Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil

Tool and techniques study to plant microbiome current understanding and future needs: an overview

Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

Exploring microbial communities, assessment methodologies and applications of animal's carcass decomposition: a review

Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is well explored and studied, but there is a scarcity of knowledge and research related to their role in decomposing animal carcasses. Microbes play an important role in carcass decomposition. The origins of microbial communities associated with a carcass, including the internal and external microbiome, are discussed in this review. The succession and methods used for the detection and exploration of decomposition-associated microbial communities have been briefly described. Also, the applications of carcass-associated microbial taxa have been outlined. This review is intended to understand the dynamics of microbial communities associated with the carcass and pave the way to estimate postmortem interval and its role in recycling nutrients.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

This review describes the researches performed in the last years to assess the impact of pesticide sub-lethal doses on soil microorganisms and non-target organisms in agricultural soil ecosystems. The overview was developed through the careful description and a critical analysis of three methodologies based on culture-independent approaches involving DNA extraction and sequencing (denaturing gradient gel electrophoresis, DGGE; next-generation sequencing, NGS) to characterize the microbial population and DNA damage assessment (comet assay) to determine the effect on soil invertebrates. The examination of the related published articles showed a continuous improvement of the possibility to detect the detrimental effect of the pesticides on soil microorganisms and non-target organisms at sub-lethal doses, i.e., doses which have no lethal effect on the organisms. Considering the overall critical discussion on microbial soil monitoring in the function of pesticide treatments, we can confirm the usefulness of PCR-DGGE as a screening technique to assess the genetic diversity of microbial communities. Nowadays, DGGE remains a preliminary technique to highlight rapidly the main differences in microbial community composition, which is able to give further information if coupled with culture-dependent microbiological approaches, while thorough assessments must be gained by high-throughput techniques such as NGS. The comet assay represents an elective technique for assessing genotoxicity in environmental biomonitoring, being mature after decades of implementation and widely used worldwide for its direct, simple, and affordable implementation. Nonetheless, in order to promote the consistency and reliability of results, regulatory bodies should provide guidelines on the optimal use of this tool, strongly indicating the most reliable indicators of DNA damage. This review may help the European Regulation Authority in deriving new ecotoxicological endpoints to be included in the Registration Procedure of new pesticides.

Biodegradación de dos residuos de estaciones de servicio en Río Gallegos - Argentina

La producción de efluentes contaminados con hidrocarburos en las estaciones de servicio es un inconveniente a controlar y dar un tratamiento adecuado. Este trabajo tuvo como objetivo estudiar la biorremediación de dos residuos de estaciones de servicio de la ciudad de Río Gallegos, Santa Cruz, Argentina por medio de biodegradación. Se realizó la caracterización de la fase oleosa obtenida de efluentes de dos estaciones de servicio y se realizó una biorremediación con microcosmos de los mismos. El seguimiento se realizó con análisis de GC/MS para hidrocarburos y perfiles de ácidos grasos microbianos, como también se realizó un seguimiento de las bacterias degradadoras de hidrocarburos. Los dos residuos mostraron diferente perfil cromatográfico; esto impactó sobre la degradación de los mismos que fue para el Residuo 1 de 79,68 % y para el Residuo 2 de 29,23 %. Este último poseía un perfil más rico en hidrocarburos policíclicos que son tóxicos para las bacterias. El impacto sobre la comunidad bacteriana debido a la composición de los residuos también se evidenció en la evolución del índice de Shannon determinado, y de los diferentes grupos microbianos estudiados a partir de los ácidos grasos obtenidos desde el suelo, encontrándose un predominio de bacterias Gram positivas responsables de llevar adelante el proceso de biorremediacón. Los principales resultados obtenidos demostraron que la fase líquida no acuosa obtenida a partir de los efluentes de estaciones de servicio es posible ser biorremediada por la comunidad bacteriana presente en el suelo de estudio.

