Persistence of antibiotic-resistant and -sensitive Proteus mirabilis strains in the digestive tract of the housefly (Musca domestica) and green bottle flies (Calliphoridae)

Synanthropic flies have been implicated in the rapid dissemination of antibiotic-resistant bacteria and resistance determinants in the biosphere. These flies stably harbor a considerable number of bacteria that exhibit resistance to various antibiotics, but the mechanisms underlying this phenomenon remain unclear. In this study, we investigated the persistence of antibiotic-resistant bacteria in the digestive tract of houseflies and green bottle flies, using Proteus mirabilis as a model microorganism. One resistant strain carried the blaTEM and aphA1 genes, and another carried a plasmid containing qnrD gene. Quantitative PCR and 454 pyrosequencing were used to monitor the relative abundance of the Proteus strains, as well as potential changes in the overall structure of the whole bacterial community incurred by the artificial induction of Proteus cultures. Both antibiotic-resistant and -sensitive P. mirabilis strains persisted in the fly digestive tract for at least 3 days, and there was no significant difference in the relative abundance of resistant and sensitive strains despite the lower growth rate of resistant strains when cultured in vitro. Therefore, conditions in the fly digestive tract may allow resistant strains to survive the competition with sensitive strains in the absence of antibiotic selective pressure. The composition of the fly-associated bacterial community changed over time, but the contribution of the artificially introduced P. mirabilis strains to these changes was not clear. In order to explain these changes, it will be necessary to obtain more information about bacterial interspecies antagonism in the fly digestive tract.     

Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake

We examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic Lake Mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). Microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (BCC) change or community activity response (assessed via alkaline phosphatase activity, APA) relative to the controls during any season. Treatments enriched with carbon‐ and nitrogen‐containing compounds resulted in a dramatic BCC change and a large APA increase in the autumn and spring seasons, but only treatments receiving carbon, nitrogen and phosphorus (CNP) exhibited similar responses in the summer season. Despite the fact that the amendments created similar CNP concentration conditions across seasons, the BCC following amendment greatly varied among seasons. 16S rRNA gene sequence analysis indicated that many common freshwater bacterial lineages from the Alpha‐ and Betaproteobacteria class and Bacteroidetes phylum were favoured following nutrient (CNP) addition, but individual taxa were generally not favoured across all seasons. Targeted quantitative PCR analysis revealed that the abundance of the Actinobacteria acIB1 cluster decreased in all microcosms during all three seasons, while the Flavobacterium aquatile (spring) and ME‐B0 (summer) clusters of Bacteroidetes increased following CNP addition. These results suggest a particular bacterial group is not universally favoured by increased nutrient loads to a lake; therefore, efforts to predict which bacteria are involved in nutrient cycling during these periods must take into account the seasonality of freshwater bacterial communities.     

Comparative analysis of bacterial community and antibiotic-resistant strains in different developmental stages of the housefly (Musca domestica)

The housefly (Musca domestica) is an important host for a variety of bacteria, including some pathogenic and antibiotic-resistant strains. To further investigate the relationship between the housefly and the bacteria it harbors, it is necessary to understand the fate of microorganisms during the larval metamorphosis. The major bacterial communities in three developmental stages of the housefly (maggot, pupa, and adult fly) were investigated by a culture-independent method, polymerase chain reaction–denaturing gradient gel electrophoresis (PCR?DGGE) analysis of 16S rRNA genes. The bacteria that were identified using DGGE analysis spanned phyla Proteobacteria, Firmicutes, and Bacteroidetes. Changes in the predominant genera were observed during the housefly development. Bacteroides, Koukoulia, and Schineria were detected in maggots, Neisseria in pupae, and Macrococcus, Lactococcus, and Kurthia in adult flies. Antibiotic-resistant bacteria were screened using a selective medium and tested for antibiotic susceptibility. Most resistant isolates from maggots and pupae were classified as Proteus spp., while those from adult flies were much more diverse and spanned 12 genera. Among 20 tested strains across the three stages, 18 were resistant to at least two antibiotics. Overall, we demonstrated that there are changes in the major bacterial communities and antibiotic-resistant strains as the housefly develops.     

Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe,China)

1. Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood.
2. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China.
3. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities.
4. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability.

     

Role of House Flies in the Ecology of Enterococcus faecalis from Wastewater Treatment Facilities

Enterococci are important nosocomial pathogens, with Enterococcus faecalis most commonly responsible for human infections. In this study, we used several measures to test the hypothesis that house flies, Musca domestica (L.), acquire and disseminate antibiotic-resistant and potentially virulent E. faecalis from wastewater treatment facilities (WWTF) to the surrounding urban environment. House flies and sludge from four WWTF (1–4) as well as house flies from three urban sites close to WWTF-1 were collected and cultured for enterococci. Enterococci were identified, quantified, screened for antibiotic resistance and virulence traits, and assessed for clonality. Of the 11 antibiotics tested, E. faecalis was most commonly resistant to tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin, and these traits were intra-species horizontally transferrable by in vitro conjugation. Profiles of E. faecalis (prevalence, antibiotic resistance, and virulence traits) from each of WWTF sludge and associated house flies were similar, indicating that flies successfully acquired these bacteria from this substrate. The greatest number of E. faecalis with antibiotic resistance and virulence factors (i.e., gelatinase, cytolysin, enterococcus surface protein, and aggregation substance) originated from WWTF-1 that processed meat waste from a nearby commercial meat-processing plant, suggesting an agricultural rather than human clinical source of these isolates. E. faecalis from house flies collected from three sites 0.7–1.5 km away from WWTF-1 were also similar in their antibiotic resistance profiles; however, antibiotic resistance was significantly less frequent. Clonal diversity assessment using pulsed-field gel electrophoresis revealed the same clones of E. faecalis from sludge and house flies from WWTF-1 but not from the three urban sites close to WWTF-1. This study demonstrates that house flies acquire antibiotic-resistant enterococci from WWTF and potentially disseminate them to the surrounding environment.     

Remediation of Urban River Water by Pontederia Cordata Combined with Artificial Aeration: Organic Matter and Nutrients Removal and Root-Adhered Bacterial Communities

Macrophyte combined with artificial aeration is a promising in situ remediation approach for urban rivers polluted with nutrients and organic matter. However, seasonal variations and aeration effects on phytoremediation performance and root-adhered microbial communities are still unclear. In this study, Pontederia cordata was used to treat polluted urban river water under various aeration intensities. Results showed that the highest removal efficiencies of chemical oxygen demand (COD_Cr) and total nitrogen (TN) were attained under aeration of 30 L min^?1 in spring and summer and 15 L min^?1 in autumn, while total phosphorus (TP) removal reached maximum with aeration of 15 L min^?1 in all seasons. Moderate aeration was beneficial for increasing the diversity of root-adhered bacteria communities, and the shift of bacterial community structure was more pronounced in spring and autumn with varying aeration intensity. The dual effect, i.e. turbulence and dissolved oxygen (DO), of aeration on the removal of COD_Cr and TN prevailed over the individual effect of DO, while DO was the most influential factor for TP removal and the root-adhered bacterial community diversity. P. cordata combined with 15 L min^?1 aeration was deemed to be the best condition tested in this study.     

Presence of sourdough lactic acid bacteria in commercial total mixed ration silage as revealed by denaturing gradient gel electrophoresis analysis

