Aluminum tolerance of wheat does not induce changes in dominant bacterial community composition or abundance in an acidic soil

Aims

Aluminum-tolerant wheat plants often produce more root exudates such as malate and phosphate than aluminum-sensitive ones under aluminum (Al) stress, which provides environmental differences for microorganism growth in their rhizosphere soils. This study investigated whether soil bacterial community composition and abundance can be affected by wheat plants with different Al tolerance.

Methods

Two wheat varieties, Atlas 66 (Al-tolerant) and Scout 66 (Al-sensitive), were grown for 60 days in acidic soils amended with or without CaCO₃. Plant growth, soil pH, exchangeable Al content, bacterial community composition and abundance were investigated.

Results

Atlas 66 showed better growth and lower rhizosphere soil pH than Scout 66 irrespective of CaCO₃ amendment or not, while there was no significant difference in the exchangeable Al content of rhizosphere soil between the two wheat lines. The dominant bacterial community composition and abundance in rhizosphere soils did not differ between Atlas 66 and Scout 66, although the bacterial abundance in rhizosphere soil of both wheat lines was significantly higher than that in bulk soil. Sphingobacteriales, Clostridiales, Burkholderiales and Acidobacteriales were the dominant bacteria phylotypes.

Conclusions

The difference in wheat Al tolerance does not induce the changes in the dominant bacterial community composition or abundance in the rhizosphere soils.     

Isolation of facultatively anaerobic soil bacteria from Ny-Ålesund, Svalbard

Anaerobic conditions in soil commonly occur even in upland environments. Physiological and biogeochemical properties of individual anaerobic bacteria, however, have been poorly understood due to difficulties in culture. This study aimed to isolate anaerobic bacteria in the Arctic tundra soil and to identify their physiological characteristics. Anaerobic culture and 16S rRNA gene sequence-based phylogenetic analysis showed that total 33 bacterial strains were affiliated with 15 species from the following 8 genera: Bacillus, Carnobacterium, Clostridium, Paenibacillus, and Trichococcus (Firmicutes), Pseudomonas and Rahnella (Gamma-proteobacteria), and Cellulomonas (Actinobacteria). All isolates were identified as facultatively anaerobic bacteria; this finding might be partially attributed to the characteristics of sampling sites, which temporarily developed anaerobic conditions because of the presence of stagnant melting snow. Six of the 33 bacterial strains were revived subsequently from glycerol stocks held ?80 °C, and these were used for the physiological study: four isolates from Firmicutes, one isolate from Gamma-proteobacteria, and one isolate from Actinobacteria. Five isolates except KOPRI 80146 (Bacillus sp.) could grow at either 4 or 10 °C within a week. All six isolates showed cellulase or protease activities at 10 or 15 °C. Endospores were observed from four isolates belonging to Firmicutes. These physiological characteristics may contribute to the survival of these organisms at low temperatures and to their involvement in biogeochemical cycles in the tundra soil. These isolates may be used for further detailed studies for identifying their cold adaptation mechanisms and ecological roles in the Arctic.     

Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil

Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2 % (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3 %) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1^T, was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.     

Effects of variation in precipitation on the distribution of soil bacterial diversity in the primitive Korean pine and broadleaved forests

Patterns of precipitation have changed as a result of climate change and will potentially keep changing in the future. Therefore, it is critical to understand how ecosystem processes will respond to the variation of precipitation. However, compared to aboveground processes, the effects of precipitation change on soil microorganisms remain poorly understood. Changbai Mountain is an ideal area to study the responses of temperate forests to the variations in precipitation. In this study, we conducted a manipulation experiment to simulation variation of precipitation in the virgin, broad-leaved Korean pine mixed forest in Changbai Mountain. Plots were designed to increase precipitation by 30 % [increased (+)] or decrease precipitation by 30 % [decreased (?)]. We analyzed differences in the diversity of the bacterial community in surface bulk soils (0–5 and 5–10 cm) and rhizosphere soils between precipitation treatments, including control. Bacteria were identified using the high-throughput 454 sequencing method. We obtained a total 271,496 optimized sequences, with a mean value of 33,242 (±1,412.39) sequences for each soil sample. Being the same among the sample plots with different precipitation levels, the dominant bacterial communities were Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Bacterial diversity and abundance declined with increasing soil depth. In the bulk soil of 0–5 cm, the bacterial diversity and abundance was the highest in the control plots and the lowest in plots with reduced precipitation. However, in the soil of 5–10 cm, the diversity and abundance of bacteria was the highest in the plots of increased precipitation and the lowest in the control plots. Bacterial diversity and abundance in rhizosphere soils decreased with increased precipitation. This result implies that variation in precipitation did not change the composition of the dominant bacterial communities but affected bacterial abundance and the response patterns of the dominant communities to variation in precipitation.     

