Microbial Diversity Structure Research Articles

Effects of water hyacinth biochar on lettuce growth in cadmium-contaminated soil

Recently, the excessive propagation of water hyacinth has led to serious ecological and environmental problems; thereby, its treatment and disposal are of great significance. Moreover, the remediation of heavy metals in soil is a hot topic at present. Thus, water hyacinth was adopted to prepare biochar to investigate its effect on Cd accumulation in lettuce by pot experiments in this study. The optimal application amount of water hyacinth biochar was 1% (30 t ha−1), considering the Cd absorption and yield of lettuce plants. Compared with those of control, the application of biochar prepared at 700°C for 2 h with an amount of 3% (90 t ha−1) resulted in a reduction in Cd by 73.6% and 38.1%, respectively, in the shoots and roots of lettuce. Within a certain carbonization time (0.5~2 h) and carbonization temperature (300°C~700°C), the content of available Cd in the soil decreases with the increase of the carbonization temperature and time, which might be the main reason for the lower Cd concentration in lettuce after applying the biochar. Furthermore, scanning electron microscopy (SEM) and energy-dispersive X-ray fluorescence spectroscopy (EDS) analyses showed that Cd was fixed on the biochar in a state of passivation, leading to a sharp decrease in the available Cd in the soil. Moreover, it was concluded that the application of biochar brings with it an obvious increase in the enzyme activity increment in the soil up to 2.3 times. Lastly, 16sRNA sequencing has shown that biochar addition leads to variations in microbial structure and abundance in soil. Accordingly, biochar prepared by water hyacinth can increase lettuce yield and reduce the concentration of heavy metals in lettuce.

Litter mixing promoted decomposition rate through increasing diversities of phyllosphere microbial communities.

Decomposition of forest litter is an essential process for returning nutrients to the soil, which is crucial for preserving soil fertility and fostering the regular biological cycle and nutrient balance of the forest ecosystem. About 70% of the land-based forest litter is made up primarily of leaf litter. However, research on the complex effects and key determinants of leaf litter decomposition is still lacking. In this study, we examined the characteristics of nutrient release and microbial diversity structure during the decomposition of three types of litter in arid and semi-arid regions using 16S rRNA and ITS sequencing technology as well as nutrient content determination. It was revealed that the nutrient content and rate of decomposition of mixed litters were significantly different from those of single species. Following litter mixing, the richness and diversity of the microbial community on leaves significantly increased. It was determined that there was a significant correlation between bacterial diversity and content (Total N, Total P, N/P, and C/P). This study provided a theoretical framework for investigating the decomposition mechanism of mixed litters by revealing the microbial mechanism of mixed decomposition of litters from the microbial community and nutrient levels.

Dynamics of fungal and bacterial communities in different types of soil ageing with different dosages of cadmium

This study investigated the structure of fungal and bacterial communities in different types of Cd-contaminated soils. The results showed that obvious variations in microbial structure between contaminated alkaline soils and acidic soils. Proteobacteria, Gemmatimonadetes, Bacteroidetes and Basidiomycota dominated the studied communities in the alkaline soils, whereas Actinobacteria, Chloroflexi, Firmicutes, Acidobacteria, Saccharibacteria and Ascomycota were more abundant in the acidic soils. Additionally, Cd tolerant (Proteobacteria, Bacteroidetes, Ascomycota) and sensitive (Actinobacteria, Acidobacteria, Basidiomycota) in alkaline soils and JL-soils, Cd tolerant (Actinobacteria, Acidobacteria, Basidiomycota) and sensitive (Saccharibacteria, Proteobacteria, Bacteroidetes, Ascomycota, Mucoromycota) in the acidic soils were identified. Redundancy analysis and correlation analysis demonstrated that it was significantly affected by different environment parameters in alkaline soils and acidic soils. Varied bacterial community structures in all soils were dominantly influenced by pH and SOM. The similarities among different groups indicated the effect of soil type on microbial community structure was greater than that of Cd level. The above conclusions may provide a new perspective for the bio-remediation of Cd in different types of soils.