Recovery of Fatty Acids from Mineralogic Mars Analogs by TMAH Thermochemolysis for the Sample Analysis at Mars Wet Chemistry Experiment on the Curiosity Rover

The Mars Curiosity rover carries a diverse instrument payload to characterize habitable environments in the sedimentary layers of Aeolis Mons. One of these instruments is Sample Analysis at Mars (SAM), which contains a mass spectrometer that is capable of detecting organic compounds via pyrolysis gas chromatography mass spectrometry (py-GC-MS). To identify polar organic molecules, the SAM instrument carries the thermochemolysis reagent tetramethylammonium hydroxide (TMAH) in methanol (hereafter referred to as TMAH). TMAH can liberate fatty acids bound in macromolecules or chemically bound monomers associated with mineral phases and make these organics detectable via gas chromatography mass spectrometry (GC-MS) by methylation. Fatty acids, a type of carboxylic acid that contains a carboxyl functional group, are of particular interest given their presence in both biotic and abiotic materials. This work represents the first analyses of a suite of Mars-analog samples using the TMAH experiment under select SAM-like conditions. Samples analyzed include iron oxyhydroxides and iron oxyhydroxysulfates, a mixture of iron oxides/oxyhydroxides and clays, iron sulfide, siliceous sinter, carbonates, and shale. The TMAH experiments produced detectable signals under SAM-like pyrolysis conditions when organics were present either at high concentrations or in geologically modern systems. Although only a few analog samples exhibited a high abundance and variety of fatty acid methyl esters (FAMEs), FAMEs were detected in the majority of analog samples tested. When utilized, the TMAH thermochemolysis experiment on SAM could be an opportunity to detect organic molecules bound in macromolecules on Mars. The detection of a FAME profile is of great astrobiological interest, as it could provide information regarding the source of martian organic material detected by SAM.

Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods

The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.

Soil Microbial Forensics

Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia

Characterization of commercial microbial consortia products for human and environmental health risk assessment is a major challenge for regulatory agencies. As a means to develop an approach to assess the potential environmental risk of these products, research was conducted to compare four genomics methods for characterizing bacterial communities; (i) Denaturing Gradient Gel Electrophoresis (DGGE), (ii) Clonal-Restriction Fragment Length Polymorphism (C/RFLP), (iii) partial 16S rDNA amplification, cloning followed by Sanger sequencing (PRACS) and (iv) Next-Generation Sequencing (NGS) based on Ion Torrent technology. A commercially available microbial consortium, marketed as a remediation agent for degrading petroleum hydrocarbon contamination in soil and water, was assessed. The bacterial composition of the commercial microbial product was characterized using the above four methods. PCR amplification of 16S rDNA was performed targeting the variable region V6 for DGGE, C/RFLP and PRACS and V5 for Ion Torrent sequencing. Ion Torrent technology was shown to be a promising tool for initial screening by detecting the majority of bacteria in the consortium that were also detected by DGGE, C/RFLP and PRACS. Additionally, Ion Torrent sequencing detected some of the bacteria that were claimed to be in the product, while three other methods failed to detect these specific bacteria. However, the relative proportions of the microbial composition detected by Ion Torrent were found to be different from DGGE, C/RFLP and PRACS, which gave comparable results across these three methods. The discrepancy of the Ion Torrent results may be due to the short read length generated by this technique and the targeting of different variable regions on the 16S rRNA gene used in this study. Arcobacter spp. a potential pathogenic bacteria was detected in the product by all methods, which was further confirmed using genus and species-specific PCR, RFLP and DNA-based sequence analyses. However, the viability of Arcobacter spp. was not confirmed. This study suggests that a combination of two or more methods may be required to ascertain the microbial constituents of a commercial microbial consortium reliably and for the presence of potentially human pathogenic contaminants.

