Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis

Applied Microbiology and Biotechnology - Spent mushroom substrate (SMS) is the residue of edible mushroom production occurring in huge amounts. The SMS residue can be digested for biogas production...     

Performance and microbial community analysis of two-stage process with extreme thermophilic hydrogen and thermophilic methane production from hydrolysate in UASB reactors

The two-stage process for extreme thermophilic hydrogen and thermophilic methane production from wheat straw hydrolysate was investigated in up-flow anaerobic sludge bed (UASB) reactors. Specific hydrogen and methane yields of 89 ml-H₂/g-VS (190 ml-H₂/g-sugars) and 307 ml-CH₄/g-VS, respectively were achieved simultaneously with the overall VS removal efficiency of 81% by operating with total hydraulic retention time (HRT) of 4 days . The energy conversion efficiency was dramatically increased from only 7.5% in the hydrogen stage to 87.5% of the potential energy from hydrolysate, corresponding to total energy of 13.4 kJ/g-VS. Dominant hydrogen-producing bacteria in the H₂-UASB reactor were Thermoanaerobacter wiegelii, Caldanaerobacter subteraneus, and Caloramator fervidus. Meanwhile, the CH₄-UASB reactor was dominated with methanogens of Methanosarcina mazei and Methanothermobacter defluvii. The results from this study suggest the two stage anaerobic process can be effectively used for energy recovery and for stabilization of hydrolysate at anaerobic conditions.     

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis

Analysis of microbial community structure in complex environmental samples using nucleic acid techniques requires efficient unbiased DNA extraction procedures; however, humic acids and other contaminants complicate the isolation of PCR-amplifiable DNA from compost and other organic-rich samples. In this study, combinations of DNA extraction and purification methods were compared based on DNA yield, humic acid contamination, PCR amplifiability, and microbial community structure assessed by terminal restriction fragment length polymorphisms (TRFLP) of amplified 16S rRNA genes. DNA yield and humic acid contamination, determined by A230, varied significantly between extraction methods. Humic acid contamination of DNA obtained from compost decreased with increasing salt concentration in the lysis buffer. DNA purified by gel permeation chromatography (Sepharose 4B columns) gave satisfactory PCR amplification with universal eubacterial 16S rRNA gene primers only when A260/A280 ratios exceeded 1.5. DNA purified with affinity chromatography (hydroxyapatite columns), and showing A260/A280 ratios as high as 1.8, did not show consistently satisfactory PCR amplification using the same 16S rRNA primers. Almost all DNA samples purified by agarose gel electrophoresis showed satisfactory PCR amplification. Principal components analysis (PCA) of TRFLP patterns differentiated compost types based on the presence/absence of peaks and on the height of the peaks, but differences in TRFLP patterns were not appreciable between extraction methods that yielded relatively pure DNA. High levels of humic acid contamination in extracted DNA resulted in TRFLP patterns that were not consistent and introduced a bias towards lower estimates of diversity.     

Anthracene biodegradation under nitrate-reducing condition and associated microbial community changes

Anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) and degraders in the subsurface environment have aroused increasing attention. Molecular techniques are especially useful when isolates are hard to obtain. Nitrate-reducing microcosms inoculated with aquifer sediment were constructed to investigate anthracene biodegradation. The associated microbial community changes were characterized using terminal restriction fragment length polymorphism analysis (TRFLP) in combination with 16S rRNA gene clone library analysis. A nearly complete removal of anthracene was achieved after an eighty day incubation under the nitrate-reducing condition. The two molecular techniques revealed a significant shift of microbial community structure, coupled with anthracene biodegradation. Species of genera Paracoccus, Herbaspirillum, Azotobacter, and Rhodococcus were grouped into four major operational taxonomic units (OTUs) in the library that was constructed with the microcosm sample on day 80. The enrichment of these genera might have links to anthracene biodegradation under the nitrate-reducing condition. Microbial consortia likely played a part in anthracene degradation.     

