Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms

Bacterial contamination of raw milk can originate from different sources: air, milking equipment, feed, soil, faeces and grass. It is hypothesized that differences in feeding and housing strategies of cows may influence the microbial quality of milk. This assumption was investigated through comparison of the aerobic spore-forming flora in milk from organic and conventional dairy farms. Laboratory pasteurized milk samples from five conventional and five organic dairy farms, sampled in late summer/autumn and in winter, were plated on a standard medium and two differential media, one screening for phospholipolytic and the other for proteolytic activity of bacteria. Almost 930 isolates were obtained of which 898 could be screened via fatty acid methyl ester analysis. Representative isolates were further analysed using 16S rRNA gene sequencing and (GTG)(5)-PCR. The majority of aerobic spore-formers in milk belonged to the genus Bacillus and showed at least 97% 16S rRNA gene sequence similarity with type strains of Bacillus licheniformis, Bacillus pumilus, Bacillus circulans, Bacillus subtilis and with type strains of species belonging to the Bacillus cereus group. About 7% of all isolates may belong to possibly new spore-forming taxa. Although the overall diversity of aerobic spore-forming bacteria in milk from organic vs. conventional dairy farms was highly similar, some differences between both were observed: (i) a relatively higher number of thermotolerant organisms in milk from conventional dairy farms compared to organic farms (41.2% vs. 25.9%), and (ii) a relatively higher number of B. cereus group organisms in milk from organic (81.3%) and Ureibacillus thermosphaericus in milk from conventional (85.7%) dairy farms. One of these differences, the higher occurrence of B. cereus group organisms in milk from organic dairy farms, may be linked to differences in housing strategy between the two types of dairy farming. However, no plausible clarification was found for the relatively higher number of thermotolerant organisms and the higher occurrence of U. thermosphaericus in milk from conventional dairy farms. Possibly this is due to differences in feeding strategy but no decisive indications were found to support this assumption.     

Distinct soil microbial diversity under long-term organic and conventional farming

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.     

Transient peak in moth diversity as a response to organic farming

Few initiatives to preserve and enhance biodiversity on farmland have been as thoroughly evaluated and debated as the agri-environment schemes (AES). Yet, little is known how confounding factors co-varying with the specific AES measures may affect species responses. Here, we quantify the influence of one such factor, the time since transition to organic farming, on moth diversity patterns. We found that species richness and abundance of moths were higher on new organic farms (years since transition ≤6) compared to old organic (≥15 years) and conventional farms, indicating a transient diversity peak. This correlates with the abundance patterns of the weed Cirsium arvense, which also reached its highest densities on new organic farms. Weeds such as C. arvense constitute a notorious problem in organic farming. However, they also provide various resources for farmland biodiversity, and our results strongly suggest that the transient weed peak may be important in influencing the parallel peak among the moths. This stresses the problem in balancing out production and conservation values. More generally, our results show that rather than having static effects on the environment, AES can have an important temporal component and result in a dynamic interplay between different trophic levels.     

Influence of antibiotic selection on genetic composition of Escherichia coli populations from conventional and organic dairy farms

The widespread agricultural use of antimicrobials has long been considered a crucial influence on the prevalence of resistant genes and bacterial strains. It has been suggested that antibiotic applications in agricultural settings are a driving force for the development of antimicrobial resistance, and epidemiologic evidence supports the view that there is a direct link between resistant human pathogens, retail produce, farm animals, and farm environments. Despite such concerns, little is understood about the population processes underlying the emergence and spread of antibiotic resistance and the reversibility of resistance when antibiotic selective pressure is removed. In this study, hierarchical log-linear modeling was used to assess the association between farm type (conventional versus organic), age of cattle (calf versus cow), bacterial phenotype (resistant versus susceptible), and the genetic composition of Escherichia coli populations (E. coli Reference Collection [ECOR] phylogroup A, B1, B2, or D) among 678 susceptible and resistant strains from a previously published study of 60 matched dairy farms (30 conventional and 30 organic) in Wisconsin. The analysis provides evidence for clonal resistance (ampicillin resistance) and genetic hitchhiking (tetracycline resistance [Tet(r)]), estimated the rate of compositional change from conventional farming to organic farming (mean, 8 years; range, 3 to 15 years), and discovered a significant association between low multidrug resistance, organic farms, and strains of the numerically dominant phylogroup B1. These data suggest that organic farming practices not only change the frequency of resistant strains but also impact the overall population genetic composition of the resident E. coli flora. In addition, the results support the hypothesis that the current prevalence of Tet(r) loci on dairy farms has little to do with the use of this antibiotic.     