Changes in the microbial community during repeated anaerobic microbial dechlorination of pentachlorophenol

Pentachlorophenol (PCP) has been widely used as a pesticide in paddy fields and has imposed negative ecological effect on agricultural soil systems, which are in typically anaerobic conditions. In this study, we investigated the effect of repeated additions of PCP to paddy soil on the microbial communities under anoxic conditions. Acetate was added as the carbon source to induce and accelerate cycles of the PCP degradation. A maximum degradation rate occurred at the 11th cycle, which completely transformed 32.3 μM (8.6 mg L^?1) PCP in 5 days. Illumina high throughput sequencing of 16S rRNA gene was used to profile the diversity and abundance of microbial communities at each interval and the results showed that the phyla of Bacteroidates, Firmicutes, Proteobacteria, and Euryarchaeota had a dominant presence in the PCP-dechlorinating cultures. Methanosarcina, Syntrophobotulus, Anaeromusa, Zoogloea, Treponema, W22 (family of Cloacamonaceae), and unclassified Cloacamonales were found to be the dominant genera during PCP dechlorination with acetate. The microbial community structure became relatively stable as cycles increased. Treponema, W22, and unclassified Cloacamonales were firstly observed to be associated with PCP dechlorination in the present study. Methanosarcina that have been isolated or identified in PCP dechlorination cultures previously was apparently enriched in the PCP dechlorination cultures. Additionally, the iron-cycling bacteria Syntrophobotulus, Anaeromusa, and Zoogloea were enriched in the PCP dechlorination cultures indicated they were likely to play an important role in PCP dechlorination. These findings increase our understanding for the microbial and geochemical interactions inherent in the transformation of organic contaminants from iron rich soil, and further extend our knowledge of the PCP-transforming microbial communities in anaerobic soil conditions.     

Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter

The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m³ digester produced biogas with 57 % methane, and chemical oxygen demand removal of 54 %. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93 % of the clones and 76 % of the pyrotags. Of the Firmicutes, class Clostridia (52 % pyrotags) was most abundant followed by class Bacilli (13 % pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97 % minimum similarity level. Fifteen OTUs were dominant (≥2 % abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5 % abundance), 75 % were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99 % of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.     

Endophytic and mycorrhizal fungi associated with roots of endangered native orchids from the Atlantic Forest, Brazil

The composition and diversity of fungal communities associated with three endangered orchid species, Hadrolaelia jongheana, Hoffmannseggella caulescens, and Hoffmannseggella cinnabarina, found in different vegetation formations of the Atlantic Forest were determined by constructing clone libraries and by applying diversity and richness indices. Our results demonstrated the presence of Basidiomycetes. Sebacinales (81.61 %) and Cantharellales (12.10 %) were the dominant orders and are potential candidates for orchid mycorrhizal fungi. The Ascomycetes identified included the Helotiales (29.31 %), Capnodiales (18.10 %), and Sordariales (10.34 %), among others. These orders may represent potentially endophytic fungi. A Shannon–Wiener diversity index (H′) analysis showed a relatively high fungal community diversity associated with these tropical orchids. This diversity may offer greater flexibility in terms of the adaptation of the plants to changing environmental conditions and the potential facilitation of reintroduction programs. The Simpson diversity index values showed that all of the libraries included dominant species, and a LIBSHUFF analysis showed that the fungal communities were structurally different from each other, suggesting an influence of local factors on this diversity. This study offers important information for the development of conservation strategies for threatened and endemic species of Brazilian flora in an important and threatened hotspot.     

