Velvetleaf (Abutilon theophrasti Medik. # ABUTH) seeds were bioassayed on 241 microbial isolates to assess their antimicrobial activity. Seeds placed on agar plates inoculated with test microorganisms released a diffusible substance(s) that inhibited the growth of 117 of 202 (58%) bacteria and all of the fungi tested. Antimicrobial activity of the seeds appeared to be nonselective as the extent of inhibition was not related to type of microorganism nor their origin. Hard, water-impermeable seeds had greater inhibitory activity than imbibed (soft) seeds. The intensity of inhibition was affected by prior leaching of seeds with various solvents and by the stage of seed development. Chemical analysis of diffusion zones from agar plates and seed leachates revealed the presence of phenolic compounds. The presence of antimicrobial substances in velvetleaf seeds may contribute to the persistence of viable seeds in soil by inhibiting potential seed-deteriorating microorganisms.

Field infestations of a seed-feeding insect developed from overwintered populations reduced viability of velvetleaf seed to 17.5 and 15.5% at two locations in central Missouri, compared to 95.5 and 87.5% at insect-free sites. Insect feeding enhanced the proportion of seedborne microorganisms in seed up to 98% compared to the average fungal infection of 8% for seed not exposed to the insect. There was a strong negative correlation between fungal infection associated with insect feeding and percent velvetleaf seed viability. The insect transmits microorganisms externally just as pollen is carried by various other insect species and not by ingestion and regurgitation. The effectiveness of the insect on reducing seed viability and seed production in central Missouri is mainly limited by the time required to build up populations capable of significantly affecting early-season velvetleaf seed production.

There is a current need to develop alternative weed management techniques in response to demands for reduction in herbicide use due mainly to health and environmental concerns. Therefore, all possible nonchemical strategies for weed control should be considered, including biological control. Deleterious rhizobacteria (DRB), largely overlooked as potential biological control agents for weeds until recently, are able to colonize root surfaces of weed seedlings and suppress plant growth. Limited field studies indicate that DRB suppressed weed growth, and reduced weed density, biomass, and seed production. In this manner, crops out-compete the suppressed weeds for growth requirements, eliminating the necessity for eradication of weeds in the crop. Establishment of DRB as a viable biological control strategy initially will require integration with other weed control approaches including other biocontrol agents, agrichemicals, and cultural and residue management practices. To achieve success, more in-depth research is needed on ecology of bacteria-plant relationships, mechanisms of action (including characterization of phytotoxins), inocula formulations, and methods to enhance crop competition.

Soil microbial community structure and activity are linked to plant communities. Weeds may alter their soil environment, selecting for specific rhizosphere microbial communities. Rhizosphere modification occurs for many crop and horticultural plants. However, impacts of weeds in agroecosystems on soil biology and ecology have received less attention because effective weed management practices were developed to minimize their impacts on crop production. The recent development of herbicide resistance (HR) in several economically important weeds leading to widespread infestations in crop fields treated with a single herbicide has prompted a re-evaluation of the effects of weed growth on soil biology and ecology. The objective of this article is to review the potential impacts of herbicide-resistant weeds on soil biological and ecological properties based on reports for crops, weeds, and invasive plants. Persistent weed infestations likely establish extensive root systems and release various plant metabolites through root exudation. Many exudates are selective for specific soil microbial groups mediating biochemical and nutrient acquisition processes. Exudates may stimulate development of microbial groups beneficial to weed but detrimental to crop growth or beneficial to both. Changes in symbiotic and associative microbial interactions occur, especially for arbuscular mycorrhizal fungi (AMF) that are important in plant uptake of nutrients and water, and protecting from phytopathogens. Mechanisms used by weeds to disrupt symbioses in crops are not clearly described. Many herbicide-resistant weeds including Amaranthus and Chenopodium do not support AMF symbioses, potentially reducing AMF propagule density and establishment with crop plants. Herbicides applied to control HR weeds may compound effects of weeds on soil microorganisms. Systemic herbicides released through weed roots may select microbial groups that mediate detrimental processes such as nutrient immobilization or serve as opportunistic pathogens. Understanding complex interactions of weeds with soil microorganisms under extensive infestations is important in developing effective management of herbicide-resistant weeds.