Plant-parasitic nematodes associated with organic and conventional vegetable farms in Laguna Province,Philippines

A survey was conducted to determine the prevalence of plant-parasitic nematodes associated with vegetable crops grown in organic and conventional farms in Laguna province, Philippines. Seven nematode genera (Aphelenchoides, Aphelenchus, Helicotylenchus, Meloidogyne, Pratylenchus, Rotylenchulus and Tylenchus) from organic farms and five (all those found in organic except Aphelenchoides and Pratylenchus) from conventional farms were isolated using modified Baermann tray method. Among these taxa, Meloidogyne and Rotylenchulus were the most prevalent and abundant in both organic and conventional farms. Pratylenchus was also prevalent in organic farms and Helicotylenchus in conventional farms. Rotylenchulus was found associated with every vegetable in both organic and conventional farms and Meloidogyne was also observed with all vegetables in conventional farms. Organic vegetable farms were more diverse in terms of genera of plant-parasitic nematodes than conventional farms.     

Impact of long-term conventional and organic farming on the diversity of arbuscular mycorrhizal fungi

Previous work has shown considerably enhanced soil fertility in agroecosystems managed by organic farming as compared to conventional farming. Arbuscular mycorrhizal fungi (AMF) play a crucial role in nutrient acquisition and soil fertility. The objective of this study was to investigate the diversity of AMF in the context of a long-term study in which replicated field plots, at a single site in Central Europe, had been cultivated for 22 years according to two organic and two conventional farming systems. In the 23rd year, the field plots, carrying an 18-month-old grass-clover stand, were examined in two ways with respect to AMF diversity. Firstly, AMF spores were isolated and morphologically identified from soil samples. The study revealed that the AMF spore abundance and species diversity was significantly higher in the organic than in the conventional systems. Furthermore, the AMF community differed in the conventional and organic systems: Glomus species were similarly abundant in all systems but spores of Acaulospora and Scutellospora species were more abundant in the organic systems. Secondly, the soils were used to establish AMF-trap cultures using a consortium of Plantago lanceolata, Trifolium pratense and Lolium perenne as host plants. The AMF spore community developing in the trap cultures differed: after 12 months, two species of the Acaulosporaceae (A. paulinae and A. longula) were consistently found to account for a large part of the spore community in the trap cultures from the organic systems but were found rarely in the ones from the conventional systems. The findings show that some AMF species present in natural ecosystems are maintained under organic farming but severely depressed under conventional farming, indicating a potentially severe loss of ecosystem function under conventional farming.     

Plant diversity in three types of hedgerows adjacent to cropfields

The farming landscape of eastern Canada is dotted with three main types of hedgerows: (1) natural woody, (2) planted woody and (3) herbaceous. The objective of this study was to compare the value of these habitats as a repository of plant biodiversity in agricultural areas of southern Quebec. The overall plant diversity was higher in natural hedgerows and they contained more plant species of conservation values than other hedgerow types. Plant species richness per quadrat was, however, higher in planted woody hedgerows, and together with the species composition, lead to the conclusion that planted hedgerows in their entirety consisted of an ecotone type of vegetation such as is found in field edges which usually support high plant diversity and productivity but where transient plant species predominate. Consequently, this study indicated that natural hedgerows fare better than planted hedgerows in terms of diversity of plants of conservation interest. In spite of that, planted woody hedgerows contained plant (and bird) species of some interest and should be favoured over more desolate herbaceous hedgerows. In areas where hedgerows were removed and are not re-establishing naturally, a mixture of deciduous trees and conifers should be encouraged in further windbreak planting programs so as to conciliate both the conservation and agronomic objectives. Furthermore, management practices should optimise the growth of establishing plants of conservation values.     