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from aged refuse for microbial community analysis

In order to develop and establish a method for isolation of PCR-amplifiable DNA from aged refuse, the orthogonal experiment was conducted to evaluate systematically the effects of various steps within each method in terms of DNA yield, purity, fragment size, humus contamination, PCR amplifiability using universal eubacterial and archaeal 16S rDNA prime pairs, and genetic diversity estimate from denaturing gradient gel electrophoresis. The inclusion of the pretreatment step was demonstrated to be crucial for the recovery of high-quality DNA preparations from the aged refuse and the pre-washing with TENP-PBS buffer was recommended. Satisfactory DNA yields and unbiased DNA extraction required the introduction of lysis by bead-beating treatment. The modified Sephadex G-200 spin column was effective in obtaining relatively stable DNA preparations from the aged refuse. It was established that a combination of pre-washes with TENP-PBS buffer plus gentle bead lysis and proteinase K treatment followed by SDS-based extraction and subsequent modified Sephadex G-200 spin column purification could ensure the acquisition of PCR-amplifiable DNA from the aged refuse expediently and cheaply.     

Comparison of molecular fingerprinting methods for analysis of soil microbial community structure

Denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP) analysis, and automated ribosomal intergenic spacer analysis (ARISA) have been widely used as molecular fingerprinting methods for analysis of microbial communities. To find suitable methods, we compared the three fingerprinting methods by analyzing soil fungal communities in four differing land-use types: bare ground, crop fields, grasslands, and forests. We also examined optimal primer pairs for DGGE analysis by comparing single and mixed DNA samples of cultured fungal populations. Principal coordinate analysis (PCO), nonmetric multidimensional scaling method (NMDS), and analysis of similarities (ANOSIM), which are major multivariate statistical analyses for quantifying fingerprint patterns, were compared. All three fingerprinting methods yielded clear discrimination of soil fungal communities among the four land-use types, irrespective of statistical methods. The advantages and disadvantages of the three fingerprinting methods were discussed.     

Systematic analysis of biochemical performance and the microbial community of an activated sludge process using ozone-treated sludge for sludge reduction

Two lab-scale bioreactors (reactors 1 and 2) were employed to examine the changes in biological performance and the microbial community of an activated sludge process fed with ozonated sludge for sludge reduction. During the 122 d operation, the microbial activities and community in the two reactors were evaluated. The results indicated that, when compared with the conventional reactor (reactor 1), the reactor that was fed with the ozonated sludge (reactor 2) showed good removal of COD, TN and cell debris, without formation of any excess sludge. In addition, the protease activity and intracellular ATP concentration of reactor 2 were increased when compared to reactor 1, indicating that reactor 2 had a better ability to digest proteins and cell debris. DGGE analysis revealed that the bacterial communities in the two reactors were different, and that the dissimilarity of the bacterial population was nearly 40%. Reactor 2 also contained more protozoa and metazoa, which could graze on the ozone-treated sludge debris directly.     

中高温污泥厌氧消化系统中微生物群落比较

【目的】结合中温与高温消化两者优势的两相厌氧消化工艺可能是推进污泥厌氧消化发展的重要方向,因此,探究和比较中温和高温污泥厌氧消化系统中微生物群落组成的异同具有重要意义。【方法】利用高通量测序技术检测中温和高温厌氧消化系统中细菌与古菌的16S r RNA基因序列信息和真菌的内转录间隔(ITS)序列信息,利用基因芯片(Geo Chip 5.0)检测病毒和病原菌致病基因的信息,以对比中温和高温条件下微生物群落在物种组成和功能基因层面上的异同。【结果】中温和高温条件下细菌和古菌在群落物种组成上存在显著差异,病毒和病原菌毒性基因也显著不同,而两种系统中真菌群落的物种组成相似且丰度相对较低。中温条件下产甲烷古菌和未分类微生物相对丰度较高,而高温条件下产酸及嗜热菌相对丰度较高,且高温消化后病毒和病原菌毒性基因相对丰度下降。微生物群落结构与COD、TS和VS有着显著相关性。【结论】微生物群落组成和功能基因在中高温的污泥厌氧消化系统中显著不同,从而解释了两个系统功能的差异。微生物群落的形成与进水参数相关,说明微生物对进水条件敏感。     