The annual variations in body-size spectra of planktonic ciliate communities and their relationships to environmental conditions were studied based on a 12-month dataset (June 2007 to May 2008) from Jiaozhou Bay on the Yellow Sea coast of northern China. Based on the dataset, the body sizes of the ciliates, expressed as equivalent spherical diameters, included five ranks: S1 (5–35 μm); S2 (35–55 μm); S3 (55–75 μm); S4 (75–100 μm); and S5 (100–350 μm). These body-size ranks showed a clear temporal succession of dominance in the order of S2 (January–April) → S1 (May–July) → S4 (August–September) → S3 (October–December). Multivariate analyses showed that the temporal variations in their body-size patterns were significantly correlated with changes in environmental conditions, especially water temperature, salinity, dissolved oxygen concentration (DO) and nutrients. In terms of abundance, rank S2 was significantly correlated with water temperature, DO and nutrients, whereas ranks S4 and S5 were correlated with the salinity and nutrients respectively (P < 0.05). These results suggest that the body-size patterns of planktonic ciliate communities showed a clear temporal pattern during an annual cycle and significantly associated with environmental conditions in marine ecosystems.

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto- and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e.g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manner.

The growing public concerns over chemical residues in animal-derived foods and threats of antibiotic-resistant bacteria have renewed interest in exploring safer alternatives to chemical feed additives in ruminant livestock. Various bioactive phytochemicals including saponins appear to be potential ‘natural’ alternatives to ‘chemical’ additives in modulating rumen fermentation favourably and animal performance. Saponins are a diverse group of glycosides present in many families of plants. The primary effect of saponins in the rumen appears to be to inhibit the protozoa (defaunation), which might increase the efficiency of microbial protein synthesis and protein flow to the duodenum. Furthermore, saponins may decrease methane production via defaunation and/or directly by decreasing the activities (i.e. rate of methanogenesis or expression of methane-producing genes) and numbers of methanogens. Saponins may also selectively affect specific rumen bacteria and fungi, which may alter the rumen metabolism beneficially or adversely. The ammonia-adsorption and modulation of digesta passage in the rumen by saponins have also been implicated in altering rumen metabolism, but their physiological responses are likely to be negligible compared with microbiological effects. The effects of saponins on rumen fermentation have not been found to be consistent. These discrepancies appear to be related to the chemical structure and dosage of saponins, diet composition, microbial community and adaptation of microbiota to saponins. There is need for systematic research based on chemical structures of saponins, nutrient composition of diets and their effects on rumen microbial ecosystem to obtain consistent results. The present paper reviews and discusses the effects and mode of action of saponins on microbial community and fermentation in the rumen, and ruminant performance.

Structural parameters of periphytic ciliate communities on a modified substrate were studied in Korean coastal waters during the period August–November 2007. In order to reduce the strong disturbances from tidal current and circulation in marine ecosystems, a modified slide method, named the polyurethane foam enveloped slide (PFES) system, was used to host ciliate communities. A total of 37 ciliate species, about half of which belong to the orders Hypotrichida and Cyrtophorida, were identified using living observation and silver impregnation method with this system. The sessile ciliates belonged to the orders Peritrichida and Suctorida, while the motile forms were represented primarily by the species of the orders Hypotrichida, Cyrtophorida and Pleurostomatida. The species diversity and evenness were significantly higher in the PFES system than those on the conventional slides (paired t-test: t = 2.384, 2.415; P < 0.05). Multivariate analysis revealed that the ciliate communities from both sampling systems had similar species composition, but represented significant differences in species distribution and temporal dynamics mainly due to the most dominant peritrich Zoothaminium duplicatum, which overly colonized the conventional slides. Results suggest that the PFES system is more effective than the conventional slide method for periphytic ciliate colonization with high species diversity, evenness and sensitive temporal dynamics mainly due to the reduction of disturbances from tidal current and circulation in marine ecosystems.

