16S rDNA Clone Libraries Research Articles

Screening of a microbial consortium with efficient corn stover degradation ability at low temperature

To speed up the degradation of corn stover directly returned to soil at low temperature, the corn stover-degrading microbial consortium GF-20, acclimated to biological decomposition in the frigid region, was successfully constructed under a long-term limiting substrate. To evaluate its potential in accelerating the decomposition of un-pretreated corn stover, the decomposing property, fermentation dynamic and the microbial diversity were analyzed. GF-20 degraded corn stover by 32% after 15-day fermentation at 10°C. Peak activities of filter paperlyase (FPA), β-glucosidases (CB), endoglucanases (Cx), and cellobiohydrolases (C1) were 1.15, 1.67, 1.73, and 1.42 U mL−1, appearing at the 6th, 3rd, 11th, and 9th d, respectively. The pH averaged at 6.73–8.42, and the optical density (OD) value peaked at 1.87 at the 120 h of the degradation process. Cellulase, hemicellulase and lignin in corn stover were persistently degraded by 44.85, 43.85 and 25.29% at the end of incubation. Result of denaturing gradient gel electrophoresis (DGGE) profiles demonstrated that GF-20 had a stable component structure under switching the temperature and pH. The composition of the GF-20 was also analyzed by constructing bacterial 16S rDNA clone library and fungal 18SrDNA-PCR-DGGE. Twenty-two bacterial clones and four fungal bands were detected and identified dominant bacteria represented by Cellvibrio mixtus subsp., Azospira oryzae, Arcobacter defluyii, and Clostridium populeti and the fungi were mainly identified as related to Trichosporon sp.

Understanding biofilm diffusion profiles and microbial activities to optimize integrated fixed-film activated sludge process

The integrated fixed-film activated sludge (IFAS) process is widely used in wastewater treatment plants (WWTPs) of China to ensure complete nitrification. However, high aeration intensity in this process requires optimization to reduce its energy footprint. Moreover, understanding microbial activity is also critical for process operation, especially for the biofilm on the carriers which play an important role for nitrogen removal. Here, we integrated process modeling, biomass activity and microbial community analysis in a full-scale IFAS plant, in order to investigate and optimize the process operation for better performance especially in cold climate. The field surveys indicated complete nitrification in the IFAS process, with biofilm contributed two thirds of it. Parameter sensitivity analysis also emphasized the importance of biofilm diffusion profile for process operation, and ammonia limited diffusion profile implied the bulk dissolved oxygen (DO) can be reduced from 8mg/L to 4mg/L. Furthermore, simplified respirometric tests revealed the variation of biomass activity over long time, proving attached biomass had much higher nitrification activity than suspended biomass, with almost no change after DO dropped to 4mg/L. Meanwhile, the microbial community by 16S rDNA clone library also indicated the accumulation of abundant nitrifiers in the biofilm, supporting the process optimization. The integrated methods of process modeling, biomass activity evaluation and microbial community analysis showed great potential in engineering practice for process optimization.

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area

The purpose of this study was to determine the first-order rate constants and half-lives of aerobic and anaerobic biomineralization of atrazine in soil samples from an agricultural farm site that had been previously used for mixing pesticide formulations and washing application equipment. Atrazine catabolic genes and atrazine-degrading bacteria in the soil samples were analyzed by molecular methods. Biomineralization of atrazine was measured in soil samples with a [U-ring-14C]-atrazine biometer technique in soil samples. Enrichment cultures growing with atrazine were derived from soil samples and they were analyzed for bacterial diversity by constructing 16S rDNA clone libraries and sequencing. Bacterial isolates were also obtained and they were screened for atrazine catabolic genes. The soils contained active atrazine-metabolizing microbial communities and both aerobic and anaerobic biomineralization of [U-ring-14C]-atrazine to 14CO2 was demonstrated. In contrast to aerobic incubations, anaerobic biometers displayed considerable differences in the kinetics of atrazine mineralization between duplicates. Sequence analysis of 16S rDNA clone libraries constructed from the enrichment cultures revealed a preponderance of Variovorax spp. (51 %) and Schlesneria (16 %). Analysis of 16S rRNA gene sequences from pure cultures (n = 12) isolated from enrichment cultures yielded almost exclusively Arthrobacter spp. (83 %; 10/12 isolates). PCR screening of pure culture isolates for atrazine catabolic genes detected atzB, atzC, trzD, trzN, and possibly atzA. The presence of a complete metabolic pathway was not demonstrated by the amplification of catabolic genes among these isolates. The soils contained active atrazine-metabolizing microbial communities. The anaerobic biometer data showed variable response of atrazine biomineralization to external electron acceptor conditions. Partial pathways are inevitable in soil microbial communities, with metabolites linking into other catabolic and assimilative pathways of carbon and nitrogen. There was no evidence for the complete set of functional genes of the known pathways of atrazine biomineralization among the isolates.

Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria.

Three soil samples obtained from different sites adjacent to a chromium slag heap in a steel alloy factory were taken to examine the effect of chromium contamination on soil bacterial diversity as determined by construction of 16S rDNA clone libraries and sequencing of selected clones based on restriction fragment length polymorphism (RFLP) analysis. Results revealed that Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Alphaproteobacteria occurred in all three soil samples, although the three samples differed in their total diversity. Sample 1 had the highest microbial diversity covering 12 different classes, while Sample 3 had the lowest microbial diversity. Strains of six different species were successfully isolated, one of which was identified as Zobellella denitrificans. To our knowledge, this is the first report of a strain belonging to the genus Zobellella able to resist and reduce chromium. Among all isolates studied, Bacillus odysseyi YH2 exhibited the highest Cr(VI)-reducing capability, with a total removal of 23.5% of an initial Cr(VI) concentration of 350mgL(-1).

Effect of domestication on microorganism diversity and anaerobic digestion of food waste.

To accomplish the rapid start-up and stable operation of biogas digesters, an efficient inoculum is required. To obtain such an inoculum for food waste anaerobic digestion, we domesticated dairy manure anaerobic digestion residue by adding food waste every day. After 36 days, the pH and biogas yield stabilized signifying the completion of domestication. During domestication, the microbial communities in the inocula were investigated by constructing 16S rDNA clone libraries. We evaluated the effect of the domesticated inoculum by testing batch food waste anaerobic digestion with a non-domesticated inoculum as a control. The pH and methane yield of the digestion systems were determined as measurement indices. Domestication changed the composition and proportion of bacteria and archaea in the inocula. Of the bacteria, Clostridia (49.3%), Bacteroidales (19.5%), and Anaerolinaceae (8.1%) species were dominant in the seed sludge; Anaerolinaceae (49.0%), Clostridia (28.4%), and Bacteroidales (9.1%), in domestication sludge. Methanosaeta was the dominant genus in both of the seed (94.3%) and domestication (74.3%) sludge. However, the diversity of methanogenic archaea was higher in the domestication than in seed sludge. Methanoculleus, which was absent from the seed sludge, appeared in the domestication sludge (21.7%). When the domesticated inoculum was used, the digestion system worked stably (organic loading rate: 20 gVS/L; methane yield: 292.2 ± 9.8 mL/gVS; VS = volatile solids), whereas the digestion system inoculated with seed sludge failed to generate biogas. The results indicate that inoculum domestication ensures efficient and stable anaerobic digestion by enriching the methanogenic strains.

Phylogenetic analysis of bacterial species compositions in sand dunes and dust aerosol in an Asian dust source area, the Taklimakan Desert

