Antimicrobial activities and phytochemical analysis of Harrisonia abyssinica (Oliv) and Vepris simplicifolia (Verd) extracts used as traditional medicine in Tanzania

The present study aimed to determine in vitro antimicrobial activities and phytochemical analysis of Harrisonia abyssinica and Vepris simplifolia which are commonly used as traditional medicine in Tanzania. Sensitivity of bacterial and fungal species against plants extracts were determined using serial microdilution method. In this method, the lowest inhibitory concentration which prevented microbial growth considered as minimum inhibitory concentration (MIC). The study also evaluated phytochemical compounds present in the leaf, stem and root barks of H. abyssinica. It was revealed that eight extracts from H. abyssinica inhibited growth of three bacteria namely Staphylococcus aureus, Enterococcus faecium and Streptococcus uberis at MIC value less than 1 mg/mL. It was further revealed that, three extracts from V. simplifolia exhibited high antibacterial and antifungal activity. The preliminary phytochemical analysis revealed presence of various phytochemicals namely alkaloids, terpenoid, flavonoid, tannin and saponin. It was concluded that presence of large number of phytochemicals in the plant extracts may be associated with pharmacological properties of H. abyssinica and V. simplifolia and therefore this study provide alternative to synthetic antimicrobial agents.     

Pyrosequencing reveals the inhibitory impact of chronic exposure to erythromycin on activated sludge bacterial community structure

The study investigated changes in the microbial population structure sustained at two different sludge ages of 10 d and 2 d under chronic impact of erythromycin. It intended to observe the experimental correlation between variable process kinetics and changes in the composition of the microbial community induced by erythromycin. Samples from two fill/draw reactors operated with continuous erythromycin dosing of 50 mg/L were collected for the analysis of microbial population structure using high-throughput sequencing of 16SrRNA gene. Significant changes were observed in the composition of microbial community during the exposure period. Richness analysis for slower growing culture indicated that most microbial fractions were inactivated and eliminated in favor of fewer more resistant species in different phyla. Sludge age appeared to control the impact of erythromycin on microbial composition. At a sludge age of 2 d, erythromycin appeared to generate richer community with faster growing and more compatible species. For slower growing culture, elimination of vulnerable species was supported by decrease in the number of shared level OTUs. For faster growing culture, shared species level OTUs also decreased significantly upon exposure to erythromycin, suggesting rapid washout and replacement by more resistant species. Resistance gene analysis yielded positive results for mph(A) gene indicating presence of erythromycin-resistant components in the microbial community.     

Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil

Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity.     

Genotypic and Phenotypic Diversity of Cyanobacteria in Biological Soil Crusts of the Succulent Karoo and Nama Karoo of Southern Africa

Biological soil crusts (BSCs) are communities of cryptogamic organisms, occurring in arid and semiarid regions all over the world. Based on both morphological identification and genetic analyses, we established a first cyanobacterial inventory using the biphasic approach for BSCs within two major biomes of southern Africa. The samples were collected at two different sites in the Succulent Karoo and one in the Nama Karoo. After cultivation and morphological identification, the 16S rRNA gene was sequenced from the cyanobacterial cultures. From the soil samples, the DNA was extracted, and the 16S rRNA gene sequenced. All the sequences of the clone libraries from soil and cultures were compared with those of the public databases. Forty-five different species were morphologically identified in the samples of the Succulent Karoo (observatories of Soebatsfontein and Goedehoop). Based on the genetic analyses, 60 operational taxonomic units (OTUs) were identified for the Succulent Karoo and 43 for the Nama Karoo (based on 95 % sequence similarity). The cloned sequences corresponded well with the morphologically described taxa in cultures and sequences in the public databases. Besides known species of typical crust-forming cyanobacterial genera (Microcoleus, Phormidium, Tolypothrix and Scytonema), we found sequences of so far undescribed species of the genera Leptolyngbya, Pseudanabaena, Phormidium, Oscillatoria, Schizothrix and Microcoleus. Most OTUs were restricted to distinct sites. Grazed soils showed lower taxa numbers than undisturbed soils, implying the presence of early successional crust types and reduced soil surface protection. Our combined approach of morphological identification and genetic analyses allowed both a taxa inventory and the analysis of species occurring under specific habitat conditions.     

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System,and Antibiotic Sensitivity Profiling

Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.     