Biodiversity analysis of microbial community in the chem-bioflocculation treatment process

Total DNA was directly extracted from environmental samples and amplified with polymerase chain reaction (PCR) technique. The PCR products were fingerprinted via denaturing gradient gel electrophoresis (DGGE). Significant differences were observed in the microbial community structures between traditional treatment process and chem-bioflocculation process. The microbial community structure shift at different sampling locations in chem-bioflocculation process and on two typical operational conditions was studied. 16S rDNA V3 regions of some dominant species were sequenced and the species were identified. The microbial communities were stable in both the chem-bioflocculation process and the activated sludge process under various experimental conditions presented in this work. The attached growth treatment process was less stable when operational conditions changed.     

DG-DGGE分析产氢发酵系统微生物群落动态及种群多样性

应用双梯度-变性梯度凝胶电泳(DG-DGGE)对生物制氢反应器微生物种群的动态变化及多样性进行监测。间隔7d从反应器取厌氧活性污泥,以细菌16SrDNA通用引物进行V2～V3区域PCR扩增,长约450bp的PCR产物经DGGE分离后,获得污泥微生物群落的16SrDNA指纹图谱。污泥接种到反应器后微生物群落中既有原始种群的消亡和增长,也有次级种群的强化和演变。反应器在运行初期群落演替迅速,15d时微生物群落结构变化最大。群落结构的相似性随着演替时间的增加而逐渐升高,种群动态变化后形成稳定的群落结构。29d时微生物多样性基本保持不变,微生物优势种属达到19个OTU。在细菌竞争和协同作用制约下,种群多样性降低后趋于稳定,形成顶级群落。有些种群在群落结构中一直存在,是群落建成的原始种群,原始种群与次级种群在代谢过程中具有协同作用,表现出群落的综合生态特征。     

Biofilm microbial community of a thermophilic trickling biofilter used for continuous biohydrogen production

Molecular methods were employed to investigate the microbial community of a biofilm obtained from a thermophilic trickling biofilter reactor (TBR) that was operated long-term to produce H(2). Biomass concentration in the TBR gradually decreased as reactor bed height increased. Despite this difference in biomass concentration, samples from the bottom and middle of the TBR bed revealed similar microbial populations as determined by PCR-DGGE analysis of 16S rRNA genes. Nucleotide sequences of most DGGE bands were affiliated with the classes Clostridia and Bacilli in the phylum Firmicutes, and the most dominant bands showed a high sequence similarity to Thermoanaerobacterium thermosaccharolyticum.     

Quantitative analysis of a high-rate hydrogen-producing microbial community in anaerobic agitated granular sludge bed bioreactors using glucose as substrate

Fermentative H₂ production microbial structure in an agitated granular sludge bed bioreactor was analyzed using fluorescence in situ hybridization (FISH) and polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). This hydrogen-producing system was operated at four different hydraulic retention times (HRTs) of 4, 2, 1, and 0.5 h and with an influent glucose concentration of 20 g chemical oxygen demand/l. According to the PCR-DGGE analysis, bacterial community structures were mainly composed of Clostridium sp. (possibly Clostridium pasteurianum), Klebsiella oxytoca, and Streptococcus sp. Significant increase of Clostridium/total cell ratio (68%) was observed when the reactor was operated under higher influent flow rate. The existence of Streptococcus sp. in the reactor became more important when operated under a short HRT as indicated by the ratio of Streptococcus probe-positive cells to Clostridium probe-positive cells changing from 21% (HRT 4 h) to 38% (HRT 0.5 h). FISH images suggested that Streptococcus cells probably acted as seeds for self-flocculated granule formation. Furthermore, combining the inspections with hydrogen production under different HRTs and their corresponding FISH analysis indicated that K. oxytoca did not directly contribute to H₂ production but possibly played a role in consuming O₂ to create an anaerobic environment for the hydrogen-producing Clostridium.     