In the natural environment, microbial community structure of river biofilm is controlled by biotic and abiotic factors. This study explored the capacity to manipulate the structure of microbial communities by modifying environmental conditions during the course of biofilm development. River epilithic biofilm was cultivated in situ on artificial substrates placed parallel to river water flow. Substrates were incubated for 3 and 5.5 weeks in river to allow natural biofilm development, at two sites with contrasting physico-chemical characteristics. The first site (Auradé, Gers, France) was located in an agricultural watershed basin and the second site (Larroque, Haute-Garonne, France) was located in a forested watershed basin. After 3 weeks of biofilm development, a subset of substrates was collected from one site and transplanted to the second site where they remained for 2.5 further weeks. Epilithic bacterial community structure (at 3 weeks from each site and at 5.5 weeks from biofilms with and without transplantation) was assessed using PCR-DGGE of 16S rDNA fragment. Biofilm biomass was estimated using ash free dry mass (AFDM). After 3 weeks of development, biofilms from the two sites exhibited comparable AFDM values (average of 1.4±0.2 g.m-2). A difference between the two sites was observed after 5.5 weeks of development: AFDM decreased for biofilms from the agricultural watershed basin (from 1.4 to 0.18 g.m-2) as a consequence of grazing pressure (Bithynia), and increased for biofilms from the forested agricultural watershed (from 1.4 to 2.6 g.m-2). Microbial community analyses revealed a differentiated community structure between biofilms from the different sites and exhibited a change of microbial community structure after 5.5 weeks of biofilm development. These observations confirm a process of ecological succession in microbial communities. Changing the incubation site during biofilm development modified the trajectory of these ecological successions, suggesting that site characteristics mainly conditioned the structure of these microbial communities.

The microbial population of the intestinal tract is a complex natural resource that can be utilized in an effort to reduce the impact of pathogenic bacteria that affect animal production and efficiency, as well as the safety of food products. Strategies have been devised to reduce the populations of food-borne pathogenic bacteria in animals at the on-farm stage. Many of these techniques rely on harnessing the natural competitive nature of bacteria to eliminate pathogens that negatively impact animal production or food safety. Thus feed products that are classified as probiotics, prebiotics and competitive exclusion cultures have been utilized as pathogen reduction strategies in food animals with varying degrees of success. The efficacy of these products is often due to specific microbial ecological factors that alter the competitive pressures experienced by the microbial population of the gut. A few products have been shown to be effective under field conditions and many have shown indications of effectiveness under experimental conditions and as a result probiotic products are widely used in all animal species and nearly all production systems. This review explores the ecology behind the efficacy of these products against pathogens found in food animals, including those that enter the food chain and impact human consumers.

In order to evaluate the environmental status within a mariculture pond, temporal variations of physico-chemical factors, protist community structure and interactions between biota and environmental conditions were investigated during a complete cycle in semi-enclosed shrimp-farming waters near Qingdao, north China. Results revealed that: (1) a total of 54 protist taxa with ten dominant species was present, comprising 4 chlorophyceans, 2 chrysophyceans, 5 cryptophyceans, 10 dinoflagellates, 3 euglenophyceans, 10 diatoms, 18 ciliates and 2 sarcodines; (2) a single peak of protist abundance occurred in October, mainly due to the chlorophyceans, diatoms and chrysophyceans, while the bimodal peaks of biomass in July and October were mainly due to the ciliates, dinoflagellates and diatoms; (3) the succession of protist communities significantly correlated with the changes of nutrients, salinity and temperature, especially phosphate, either alone or in combination with NO3; (4) species diversity and evenness indices were found to be relatively independent of physico-chemical factors, whereas species richness and the ratio of biomass to abundance were strongly correlated with water temperature and abundances of bacteria. It was concluded that planktonic protists are potentially useful bioindicators of water quality in a semi-enclosed mariculture system.

Methanol-toluene extracts of 17 common Antarctic marine sponges collected from shallow waters in McMurdo Sound in October–December 1989 were tested for suppression of growth of bacteria (gram-positive and negative), yeasts and fungi. Weak to moderate levels of antimicrobial activity occurred in all sponges. Antimicrobial activity was more common when gram-negative bacteria were exposed to sponge extracts; 47% of the sponge extracts caused growth inhibition in one or more gram-positive bacteria, while 100% of the extracts caused growth inhibition in gram-negative bacteria. Particularly strong activity was observed against two species of gram-positive bacteria exposed to extracts of the sponge Latrunculia apicalis and against one strain of gram-negative bacterium exposed to extracts of the sponge Haliclona sp. Antimicrobial responses against yeasts and fungi were generally non-existent or weak, with the exception of the yeast Candida tropicalis, which was strongly inhibited by extracts of the sponges Homaxonella balfourensis, Dendrilla membranosa, Kirkpatrickia variolosa, Gellius benedeni, Cinachyra antarctica and Scolymastia joubinia. Antimicrobial activity in these polar sponges is widespread but generally weaker than that found in temperate and tropical sponges.