Airborne microorganisms (bioaerosol) from the China desert region, which are released into the atmosphere, disperse by the Asian dust event and affect ecosystems, human life, and atmospheric processes in downwind areas. However, the dynamics of airborne bacteria over the China desert regions have rarely been investigated. In this study, we analyzed bacterial communities in aerosols of the Asian dust source region (Taklimakan Desert) and compared them with the bacterial communities in sand dunes, for evaluating the mixtures from sand area to atmosphere. Air samples were collected at 10 m above the ground level from Dunhuang City during a dust event. The cell densities of airborne bacteria during a dust event were ten times more than that in non-dust periods. The 16S rDNA clone libraries from four air samples mainly belonged to two phyla, Firmicutes and Proteobacteria. During a dust event, the proportion of Proteobacteria clones decreased, whereas that of Firmicutes clones increased. Sand samples were collected from the sand dunes in four sampling sites of the Taklimakan Desert. The bacterial communities in sand samples comprised of the members of Firmicutes and Actinobacteria. The clones of Firmicutes in both air and sand samples included Bacillus species, constituting more than 10 % of total clones. Airborne bacterial communities would be carried by the dust events from sand dunes. Propionibacterium species from the class Actinobacteria that were dominant in sand samples were not detected in the air samples, suggesting that atmospheric stressors eliminate some bacterial species. Presumably, airborne bacterial communities in the Asian dust source region are composed of local environmental bacteria, and their dynamics depend on the occurrence of a dust event.

Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals

Gorgonian corals serve as key engineering species within Mediterranean rocky-shore communities that have recently suffered from repeated mortality events during warm temperature anomalies. Among the factors that may link thermal conditions with disease outbreaks, a number of bacterial pathogens have been implicated; they may take advantage of decreases in the defenses and/or overall health of the gorgonian hosts. Considering the beneficial role of the resident bacteria in tropical coral holobionts, a detailed characterization of the gorgonian-associated microbial populations is required to better understand the relationships among native microbiota, host fitness, and pathogen susceptibility. In this study, the bacterial communities associated with three sympatric gorgonian species, Eunicella singularis, Eunicella cavolini, and Corallium rubrum, were investigated to provide insight into the stability and the specificity of host–microbe interactions. Natural variations in bacterial communities were detected using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal DNA. No major differences were identified between individual colonies sampled in winter or in summer within each gorgonian species. Although hierarchical cluster analysis of the T-RFLP profiles revealed that the three species harbor distinct communities, comparison of the T-RFLP peaks indicated the presence of common bacterial ribotypes. From phylogenetic analysis of 16S rDNA clone libraries, we identified a bacterial lineage related to the Hahellaceae family within the Oceanospirillales that is shared among E. singularis, E. cavolini, and C. rubrum and that dominates the communities of both species of Eunicella. However, distinct clades of Hahellaceae are harbored by various gorgonian species from Mediterranean and tropical waters, suggesting that these bacteria have formed host-specific symbiotic relationships with gorgonian octocorals. In addition, the relatedness of symbionts from host species belonging to the same taxon but occurring in geographically remote areas is consistent with codivergence between gorgonians and their associated bacteria.

Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)

The central Mediterranean Sea is among the most oligotrophic habitats in the marine environment. In this study, we investigated the abundance, diversity and activity of prokaryoplankton in the water column (25–3000-m depth) at Station Vector (Tyrrhenian Sea, 39°32.050′ N; 13°22.280′ E). This specific water column consists of three different water masses (Modified Atlantic Water (MAW), Levantine Intermediate Water (LIW) and Tyrrhenian Deep Water (TDW), possessing a typical stratification of the Central Mediterranean basin. CARD-FISH showed that the metabolically-active fraction of bacterial populations exceeded the archaeal fraction along the whole water column, except at the deepest water masses. 16S rDNA and 16S rRNA clone libraries obtained from each type of water mass were used to analyse the prokaryoplankton community structure and to distinguish between active and “less active” microbial fractions. Our results showed that the rRNA-derived bacterial libraries seemed to be more depth specific compared to 16S rDNA-derived counterparts. Major differences were detected between the active fractions of bacterioplankton thriving in photic (25 m, MAW) and aphotic layers (500–3000 m, LIW and TDW respectively), whereas no statistically-significant differences were detected within the deep, aphotic layers (500–3000 m, LIW and TDW). Archaeal communities possessed more depth-specific distribution patterns with both total and active fractions showing depth stratification. Cyanobacteria and Marine Group II MAGII of Euryarchaea dominated the MAW prokaryoplankton. A notable fraction of Geitlerinema-related cyanobacteria was detected among the metabolically-active bacterial population recovered from the mesopelagic (500 m, LIW) aphotic layer, which is indicative of their mixotrophic behaviour. Heterotrophic Gammaproteobacteria and members of Marine Group 1.1a and the PSL12-related ALOHA group of Thaumarchaeota were both abundant in the aphotic layers (both LIW and TDW). Discrepancies observed between 16S rDNA- and 16S rRNA-based libraries are most likely linked to different physiological states of the prokaryoplankton community members recovered from different layers. Taking into account the relative homogeneity of the main physicochemical parameters throughout the whole water column, light and energy source are likely the most relevant environmental variables shaping microbial biodiversity through the Station Vector water column.