Impacts of land-use and management histories of maize fields on the structure, composition, and metabolic potentials of microbial communities

Microbial diversity and functionality are impacted by land-use and management practices, with studies reporting reduced microbial activities due to anthropogenic activities. In this study, we analyzed and compared the composition, diversity, and metabolic profiles of microbial communities in maize rhizosphere soils of a former grassland and an intensively cultivated land. Metagenomic DNA was extracted from maize rhizosphere and bulk samples and sequencing was performed using the shotgun metagenomic approach. Comparative analyses of the metagenomes revealed differences in the distribution of microbial communities across the soils. Alpha diversity indices (Simpson, Shannon, and Evenness) were higher in the former grassland soils and beta diversity analysis revealed a significant difference (p = 0.01) in microbial community structure between the fields, with the highest dissimilarity (21.03%) observed between the rhizosphere soils. Among all taxonomic levels in the study, a total of 23 taxa were observed to be differentially abundant in the samples. Soil pH, with a contribution of 51% and a p-value of 0.002 was the most influential soil parameter that determined microbial distribution across the soils. Differences were also observed in the abundance of metabolic pathways (alpha = 0.05) across the samples. Overall, differences in the soils’ chemical properties were attributed to land-use and management histories, which contributed to the dissimilarities observed in the microbial structural diversity and metabolic pathways. These results provide knowledge on the impact of land-use practices on microbial diversity and function in cultivated soils and create opportunities for future experiments to mine the unclassified bacteria/sequences, with the intention of discovering novel microbes of agricultural importance.

The Response of Soil Nutrients and Microbial Community Structures in Long-Term Tea Plantations and Diverse Agroforestry Intercropping Systems

During tea cultivation, diverse agroforestry is an important and established intercropping measure, with most studies concentrating on ecological service provision and economic returns. However, the response of soil nutrients and microbial community structures in long-term tea plantations with diverse agroforestry intercropping systems is poorly understood. In the present field study (2015), three intercropping agroforestry-tea patterns (Osmanthus-Tea (OT), Michelia-Tea (MT), Osmanthus-Michelia-Tea (OMT)) along with a study control (C) were examined in terms of these two knowledge gaps. Results showed that, in terms of tea cultivation, the OMT system is more suitable than the OT and MT systems. The OMT system significantly increased the total nitrogen (TN, 16.4%), total potassium (TK, 10.5%), available nitrogen (AN, 14.2%), available phosphorus (AP, 26.7%) and soil organic matter (SOM, 28.9%). The OMT system increased phylum Firmicutes and Bacteroidetes abundance by 35.8% and 9.6%. In addition, the OMT system enhanced the abundance of class Bacteroidia (99.5%), Erysipelotrichia (96.9%), Clostridia (93.5%) and Actinobacteria (19.6%), respectively. In general, the phylum bacteria Proteobacteria, Firmicutes, Actinobacteria accounted for the largest proportion of bacteria in all three intercropping systems. In this study, the abundance of Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were positively correlated with AN, SOM and TP. The results of the present study will help to develop a better understanding of the benefits imposed by different agroforestry intercropping systems on nutrient dynamics and microbial structural diversity during tea cultivation.

Metagenomic insights into taxonomic diversity and metabolic potential of bacterial communities associated with tannery waste-contaminated soils

Long-term exposure to anthropogenic stressors can lead to perturbations in microbiomes, either selecting for novel and biotechnologically important biotypes, or reductions in the microbial diversity and disequilibrium of ecosystem services. Consequently, analysis of variations in microbial structure and function in stressful environments remains a critical issue in microbial ecology. In this study, the taxonomic structure of bacterial communities inhabiting tannery waste dumpsite soils was evaluated comparatively with those from non-contaminated soils using 16S rRNA gene sequencing. Furthermore, the metabolic potential of these communities was inferred from community level physiological profiling fingerprints. The dumpsite has been receiving tannery waste since 1982; hence, the soils are laden with heavy metals including chromium, zinc, sodium, and potassium. Consequently, the following significant differences between bacterial communities from contaminated and non-contaminated soils were observed: (1) bacterial communities from the contaminated soils were characterized by lower species diversity, albeit at comparable species evenness (Simpson index); (2) long term contamination of soil shifted the bacterial community structure to a distinct core microbiome dominated by bacterial groups such as Halomonas, Balneolaceae, Aliifodinibius, Serinicoccus, Gracilimonas, Marinobater, Penticoccus, Fordinicurvata, Dietzia, and Norcadioides. These are characteristic of saline, metal-laden environments and have potentially high organo-pollutant degradative properties; and (3) bacterial communities from the contaminated soils exhibited a robust metabolic potential utilizing both natural and anthropogenically derived polymers at a higher rate. Overall, these results highlight tannery waste dumpsite soils as microbial diversity hotspots and potential reservoirs for exploration of novel biotechnological tools for bioremediation and industrial applications.

