Comprehensive study on dynamics of microbial community in Anaerobic-Oxic-Oxic process using PCR-DGGE, gas chromatography analysis, and dehydrogenase activity assays

This study was conducted to evaluate the relationship between the function of microbes and the change in their communities during the treatment of coking wastewater using a bio-fluidized bed Anaerobic-Oxic-Oxic (A/O/O) process. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), Gas Chromatography (GC) analysis, and the triphenyl-tetrazolium chloride (TTC) dehydrogenase activity test (TTC test) were simultaneously conducted to analyze the dynamics of microbe communities during the process of coking wastewater treatment. The study suggests that combined approaches of PCR-DGGE, GC, and TTC provided a simple and accurate method to evaluate the changes in microbial activity, microbial structure, and population size with the shifting of contaminants in different treatment processes. It demonstrates that the structure and components of a microbial community are influenced by selecting pressure during the wastewater treatment process, which in turn determines the overall functionality of the system.     

Adaptations in bacterial catabolic enzyme activity and community structure in membrane-coupled bioreactors fed simple synthetic wastewater

Membrane-coupled bioreactors (MBRs) offer substantial benefits compared to conventional reactor designs for biological wastewater treatment. MBR treatment efficiency, however, has not been optimized because the effects of the MBR on process microbiology are poorly understood. In this study, the structure and function of the microbial communities growing in MBRs fed simple synthetic wastewater were investigated. In four starch-fed MBRs, the bacterial community substantially increased its alpha-glucosidase affinity (>1000-fold), while the leucine aminopeptidase and heptanoate esterase affinities increased slightly (<40-fold) or remained relatively constant. Concomitant to these physiological adaptations, shifts in the bacterial community structure in two of the starch-fed MBRs were detected by PCR-DGGE. Four of the bacterial populations detected by PCR-DGGE were isolated and exhibited specific growth rates in batch culture ranging from 0.009 to 0.22 h(-1). Our results suggest that bacterial communities growing under increasingly stringent nutrient limitation adapt their enzyme activities primarily for the nutrients provided, but that there is also a more subtle response not linked to the substrates included in the feed medium. Our research also demonstrates that MBRs can support relatively complex bacterial communities even on simple feed media.     

PCR-DGGE Comparison of Bacterial Community Structure in Fresh and Archived Soils Sampled along a Chihuahuan Desert Elevational Gradient

The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.     

Estimation of dominant microbial population sizes in the anaerobic granular sludge of a full-scale UASB treating streptomycin wastewater by PCR-DGGE

Although the dominant members of microbial communities in wastewater bio-treatment systems were often paid attention due to their possible important roles in treatment performance, their population sizes, especially the unculturable species, were still little known. Then PCR-DGGE was used in an attempt to estimate the dominant microbial population sizes in the anaerobic granular sludge treating streptomycin wastewater, coupled with an inoculated strain (Esherichia coli) with known population sizes as an internal standard. The results indicated that the band intensities of the inoculated strain in DGGE profiles showed good correlation with population sizes. Then it was possible to estimate the dominant microbial population sizes by means of comparing their DGGE band intensities with the inoculated strain. The estimated results demonstrated that the sizes of major dominant microbial populations in the sludge sample were at the level of 10⁷–10⁸ CFU/g. The sizes of secondary dominant microbial populations were at the level of 10⁵–10⁶ CFU/g. The microbial populations with the size level lower than 10³ CFU/g were undetectable by PCR-DGGE. These results provided a potential approach to evaluate dominant microbial population sizes in complex microbial communities.     