Novel MBR_based main stream biological nutrient removal process: high performance and microbial community

For municipal wastewater treatment, main stream biological nutrient removal (BNR) process is becoming more and more important. This lab-scale study, novel MBR_based BNR processes (named A₂N-MBR and A₂NO-MBR) were built. Comparison of the COD removal, results obtained demonstrated that COD removal efficiencies were almost the same in three processes, with effluent concentration all bellowed 30 mg L^?1. However, the two-sludge systems (A₂N-MBR and A₂NO-MBR) had an obvious advantage over the A²/O for denitrification and phosphorus removal, with the average TP removal rates of 91.20, 98.05% and TN removal rates of 73.00, 79.49%, respectively, higher than that of 86.45 and 61.60% in A²/O process. Illumina Miseq sequencing revealed that Candidatus_Accumulibacter, which is capable of using nitrate as an electron acceptor for phosphorus and nitrogen removal simultaneously, was the dominant phylum in both A₂N-MBR and A₂NO-MBR process, accounting for 28.74 and 23.98%, respectively. Distinguishingly, major organism groups related to nitrogen and phosphorus removal in A²/O system were Anaerolineaceae_uncultured, Saprospiraceae_uncultured and Thauera, with proportions of 11.31, 8.56 and 5.00%, respectively. Hence, the diversity of dominant PAOs group was likely responsible for the difference in nitrogen and phosphorus removal in the three processes.     

Shift of microbial community in gas-phase biofilters with different inocula,inlet loads and nitrogen sources

The research on gaseous VOCs biofilters has often concentrated on process optimization. However, the microbial community change upon operating conditions is not well understood. In this study, three lab-scale biofilters treating gaseous toluene were operated for 66 days with different inocula under changes in inlet loads and nitrogen sources. Three biofilters were inoculated with activated sludge, river sediment or microbial consortia, respectively. The microbial community differed a lot initially but gradually deviated toward similar structures with the same dominant microorganisms, i.e. Proteobacteria, Actinobacteria (phylum level) and Rhodococcus,Pseudomonas(genus level). Among three biofilters, the two biofilters inoculated with activated sludge and river sediment showed higher microbial diversity, better VOCs removal performance and higher metabolic activity. Higher relative abundance of Alcanivorax (3% compared with lower than 0.03%), Pimelobacte (0.05% compared with lower than 0.01%)were detected under low inlet load, and Zoogloea(0.1%), Alkaliphilus(0.2%) were detected when the inlet load was increased. the abundance of Pseudomonasdecreased from 14% to 2% when ammonia was used as nitrogen source instead of nitrate, meanwhile the abundance of Bacillus and Gordoniaincreased from 0.01% to 0.05% and 0.8% to 5.8% respectively. Some special organisms were observed i.e. the intestinal microorganism.     

Microarrays for bacterial detection and microbial community analysis

Several types of microarrays have recently been developed and evaluated for bacterial detection and microbial community analysis. These studies demonstrated that specific, sensitive and quantitative detection could be obtained with both functional gene arrays and community genome arrays. Although single-base mismatch can be differentiated with phylogenetic oligonucleotide arrays, reliable specific detection at the single-base level is still problematic. Microarray-based hybridization approaches are also useful for defining genome diversity and bacterial relatedness. However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial detection and community analysis.     