Effective anaerobic treatment of fresh leachate from MSW incineration plant and dynamic characteristics of microbial community in granular sludge

We investigated the treatment of fresh leachate from municipal solid waste incineration plants with high-strength organics using a lab-scale expanded granular sludge bed (EGSB) reactor. The reactor was operated at a mesophilic temperature (33 °C) for 118 days. The influent chemical oxygen demand (COD) of the leachate gradually increased to over 70,000 mg/L, and the organic loading rate increased to 18 kg COD/(m³?day). An average COD removal efficiency of 86.7 % was achieved when the reactor was fed with raw leachate, which suggests the feasibility of the EGSB process for leachate treatment. The microbial communities in the sludge from the reactor during the trial operation were constructed by denaturing gradient gel electrophoresis, clone libraries, and real-time quantitative polymerase chain reaction. The dominant group for archaea was Methanosaeta, with 68.4 % proportion at the start of the operation, and then changed to Methanosarcina, with a proportion of 62.3 %, after 118 days of operation. The dominant group of eubacteria was confirmed to be Firmicutes throughout the operation process, with the proportion increasing from >50 to 81.2 %. Almost all the operational taxonomic units of Firmicutes belonged to the order Clostridiales, with characteristic spore formation. The microbial diversity of the population was low under raw leachate as feed in the reactor. The dynamics of the microbial community in the anaerobic granular sludge was discussed relating with the operating status of the EGSB reactor.     

Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China

The anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0–5 cm) and subsurface (20–25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China.     

Unique Microbial Community in Drilling Fluids from Chinese Continental Scientific Drilling

Circulating drilling fluid is often regarded as a contamination source in investigations of subsurface microbiology. However, it also provides an opportunity to sample geological fluids at depth and to study contained microbial communities. During our study of deep subsurface microbiology of the Chinese Continental Scientific Deep drilling project, we collected 6 drilling fluid samples from a borehole from 2290 to 3350 m below the land surface. Microbial communities in these samples were characterized with cultivation-dependent and -independent techniques. Characterization of 16S rRNA genes indicated that the bacterial clone sequences related to Firmicutes became progressively dominant with increasing depth. Most sequences were related to anaerobic, thermophilic, halophilic or alkaliphilic bacteria. These habitats were consistent with the measured geochemical characteristics of the drilling fluids that have incorporated geological fluids and partly reflected the in-situ conditions. Several clone types were closely related to Thermoanaerobacter ethanolicus, Caldicellulosiruptor lactoaceticus, and Anaerobranca gottschalkii, an anaerobic metal-reducer, an extreme thermophile, and an anaerobic chemoorganotroph, respectively, with an optimal growth temperature of 50–68°C. Seven anaerobic, thermophilic Fe(III)-reducing bacterial isolates were obtained and they were capable of reducing iron oxide and clay minerals to produce siderite, vivianite, and illite. The archaeal diversity was low. Most archaeal sequences were not related to any known cultivated species, but rather to environmental clone sequences recovered from subsurface environments. We infer that the detected microbes were derived from geological fluids at depth and their growth habitats reflected the deep subsurface conditions. These findings have important implications for microbial survival and their ecological functions in the deep subsurface.     

Highly thermo–halo–alkali-stable β-1,4-endoxylanase from a novel polyextremophilic strain of Bacillus halodurans