A survey of ammonia-assimilating micro-organisms in cattle manure composting

AIMS: To evaluate the ammonia-assimilating abilities of micro-organisms isolated from cattle manure composting processes and to determine the distribution of cultivable species of ammonia-assimilating micro-organisms in microbial communities during the composting processes. METHODS AND RESULTS: Compost samples were collected from four stages of treatment. Trypto soya agar was used for the isolation of ammonia-assimilating aerobes. Many of the isolates showed high ammonia-assimilating ability in a medium containing basal components and a compost extract. Partial 16S ribosomal DNA sequencing showed that the cultivable species of highly efficient ammonia-assimilating isolates changed during the composting process. The community structure of micro-organisms and actinomycetes was analysed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Two species of actinomycetes identified by PCR-DGGE coincided with those found among the cultured isolates. CONCLUSIONS: Ammonia-assimilating micro-organisms obtained by the cultivation method were not predominant in the microbial community during the composting process: however certain cultured actinomycetes were members of predominant species in the actinomycetes community. SIGNIFICANCE AND IMPACT OF THE STUDY: Ammonia assimilation by micro-organisms is one of the important mechanisms for ammonia retention in the composting process. Cultivable actinomycetes are a means for preventing ammonia emission from the composting process.     

Relative roles of niche and neutral processes on turnover of plant,fungal and bacterial communities in arid and semi-arid areas at the regional scale

The mechanisms that determine the spatial structure of macroscopic and microbial communities and how they respond to environmental changes are central themes that have been explored in ecological research. However, little is known about the relative roles and importance of neutral and niche-related factors in the assemblage of bacterial, fungal, and plant communities. Here partial Mantel, null model, and variation partitioning analysis were used to compare mechanisms driving the beta diversity of bacteria, fungi and plant communities at the regional scale in arid and semi-arid areas. Denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the distribution pattern of microbial communities, and vegetation survey were conducted to evaluate the characteristics of plant communities. We found that bacterial, fungal, and plant communities were strongly influenced by niche processes at the regional scale in arid and semi-arid areas. Bacteria had a stronger habitat association, indicating community assembly is strongly affected by niche processes. Fungi, with their body size between plants and bacteria, had moderate environment correlation, and plants had less environment association than fungi or bacteria, which suggests that body size may determine the association between organism and environment. We concluded that the pivotal niche process, environmental filtering, weakened with increasing body size, and it should be considered when we evaluate the relative roles of deterministic and stochastic processes in community assemblage.     

Changes in composition and microbial communities in excess sludge after heat-alkaline treatment and acclimation

This study examined the effects of combining heat-alkaline treatment (HAT) with an acclimation process on sludge reduction. Changes in sludge components and microbial communities in both the mixed liquor suspended solids (MLSS) and supernatant fractions were monitored throughout the process. HAT was performed under different pH conditions (pH 7, pH 11 and pH 13) at 60 °C. Approximately 42–62% of the released materials were proteins. After an 8-day acclimation of sludge, the protein concentration in the supernatant had significantly decreased under all conditions. Treatment conditions at pH 11 were optimal for sludge reduction due to the increased efficiency and reduced consumption of chemicals to adjust the pH. A molecular analysis showed that the microbial consortia in both fractions after the cell lysis differed depending on the pH and temperature, and only a few types of bacteria were resistant under extreme conditions. The microbial communities in the MLSS under different conditions were similar after the 8-day acclimation.     

复合菌系RSS-4腐解稻秆过程中的菌系动态变化

采用传统平扳分离培养方法和PCR—DGGE技术研究了水稻秸秆腐解复合菌系RSS-4在腐解稻秆过。程中菌种区系变化情况。结果表明：平板分离培养方法显示,在稻秆腐解过程中,微生物的数量呈现出先升后降的变化趋势,在整个腐解过程中细菌的数量占优势;DGGE图谱显示,至少有12种细菌和18种真菌的近缘种参与到稻秆的腐解过程。在其腐解过程中,不同腐解阶段真菌的组成呈现出多样性,数量变化差异也较大：细菌DGGE图谱中的条带1、9、10等以及真菌DGGE图谱中的条带8、9、13等为优势菌株,它们贯穿于稻秤腐解的整个过程;细菌中的条带12以及真菌中的条带4在腐解的前期起作用,而后迅速消失;细菌中的条带3、11等以及真菌中的条带3、10等在腐解的后期才出现而起作用;而细菌中的条带2以夏真菌中的条带1、5等仅出现在腐解的莱一时期。     

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.     