Structure and conservation value of high-diversity hedgerows in southeastern Brazil

We studied the tree component of hedgerows resulting from the natural colonization of land plot boundaries’ ditches. These three-meter wide ditches were dug during the European occupation of southeastern Brazil, and are a prominent feature of the landscape. The hedgerows are connected to forest fragments within a farmland matrix. In two systems of hedgerows, we sampled a total of 2.28 ha (114 plots of 200 m²), where we evaluated the structural and floristic similarity between fragments and hedgerows, the similarities between the hedgerows and the fragments’ edges and interior, and the relationships between distribution of tree species and soil variables. The systems presented similar richness and diversity; hedgerows had greater similarity to the fragments included in the same system than to hedgerows of the other system, indicating possible functional linkages between their components (fragments and hedgerows). Tree species composition in the hedgerows was not more similar to the fragment edges as we expected. The hedgerows exhibited greater density and basal area than the fragments. For either single system, species showed preferences for fragments or hedgerows or for sections of the ditch (edge, wall and bottom of the ditch), but for species common in both systems, those preferences were rarely held. The environmental conditions in the ditches seem to favor the establishment of species from the fragments, even those more common in fragment interior, suggesting that, in spite of their narrow widths, these hedgerows may play an important role in the conservation of flora without negatively impacting agriculturally productive rural areas.     

Functional and structural microbial diversity in organic and conventional viticulture: organic farming benefits natural biocontrol agents

Statistically significant differences in the structure and function of above-ground grapevine-associated microorganisms from organically and conventionally managed vineyards were found. Aureobasidium pullulans, a copper-detoxifying fungus and biocontrol agent, plays a key role in explaining these differences. The black fungus was strongly enriched in the communities of organically managed plants and yielded a higher indigenous antiphytopathogenic potential.     

Decreased functional diversity and biological pest control in conventional compared to organic crop fields

Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid densities but long-term negative effects on biological pest control. Therefore conventional farmers should restrict insecticide applications to situations where thresholds for pest densities are reached.     

The value of microbial diversity

In the past few years, due to the use of molecular methods, our knowledge of microbial diversity has increased dramatically, not only from a phylogenetic and taxonomic perspective but also from an ecological basis. We now know that microorganisms exist in every conceivable place on Earth, even in extreme environments. Temperature may be the only limitation as to where they can and cannot exist and/or function. As more small subunit rDNA sequence information becomes available there is a real need to start turning the information into knowledge that can be applied to better elucidate and understand structure-function relationships within ecosystems, develop new culturing methods, and discover new products and processes. It has been stated on numerous occasions that the 21(st) century is the century for biology. Within that context, we must address the real value of microbial diversity.     

Comparison of microbial diversity of edible flowers and basil grown with organic versus conventional methods

The consumption and use of edible flowers as food is growing; however, no study has been conducted to evaluate their role in the cause of food-borne illness or in food safety. Recent food-borne outbreaks traced to fresh herbs have raised concern about their processing and handling. Basil, one of the most commonly used fresh herbs, has been identified as a source of food-borne illness. Baseline assessments of microflora were performed, and the microbial diversity between growing methods (organic vs. conventional) was compared. DNA sequencing was used to identify the microbial flora present on fresh edible flower and basil samples. The most predominant species identified were Enterobacter hormaechei (10%), Acinetobacter calcoaceticus (10%), Enterobacter ludwigii (10%), Enterobacter asburiae (6%), and Enterobacter cowanii (6%). Pseudomonas aeruginosa (6%), Salmonella enterica (6%), and Bacillus amyloliquefaciens (2%) were also isolated. Phylogenetic analysis showed that most species of isolated bacteria belonged to the phyla Gammaproteobacteria (81.2%) and Firmicutes (18.8%). Statistical analysis, diversity index for species richness, and lineage-per-time plots showed that for basil, organically grown samples had a higher microbial diversity than conventionally grown samples. Edible flowers and basil are often grown using organic methods and are commonly consumed raw without any washing or cooking, to preserve aesthetic value, but these practices may pose a potential risk for food-borne illness. The baseline assessment, together with phylogenetic and statistical analyses, indicated possible microbial contamination in edible flowers and basil. The use of statistical estimation of molecular diversity based on the 16S rRNA sequences and lineage-per-time plots with phylogenetic analysis well served as a means for comparing microbial diversity in food samples between the growing methods (organic vs. conventional).     