Bacterial communities during the process of high-temperature Daqu production of roasted sesame-like flavour liquor

Bacterial communities in fermentative high-temperature Daqu play an important role in the Chinese roasted sesame-like flavour liquor brewing process. A culture-independent method of 16S rDNA clone library was applied to investigate the changes in bacterial diversity during the process of a Daqu fermentation. The results indicated that the types of bacteria species gradually increased with prolonged fermentation time. The first dominant bacterium, Pantoea sp. (73.68%), in the raw material was only detected at the beginning of the fermentation stage (8 days) in small quantities. The second dominant bacterium, Weissella sp. (16.99%) and the third, Lactobacillus sp. (4.57%), were both detected in the beginning fermentation sample (3.22, 11.29%), in the ripening fermentation sample (24 days; 6.89, 25.11%) and in the drying stage (49 days; 3.74, 7.47%). In the beginning fermentation, Thermoactinomyces sp. (47.57%) was detected as the first predominant bacterium, and it was also detected in the ripening fermentation stage (4.93%) and in the drying stage (15.68%). The bacterial communities in the Daqu fermentation process affected the physicochemical index of Daqu. A molecular analysis of the bacterial community from the Daqu fermentation process will benefit studies on the aroma production mechanisms from these bacteria. Copyright © 2015 The Institute of Brewing & Distilling

A preliminary and qualitative study of resource ratio theory to nitrifying lab-scale bioreactors.

The incorporation of microbial diversity in design would ideally require predictive theory that would relate operational parameters to the numbers and distribution of taxa. Resource ratio-theory (RRT) might be one such theory. Based on Monod kinetics, it explains diversity in function of resource-ratio and richness. However, to be usable in biological engineered system, the growth parameters of all the bacteria under consideration and the resource supply and diffusion parameters for all the relevant nutrients should be determined. This is challenging, but plausible, at least for low diversity groups with simple resource requirements like the ammonia oxidizing bacteria (AOB). One of the major successes of RRT was its ability to explain the ‘paradox of enrichment’ which states that diversity first increases and then decreases with resource richness. Here, we demonstrate that this pattern can be seen in lab-scale-activated sludge reactors and parallel simulations that incorporate the principles of RRT in a floc-based system. High and low ammonia and oxygen were supplied to continuous flow bioreactors with resource conditions correlating with the composition and diversity of resident AOB communities based on AOB 16S rDNA clone libraries. Neither the experimental work nor the simulations are definitive proof for the application of RRT in this context. However, it is sufficient evidence that such approach might work and justify a more rigorous investigation.

Molecular analysis of in situ diets of coral reef copepods: evidence of terrestrial plant detritus as a food source in Sanya Bay, China

Knowledge of copepod in situ diet is critical for accurate assessment of trophic linkages and transfer efficiencies of the marine food web but is limited due to technical challenges. Here we report, using a recently developed eukaryote-universal copepod-excluding ectobiotic ciliate-blocking protocol, to investigate the natural diets of the copepods Temora turbinata, Subeucalanus subcrassus and Canthocalanus pauper in coastal waters in Sanya Bay, China. Analysis of the resultant 18S rDNA clone libraries revealed diverse diet composition for all the three copepod species, with 11 prey species for C. pauper, 9 for T. turbinata and 9 for S. subcrassus. The ingested materials included land plants, green algae, Metazoa, Euglenozoa and Rhizaria, although species numbers from each of these lineages differed. Broussonetia sp. (land plant), which might have been ingested in the form of pollen or fresh detritus were common among all three copepods, and accounted for a significant proportion (>55%) of the clones sequenced. These results suggest that copepods in Sanya coastal waters might use terrigenous detritus as supplementary food sources when phytoplankton production is limited. However, the significance of the plant detritus as a nutrition source of these copepods remains to be determined by analyzing carbon-based proportion and digestion/assimilation rate of the ingested plant materials.