A novel bacterial isolate, capable of producing extracellular highly thermostable, halo-alkali-stable and cellulase-free xylanase, was isolated from soil and identified as Bacillus halodurans TSPV1 by polyphasic approach. The Plackett–Burman design identified wheat bran, lactose, tryptone and NaCl as the factors that significantly affect xylanase production, and thus, these were optimized by response surface methodology. The data analysis suggested that optimum levels of wheat bran (15–20 g L^?1), lactose (1.0–1.5 g L^?1), tryptone (2–2.5 g L^?1) and NaCl (7.0–8.0 g L^?1) support 6.75-fold higher xylanase production than that in the un-optimized medium. The xylanase is optimally active at 90 °C and pH 10, and stable for 4 h at 90 °C (T _1/2 60 h) over a broad range of NaCl concentrations (0–29 %). This is the first report on the isolation of polyextremophilic B. halodurans strain that produces thermo-halo-alkali-stable xylanase in submerged fermentation. This enzyme efficiently saccharifies agro residues like wheat bran and corncobs. Fifty-six percent of hemicellulose of wheat bran could be hydrolyzed by xylanase (100 U g^?1 substrate) along with cellulase (22 U FPase and 50 U CMCase g^?1). The xylanase, being thermo-alkali stable and cellulase free, can find applications in pre-bleaching of paper pulps and hydrolysis of xylan in agricultural residues.     

Diversity of prokaryotes associated with soils around coal-fire gas vents in MaNasi county of Xinjiang, China

Bacterial and archaeal diversity in surface soils of three coal-fire vents was investigated by T-RFLP analysis and clone libraries of 16S rRNA genes. Soil analysis showed that underground coal fires significantly influenced soil pH, moisture and NO₃ ^? content but had little effect on other elements, organic matter and available nutrients. Hierarchical cluster analysis showed that bacterial community patterns in the soils were very similar, but abundance varied with geographic distance. A clone library from one soil showed that the bacterial community was mainly composed of Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, Planctomycetes, Actinobacteria, and unidentified groups. Of these, Firmicutes was the most abundant, accounting for 71.4 % of the clones, and was mainly represented by the genera Bacillus and Paenibacillus. Archaeal phylotypes were closely related to uncultivated species of the phyla Crenarchaeota (97.9 % of clones) and Thaumarchaeota (2.1 %). About 28 % of archaeal phylotypes were associated with ammonia oxidization, especially phylotypes that were highly related to a novel, ammonia-oxidizing isolate from the phylum Thaumarchaeota. These results suggested that microbial communities in the soils were diverse and might contain a large number of novel cultivable species with the potential to assimilate materials by heterotrophic metabolism at high temperature.     

Comparison of Soil Bacterial Communities of Pinus patula of Nilgiris, Western Ghats with Other Biogeographically Distant Pine Forest Clone Libraries

The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.     

Field response of rice paddy crop to Azospirillum inoculation: physiology of rhizosphere bacterial communities and the genetic diversity of endophytic bacteria in different parts of the plants

The response of rice plants to the application of inoculant containing two Azospirillum brasilense strains was studied under field conditions. The experiment was performed as three treatments with four replicates in randomized complete blocks arranged as plots of 60 m² in an area on a Vertic Argiudol soil type in the province of Entre Ríos, Argentina. The bacterial rhizosphere community and also the diazotrophic isolates obtained from control and inoculated rice plants were analyzed in relation to their physiology and biological nitrogen fixation (BNF). The MPN of diazotrophs in the rhizosphere varied during the ontogenic cycle. The patterns of distribution of the microbial physiological activities obtained by principal component analysis of community-level physiological profiles (CLPP) showed differences in the utilization of carbon sources by the rhizosphere communities among treatments. Although the analyses of DGGE 16S and nifH profiles have not indicated that the inoculation influenced the genetic diversity of bacterial communities among treatments, they revealed that the banding profiles were altered in different parts of the rice plant by each Azospirillum inoculation treatment. These observations suggest that physiological responses of plant tissues to the inoculation may have occurred. According to agronomic parameters of each treatment, the Azospirillum inoculation increased aerial biomass at the tillering and grain-filling stages. Although the N content accumulated in rice plants increased by 16 and 50 kg ha^?1, the BNF contribution could not be estimated under our experimental conditions by the ¹⁵N balance technique. Based on this field inoculation experiment to rice plants, it is noteworthy that our data suggest that due to Azospirillum inoculation the increase of total N accumulated in rice plants could be a tool to help farmers to improve production and maintain high input of plant residues, providing more organic matter to the soil and guaranteeing sustainability of the system.     