Detection of filamentous genus Gordonia in foam samples using genus-specific primers combined with PCR--denaturing gradient gel electrophoresis analysis

A nested-PCR amplification combined with denaturing gradient gel electrophoresis (PCR-DGGE) approach was used to detect and identify Gordonia populations from wastewater treatment plant foam samples. The PCR-amplified region (position 722-1119) by specifically designed primers G699F and G1096R covered the hypervariable region of the Gordonia 16S rRNA gene sequence. This approach successfully distinguished Gordonia species to the interspecies level. The differential ability of PCR-DGGE analysis was effectively used to separate 12 Gordonia species belonging to different 16S rRNA gene-based phylogenetic lineages into 8 groups. Based on this method, the minimum limit of Gordonia detection was 5 x 10(4) CFU.g -1 in the seeded soil samples. The PCR-DGGE bands obtained were excised and identified by sequence analysis. Gordonia polyisoprenivorans, Gordonia amicalis, DGGE type II Gordonia species, and an uncertain Gordonia species dominated the activated sludge foam samples. Results of this study indicate that the detection and analyses of genus Gordonia within a complex microbial community could be accomplished using the PCR-DGGE approach to a larger extent, with certain limitations. Detection of diverse Gordonia populations in foam samples from wastewater treatment plants revealed the significant role of Gordonia in biological foaming during wastewater treatment. The nested-PCR amplification and DGGE can be used as a diagnostic tool for the early detection of foaming incidents in wastewater treatment plants using Gordonia as indicator organism.     

Responses of pea and wheat to textile wastewater reclaimed by suspended sequencing batch bioreactors

Availability of good quality water for crop irrigation is a big challenge in developing countries due to limited resources of clean water. Textile industry consumes a huge amount of water during dyeing process and consequently it releases high strength wastewater into wastewater streams. The present study was designed with the objective to use textile wastewater treated in sequencing batch bioreactor for irrigation purpose. Wastewater containing 100 mg/L reactive black-5 azo dye amended with different co-substrates was treated using mixed liquor suspended solids (MLSS) and two previously isolated dye-degrading bacterial strains (Psychrobacter alimentarius KS23 and Staphylococcus equorum KS26). About 90% color and COD removal in case of dye-containing wastewater amended either with mineral salts + yeast extract or only yeast extract was achieved in 24 h after treatment with mixed culture (MLSS + KS23 + KS26). The treated wastewater was applied for irrigation of pea and wheat plants under controlled conditions. Untreated dye-contaminated wastewater was used as a control for comparison. A significant positive effect of treated dye wastewater amended with different co-substrates on the seed germination index, root and shoot length and biomass was observed in response to application of dye-containing wastewater treated with MLSS and dye-degrading bacterial strains compared to untreated control. Results of this study reveal that the dye-degrading microbial cultures could be used to enhance the treatment efficiency of dye-contaminated wastewater that can be utilized for irrigation of crops and biomass production.     

Microbial community dynamics in anaerobic bioreactors and algal tanks treating piggery wastewater

Integrated biosystem is becoming a major aspect of wastewater management practice. Microbial communities in piggery wastewater sampled from anaerobic (thermophilic and mesophilic) and aerobic digesters (algal tanks) during waste remediation were analyzed by culture-independent techniques based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The use of Muyzer's 314F-GC, 518R bacterial primers, and archaeal A934F, 1309R primers followed by partial 16s rDNA sequence analysis of the main bands from DGGE revealed the presence of unknown and as yet uncultured microorganisms but also showed functional and ecologically significant denitrifying, acetogenic bacteria along with autotrophic, hydrogenotrophic, and acetoclastic methanogen archaea. Thermophilic digesters were dominated by γ-Proteobacteria, Methanothermobacter sp., while mesophilic digesters showed dominance by Firmicutes, uncultured bacteria, Methanosarcina, and Methanoculleus genera. Under aerobic conditions within algal tanks, pH rose from 7.17 to 9.32, with a significant decrease in total ammonia nitrogen, chemical oxygen demand, and soluble phosphorus levels. PCR-DGGE proved a useful tool for investigating the dynamics of microbial community in the bio-processing of piggery wastewater. Knowledge of the microbial communities involved in digestion of piggery wastewater will allow optimization of integrated biosystem by removing the main pollutants like inorganic ammonium-nitrogen, phosphorus, and pathogens from intensive farming system.     