Changes in bird populations on sample lowland English farms in relation to loss of hedgerows and other non-crop habitats

Farmland bird population trends were examined on a sample of lowland English farms to assess the relative importance of habitat loss and habitat degradation. Data were extracted from 11 farms surveyed by territory mapping between 1966 and 1986 as part of the British Trust for Ornithology's Common Birds Census. The population size of 38 bird species was quantified for each farm in each year. The extents of five non-crop habitats were measured at 4-yearly intervals on each farm. The farms were selected because some had undergone extensive removal of non-crop habitats while others had undergone little or none. Although declines were commonest on farms where the severest habitat loss had taken place, we found no evidence that habitat loss was the main factor causing population declines: all 11 farms had significant numbers of declining species, even where habitat loss was minimal. Furthermore, general linear modelling found no significant effects of habitat loss on population trends and principal-components analysis found limited effects of habitat extent on community composition. These results suggest that habitat loss is of secondary importance in causing farmland bird population declines. We suggest that other processes, such as habitat degradation, may have caused a baseline population decline in at least 10 farmland bird species and that declines may have been exacerbated by localised habitat loss. Received: 4 February 1998 / Accepted: 1 April 1998     

The diversity of Listeria monocytogenes strains from 10 Icelandic sheep farms

AIMS: The purpose of this study was to examine the diversity of Listeria monocytogenes strains from healthy sheep, winter feed and environment of sheep farms in Iceland. METHODS AND RESULTS: A total of 104 L. monocytogenes isolates from animals, winter feed and environment on 10 Icelandic sheep farms were compared by serotyping, ribotyping, and pulsed-field gel electrophoresis with ApaI and AscI. The isolates were divided into 24 genotypes, all identified as serovars 1/2a, 1/2b, or 4b. Nine genotypes were detected on more than one farm. On three of the farms there seemed to be a dominant strain of L. monocytogenes. Isolates from incidents of listeriosis in animals occurring on two of the farms belonged to the genotype most commonly found on the particular farm. Nine of the 24 genotypes found on the sheep farms have been associated with disease in animals and/or humans elsewhere in Iceland. CONCLUSIONS: Certain strains of L. monocytogenes seem to be widely distributed on Icelandic sheep farms. On some farms there appears to be a dominant strain of L. monocytogenes. Incidents of listeriosis in animals may tend to be associated with strains commonly found on the farm. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates the diversity of L. monocytogenes present in healthy sheep and their environment.     

Effects of geographical extent on the determinants of woody plant diversity

Despite a long history of study, the mechanisms underlying the geographical patterns of species richness are still controversial. Patterns and determinants of species richness are well‐known to vary with spatial scale. However, most studies on the effects of scale have focused on grain size whereas the quantitative effects of geographical extent are rarely tested. Here, using distribution maps of 11 405 woody species found in China and associated environmental data to the domain, we investigated the influence of geographical extent on the determinants of species richness patterns. Our results revealed consistent extent dependence of all species, narrow‐ and wide‐ranged species: with the expansion of geographical extents, the explanatory power of climate (i.e. environmental energy, water availability and climatic seasonality) increased, while the explanatory power of habitat heterogeneity and human activities decreased. Although the primary determinant of species richness patterns varied significantly at small to meso‐geographical extent, we showed that species richness was predominantly determined by environmental energy at large extent. Our findings indicate that differences in geographical extent may have led to the controversies regarding the primary determinants of richness patterns in previous studies, and that a multi‐scale perspective not only with regard to grain‐size but also extent is likely to shed new light on this old debate of what determines richness patterns.