Biocontrol of the toxigenic plant pathogen <Emphasis Type="Italic">Fusarium culmorum</Emphasis> by soil fauna in an agroecosystem

In 2011 and 2013, a field experiment was conducted in a winter wheat field at Adenstedt (northern Germany) to investigate biocontrol and interaction effects of important members of the soil food web (Lumbricus terrestris, Annelida; Folsomia candida, Collembola and Aphelenchoides saprophilus, Nematoda) on the phytopathogenic fungus Fusarium culmorum in wheat straw. Therefore, soil fauna was introduced in mesocosms in defined numbers and combinations and exposed to either Fusarium-infected or non-infected wheat straw. L. terrestris was introduced in all faunal treatments and combined either with F. candida or A. saprophilus or both. Mesocosms filled with a Luvisol soil, a cover of different types of wheat straw and respective combinations of faunal species were established outdoors in the topsoil of a winter wheat field after harvest of the crop. After a time span of 4 and 8 weeks, the degree of wheat straw coverage of mesocosms was quantified to assess its attractiveness for the soil fauna. The content of Fusarium biomass in residual wheat straw and soil was determined using a double-antibody sandwich (DAS)-ELISA method. In both experimental years, the infected wheat straw was incorporated more efficiently into the soil than the non-infected control straw due to the presence of L. terrestris in all faunal treatments than the non-infected control straw. In addition, Fusarium biomass was reduced significantly in all treatments after 4 weeks (2011: 95–99%; 2013:15–54%), whereupon the decline of fungal biomass was higher in faunal treatments than in non-faunal treatments and differed significantly from them. In 2011, Fusarium biomass of the faunal treatments was below the quantification limit after 8 weeks. In 2013, a decline of Fusarium biomass was observed, but the highest content of Fusarium biomass was still found in the non-faunal treatments after 8 weeks. In the soil of all treatments, Fusarium biomass was below the quantification limit. The earthworm species L. terrestris revealed a considerable potential as an effective biocontrol agent contributing to a sustainable control of a Fusarium plant pathogen in wheat straw, thus reducing the infection risk for specific plant diseases in arable fields.     

The Gut Bacterial Communities Associated with Lab-Raised and Field-Collected Ants of Camponotus fragilis (Formicidae: Formicinae)

Camponotus is the second largest ant genus and known to harbor the primary endosymbiotic bacteria of the genus Blochmannia. However, little is known about the effect of diet and environment changes on the gut bacterial communities of these ants. We investigated the intestinal bacterial communities in the lab-raised and field-collected ants of Camponotus fragilis which is found in the southwestern United States and northern reaches of Mexico. We determined the difference of gut bacterial composition and distribution among the crop, midgut, and hindgut of the two types of colonies. Number of bacterial species varied with the methods of detection and the source of the ants. Lab-raised ants yielded 12 and 11 species using classical microbial culture methods and small-subunit rRNA genes (16S rRNAs) polymerase chain reaction-restriction fragment-length polymorphism analysis, respectively. Field-collected ants yielded just 4 and 1–3 species using the same methods. Most gut bacterial species from the lab-raised ants were unevenly distributed among the crop, midgut, and hindgut, and each section had its own dominant bacterial species. Acetobacter was the prominent bacteria group in crop, accounting for about 55 % of the crop clone library. Blochmannia was the dominant species in midgut, nearly reaching 90 % of the midgut clone library. Pseudomonas aeruginosa dominated the hindgut, accounting for over 98 % of the hindgut clone library. P. aeruginosa was the only species common to all three sections. A comparison between lab-raised and field-collected ants, and comparison with other species, shows that gut bacterial communities vary with local environment and diet. The bacterial species identified here were most likely commensals with little effect on their hosts or mild pathogens deleterious to colony health.     