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1–V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4–99.9% of OTUs represented by more than one read, using Good’s coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.     

闽江口芦苇沼泽湿地土壤产甲烷菌群落结构的垂直分布

应用PCR-RFLP技术及测序分析对闽江口芦苇湿地土壤产甲烷菌群落结构的垂直分布特征进行了研究。在构建的6个克隆文库中,每个克隆文库随机挑选100个克隆进行菌落PCR验证,共得到591个阳性克隆。PCR产物经限制性内切酶MspⅠ进行RFLP分析后得到37个不同的分类操作单元(OTUs)。对37个克隆子进行了序列测定,与GenBank数据库中的序列进行比对,最近相似性在91%—99%之间。RFLP分析和系统发育分析表明,闽江口芦苇湿地土壤中产甲烷菌群落包括3大类群:甲烷杆菌目(Methanobacteriales)、甲烷微菌目(Methanomirobiales)和甲烷八叠球菌目(Methanosarcinales)。不同土壤深度中产甲烷菌群落的分布呈现出不同的特征。土壤表层(0—10 cm)优势产甲烷菌类群为Methanoregula,约占76%;10—20 cm土层主要的产甲烷菌类群为Methanolinea和Methanoregula,分别约占23%和29%;20—30cm土层优势的产甲烷菌类群为Methanolinea,约占66%。Shannon指数(H’)和Simpson多样性指教(D)表明,10—20cm土层产甲烷菌多样性高于土壤表层(0—10 cm)和20—30 cm土层。37个测序OTUs中有26个OTUs属于不可培养的产甲烷菌序列,表明闽江口芦苇湿地土壤中存在大量不可培养的产甲烷菌。     

In vitro conservation,phytochemistry, and medicinal activity of Artemisia tridentata Nutt.: metabolomics as a hypothesis-generating tool for plant tissue culture

Artemisia tridentata Nutt. and related species in the subgenus Tridentatae are ecologically important plants with a rich history of ceremonial and medicinal use by the indigenous people of North America. With the exception of antimicrobial and insecticidal bioassays, there is limited data to support the traditional uses of A. tridentata. Additionally, wild A. tridentata populations are declining and conservation of genetic resources is warranted. The current study was designed to (a) develop in vitro protocols to conserve A. tridentata in axenic culture and to provide plant tissues for phytochemical analysis, (b) to investigate the presence of neurologically-active phytochemicals in A. tridentata and (c) to develop metabolomics as a tool for understanding secondary metabolite biosynthesis under aseptic conditions. A collection of in vitro-grown germplasm lines was established from wild-harvested seeds of A. tridentata. Neurotransmitters acetylcholine, GABA, melatonin and serotonin were identified and quantified in the plant tissues. Crude extracts of A. tridentata inhibited acetylcholinesterase in a bioassay. A metabolomics analysis with chemometric statistics quantified changes in the phytochemical profiles of wild-harvested plants and plantlets in axenic culture. A total of 1,543 phytochemicals were found in all samples of A. tridentata including 52 significant ions putatively identified as monoterpene, phenolic or sesquiterpene compounds. Together, these data provide the foundation for further investigations of the phytochemical diversity and medicinal activity of A. tridentata and demonstrate a research approach for use of metabolomics as a tool for understanding secondary metabolite biosynthesis under aseptic conditions.     

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.     

Impact of Soil Drying-Rewetting Stress on Microbial Communities and Activities and on Degradation of Two Crop Protection Products

Prior to registration of crop protection products (CPPs) their persistence in soil has to be determined under defined conditions. For this purpose, soils are collected in the field and stored for up to 3 months prior to the tests. During storage, stresses like drying may induce changes in microbiological soil characteristics (MSCs) and thus may influence CPP degradation rates. We investigated the influence of soil storage-related stress on the resistance and resilience of different MSCs by assessing the impact of a single severe drying-rewetting cycle and by monitoring recovery from this event for 34 days. The degradation and mineralization of the fungicide metalaxyl-M and the insecticide lufenuron were delayed by factors of 1.5 to 5.4 in the dried and rewetted soil compared to the degradation and mineralization in an undisturbed reference. The microbial biomass, as estimated by direct cell counting and from the soil DNA content, decreased on average by 51 and 24%, respectively. The bulk microbial activities, as determined by measuring substrate-induced respiration and fluorescein diacetate hydrolysis, increased after rewetting and recovered completely within 6 days after reequilibration. The effects on Bacteria, Archaea, and Pseudomonas were investigated by performing PCR amplification of 16S rRNA genes and reverse-transcribed 16S rRNA, followed by restriction fragment length polymorphism (RFLP) and terminal RFLP (T-RFLP) fingerprinting. Statistical analyses of RFLP and T-RFLP profiles indicated that specific groups in the microbial community were sensitive to the stress. In addition, evaluation of rRNA genes and rRNA as markers for monitoring the stress responses of microbial communities revealed overall similar sensitivities. We concluded that various structural and functional MSCs were not resistant to drying-rewetting stress and that resilience depended strongly on the parameter investigated.     