Use of length heterogeneity polymerase chain reaction (LH-PCR) as non-invasive approach for dietary analysis of Svalbard reindeer, Rangifer tarandus platyrhynchus

To efficiently investigate the forage preference of Svalbard reindeer (Rangifer tarandus platyrhynchus), we applied length-heterogeneity polymerase chain reaction (LH-PCR) based on length differences of internal transcribed spacer (ITS) regions of ribosomal RNA (rRNA) to fecal samples from R. tarandus platyrhynchus. A length-heterogeneity (LH) database was constructed using both collected potential food sources of Svalbard reindeer and fecal samples, followed by PCR, cloning and sequencing. In total, eighteen fecal samples were collected between 2011 and 2012 from 2 geographic regions and 15 samples were successfully amplified by PCR. The LH-PCR analysis detected abundant peaks, 18.6 peaks on an average per sample, ranging from 100 to 500 bp in size and showing distinct patterns associated with both regions and years of sample collection. Principal component analysis (PCA) resulted in clustering of 15 fecal samples into 3 groups by the year of collection and region with a statistically significant difference at 99.9% level. The first 2 principal components (PCs) explained 71.1% of the total variation among the samples. Through comparison with LH database and identification by cloning and sequencing, lichens (Stereocaulon sp. and Ochrolechia sp.) and plant species (Salix polaris and Saxifraga oppositifolia) were detected as the food sources that contributed most to the Svalbard reindeer diet. Our results suggest that the use of LH-PCR analysis would be a non-invasive and efficient monitoring tool for characterizing the foraging strategy of Svalbard reindeer. Additionally, combining sequence information would increase its resolving power in identification of foraged diet components.

New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano

Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the composition of microbial population changes under the influence of continuous shifts in environmental conditions and microorganisms interactions during manufacturing and ripening, the characteristics of a given cheese depend also on microflora dynamics. The microbiota present in cheese is complex and its growth and activity represent the most important, but the least controllable steps. In the past, research in this area was dependent on classical microbiological techniques. However, culture-dependent methods are time-consuming and approaches that include a culturing step can lead to inaccuracies due to species present in low numbers or simply uncultivable. Therefore, they cannot be used as a unique tool to monitor community dynamics. For these reasons approaches to cheese microbiology had to change dramatically. To address this, in recent years the focus on the use of culture-independent methods based on the direct analysis of DNA (or RNA) has rapidly increased. Application of such techniques to the study of cheese microbiology represents a rapid, sound, reliable, and effective way for the detection and identification of the microorganisms present in dairy products, leading to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality. In this article, an overview on the recent advances in the use of molecular methods for thorough analysis of microbial communities in cheeses is given. Furthermore, applications of culture-independent approaches to study the microbiology of two important raw-milk, long-ripened cheeses such as Grana Padano and Parmigiano Reggiano, are presented.

Soil microbial diversity, site conditions, shelter forest land, saline water drip-irrigation, drift desert

Soil microbes in forest land are crucial to soil development in extreme areas. In this study, methods of conventional culture, PLFA and PCR-DGGE were utilized to analyze soil microbial quantity, fatty acids and microbial DNA segments of soils subjected to different site conditions in the Tarim Desert Highway forest land. The main results were as follows: the soil microbial amount, diversity indexes of fatty acid and DNA segment differed significantly among sites with different conditions (F < F0.05 ). Specifically, the values were higher in the middle and base of dunes than the top part of dunes and hardened flat sand, but all values for dunes were higher than for drift sand. Bacteria was dominant in the soil microbial community (>84%), followed by actinomycetes and then fungi (<0.05%). Vertical differences in the soil microbial diversity were insignificant at 0-35 cm. Correlation analysis indicated that the forest trees grew better as the soil microbial diversity index increased. Therefore, construction of the Tarim Desert Highway shelter-forest promoted soil biological development; however, for enhancing sand control efficiency and promoting sand development, we should consider the effects of site condition in the construction and regeneration of shelter-forest ecological projects.

Arbitrary single primer amplification of trace DNA substrates yields sequence content profiles that are discriminatory and reproducible

Single primer amplification is shown to yield a DNA profile that is reproducible when based on the sequence content of the amplicons rather than on the pattern of length polymorphism. The sequence-based profile increases in reliability with increasing numbers of cycles of amplification. This process uses an arbitrarily chosen primer and a low initial annealing temperature in order to amplify sequences from the whole metagenome present in a sample that may contain only trace DNA, and a large number of cycles to select subsets of sequences based on variable amplification efficiency. Using arrays, we demonstrate the utility and limitations of this approach for profiling the large metagenomes typical of soils and the trace DNA present in drug seizures. We suggest that this type of profiling will be most effective once next-generation sequencing and advanced sequence analysis becomes routine.