Aims: To characterize the bacterial communities in commercial total mixed ration (TMR) silage, which is known to have a long bunk life after silo opening. Methods and Results: Samples were collected from four factories that produce TMR silage according to their own recipes. Three factories were sampled three times at 1‐month intervals during the summer to characterize the differences between factories; one factory was sampled 12 times, three samples each during the summer, autumn, winter and spring, to determine seasonal changes. Bacterial communities were determined by culture‐independent denaturing gradient gel electrophoresis. All silages contained lactic acid as the predominant acid, and the contents appeared stable regardless of factories and product seasons. Acetic acid and 1‐propanol contents were different between factories and indicated seasonal changes, with increases in warm seasons compared to cool seasons. Both differences and similarities existed among the bacterial communities from each factory and product season. Lactobacillus parabuchneri was found in the products from three of four factories. Various sourdough lactic acid bacteria (LAB) were identified in commercial TMR silage; Lactobacillus panis, Lactobacillus hammesii, Lactobacillus mindensis, Lactobacillus pontis, Lactobacillus frumenti and Lactobacillus farciminis were detected in many products. Moreover, changes owing to product season were distinctive, and Lact. pontis and Lact. frumenti became detectable in summer products. Conclusion: Sourdough LAB are involved in the ensiling of commercial TMR silage. Silage bacterial communities vary more by season than by factory. The LAB species Lact. parabuchneri was detected in the TMR silage but may not be essential to the product’s long bunk life after silo opening. Significance and Impact of the Study: Commercial TMR silage resembles sourdough with respect to bacterial communities and long shelf life. The roles of sourdough LAB in the ensiling process and aerobic stability are worth examining.     

Long-term trends in food habits of Asiatic black bears in the Misaka Mountains on the Pacific coast of central Japan

I did the food habits of the Asiatic black bear Ursus thibetanus from 1013 fecal samples collected between 1999 and 2005 in the Misaka Mountains on the Pacific coast of central Japan. The food habits of the bears showed clear seasonal changes, and I classified the food resources of the bears into three types. Staple foods were green vegetation in spring, soft mast (Prunus spp.) and insects in summer, and hard mast (Quercus spp.) in autumn. Alternative foods were green vegetation and other soft mast (Rubus spp.) in summer and Japanese chestnuts Castanea crenata and vine fruits in autumn. Foods of opportunity were hard mast (Quercus spp.) that had been shed in the previous autumn and were found in spring and other fruits in autumn. Seasonal food habits showed yearly variations: bears used alternative foods and foods of opportunity in response to the yearly variation in staple food amount, but the magnitude of variability of food habits differed among seasons, with large variability in autumn and small variability in summer and spring. The primary influence on the yearly variation in food habit is presumably the fluctuation in fruit production among years. Summer is probably the most difficult season in terms of the bear's food supply, because the number of fruiting species is limited and staple foods such as new green vegetation and fruits are less available. Long-term studies of the availability of the main food items and food habits of bears will be critical for further understanding these animals’ feeding ecology and for determining the factors that influence their behavior.     

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors

Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.     

Kinetics of Colonization of Adult Queensland Fruit Flies (Bactrocera tryoni) by Dinitrogen-Fixing Alimentary Tract Bacteria

The average total population of bacteria remained constant in the alimentary tracts of adult laboratory-raised Queensland fruit flies (Bactrocera tryoni) although the insects had ingested large numbers of live bacteria as part of their diet. The mean number of bacteria (about 13 million) present in the gut of the insects from 12 to 55 days after emergence was not significantly modified when, at 5 days after emergence, the flies were fed antibiotic-resistant bacteria belonging to two species commonly isolated from the gut of field-collected B. tryoni. Flies were fed one marked dinitrogen-fixing strain each of either Klebsiella oxytoca or Enterobacter cloacae, and the gastrointestinal tracts of fed flies were shown to be colonized within 7 days by antibiotic-resistant isolates of K. oxytoca but not E. cloacae. The composition of the microbial population also appeared to be stable in that the distribution and frequency of bacterial taxa among individual flies exhibited similar patterns whether or not the flies had been bacteria fed. Isolates of either E. cloacae or K. oxytoca, constituting 70% of the total numbers, were usually dominant, with oxidative species including pseudomonads forming the balance of the population. Antibiotic-resistant bacteria could be spread from one cage of flies to the adjacent surfaces of a second cage within a few days and had reached a control group several meters distant by 3 weeks. Restriction of marked bacteria to the population of one in five flies sampled from the control group over the next 30 days suggested that the bacterial population in the gut of the insect was susceptible to alteration in the first week after emergence but that thereafter it entered a steady state and was less likely to be perturbed by the introduction of newly encountered strains. All populations sampled, including controls, included at least one isolate of the dinitrogen-fixing family Enterobacteriaceae; many were distinct from the marked strains fed to the flies. Nitrogenase activity detected by the acetylene reduction assay was associated with flies fed dinitrogen-fixing bacteria as well as with control groups given either no supplement or free access to a yeast hydrolysate preparation. Nitrogen fixed from the atmosphere may supplement the nutrition of the alimentary tract microbial population of B. tryoni. Transmission electron microscopy showed that the principal site of bacterial colonization in the abdominal alimentary tract was the lumen of the midgut inside the peritrophic membrane. No intracellular symbionts were seen in the gut tissues nor were bacteria found attached to the cuticular folds of the hindgut. The ultrastructure of the gut resembled that of other fly genera except that the intercellular spaces between rectal epithelial cells were more extensive, suggesting a role for unspecialized epithelium in water and solute uptake in B. tryoni.     