Ethnochemometric of plants traditionally utilised as local detergents in the forest dependent culture

The purpose of this study is to access the existing awareness of nearly forgotten Thai detergent plants by the use of chemometrics tool. A Northern Thai forest dependent community was chosen as it played vital role on knowledge retaining of plant utilisations. For initial perception, ethnobotanical survey was conducted to determine usage of plants by the community. Then the utilised plant parts were screened for phytochemicals and their relationships with the defined cleansing terms (viz., shampoo, scrub, detergent, soap, scent and spiritual) were analysed by Principal Component Analysis (PCA). From the results, the most cited plants as known, used and found were Acacia concinna, Clitoria ternetea, Oryza sativa and Citrus hystrix. Biometric analyses advised that knowledge of detergent plant utilisation was well preserved at all age ranges and it was not variable with genders. Cluster analysis described that term ‘spiritual’ was not narrated with cleansing properties. For phytochemical analysis, plant extracts showed positive variable of bioactive ingredients and the main compounds in the extracts was saponins. These findings confirmed that the knowledge of indigenous plant utilisation was reserved by the forest dependent community and the information is beneficial toward local plant conservation movement.     

Synergistic effects of floral phytochemicals against a bumble bee parasite

Floral landscapes comprise diverse phytochemical combinations. Individual phytochemicals in floral nectar and pollen can reduce infection in bees and directly inhibit trypanosome parasites. However, gut parasites of generalist pollinators, which consume nectar and pollen from many plant species, are exposed to phytochemical combinations. Interactions between phytochemicals could augment or decrease effects of single compounds on parasites. Using a matrix of 36 phytochemical treatment combinations, we assessed the combined effects of two floral phytochemicals, eugenol and thymol, against four strains of the bumblebee gut trypanosome Crithidia bombi. Eugenol and thymol had synergistic effects against C. bombi growth across seven independent experiments, showing that the phytochemical combination can disproportionately inhibit parasites. The strength of synergistic effects varied across strains and experiments. Thus, the antiparasitic effects of individual compounds will depend on both the presence of other phytochemicals and parasite strain identity. The presence of synergistic phytochemical combinations could augment the antiparasitic activity of individual compounds for pollinators in diverse floral landscapes.     

How effective are Mesocyclops aspericornis (Copepoda: Cyclopoida) in controlling mosquito immatures in the environment with an application of phytochemicals?

We investigated the susceptibility of Mesocyclops aspericornis and Aedes aegypti larvae to mosquito larvicidal phytochemicals: piperine and eugenol and the predation efficiency of the adult female M. aspericornis on Ae. aegypti larval instar-I and late II at the sublethal concentration of piperine and eugenol. Both prey and predator were susceptible to both the phytochemicals; however, the lethal concentration of either phytochemicals recorded for Ae. aegypti did not exert mortality on the copepods. The predator’s latent time was significantly longer in the phytochemical medium than control. The encounter frequency was significantly higher in control than in the phytochemical medium. For instar-I larvae, the post-encounter attack probabilities were not affected by the tested phytochemicals. However, for instar-II, the post-encounter attack probability was lower in eugenol treatment than in either the control or piperine. The escape and post-escape survival probabilities of larvae were substantially lower in phytochemical treatments than in the control. However, the overall copepod-imposed mortality did not differ significantly between the control and the phytochemical medium. In conclusion, both the phytochemicals modify the copepod feeding behavior without affecting the copepod incurred total larval mortality. Therefore, application of these phytochemicals along with M. aspericornis for mosquito control is advisable.     