Bacterial endosymbiont localization in Hyalesthes obsoletus, the insect vector of Bois noir in Vitis vinifera

One emerging disease of grapevine in Europe is Bois noir (BN), a phytoplasmosis caused by "Candidatus Phytoplasma solani" and spread in vineyards by the planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae). Here we present the first full characterization of the bacterial community of this important disease vector collected from BN-contaminated areas in Piedmont, Italy. Length heterogeneity PCR and denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene revealed the presence of a number of bacteria stably associated with the insect vector. In particular, symbiotic bacteria detected by PCR with high infection rates in adult individuals fell within the "Candidatus Sulcia muelleri" cluster in the Bacteroidetes and in the "Candidatus Purcelliella pentastirinorum" group in the Gammaproteobacteria, both previously identified in different leafhoppers and planthoppers. A high infection rate (81%) was also shown for another symbiont belonging to the Betaproteobacteria, designated the HO1-V symbiont. Because of the low level of 16S rRNA gene identity (80%) with the closest relative, an uncharacterized symbiont of the tick Haemaphysalis longicornis, we propose the new name "Candidatus Vidania fulgoroideae." Other bacterial endosymbionts identified in H. obsoletus were related to the intracellular bacteria Wolbachia pipientis, Rickettsia sp., and "Candidatus Cardinium hertigii." Fluorescent in situ hybridization coupled with confocal laser scanning microscopy and transmission electron microscopy showed that these bacteria are localized in the gut, testicles, and oocytes. As "Ca. Sulcia" is usually reported in association with other symbiotic bacteria, we propose that in H. obsoletus, it may occur in a bipartite or even tripartite relationship between "Ca. Sulcia" and "Ca. Purcelliella," "Ca. Vidania," or both.

Removal of pyridine and quinoline by bio-zeolite composed of mixed degrading bacteria and modified zeolite

In the process of the biodegradation of pyridine and quinoline, ammonium is often generated because of the transformation of N from pyridine and quinoline. Zeolite has been proven to be an effective sorbent for the removal of the ammonium. The natural zeolite can be modified to be the macroporous carrier in the biological wastewater treatment process. In this study, a specific bio-zeolite composed of mixed bacteria (a pyridine-degrading bacterium and a quinoline-degrading bacterium) and modified zeolite was used for biodegradation and adsorption in two types of wastewater: sterile synthetic and coking wastewater. The experimental results indicated that pyridine and quinoline could be degraded simultaneously by the mixed bacteria. Furthermore, NH(4)(+)-N transformed from pyridine and quinoline could be removed by the modified zeolite. In addition, the bacterial community structures of the coking wastewater and the bio-zeolite were monitored by the amplicon length heterogeneity polymerase-chain reaction (LH-PCR) technique. Both LH-PCR results and scanning electron microscope (SEM) observations indicated that the microorganisms, including BW001 and BW003, could be easily attached on the surface of the modified zeolite and that the bio-zeolite could be used in the treatment of wastewater containing pyridine and/or quinoline.

Effect of pesticide inoculation, duration of composting, and degradation time on the content of compost fatty acids, quantified using two methods

Compost biobeds can promote biodegradation of pesticides. The microbial community structure changes during the composting process, and simple methods can potentially be used to follow these changes. In this study the microbial identification (MIDI) and ester-linked (EL) procedures were used to determine the composition of fatty acid methyl esters (FAMEs) in composts aged 3 and 12 months, inoculated with 3 recalcitrant pesticides (azoxystrobin, chlorotoluron, and epoxyconazole and a coapplication of all three) after 0, 56, and 125 days of degradation. Pesticide persistence was high, and after 125 days the residue was 22 to 70% of the applied amount depending mostly on the composting age. Seventy-one FAMEs belonging to nine groups were detected. The EL method provided three times as many detections as did the MIDI method and was more sensitive for all FAME groups except alcohol. Thirty-six and five FAMEs were unique to the EL and MIDI methods, respectively. The extraction method was of importance. The EL method provided a higher number of detections for 57 FAMEs, and the MIDI method provided a higher number for 9 FAMEs, while the two methods were equal for 5 FAMEs; thus, the EL method provided a more uniform overall FAME profile. Effects of the other factors were not always clear. Inoculation with pesticide did not influence the FAME profile with the MIDI method, while it influenced cyclopropane and monounsaturated content with the EL method. Composting age and degradation time had an effect on some groups of FAMEs, and this effect was greater with the EL method. The use of some FAMEs as biomarkers to follow microbial community succession was likely influenced by the type of compost and other factors.

Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p < 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 +/- 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 +/- 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (integral-libshuff, p < 0.001) and exhibited low similarities on both a presence/absence (0.145 +/- 0.019) and abundance (0.420 +/- 0.081) basis. Seventeen OTUs showed a strong positive (r > 0.600) or negative (r < -0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.

Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients

Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, Pseudomonas aeruginosa was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.

Bioaugmentation treatment for coking wastewater containing pyridine and quinoline in a sequencing batch reactor

Two pyridine-degrading bacteria and two quinoline-degrading bacteria were introduced for bioaugmentation to treat the coking wastewater. Sequencing batch reactors (SBRs) were used for a comparative study on the treatment efficiency of pyridine, quinoline, and chemical oxygen demand. Results showed that the treatment efficiency with coking-activated sludge plus a mixture of the four degrading bacteria was much better than that ones with coking-activated sludge only or mixed degrading bacteria only. Moreover, a 52-day continuous operation of the bioaugmented and general SBRs was investigated. The bioaugmented SBR showed better treatment efficiency and stronger capacity to treat high pyridine and quinoline shock loading. The general SBR failed to cope with the shock loading, and the biomass of the activated sludge decreased significantly. In order to monitor the microbial ecological variation during the long-term treatment, the bacterial community in both reactors was monitored by the amplicon length heterogeneity polymerase chain reaction technique. The diversity of the bacterial community decreased in both reactors, but the introduced highly efficient bacteria were dominant in the bioaugmented SBR. Our experiment showed clearly that the use of highly efficient bacteria in SBR process could be a feasible method to treat wastewater containing pyridine or/and quinoline.

Quantitative assessment of the human gut microbiome using multitag pyrosequencing

Recent advances in molecular techniques have now made it possible to interrogate the human microbiome in depth to better understand the interactions with the host organism and its role in diseases. We now report the utility of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to survey samples and a proprietary Multitagged Pyrosequencing (MTPS) methodology to interrogate the gut microbiome in healthy and disease states. We present an overview of our studies demonstrating the application of these molecular-biology techniques to an example disease state such as Inflammatory Bowel Disease (IBD). The findings show that there is a core mucosal bacterial microbiome (i.e., a mucosal biofilm) that is distinct from the luminal microbiome in health, and that the mucosal microbiome appears to be dysbiotic in IBD. We propose that the mucosal microbiome forms a synergistic and stable interaction with the host immune system, while the lumen microbiome varies based on diet or other environmental factors. We define this composite ecosystem of the human microbiome and human host as the Human Metabiome.

Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR

Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing best sequence matches with gamma-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria, genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially for diversity survey on a large number of samples.

Intestinal dysbiosis: a possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in rats

BACKGROUND

Clinical and animal data indicate that gut-derived endotoxin and other luminal bacterial products are necessary cofactors for development of alcoholic liver disease (ALD). Although gut leakiness is clearly an important cause of endotoxemia in ALD, it cannot fully explain endotoxemia in all ALD subjects and thus other factors may be involved. One possible factor is a change in gut microbiota composition (dysbiosis). Thus, the aim of our study was to interrogate the gut bacterial microbiota in alcohol-fed rats to see if chronic alcohol consumption affects gut bacteria composition.

METHOD

Male Sprague-Dawley rats were given either alcohol or dextrose intragastrically by gavage twice daily for up to 10 weeks. A subgroup of rats was also given either a probiotic (lactobacillus GG) or a prebiotic (oats) by gavage. Ileal and colonic mucosal-attached microbiota composition were interrogated by Length Heterogeneity PCR (LH-PCR) fingerprinting.

