative synthesis identified a range of psychological effects common to families that have experienced stillbirth. Both methods revealed the persistent nature of these effects and the subsequent economic burden. CONCLUSIONS: The psychological effects of stillbirth adversely impacts on the daily functioning, relationships and employment of those affected with far-reaching economic implications. Knowledge of the intangible costs of stillbirth is therefore important to accurately estimate the size of the impact on families and health services and to inform policy and decision making. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12884-015-0617-x) contains supplementary material, which is available to authorized users

Impact of antenatal antiretroviral drug exposure on the growth of children who are HIV-exposed uninfected: the national South African Prevention of Mother to Child Evaluation cohort study.

BACKGROUND: The relationship between in-utero antiretroviral (ARV) drug exposure and child growth needs further study as current data provide mixed messages. We compared postnatal growth in the first 18-months of life between children who are HIV-exposed uninfected (CHEU) with fetal exposure to ARV drugs (prophylaxis or triple-drug therapy (ART)) and CHEU not exposed to ARVs. We also examined other independent predictors of postnatal growth. METHODS: We analysed data from a national prospective cohort study of 2526 CHEU enrolled at 6-weeks and followed up 3-monthly till 18-months postpartum, between October 2012 and September 2014. Infant anthropometry was measured, and weight-for-age (WAZ) and length-for-age (LAZ) Z-scores calculated. Generalized estimation equation models were used to compare Z-scores between groups. RESULTS: Among 2526 CHEU, 617 (24.4%) were exposed to ART since -pregnancy (pre-conception ART), 782 (31.0%) to ART commencing post-conception, 879 (34.8%) to maternal ARV prophylaxis (Azidothymidine (AZT)), and 248 (9.8%) had no ARV exposure. In unadjusted analyses, preterm birth rates were higher among CHEU with no ARV exposure than in other groups. Adjusting for infant age, the mean WAZ profile was lower among CHEU exposed to pre-conception ART [-0.13 (95% confidence interval - 0.26; - 0.01)] than the referent AZT prophylaxis group; no differences in mean WAZ profiles were observed for the post-conception ART (- 0.05 (- 0.16; 0.07)), None (- 0.05 (- 0.26; 0.16)) and newly-infected (- 0.18 (- 0.48; 0.13)) groups. Mean LAZ profiles were similar across all groups. In multivariable analyses, mean WAZ and LAZ profiles  for the ARV exposure groups were completely aligned. Several non-ARV factors including child, maternal, and socio-demographic factors independently predicted mean WAZ. These include child male (0.45 (0.35; 0.56)) versus female, higher maternal education grade 7-12 (0.28 (0.14; 0.42) and 12 + (0.36 (0.06; 0.66)) versus ≤ grade7, employment (0.16 (0.04; 0.28) versus unemployment, and household food security (0.17 (0.03; 0.31). Similar predictors were observed for mean LAZ. CONCLUSION: Findings provide evidence for initiating all pregnant women living with HIV on ART as fetal exposure had no demonstrable adverse effects on postnatal growth. Several non-HIV-related maternal, child and socio-demographic factors were independently associated with growth, highlighting the need for multi-sectoral interventions. Longer-term monitoring of CHEU children is recommended

Which agricultural management interventions are most influential on soil organic carbon (using time series data)?

Background Loss of soil organic carbon (SOC) from agricultural land is identified as one of the major threats to soils, as it influences both fertility and the production of ecosystem services from agriculture. Losses of SOC across regions are often determined by monitoring in different land use systems. Results from agricultural field experiments can reveal increasing SOC stocks after implementation of specific management practices compared to a control, though in time series experiments the relative rate of change is often negative and implying an overall loss. Long-term agricultural field experiments are indispensable for quantifying absolute changes in SOC stocks under different management regimes. Since SOC responses are seldom linear over time, time series data from these experiments are particularly valuable. Methods This systematic review is based on studies reporting time series data collated in a recently completed systematic map on the topic restricted to the warm temperate climate zone and the snow climate zone. These 53 studies were identified and selected systematically according to CEE guidelines. An update of the original search for studies will be repeated using Web of Science and Google Scholar to include newly published academic and grey literature in the time since the original search was performed in September 2013. Studies will be subject to critical appraisal of the internal and external validity, followed by full data extraction (meta-data describing study settings and quantitative study results). Where possible, studies will be included in a quantitative synthesis using time series meta-analytical approaches. The implications of the meta-analytical findings will be discussed in terms of policy, practice and research along with a discussion of the nature of the evidence base