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico

This study investigated the intestinal microbial community structure of Litopenaeus vannamei at six different stages during shrimp farming. Our goal was to elucidate the bacterial profile and the changes in the relative abundance of taxa during an atypical massive mortality event in Sonora, Mexico. High-throughput sequencing of the 16S rRNA gene and denaturing gradient gel electrophoresis showed that Vibrionaceae was persistent with high relative abundances in the intestine from cultivated shrimp during all the studied stages. The massive mortality observed at day 63 could be related to an overabundance of different Operational Taxonomic Units (OTUs) of Vibrio, Shewanella and Clostridium. Principal coordinate analysis (PCoA) showed variations in microbial structure at different culture times. These findings suggest that OTUs of different taxa contributed to the community switch from healthy to diseased individuals, questioning the hypothesis that single bacterial species is the cause of disease outbreaks. This study provided data to improve the understanding of disease outbreaks during shrimp farming.

Microbial Community Structure Diversity in the Dewatered Sludge from 4 Different Waste Water Treatment Plants used for CSRB in Colder Season

Compacted Sludge Reducing Barrier (CSRB) was tested to be a feasible barrier for Acid Mine Drainage (AMD) from tailings in case the ground water contamination. Because of its double function (encapsuling and reducing), the microbial community structure diversity in the sludge played a key role. In this paper, we researched the correlation between heavy metals and microbial structure diversity in the dewatered sludge from 4 different sewage treatment process plants in Lanzhou city, a developing area of northwest China, in the colder season. The results indicated that the microbial community structure diversity differed and were unique among the different sewage plants; their correlation with heavy metals was also unique independently.

Responses of soil microbial community structure to stand densities of Chinese fir plantations

ABSTRACTPlant-microorganism interactions have an important effect on plant growth and yield. However, how stand densities of Chinese fir plantations to drive change in the microbial structure remains unclear. This study used gas chromatography (GC) to determine the biomass of Phospholipid Fatty Acids (PLFA) of soil microorganisms in the topsoil (0–20 cm) of Chinese fir plantations of five initial densities (D1: 1667 stems/hm2, D2: 3333 stems/hm2, D3: 5000 stems/hm2, D4: 6667 stems/hm2, and D5: 10,000 stems/hm2); stand densities at sampling were D1: 1578 stems/hm2, D2: 2294 stems/hm2, D3: 2617 stems/hm2, D4: 2789 stems/hm2, and D5: 2461 stems/hm2. We found that the microbial biomass was significantly affected by both the initial density and the subsequent density of Chinese fir plantation. Overall, the low-density plantation was more conducive to increasing the microbial structure diversity. The ratio of fungal biomass to bacterial biomass was higher at the low density (D1 and D2) compared to the high density (D3, D4, and D5), while the ratio of the biomass of Gram-positive bacteria to the biomass of Gram-negative bacteria was opposite, which suggest that high-density Chinese fir plantations are exposed to greater environmental stresses than low-density Chinese fir plantations. We showed that the biomass of PLFA is significantly affected by soil capillary porosity, maximum water-holding capacity, pH, alkali available N, and available P. Together, we provide a theoretical basis for the management of Chinese fir plantations and a broader perspective for better understanding and estimating the influences of stand densities on plantations in the regional and world scales.