RESULTS

Bacterial microbiota composition in alcohol-fed rats is not different from dextrose-fed rats at weeks 4 and 6. Mucosa-associated microbiota composition in the colon is altered at 10 weeks of daily alcohol gavage. Both LGG and oats prevented alcohol-induced dysbiosis up to 10 weeks of alcohol treatment.

CONCLUSION

Daily alcohol consumption for 10 weeks alters colonic mucosa-associated bacterial microbiota composition in rats. Our data showed, for the first time, that daily alcohol consumption can affect colonic microbiome composition and suggest that dysbiosis may be an important mechanism of alcohol-induced endotoxemia. Further studies are needed to determine how dysbiotic microbiota contributes to development of ALD and whether therapeutic interventions targeted towards dysbiotic microbiota can prevent complications of alcoholism like ALD.

Intestinal dysbiosis: a possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in rats

BACKGROUND

Clinical and animal data indicate that gut-derived endotoxin and other luminal bacterial products are necessary cofactors for development of alcoholic liver disease (ALD). Although gut leakiness is clearly an important cause of endotoxemia in ALD, it cannot fully explain endotoxemia in all ALD subjects and thus other factors may be involved. One possible factor is a change in gut microbiota composition (dysbiosis). Thus, the aim of our study was to interrogate the gut bacterial microbiota in alcohol-fed rats to see if chronic alcohol consumption affects gut bacteria composition.

METHOD

Male Sprague-Dawley rats were given either alcohol or dextrose intragastrically by gavage twice daily for up to 10 weeks. A subgroup of rats was also given either a probiotic (lactobacillus GG) or a prebiotic (oats) by gavage. Ileal and colonic mucosal-attached microbiota composition were interrogated by Length Heterogeneity PCR (LH-PCR) fingerprinting.

RESULTS

Bacterial microbiota composition in alcohol-fed rats is not different from dextrose-fed rats at weeks 4 and 6. Mucosa-associated microbiota composition in the colon is altered at 10 weeks of daily alcohol gavage. Both LGG and oats prevented alcohol-induced dysbiosis up to 10 weeks of alcohol treatment.

CONCLUSION

Daily alcohol consumption for 10 weeks alters colonic mucosa-associated bacterial microbiota composition in rats. Our data showed, for the first time, that daily alcohol consumption can affect colonic microbiome composition and suggest that dysbiosis may be an important mechanism of alcohol-induced endotoxemia. Further studies are needed to determine how dysbiotic microbiota contributes to development of ALD and whether therapeutic interventions targeted towards dysbiotic microbiota can prevent complications of alcoholism like ALD.

Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung

Microbial communities play vital roles in many aspects of our lives, although our understanding of microbial biogeography and community profiles remains unclear. The number of microbes or the diversity of the microbes, even in small environmental niches, is staggering. Current microbiological methods used to analyse these communities are limited, in that many microorganisms cannot be cultured. Even for the isolates that can be cultured, the expense of identifying them definitively is much too high to be practical. Many recent molecular technologies, combined with bioinformatic tools, are raising the bar by improving the sensitivity and reliability of microbial community analysis. These tools and techniques range from those that attempt to understand a microbial community from their length heterogeneity profiles to those that help to identify the strains and species of a random sampling of the microbes in a given sample. These technologies are reviewed here, using the microbial communities present in the lungs of cystic fibrosis patients as a paradigm.

Are basidiomycete laccase gene abundance and composition related to reduced lignolytic activity under elevated atmospheric NO3(-) deposition in a northern hardwood forest?