Archaeal community structure in the tropical coastal waters of Peninsular Malaysia

In this study, we used a direct cloning method to explore the archaeal diversity at four locations along the Straits of Malacca. Four 16S rDNA clone libraries were constructed with archaeal specific primers (Arc21F and Arc958R) and, in total, 1,074 randomly selected clones were screened by PCR-restriction fragment length polymorphism analysis using three different restriction enzymes (RsaI, CfoI and DdeI). Good’s coverage suggested that >85 % of archaeal sequence types were obtained in our libraries. The majority of the sequences from Port Dickson and Sungai Muar were affiliated to Euryarchaeota, whereas Port Klang and Kuala Selangor clone libraries were dominated by Thaumarchaeota sequences. Phylogenetic analysis of 16S rDNA sequences showed high archaeal diversity, with a Shannon index ranging from 2.16 to 3.24. Using weighted, non-normalized principal coordinate analysis, the archaeal communities of the four sites were clearly separated from each other. We also showed via canonical correspondence analysis that the distribution of archaeal operational taxonomic units could be related to environmental variables (salinity and chlorophyll a).

The Impact of Enterohemorrhagic <i>Escherichia coli</i> (EHEC) on Ciliate Protozoan Populations in Municipal Sewage

Enterohemorrhagic Escherichia coli strains (EHEC) have caused many foodborne outbreaks. Bacterivorous protozoa could remove bacteria from aquatic systems. We analyzed the ciliate protozoan population changes influenced by EHEC co-culture in activated sludge. EHEC and non-EHEC control E. coli cells were added to activated sludge samples in microcosms. The ciliate population changes were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis. EHEC and non-EHEC fed ciliate protozoan populations were different from each other and the no bacteria added controls based on the additive main effects and multiplicative interaction model (AMMI) analysis. Ciliate species were identified by 18S rDNA clone libraries. The 18S rDNA clones from the original sludge sample were identified as Epistylis wenrichi (70%) and Prorodon teres (30%), while clones from EHEC treated sludge sample were identified as P. teres (52%), Vorticella fusca (41%), Dexitrichides pangi (5%), and Opisthonecta henneguyi (2%). This study could provide helpful information about ciliate protozoan population changes caused by different E. coli strains in wastewater treatment plants, which could be useful for preventing and tracking E. coli outbreaks.

Molecular and Chemical Analyses of Cyanobacterial Blooms in Tropical Lagoons from Southeast Brazil

The genetic diversity and the potential toxicity of bloom-forming cyanobacteria were studied in four lagoons located in the state of Sao Paulo (Campinas, Limeira and Piracicaba cities). Bloom samples were collected on the water surface and cyanobacterial communities were evaluated using DGGE fingerprinting and 16S rDNA clone library. The amplification of genes encoding secondary metabolites such as microcystin (mcy), anatoxin (ana), cylindrospermopsin (cyr), saxitoxin (sxt), cyanopeptolin (mcn) and aeruginosin (aer) was performed and their production analyzed by LC-MS. The comparison of DGGE banding pattern among the different water samples suggested that some operational taxonomic units (OTUs) in these locations were predominant over others. The 16S rDNA clone libraries sequences matched with nine different known cyanobacterial genera available in NCBI, identified as Anabaena, Brasilonema, Cylindrospermopsis, Limnococcus, Microcystis, Nostoc, Pseudanabaena, Synechococcus and Woronichinia. The lagoons ESALQ2, Taquaral and Limeira had more than 80% of the cyanobacterial community assigned to the genus Microcystis. Genes encoding aeruginosin, cyanopeptolin and microcystin synthetases and saxitoxin synthase were amplified, and LC-MS/MS confirmed the production of aeruginosin, cyanopeptolin and microcystin. Rapid and sensitive methods for the detection of these secondary metabolites, especially toxins, using chemical and molecular tools together, can be used for a faster diagnostic of toxic cyanobacterial blooms.