Long-Term Nitrogen Fertilization Elevates the Activity and Abundance of Nitrifying and Denitrifying Microbial Communities in an Upland Soil: Implications for Nitrogen Loss From Intensive Agricultural Systems.

The continuous use of nitrogen (N) fertilizers to increase soil fertility and crop productivity often results in unexpected environmental effects and N losses through biological processes, such as nitrification and denitrification. In this study, multidisciplinary approaches were employed to assess the effects of N fertilization in a long-term (~20 years) field experiment in which a fertilizer gradient (0, 200, 400, and 600 kg N ha−1 yr−1) was applied in a winter wheat-summer maize rotation cropping system in the North China Plain, one of the most intensive agricultural regions in China. The potential nitrification/denitrification rates, bacterial community structure, and abundances of functional microbial communities involved in key processes of the N cycle were assessed during both the summer maize (SM) and winter wheat (WW) seasons. Long-term N fertilization resulted in a decrease in soil pH and an increase in soil organic matter (OM), total N and total carbon concentrations. Potential nitrification/denitrification and the abundances of corresponding functional N cycling genes were positively correlated with the fertilization intensity. High-throughput sequencing of the 16S rRNA gene revealed that the increased fertilization intensity caused a significant decrease of bacterial diversity in SM season, while changed the microbial community composition such as increasing the Bacteroidetes abundance and decreasing Acidobacteria abundance in both SM and WW seasons. The alteration of soil properties markedly correlated with the variation in microbial structure, as soil pH and OM were the most predominant factors affecting the microbial structure in the SM and WW seasons, respectively. Furthermore, consistently with the results of functional gene quantification, functional prediction of microbial communities based on 16S rRNA sequence data also revealed that the abundances of the key nitrificaiton/denitrification groups were elevated by long-term N inputs. Taken together, our results suggested that soil microbial community shifted consistently in both SM and WW seasons toward a higher proportion of N-cycle microbes and exhibited higher N turnover activities in response to long-term elevated N fertilizer. These findings provided new insights into the molecular mechanisms responsible for N loss in intensively N fertilized agricultural ecosystems.

Metagenomic analysis of microbial community and function involved in cd-contaminated soil

BackgroundSoil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).ResultsThe results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.ConclusionsCd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.

Microbial diversity structure in acetate single chamber microbial fuel cell for electricity generation.

This study investigates the performance of acetate feed membrane less single chamber microbial fuel cell and physical characterization of the bio film present on the anode surface using Scanning Electron Microscope (SEM) and 16S rRNA analyzer. The performance has been investigated using Teflon treated carbon paper with 0.3 mg/cm2 Pt/C loaded as a cathode and carbon paper as an anode. The maximum open circuit potential is noticed as 791 mV, the system successfully revealed a maximum power density of 86.1 mW m−2 at stable current density of 354 mA m−2 with high coulombic efficiency of 65% at maximum degradation rate of 96%. SEM showed the dense adherence of microorganisms on the anode. 16S rRNA sequencing results indicates phylogenetic mixture in the communities of anodic biofilm and there is no single dominant bacterial species. The dominant phyla are Firmicutes, Gamma Proteobacteria, Alpha Proteobacteria, Actinobacteria, with ten dominant microbial strains: Bacillus firmus, Shewanella profunda, Bacillus isronensis, Brevundimonas bullata, Pseudomonas putida, Planococcus citreus, Micrococcus endophyticus, Acinetobacter tandoii, Bacillus safensis and Shewanella xiamenensis.

Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using Ion Sequencing.