含氟有机废水处理过程活性污泥微生物群落研究进展

随着有机氟化物在各领域的广泛应用,含氟有机废水处理面临巨大挑战。活性污泥作为有机废水处理的核心技术之一,微生物在其中发挥着极其重要的作用。本综述首先聚焦在活性污泥微生物群落多样性、组成、结构和功能及其与含氟废水类型、处理工艺和处理效率之间的关系,进而讨论了功能微生物降解/转化有机氟化物的途径和作用机制,最后展望了结合分离培养降解有机氟化物的关键微生物,以及微生物组学技术解析活性污泥微生物群落构建、互作、代谢等核心问题,以提高对含氟有机废水微生物降解机理的认识,优化含氟有机废水处理工艺。     

Molecular characterization of microbial communities in Canadian pulp and paper activated sludge and quantification of a novel Thiothrix eikelboomii-like bulking filament

We examined the microbial community structure and quantified the levels of the filamentous bulking organism Thiothrix eikelboomii in samples of activated sludge mixed liquor suspended solids (MLSS) from Canadian pulp and paper mills. Libraries of chaperonin 60 (cpn60) gene sequences were prepared from MLSS total microbial community DNA and each was compared with cpnDB, a reference database of cpn60 sequences (http://cpndb.cbr.nrc.ca) for assignment of taxonomic identities. Sequences similar to but distinct from the type strain of T. eikelboomii AP3 (ATCC 49788T) (approximately 89% identity over 555 bp) were recovered at high frequency from a mill sample that was experiencing bulking problems at the time of sample collection, which corresponded to microscopic observations using fluorescent in situ hybridization with commercially available 16S rDNA-based probes. We enumerated this strain in five mill-derived MLSS samples using real-time quantitative PCR (qPCR) and found that two samples had high levels of the bulking strain (>1012 genomes/g MLSS) and two contained lower but detectable levels of this organism. None of the mill samples contained cpn60 sequences that were identical to the type strain of T. eikelboomii. This technique shows promise for monitoring pulp and paper mill wastewater treatment systems by detecting and enumerating this strain of T. eikelboomii, which may be specific to pulp and paper mill wastewater treatment systems.     

A meta-analysis of changes in bacterial and archaeal communities with time

Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species–time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and ‘macro''-bial communities alike.     

PCR-DGGE as a supplemental method verifying dominance of culturable microorganisms from activated sludge

To verify the dominance of microorganisms in wastewater biological treatment, PCR-DGGE (denaturing gradient gel electrophoresis) was performed as a supplementary support method for screening of the dominant microorganisms from activated sludge. Results suggest that the dominant microorganisms in activated sludge are primarily responsible for strengthening its effectiveness as a biological treatment system, followed by the non-main dominant microorganisms, whereas the non-dominant microorganisms showed no effects. The degree of microbial abundance present on the profile of PCR-DGGE was in line with the treatment efficiency of augmented activated sludge with isolated cultures, suggesting that PCR-DGGE can be used as an effective supplementary method for verifying culturable dominant microorganisms in activated sludge of coking wastewater.     

Influence of polyaluminum chloride on microbial characteristics in anaerobic membrane bioreactors for sludge digestion

In this study, two parallel lab-scale anaerobic membrane bioreactors (AnMBRs), one of which was dosed with polyaluminum chloride (PAC) for membrane fouling control, were operated for treating excess activated sludge collected from a wastewater treatment plant (WWTP). The AnMBRs were inoculated with anaerobic digested sludge collected from an anaerobic digester of another WWTP. The microbial community of digested sludge and cake layer in AnMBRs, as well as that of excess sludge, was analyzed through polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) and Illumina MiSeq. The dynamic variation of archaeal community in AnMBRs was not as obvious as that of bacterial community based on the PCR-DGGE results. Under the circumstance of stable operation, Cloacimonetes, Chloroflexi, Bacteroidetes, Proteobacteria, Firmicutes, and Ignavibacteriae were observed as the predominant phyla in digested sludge based on the Illumina results. In addition to that, the cake layer possessed similar predominant phyla with the digested sludge but owned a higher diversity. Furthermore, overlapping bacterial communities were discovered between the excess sludge and digested sludge. However, the abundance of aerobic bacteria was substantially reduced, while the abundance of anaerobic microorganisms like phylum Cloacimonetes and Smithella was enriched in digested sludge over time. Additional PAC dosing, on the one hand, affected the bioavailable substrate, thus further changing the microbial community structure; on the other hand, aluminum itself also affected specific microbial communities. Besides, PAC dosing indirectly influenced the bacterial diversity in AnMBR as well.