Anthropogenic release of biologically available N has increased atmospheric N deposition in forest ecosystems, which may slow decomposition by reducing the lignolytic activity of white-rot fungi. We investigated the potential for atmospheric N deposition to reduce the abundance and alter the composition of lignolytic basidiomycetes in a regional network of four northern hardwood forest stands receiving experimental NO(3)(-) deposition (30 kg NO(3)(-)-N ha(-1) year(-1)) for a decade. To estimate the abundance of basidiomycetes with lignolytic potential, we used PCR primers targeting laccase (polyphenol oxidase) and quantitative fluorescence PCR to estimate gene copy number. Natural variation in laccase gene size permitted use of length heterogeneity PCR to profile basidiomycete community composition across two sampling dates in forest floor and mineral soil. Although past work has identified significant and consistent negative effects of NO(3)(-) deposition on lignolytic enzyme activity, microbial biomass, soil respiration, and decomposition rate, we found no consistent effect of NO(3)(-) deposition on basidiomycete laccase gene abundance or community profile. Rather, laccase abundance under NO(3)(-) deposition was lower (-52%), higher (+223%), or unchanged, depending on stand. Only a single stand exhibited a significant change in basidiomycete laccase gene profile. Basidiomycete laccase genes occurring in mineral soil were a subset of the genes observed in the forest floor. Moreover, significant effects on laccase abundance were confined to the forest floor, suggesting that species composition plays some role in determining how lignolytic basidiomycetes are affected by N deposition. Community profiles differed between July and October sampling dates, and basidiomycete communities sampled in October had lower laccase gene abundance in the forest floor, but higher laccase abundance in mineral soil. Although experimental N deposition significantly suppresses lignolytic activity in these forests, this change is not related to the abundance or community composition of basidiomycete fungi with laccase genes. Understanding the expression of laccases and other lignolytic enzymes by basidiomycete fungi and other lignin-decaying organisms appears to hold promise for explaining the consistent decline in lignolytic activity elicited by experimental N deposition.

Carbon utilization profiles of bacteria colonizing the headbox water of two paper machines in a Canadian mill

Forty-one bacterial strains isolated from the headbox water of two machines in a Canadian paper mill were associated with the genera Asticcacaulis, Acidovorax, Bacillus, Exiguobacterium, Hydrogenophaga, Pseudomonas, Pseudoxanthomonas, Staphylococcus, Stenotrophomonas based on the sequence of their 16S rRNA genes. The metabolic profile of these strains were determined using Biolog EcoPlate, and the bacteria were divided into four metabolic groups. Metabolic profiles of the bacterial communities colonizing the headbox water of two paper machines was also determined weekly over a 1 year period. The only compound that was not reduced by the bacterial community was 2-hydroxybenzoic acid. Utilization frequency of the other carbon sources in the Biolog EcoPlate ranged from 3 to 100%. The metabolic profiles of the bacterial community did not vary considerably between the two paper machines. However, the metabolic profile varied among the sampling dates.

Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure

A plug-flow type anaerobic reactor consisting of eight sequential compartments was used to study shifts in a bacterial community adapted to degrade swine manure at 25 degrees C. The investigation was carried out during the first 6 months of reactor operation. The reactor successfully separated the hydrolysis/acidogenesis stage from the methanogenesis stage. Bacterial 16S rDNA- and rRNA-based fingerprints obtained through amplicon length heterogeneity PCR (LH-PCR) were analyzed with a view to characterizing the bacterial community structure and the metabolically active community, respectively. Multivariate statistical tools showed that the rDNA-based fingerprints described a more temporal than compartmentalized distribution of similar bacterial communities. By contrast, the rRNA-based multivariate analyses described a distribution that was linked more to reactor performance parameters, especially during short time periods. Diversity indices calculated from fingerprint data were used to assess overall diversity shifts. The decrease in rRNA-based diversity observed through the reactor compartments was greater than the decrease in rDNA-based diversity. This finding indicates that the analysis of metabolically active bacteria diversity was more discriminative than the analysis based on the mere presence of bacteria. The observed decrease in diversity suggests that the bacterial community became specialized in degrading less diversified substrates through the compartments. All these findings suggest that rRNA-based analyses are more appropriate for monitoring reactor performance.

Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vaginosis

BACKGROUND

Whether human immunodeficiency virus (HIV) infection is associated with a change in the diversity of genital microbiota in women was investigated.