Microbial community structures in an integrated two-phase anaerobic bioreactor fed by fruit vegetable wastes and wheat straw

The microbial community structures in an integrated two-phase anaerobic reactor (ITPAR) were investigated by 16S rDNA clone library technology. The 75L reactor was designed with a 25L rotating acidogenic unit at the top and a 50L conventional upflow methanogenic unit at the bottom, with a recirculation connected to the two units. The reactor had been operated for 21 stages to co-digest fruit/vegetable wastes and wheat straw, which showed a very good biogas production and decomposition of cellulosic materials. The results showed that many kinds of cellulose and glycan decomposition bacteria related with Bacteroidales, Clostridiales and Syntrophobacterales were dominated in the reactor, with more bacteria community diversities in the acidogenic unit. The methanogens were mostly related with Methanosaeta, Methanosarcina, Methanoculleus, Methanospirillum and Methanobacterium; the predominating genus Methanosaeta, accounting for 40.5%, 54.2%, 73.6% and 78.7% in four samples from top to bottom, indicated a major methanogenesis pathway by acetoclastic methanogenesis in the methanogenic unit. The beta diversity indexes illustrated a more similar distribution of bacterial communities than that of methanogens between acidogenic unit and methanogenic unit. The differentiation of methanogenic community composition in two phases, as well as pH values and volatile fatty acid (VFA) concentrations confirmed the phase separation of the ITPAR. Overall, the results of this study demonstrated that the special designing of ITPAR maintained a sufficient number of methanogens, more diverse communities and stronger syntrophic associations among microorganisms, which made two phase anaerobic digestion of cellulosic materials more efficient.

Analysis of endophytic bacterial community composition by 16S rDNA clone library in Achnatherum inebrians

The endophytic bacterial diversity of drunken horse grass (DHG) (Achnatherum inebrians) growing in native habitat station in Xinjiang Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of DHG, a pair of bacterial PCR primers was selected to specifically amplify bacterial 16S rDNA sequences directly from DHG root tissues. Among 249 positive clones in the 16S rDNA library of endophytes, 57 OTUs were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Flavobacteria, Actinobacteria, Sphingobacteria, and uncultured bacteria. The dominant group was Proteobacteria, whie the most numerous genus was Bacillus. More than 8.00% of the total clones showed a high similarity to uncultured bacteria, suggesting that nonculturable bacteria make a significant part of DHG endophytic bacterial community. To our knowledge, this is the first report that endophytic bacteria associated with DHG are revealed by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in DHG.

Bacterial community in semiarid hydrocarbon contaminated soils treated by aeration and organic amendments

Bioremediation of oil sludge contaminated soils may enhance the rate of petroleum hydrocarbons (PHs) biodegradation. Changes in bacterial community structure and functionality may be expected as a result of hydrocarbon contamination and bioremediation processes.A 6 month microcosm experiment was performed in which an oil sludge contaminated semi-arid soil was treated by aeration (AE), and aeration plus organic amendment (dried biosolid, DB) and composted biosolid, CB)). Hydrocarbon degradation and functional and structural changes in microbial communities were examined after submitting the soil to these bioremediation treatments. AE reduced the amount of PHs in soil from the initial 5% to 2.7% whereas the amount of PHs left in the soil with the CB and DB treatments were 2.5% and 2.4%, respectively. Bacterial abundance, measured by real-time PCR, was significantly higher in bioremediated soils (AE, DB and CB) than in the non-contaminated soil (control soil). Functional and structural differences in bacterial community measured by BIOLOG and denaturing gradient gel electrophoresis (DGGE), respectively, were observed between bioremediated soils and control soil, both at the start and end of the bioremediation process. After 6 months of bioremediation, 16S rDNA clone libraries showed less phyla in bioremediated soils than in the control soil. The most dominant phylum observed in bioremediated soils was Actinobacteria whereas in the control soil Proteobacteria was the most dominant.This study suggests that regardless of the type of bioremediation carried out and the degree of hydrocarbon degradation, the bioremediation process leads to an increase in soil bacterial abundance accompanied by a decrease in microbial diversity, as well as, to structural and functional changes in the bacterial community.