Termite gut and termite nest possess complex microbial communities. However, only limited information is available on the comparative investigation of termite gut- and nest-associated microbial communities. In the present study, we examined and compared the bacterial diversity of termite gut and their respective nest by high-throughput sequencing of V3 hypervariable region of 16S rDNA. A total of 14 barcoded libraries were generated from seven termite gut samples and their respective nest samples, and sequenced using Ion Torrent platform. The sequences of each group were pooled, which yielded 170,644 and 132,000 reads from termite gut and termite nest samples, respectively. Phylogenetic analysis revealed significant differences in the bacterial diversity and community structure between termite gut and termite nest samples. Phyla Verrucomicrobia and Acidobacteria were observed only in termite gut, whereas Synergistetes and Chlorobi were observed only in termite nest samples. These variations in microbial structure and composition could be attributed with the differences in physiological conditions prevailing in the termite gut (anoxic and alkaline) and termite nest (oxic, slightly acidic and rich in organic matter) environment. Overall, this study unmasked the complexity of bacterial population in the respective niche. Interestingly, majority of the sequence reads could be classified only up to the domain level indicating the presence of a huge number of uncultivable or unidentified novel bacterial species in both termite gut and nest samples. Whole metagenome sequencing and assessing the metabolic potential of these samples will be useful for biotechnological applications.

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.

Circadian clocks and metabolism are inextricably intertwined, where central and hepatic circadian clocks coordinate metabolic events in response to light-dark and sleep-wake cycles. We reveal an additional key element involved in maintaining host circadian rhythms, the gut microbiome. Despite persistence of light-dark signals, germ-free mice fed low or high-fat diets exhibit markedly impaired central and hepatic circadian clock gene expression and do not gain weight compared to conventionally raised counterparts. Examination of gut microbiota in conventionally raised mice showed differential diurnal variation in microbial structure and function dependent upon dietary composition. Additionally, specific microbial metabolites induced under low- or high-fat feeding, particularly short-chain fatty acids, but not hydrogen sulfide, directly modulate circadian clock gene expression within hepatocytes. These results underscore the ability of microbially derived metabolites to regulate or modify central and hepatic circadian rhythm and host metabolic function, the latter following intake of a Westernized diet.

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation.

Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats

Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.

Changes in diversity and biomass of bacteria along a shallow snow pit from Kuytun 51 Glacier, Tianshan Mountains, China

Microorganisms vary in both biomass and diversity composition along glacial depth profiles. However, it is not well known about the major processes controlling the structure diversity shift of microorganisms in a glacier, although, aeolian deposition has been widely accepted as one mechanism regulating the distribution of microorganisms in snow. To better understand the distribution of microorganisms in a glacier, variations in bacterial diversity and biomass along a pit profile from the Kuytun 51 Glacier in the Tianshan Mountains in China were investigated by using 16S rRNA gene library sequencing and flow cytometric analysis with cell sorting markers. Four clone libraries were established from each of the different sampling depths from the snow pit. A total of 311 insert clones were preliminarily screened by HaeIII‐based amplified rRNA restriction analysis (ARDRA), and 83 representatives of the unique ARDRA patterns were sequenced. Sequence analysis showed that the bacteria in the snow pit were affiliated with 23 known subphyla within the members of the Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria phyla. To examine diversity shifts in snow, the diversity structures from the snow pit were also compared with those previously recovered from the different habitats along the Kuytun 51 Glacier surface and from the deep Malan Glacier. The results showed structure shift patterns in bacterial diversity among the surface, deep snow, and deep ice. Sequence analysis displayed a dramatic diversity shift from a mixture of Cyanobacteria and other eubacteria across the glacial surface to other eubacteria without Cyanobacteria in the deep snow. However, the biogeochemical analyses showed great variability in the measured abiotic and biotic components along the pit profile, which reinforced the idea of aeolian deposition being a dominant mechanism controlling the size and diversity of microorganisms in snow. Overall, the findings indicated a significant bacterial diversity shift between the surface and deep snow, confirming our hypothesis of a postdeposition influence on the microbial diversity structures in the glacier.