Ant-cultivated Chaetothyriales in hollow stems of myrmecophytic Cecropia sp. trees – diversity and patterns

Five Cecropia tree species occupied by four Azteca ant species from Costa Rica and French Guiana were investigated to assess the diversity and host specificity of chaetothyrialean fungal symbionts. The ITS rDNA region of the symbiotic fungi was sequenced either from pure culture isolation, or from environmental samples obtained from ant colonies nesting in hollow stems of the Cecropia host plants. The investigation revealed six closely related OTUs of Chaetothyriales. Neither the four Azteca species nor the six fungal OTUs were associated with specific Cecropia species. In contrast, ants and fungi showed an association. Azteca alfari was associated with a particular OTU, and often contained only one. Azteca coeruleipennis, Azteca constructor and Azteca xanthochroa were associated with a different set of OTUs and often had multiple OTUs within colonies. Possible reasons for these differences and the role of the fungi for the Azteca-Cecropia symbiosis are discussed.     

Identification of phytochemical components from Aerva lanata (Linn.) medicinal plants and its in-vitro inhibitory activity against drug resistant microbial pathogens and antioxidant properties

This study aimed to determine the phytochemical components, microbial inhibitory effectiveness and antioxidant properties of Aerva lanata plant extracts. The whole plant showed various medicinal applications in folklore and traditional medicine in various parts of the world. The organic extracts such as ethanol, ethyl acetate, chloroform, acetone, water and methanol were subjected for various phytochemical analysis and confirmed for the existence of flavonoids, glycosides, terpenoids and alkaloid containing components. Alternatively, the extracts were performed for the antibacterial activities against the microbial pathogens and antioxidant properties. Results indicated that, the solvent extracts showed prominent activity against the tested strains. The MIC concentrations of plant were detected from 5 mg/ml to 40 mg/ml. The plant extract was highly effective against E. coli and E. aerogenes and the MIC was 5 mg/ml. In addition, the extracts noted promising antioxidant activities. The antioxidant activities were dose dependent manner. In conclusion, A. lanata extracts showed that significant major phytochemicals and effective antioxidant and anti-microbial properties.     

Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities

Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative PCR (qPCR) assays were developed for quantifying pathogenic Streptomyces scabiei and antibiotic-producing Streptomyces lavendulae strains in complex soil communities. This assay will be useful for evaluating the competitive dynamics of streptomycetes in soil.Streptomyces spp. are ubiquitous soil bacteria that are noted for their capacity to produce a vast array of bioactive compounds, including antibiotics (10). Antibiotic-mediated species interactions are believed to be important to Streptomyces fitness and plant disease biocontrol in soil, and yet quantitative data on Streptomyces interactions in soil are limited. Moreover, because the impacts of one species on another can be mediated through interactions with other microbes in the community, detecting these impacts requires a sensitive and accurate method for quantifying the target populations within a complex community. Here, we describe a sensitive and specific assay that targets a short hypervariable region of the 16S rRNA gene to distinguish among Streptomyces organisms in complex soil communities. Streptomyces strains DL93 (Streptomyces lavendulae, an antibiotic producer that is effective in plant disease biocontrol [9]) and DL87 (Streptomyces scabiei, a plant pathogen) were studied in the present work. This approach has significant potential to shed light on the diversity and complexity of Streptomyces species interactions in soil.     

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches

The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.     

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445 microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.     

The Exotic Legume Tree Species Acacia holosericea Alters Microbial Soil Functionalities and the Structure of the Arbuscular Mycorrhizal Community

The response of microbial functional diversity as well as its resistance to stress or disturbances caused by the introduction of an exotic tree species, Acacia holosericea, ectomycorrhized or not with Pisolithus albus, was examined. The results show that this ectomycorrhizal fungus promotes drastically the growth of this fast-growing tree species in field conditions after 7 years of plantation. Compared to the crop soil surrounding the A. holosericea plantation, this exotic tree species, associated or not with the ectomycorrhizal symbiont, induced strong modifications in soil microbial functionalities (assessed by measuring the patterns of in situ catabolic potential of microbial communities) and reduced soil resistance in response to increasing stress or disturbance (salinity, temperature, and freeze-thaw and wet-dry cycles). In addition, A. holosericea strongly modified the structure of arbuscular mycorrhizal fungus communities. These results show clearly that exotic plants may be responsible for important changes in soil microbiota affecting the structure and functions of microbial communities.     

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.