     

Study of Biological Activity and Process Stability in Submerged Membrane Bioreactors

Synthetic wastewater was treated in a bench scale submerged membrane bioreactor (SMBR). A long‐term experiment was conducted by varying the sludge residence time (SRT) (10–500 d) and BOD loading (1.3–0.25 kg/m³·d). The biological activity was observed in terms of the oxygen utilization rate (OUR) and adenosine triphosphate (ATP) profile; the process stability was analyzed based on the extent of organic degradation and suction pressure. The microbial population in the SMBR was dependent on the SRT and BOD loading, and its biological activity was increased with an increase in the SRT or BOD loading. At a low feed to microorganism (F/M) ratio (0.06 kg BOD/kg MLSS·d), the sludge production of the reactor was reduced to 0.04 kg MLSS/kg BOD, which is much less than in the conventional activated sludge process (0.4–0.6 kg MLSS/kg BOD). The F/M ratio influenced the biological activity (via ATP and the OUR) significantly at a short SRT (≤90 d). However, the effect of the F/M ratio ceased at a low F/M ratio (≤ 0.07 kg BOD/kg MLSS·d). The accumulation of organics in the SMBR was accompanied with an increase in the supernatant TOC, which caused a high suction pressure and an abrupt change in the operating conditions to process instability. However, the process stability of the SMBR increased with an increase in the SRT and a decrease in the BOD loading along with a concomitant decrease in the biological activity and sludge production.     

Effects of fertilization on bacterial community structure and function in a black soil of Dehui region estimated by Biolog and PCR-DGGE methods

Soil microbial community structure and function are commonly used as indicators for soil quality and fertility. In this paper, the bacterial community structure and function in a black soil of Dehui region influenced by fertilization were investigated by Biolog and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) methods. Biolog examination showed that substrate richness and catabolic diversities of bacterial communities were the highest in the treatment of farm yard manure, and the lowest in the chemical fertilizer treatment. DGGE fingerprint showed that the majority of bands were similar among all treatments, suggesting that microbial communities with those bands were stable, and not influenced by fertilization. In general, chemical fertilizer decreased the diversity of soil bacterial communities. The PCA (principal component analysis) plots of Biolog and DGGE revealed that the structure and function of bacterial communities were similar in the non-fertilized control and the treatment of farm yard manure alone, which inferred that the application of farm yard manure increased the quantity of soil microbes but had less effect on the changes of community structure. The catabolic function was similar, but the composition structure differed between the treatments of chemical fertilizer alone and combined application of farm yard manure with chemical fertilizer. These results suggest that the use of chemical fertilizer mainly decreased the catabolic activity of the fast growth bacteria or eutrophic bacteria.     

Analysis of the bacterial community in a full-scale printing and dyeing wastewater treatment system based on T-RFLP and 454 pyrosequencing

In this study, the bacterial dynamics and structure compositions in the two-stage biological process of a full-scale printing and dyeing wastewater (PDW) treatment system were traced and analyzed by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing techniques. T-RFLP analysis showed that the microbial communities experienced significant variation in the process of seed sludge adaptation to the PDW environments and were in constant evolution during the whole running period of the system, despite the constant COD and color removal effects. Pyrosequencing results indicated that the two-stage biological system harbored rather diverse bacteria, with Proteobacteria being the predominant phylum during the steady running period, although its microbial compositions differed. The first-stage aerobic tank was dominated by α-Proteobacteria (89.05% of Proteobacteria), whereas in the second-stage aerobic tank, β- and γ-Proteobacteria, besides α-Proteobacteria, were the dominant bacterial populations.