METHODS

Amplicon length heterogeneity polymerase chain reaction (LH-PCR) analysis and pyrosequencing of the 16S ribosomal RNA gene were used to analyze the diversity of the microbiota in HIV-positive (HIV(+)) and HIV-negative (HIV(-)) women with or without bacterial vaginosis (BV).

RESULTS

LH-PCR analysis revealed significantly more microbiota diversity in BV-positive (BV(+)) women than in BV-negative (BV(-)) women, but no significant difference was noted between HIV(+) women and HIV(-) women. Pyrosequencing revealed that Lactobacillus organisms constituted a median of 96% of the bacteria in BV(-) women. BV(+) women had a significantly higher number of taxa found at > or =1% of the total genital microbiota (median, 11 taxa). Common taxa in BV(+) women were Prevotella, Megasphaera, Gardnerella, Coriobacterineae, Lachnospira, and Sneathia. There was a trend (P = .07) toward the presence of a higher number of taxa in HIV(+)BV(+) women than in HIV(-)BV(+) women. Propionibacterineae, Citrobacter, and Anaerococcus were the taxa found only in HIV(+) women (P < .05).

CONCLUSIONS

The present study demonstrated that both LH-PCR analysis and pyrosequencing differentiated microbiota in BV(+) women from that in BV(-) women and that pyrosequencing indicated a trend toward increased diversity in BV(+)HIV(+) women, suggesting that HIV infection is associated with changes in the diversity of genital microbiota.

Spatial and temporal changes in Actinobacterial dominance in experimental artificial groundwater recharge

Artificial groundwater recharge (AGR) is used in the drinking water industry to supplement groundwater resources and to minimise the use of chemicals in water treatment. This study analysed the spatial and temporal changes of microbial communities in AGR using two test systems: a nutrient-amended fluidized-bed reactor (FBR) and a sand column. Structural changes in the feed lake water (Lake Roine), FBR, and sand column bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) and the length heterogeneity analysis of amplified 16S rRNA genes (LH-PCR). Two clone libraries were created to link the LH-PCR results to the dominant bacterial groups. The lake water bacterial community was relatively stable, with three bands dominating in all LH-PCR products. The most dominant fragment accounted for up to 72% and was derived from Actinobacteria. Based on the clone libraries and LH-PCR data, Actinobacteria also dominated in the unattached bacterial community of the FBR, whereas several Proteobacterial groups were more abundant on the FBR carrier particles. In the stabilised AGR system a major change in the community structure of the lake water bacteria took place during passage within the first 0.6m in the sand column as the community composition shifted from Actinobacteria-dominated populations to a diverse, mainly Proteobacterial communities. Concurrently, most of the dissolved organic carbon (DOC) was removed at this stage. In summary, the study showed that the make-up of microbial communities in experimental AGR systems responded to changes in their environment. LH-PCR showed potential as a method to determine microbial community dynamics in long-term studies at real-scale AGR sites. This is the first step to provide data on microbial community dynamics in AGR for drinking water production.

Microbial community in the rhizosphere of young maize seedlings is susceptible to the impact of introduced pseudomonads as indicated by FAME analysis

Two species of Pseudomonas (i.e. P. chlororaphis or P. putida) derived from a maize rhizosphere were studied for their impact on the structure of the microbial community in the rhizosphere of young maize seedlings after inoculation. The culturable bacteria and total microbial communities were analyzed based on profiles of whole-cell fatty acid methyl esters (MIDI-FAME). The introduction of Pseudomonas species resulted in the shift from the Gram-positive dominated culturable community in the rhizosphere of uninoculated maize to more Gram-negative populations in the rhizospheres of the inoculated plants. For the total rhizosphere communities, 43, 47 and 42 FAMEs were detected in the uninoculated maize and the samples inoculated with P. chlororaphis or P. putida, respectively. In contrast to the culturable communities, low concentrations of marker FAMEs for Gram-positives (i15:0, a15:0, i16:0) were found in the profiles of the total rhizosphere communities. The maize inoculations resulted in an enrichment of some Gram-negative isolates; however, Gram-positive bacteria, Cytophaga/Flavobacterium and saprophytic fungi were found in the uninoculated rhizosphere.