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐vs.‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.     

Can season interfere with diatom ecological quality assessment?

To understand whether seasons influence the ecological quality assessment of streams on the basis of diatoms, a study was undertaken in two lowland water courses located in northwest Portugal, between autumn 2008 and summer 2009. Temporal variation in the chemical pollution of these streams was small as revealed by a number of physical and chemical parameters analyzed. PERMANOVA global test revealed significant variation in water temperature among seasons. The diatom communities also showed a temporal variation although not all the seasons were statistically different. The multidimensional scaling analysis showed that the main differences in the diatom communities were between two groups of seasons: autumn/winter and spring/summer. Species such as Cocconeis pseudolineata, Gomphonema parvulum var. exilissimum, Fragilaria vaucheriae, Encyonema minutum, and Nitzschia recta were more abundant in spring/summer, while species such as Mayamaea atomus and Nitzschia pusilla were more abundant in autumn/winter. The BIOENV routine confirmed that the biological and temperature patterns are highly correlated. Despite the effects observed on diatom communities, these differences were buffered by the EQR (IPS) values which do not reflect seasonal differences. Therefore, the use of the index IPS seems to allow the monitoring of the streams’ ecological quality throughout the year without the interference of the natural temporal variability of diatom communities.     

The Diversity of Bacterial Communities Associated with Atlantic Cod <Emphasis Type="Italic">Gadus morhua</Emphasis>

The spatial and temporal changes in the bacterial communities associated with the Atlantic cod Gadus morhua were investigated using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S recombinant DNA (rDNA). Epidermal mucous was sampled from 366 cod caught in three harvest locations (Baltic, Icelandic, and North Seas) over three seasons (spring 2002, autumn 2002, and spring 2003), and an automated method for the high-throughput processing of environmental samples was developed using a Qiagen BioRobot. The analysis revealed that a diverse consortium of bacteria were found on fish; γ-proteobacteria and Cytophaga–Flavobacter–Bacteroides (CFB) species were dominant. T-RFLP peak profiles suggested that operational taxonomic units (OTUs) related to Photobacterium sp., Psychrobacter sp., and Bacteroides sp. were common to all sites in all three seasons, but there were intersite variations in community composition. Cod caught from different seas had distinct reproducible bacterial assemblages. Whereas communities from fish caught in the Baltic and Icelandic Seas were relatively stable over the three seasons, those from fish from the North Sea changed significantly over time.     

Strong seasonal differences of bacterial polysaccharide utilization in the North Sea over an annual cycle

Marine heterotrophic bacteria contribute considerably to global carbon cycling, in part by utilizing phytoplankton-derived polysaccharides. The patterns and rates of two different polysaccharide utilization modes – extracellular hydrolysis and selfish uptake – have previously been found to change during spring phytoplankton bloom events. Here we investigated seasonal changes in bacterial utilization of three polysaccharides, laminarin, xylan and chondroitin sulfate. Strong seasonal differences were apparent in mode and speed of polysaccharide utilization, as well as in bacterial community compositions. Compared to the winter month of February, during the spring bloom in May, polysaccharide utilization was detected earlier in the incubations and a higher portion of all bacteria took up laminarin selfishly. Highest polysaccharide utilization was measured in June and September, mediated by bacterial communities that were significantly different from spring assemblages. Extensive selfish laminarin uptake, for example, was detectible within a few hours in June, while extracellular hydrolysis of chondroitin was dominant in September. In addition to the well-known Bacteroidota and Gammaproteobacteria clades, the numerically minor verrucomicrobial clade Pedosphaeraceae could be identified as a rapid laminarin utilizer. In summary, polysaccharide utilization proved highly variable over the seasons, both in mode and speed, and also by the bacterial clades involved.     

Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains

The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of β-Proteobacteria. As a whole, α-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the α-, β-, and γ-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and β-proteobacterial isolates were most abundant during winter, while the α- and γ-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.     

Seasonal and spatial variability of sediment bacterial communities inhabiting the large shallow Lake Balaton

Seasonal studies of surface sediment bacterial communities, from two basins with differing trophic states within Lake Balaton (Hungary), were carried out using molecular (denaturing gradient gel electrophoresis, DGGE) and cultivation-based techniques. The presence of polyphosphate accumulates was tested using Neisser staining, and phosphatase activity was investigated on organic phosphorus (P) compound. Aerobic viable cell counts were significantly higher in the eutrophic than mesotrophic basin in each season. The lowest viable counts were observed in the autumn and the highest in spring and summer month in both basins. The DGGE fingerprints of the samples reflected that the composition of sediment bacterial communities in the two basins were distinct in spring and summer, and similar in autumn, but similarly diverse in all seasons. On the basis of partial 16S rDNA sequences, the 216 strains were affiliated with six major bacterial lineages: Firmicutes; Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Common species characterized from both basins constituted up to 66% of all identified phylotypes. Strains related to Bacillus sp. were dominant in all but one sample. Isolates affiliated with Aeromonas sp. prevailed in the sample taken from the mesotrophic basin in spring. The majority of the strains showed excess poly-P accumulation. Association of Neisser staining and phosphatase activity test results suggested that excess poly-P accumulation serves as P storage for sediment bacteria. Our study implied the importance of Firmicutes, Actinobacteria, Alphaproteobacteria, and Aeromonas species in benthic bacterial P retention.     

Colonization of Fungi and Bacteria in Stumps and Roots of Scots Pine after Thinning and Treatment with Rotstop

The research areas were located in the Pisz Forest District, northeast Poland, in 10‐year‐old Scots pine (Pinus sylvestris L.) plantations, established in 2004 on a clear‐cut area. Reforestation was performed without a biological treatment against root pathogens, despite the presence of Heterobasidion annosum and Armillaria ostoyae in roots and stumps of trees growing previously. The aim of this research was to evaluate how thinning and treatment with the biological control agent Rotstop influences bacterial and fungal communities within roots and stumps. Twelve months after thinning, samples were collected from five stumps in each of two seasons, autumn and spring, from stands on two types of site, one previously forested and one agricultural (20 stumps in total). Wood samples were cultured on agar media, and (i) fungi in the upper part of the stump and (ii) in roots and (iii) bacteria in roots were genetically identified. Sequences were genetically identified by comparing sequences with records held in the GenBank database. We found great differences in the frequency of both fungi and bacteria in roots: they were more frequent (i) in healthy stumps compared to stumps infected with pathogens (H. annosum and A. ostoyae), (ii) in postagricultural soil than in forest soil and (iii) after spring rather than autumn biological treatment. The introduced species Phlebiopsis gigantea was only identified in the parts of the stumps which were above ground level. The bacterium Paenibacillus pini was associated with the presence of H. annosum infecting the stumps from the roots side. In areas seriously threatened by root pathogens, biological treatment can play only a limited role. It can spread to the upper part and impede the production of fruitbodies; however, it has no impact on the development of pathogens in deeper root areas.     