The microbial signature of aerosols produced during the thermophilic phase of composting

The microbial diversity of bioaerosols released during operational activities at composting plants is poorly understood. Identification of bacteria and fungi present in such aerosols is the prerequisite for the definition of microbial indicators that could be used in dispersal and exposure studies. A culture-independent analysis of composting bioaerosols collected at five different industrial open sites during the turning of composting piles in fermentation was performed by building 16S rDNA and 18S rDNA libraries. More than 800 sequences were analysed. Although differences in the phylotypes distribution were observed from one composting site to another, similarities in the structure of microbial diversity were remarkable. The same phyla dominated in the five bioaerosols: Ascomycota among fungi, Firmicutes and Actinobacteria among bacteria. For each phylum, some dominant phylotypes were common to at least four bioaerosols. These common phylotypes belonged to Thermomyces, Aspergillus, Penicillium, Geobacillus, Planifilum, Thermoactinomyces, Saccharopolyspora, Thermobifida and Saccharomonospora. The microbial signature of aerosols produced during the thermophilic phase of composting was determined. The similarities observed may be explained by the selection of thermophilic and sporulating species. Several bacteria and fungi identified in this study may represent potential indicators of composting bioaerosols in air.

DGGE analysis of 16S rDNA of ammonia-oxidizing bacteria in chemical–biological flocculation and chemical coagulation systems

Microbial community DNA was extracted from activated sludge samples taken from a chemical bioflocculation process and a chemical coagulation process in Shanghai, China. 16S rDNA of ammonia-oxidizing bacteria (AOB)was amplified by nested polymerase chain reaction and fingerprinted by denaturing gradient gel electrophoresis for microbial structure analysis. The Shannon diversity index of each sample was determined. The results indicated that the microbial structure of AOB in chemical bioflocculation process was comparable at two operational conditions. The ammonia-oxidizing bacterial communities were similar in three channels of the chemical bioflocculation process and in three serial tanks in the chemical coagulation process at the same condition. The diversity of microbial structures in the chemical bioflocculation process was higher than in the chemical coagulation process, in which the microbial structure was similar to that in the influent. Although the microbial study provides insights to the nitrification removal, higher microbial diversity of AOB does not necessarily mean higher ammonia oxidization. Molecular analysis should be combined with chemical assays to optimize operational conditions.

Microbial community structure and function in a soil contaminated by heavy metals: effects of plant growth and different amendments

We studied the effects of in situ remediation of a heavy metal (HM) contaminated soil on some soil chemical properties, microbial function and microbial structural diversity after 18 months. The experiment was carried out at semifield scale in containers filled with HM contaminated soil from the Aznalcóllar mine accident (Southern Spain, 1998). The remediation measures consisted of the application of different amendments and/or establishment of a plant cover ( Agrostis stolonifera L.). Seven treatments were established: four organic treatments (municipal waste compost (MWC), biosolid compost (BC), leonardite (LEO) and litter (LIT)), one inorganic treatment (sugar beet lime (SL)) and two controls (control with plant cover (CTRP) and control without plant cover (CTR)). Several soil chemical (pH, soluble HM, total organic C (TOC), water-soluble C (WSC) and available-P) and biochemical properties (microbial biomass C (MBC), MBC/TOC ratio and enzyme activities) were determined. Microbial community structure was studied by means of ARDRA (amplified ribosomal DNA restriction analysis). The SL, MWC and BC treatments were the most efficient to raise soil pH and decrease soluble HM concentrations. Total organic C was increased in the organic treatments by 2 to 4-fold, whereas water-soluble C was statistically similar in the CTRP, SL and the organic treatments, probably due to the presence of a root system in all these treatments. Available-P was also increased in the BC, SL and MWC treatments due to the higher P content of the amendments applied in these treatments. Soil microbial function was generally enhanced in the amended and CTRP treatments. The MWC, BC and SL treatments were particularly efficient to increase microbial biomass C, the MBC/TOC ratio and the dehydrogenase and aryl-sulphatase enzyme activities. These results could be attributed to the amelioration of some of the soil chemical properties: increase in soil pH and water-soluble C and decrease of HM soluble concentrations. ARDRA analyses showed changes in structural diversity in both the bacterial and fungal community under the different treatments. Fingerprinting patterns of the 16S rDNA obtained with Hinf- I and of the 18S rDNA with Hpa- II revealed higher similarity percentages among samples from the same treatment compared with samples from the other treatments. In addition, a higher similarity was found between samples from all treatments under the Agrostis influence. The use of certain amendments and/or a plant cover is important for in situ remediation of HM contaminated soils, since these practices can affect soil chemical properties, as well as the microbial community function and structure.