Biohydrogen and methane production by co-digestion of cassava stillage and excess sludge under thermophilic condition

Thermophilic anaerobic hydrogen and methane production by co-digestion of cassava stillage (CS) and excess sludge (ES) was investigated in this study. The improved hydrogen and subsequent methane production were observed by co-digestion of CS with certain amount of ES in batch experiments. Compared with one phase anaerobic digestion, two phase anaerobic digestion offered an attractive alternative with more abundant biogas production and energy yield, e.g., the total energy yield in two phase obtained at VS_CS/VS_ES of 3:1 was 25% higher than the value of one phase. Results from continuous experiments further demonstrated that VS_CS/VS_ES of 3:1 was optimal for hydrogen production with the highest hydrogen yield of 74 mL/g total VS added, the balanced nutrient condition with C/N ratio of 1.5 g carbohydrate-COD/g protein-COD or 11.9 g C/g N might be the main reason for such enhancement. VS_CS/VS_ES of 3:1 was also optimal for continuous methane production considering the higher methane yield of 350 mL/g total VS added and the lower propionate concentration in the effluent.     

Effect of seed sludge microbial community and activity on the performance of anaerobic reactors during the start-up period

In this study, two laboratory-scale anaerobic batch reactors started up with different inoculum sludges and fed with the same synthetic wastewater were monitored in terms of performance and microbial community shift by denaturant gradient gel electrophoresis fingerprinting and subsequent cloning, sequencing analysis in order to reveal importance of initial quality of inoculum sludge for operation of anaerobic reactors. For this purpose, two different seed sludge were evaluated. In Reactor1 seeded with a sludge having less diverse microbial community (19 operational taxonomic unit (OTU’s) for Bacterial and 8 OTU’s for Archaeal community, respectively) and a methanogenic activity of 150 ml CH₄ g TVS⁻¹ day⁻¹, a chemical oxygen demand (COD) removal efficiency of 78.8 ± 4.17% was obtained at a substrate to microorganism (S/X) ratio of 0.38. On the other hand, Reactor2, seeded with a sludge having a much more diverse microbial community (24 OTU’s for Bacterial and 9 OTU’s for Archaeal communities, respectively) and a methanogenic activity, 450 ml CH₄ g TVS⁻¹ day⁻¹, operated in the same conditions showed a better start-up performance; a COD removal efficiency of over 98% at a S/X ratio of 0.53. Sequence analysis of Seed2 revealed the presence of diverse fermentative and syntrophic bacteria, whereas excised bands of Seed1 related to fermentative and sulfate/metal-reducing bacteria. This study revealed that a higher degree of bacterial diversity, especially the presence of syntrophic bacteria besides the abundance of key species such as methanogenic Archaea may play an important role in the performance of anaerobic reactors during the start-up period.     

Effect of pH change on the performance and microbial community of enhanced biological phosphate removal process

An acetate-rich wastewater, containing 170 mg/L of total organic carbon (TOC), 13 mg/L of N, and 15 mg/L of P, was treated using the enhanced biological phosphate removal (EBPR) process operated in a sequencing batch reactor. A slight change of pH of the mixed liquor from 7.0 to 6.5 led to a complete loss of phosphate-removing capability and a drastic change of microbial populations. The process steadily removed 94% of TOC and 99.9% of P from the wastewater at pH 7.0, but only 93% TOC and 17% of P 14 days after the pH was lowered to pH 6.5. The sludge contained 8.8% P at pH 7.0, but only 1.9% at pH 6.5. Based on 16S rDNA analysis, 64.8% of the clones obtained from the sludge at pH 7.0 were absent in the pH 6.5 sludge. The missing microbes, some of which were likely responsible for the phosphate removal at pH 7.0, included beta-Proteobacteria, Actinobacteria, Bacteriodetes/Chlorobi group, plus photosynthetic bacteria and Defluvicoccus of the alpha-Proteobacteria. Among them, the last two groups, which represented 9.3% and 10.1% of the EBPR sludge at pH 7.0, have rarely been reported in an EBPR system.