Seasonal Distribution and Diversity of Ground Arthropods in Microhabitats Following a Shrub Plantation Age Sequence in Desertified Steppe

In desertified regions, shrub-dominated patches are important microhabitats for ground arthropod assemblages. As shrub age increases, soil, vegetation and microbiological properties can change remarkably and spontaneously across seasons. However, relatively few studies have analyzed how ground arthropods respond to the microhabitats created by shrubs of different plantation ages across seasons. Using 6, 15, 24 and 36 year-old plantations of re-vegetated shrubs (Caragana koushinskii) in the desert steppe of northwestern China as a model system, we sampled ground arthropod communities using a pitfall trapping method in the microhabitats under shrubs and in the open areas between shrubs, during the spring, summer and autumn. The total ground arthropod assemblage was dominated by Carabidae, Melolonthidae, Curculionidae, Tenebrionidae and Formicidae that were affected by plantation age, seasonal changes, or the interaction between these factors, with the later two groups also influenced by microhabitat. Overall, a facilitative effect was observed, with more arthropods and a greater diversity found under shrubs as compared to open areas, but this was markedly affected by seasonal changes. There was a high degree of similarity in arthropod assemblages and diversity between microhabitats in summer and autumn. Shrub plantation age significantly influenced the distribution of the most abundant groups, and also the diversity indices of the ground arthropods. However, there was not an overall positive relationship between shrub age and arthropod abundance, richness or diversity index. The influence of plantation age on arthropod communities was also affected by seasonal changes. From spring through summer to autumn, community indices of ground arthropods tended to decline, and a high degree of similarity in these indices (with fluctuation) was observed among different ages of shrub plantation in autumn. Altogether the recovery of arthropod communities was markedly affected by seasonal variability, and they demonstrated distinctive communal fingerprints in different microhabitats for each plantation age stage.     

RAPD‐PCR DETECTION OF DNA POLYMORPHISM OF COTTON APHID*

Abstract The RAPDPCR technique was used to determine the DNA polymorphism of the aphid Aphis gossypii(Glover) collected from different host plants and in different seasons. Three primers were selected from 20 primers and used for cluster analysis based on the data of Nei's genetic distance (D). The results showed that the aphids on Chinese prickly ash differentiated obviously from the aphids on the other four host plants at DNA level. The seasonal population of cotton aphid might be clustered into three groups, i.e. the spring and autumn yellow colored aphids, the spring and autumn green colored aphids and the yellow dwarf form aphid in summer. However, the genetic relationship of dwarf form was more closely to the spring and autumn green colored aphid.     

Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods

There is a paucity of knowledge on microbial community diversity and naturally occurring seasonal variations in agricultural soil. For this purpose the soil microbial community of a wheat field on an experimental farm in The Netherlands was studied by using both cultivation-based and molecule-based methods. Samples were taken in the different seasons over a 1-year period. Fatty acid-based typing of bacterial isolates obtained via plating revealed a diverse community of mainly gram-positive bacteria, and only a few isolates appeared to belong to the Proteobacteria and green sulfur bacteria. Some genera, such as Micrococcus, Arthrobacter, and Corynebacterium were detected throughout the year, while Bacillus was found only in July. Isolate diversity was lowest in July, and the most abundant species, Arthrobacter oxydans, and members of the genus Pseudomonas were found in reduced numbers in July. Analysis by molecular techniques showed that diversity of cloned 16S ribosomal DNA (rDNA) sequences was greater than the diversity among cultured isolates. Moreover, based on analysis of 16S rDNA sequences, there was a more even distribution among five main divisions, Acidobacterium, Proteobacteria, Nitrospira, cyanobacteria, and green sulfur bacteria. No clones were found belonging to the gram-positive bacteria, which dominated the cultured isolates. Seasonal fluctuations were assessed by denaturing gradient gel electrophoresis. Statistical analysis of the banding patterns revealed significant differences between samples taken in different seasons. Cluster analysis of the patterns revealed that the bacterial community in July clearly differed from those in the other months. Although the molecule- and cultivation-based methods allowed the detection of different parts of the bacterial community, results from both methods indicated that the community present in July showed the largest difference from the communities of the other months. Efforts were made to use the sequence data for providing insight into more general ecological relationships. Based on the distribution of 16S rDNA sequences among the bacterial divisions found in this work and in literature, it is suggested that the ratio between the number of Proteobacteria and Acidobacterium organisms might be indicative of the trophic level of the soil.