Diversity of rhizosphere bacteria associated with different soybean cultivars in two soil conditions

Aiming at learning the effects of soil conditions and cultivar on the bacterial diversity in the rhizosphere of soybean (Glycine max(L.) Merr.), bacterial communities associated with four soybean cultivars grown in two soils were revealed by terminal-restriction fragment length polymorphism (T-RFLP) combined with sequencing analysis of a 16S rDNA clone library. Lower bacteria diversity was found in soil A which has higher salinity and nutrient contents, while the highest bacterial diversity was found in the rhizosphere of cv. Jidou 12 in both soils. These results revealed that both the soil conditions and soybean cultivar affected the community composition of rhizosphere bacteria, but the effect of soil conditions was greater than that of soybean cultivar as demonstrated by the principal component analysis. It also revealed that the abundant rhizosphere bacteria may also the main symbiotic or non-symbiotic nodule endophytes.

Nitrogen fixation, hydrogen production and N2O emissions

Flynn, B., Scott, N. and Dong, Z. 2014. Nitrogen fixation, hydrogen production and N2O emissions. Can. J. Plant Sci. 94: 1037–1041. H2 is a by-product of the nitrogenase reaction. Exposure to H2 is linked to increased N2O production, increased CO2 fixation and plant growth promotion in soil. The effects of H2 exposure on soil were observed using controlled H2 gas treatments and field trials with legumes. In field trials, increased N2O production was observed in soil adjacent to legume nodules and inoculation of H2-oxidizing isolates led to increased N2O emissions in corn fields. Many H2-oxidizing isolates tested positive for key denitrification genes, indicating a connection between H2 uptake and N2O emissions. H2 treatment significantly increased copy number of the nitrite reductase (nirK) gene suggesting increased denitrification as the source of N2O. There was also a significant increase in copy number and expression of the RubisCO (cbbL) gene in soil. H2-oxidizing bacterial isolates (JM63 and JM162a) were found to promote plant growth, increasing tiller number and yield in spring wheat and barley. Combined results of T-RFLP and 16S rDNA clone libraries analysis revealed bacterial community structure changes in response to H2 treatment, primarily with increases to the Gammaproteobacteria and Betaproteobacteria groups. The results of these studies help provide a better understanding of the soil bacterial community's responses to H2 exposure and may lead to the development of a commercially viable plant growth promoting inoculant.

Bacterial diversity of extremely alkaline bauxite residue site of alumina industrial plant using culturable bacteria and residue 16S rRNA gene clones.

Bauxite residue (red mud), generated during the extraction of alumina from bauxite ore is characterized by high pH, high concentrations of soluble ions with low or virtually no organic matter. These extreme conditions along with numerous nutrient deficiencies, limit the microbial growth and vegetation establishment. In the present study, diversity of both cultivable and non-cultivable bacteria present in the red mud was investigated by 16S rDNA sequence analyses. The cultivable bacteria were identified as Agromyces indicus, Bacillus litoralis, B. anthracis, Chungangia koreensis, Kokuria flava, K. polaris, Microbacterium hominis, Planococcus plakortidis, Pseudomonas alcaliphila and Salinococcus roseus based on their 16S rDNA sequence analysis. These isolates were alkali tolerant, positive for one or more of the enzyme activities tested, able to produce organic acids and oxidize wide range of carbon substrates. For non-cultivable diversity of bacteria, DNA was extracted from the bauxite residue samples and 16S rDNA clone library was constructed. The 16S rDNA clones of this study showed affiliation to three major phyla predominant being betaproteobacteria (41.1%) followed by gammaproteobacteria (37.5%) and bacteroidetes (21.4%). We are reporting for the first time about the bacterial diversity of this unique and extreme environment.