Anaerobic/aerobic conditions and biostimulation for enhanced chlorophenols degradation in biocathode microbial fuel cells

Anaerobic/aerobic conditions affected bacterial community composition and the subsequent chlorophenols (CPs) degradation in biocathode microbial fuel cells (MFCs). Bacterial communities acclimated with either 4-chlorophenol (4-CP) or 2,4-dichlorophenol (2,4-DCP) under anaerobiosis can degrade the respective substrates more efficiently than the facultative aerobic bacterial communities. The anaerobic bacterial communities well developed with 2,4-DCP were then adapted to 2,4,6-trichlorophenol (2,4,6-TCP) and successfully stimulated for enhanced 2,4,6-TCP degradation and power generation. A 2,4,6-TCP degradation rate of 0.10 mol/m³/d and a maximum power density of 2.6 W/m³ (11.7 A/m³) were achieved, 138 and 13 % improvements, respectively compared to the controls with no stimulation. Bacterial communities developed with the specific CPs under anaerobic/aerobic conditions as well as the stimulated biofilm shared some dominant genera and also exhibited great differences. These results provide the most convincing evidence to date that anaerobic/aerobic conditions affected CPs degradation with power generation from the biocathode systems, and using deliberate substrates can stimulate the microbial consortia and be potentially feasible for the selection of an appropriate microbial community for the target substrate (e.g. 2,4,6-TCP) degradation in the biocathode MFCs.     

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members

In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.     

Conversion from natural wetlands to paddy field alters the composition of soil bacterial communities in Sanjiang Plain,Northeast China

The Sanjiang Plain is the largest freshwater wetlands in Northeast China. In order to feed the growing population, about 84 % of the wetlands in this area have been converted to farmland, especially to paddy fields, since the 1950s. However, little is known about the influence of this conversion on soil microbial community composition. In this study, soil samples were collected from two natural wetlands dominated by plant species Carex lasiocarpa and Deyeuxia angustifolia and from a neighboring paddy field that was changed from wetland more than 10 years ago. The composition and diversity of bacterial communities in the soils were estimated by clone library analysis of nearly full length of 16S rDNA sequences. The results revealed that bacterial diversity was higher in paddy fields, and that the composition of bacterial communities differed among the three samples; the difference was more notable between the paddy field and two natural wetlands than between two natural wetlands. The distribution of clones into different bacterial phyla differed among soil samples, and the conversion from natural wetlands to paddy field increased the abundance of Proteobacteria and Firmicutes but decreased the abundance of Chloroflexi. About 63 % and 71 % of clones from two natural wetlands and 49 % of clones from the paddy field had <93 % similarity with known bacteria, suggesting that the majority of bacteria in natural wetland soils in the Sanjiang Plain are phylogenetically novel. In general, this study demonstrated that long-term conversion from natural wetlands to paddy field changes soil bacterial communities in the Sanjiang Plain.     

Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding

Thermophilic dry anaerobic digestion of sludge for cellulose methanization was acclimated at 53 °C for nearly 5 years using a waste paper-based medium. The stability of the microbial community structure and the microbial community responsible for the cellulose methanization were studied by 16S rRNA gene-based clone library analysis. The microbial community structure remained stable during the long-term acclimation period. Hydrogenotrophic methanogens dominated in methanogens and Methanothermobacter, Methanobacterium, Methanoculleus, and Methanosarcina were responsible for the methane production. Bacteria showed relatively high diversity and distributed mainly in the phyla Firmicutes, Bacteroidetes, and Synergistetes. Ninety percent of operational taxonomic units (OTUs) were affiliated with the phylum Firmicutes, indicating the crucial roles of this phylum in the digestion. Relatives of Clostridium stercorarium, Clostridium thermocellum, and Halocella cellulosilytica were dominant cellulose degraders. The acclimated stable sludge was used to treat garbage stillage discharged from a fuel ethanol production process, and the shift of microbial communities with the change of feed was analyzed. Both archaeal and bacterial communities had obviously changed: Methanoculleus spp. and Methanothermobacter spp. and the protein- and fatty acid-degrading bacteria became dominant. Accumulation of ammonia as well as volatile fatty acids led to the inhibition of microbial activity and finally resulted in the deterioration of methane fermentation of the garbage stillage.