Characterization of active microbes in a full-scale anaerobic fluidized bed reactor treating phenolic wastewater

Microbial insights towards understanding the role of hydrochar in enhancing phenol degradation in anaerobic digestion

Anaerobic digestion (AD) of wastewater is the most promising bioprocess for organic conversion, however, phenol is toxic and resistant to anaerobic degradation. The current study compared the effect of hydrochar and granular activated carbon (GAC) on AD of phenol at four concentrations (100 mg/L, 250 mg/L, 500 mg/L and 1000 mg/L). Results demonstrated that hydrochar significantly improved the methane production rate and reduced the lag phase at all concentrations of phenol. The methane production rate was improved by about 50% at both 100 mg/L and 250 mg/L phenol, while it was raised by >160% at 500 mg/L and 1000 mg/L phenol by hydrochar. The GAC only increased the methane production rate at 500 mg/L and 1000 mg/L due to high adsorption capacity. Further, the adsorption of phenol by hydrochar had no apparent impact on the methane production rate, even though certain amounts of phenol were adsorbed. At 500 mg/L, the amount of methane produced significantly increased, so 16S rRNA transcripts sequencing and metabolomic analysis were conducted. 16S rRNA transcripts sequencing analysis indicated that hydrochar resulted in the enrichment of syntrophic bacteria (e.g., Syntrophorhabdus &Syntrophobacter) and Methanosaeta, which might be related with direct interspecies electron transfer. Further, it was noticed that the growth of Methanobacterium was repressed at 500 mg/L phenol, while hydrochar promoted its growth. Phenol was degraded into L-tyrosine and then followed the benzoate degradation pathway for methane production as revealed by metabolomic analysis. In addition, metabolomic analysis also revealed that hydrochar promoted the degradation of all metabolites and enhanced the phenol degradation into methane.

Shifts in structure and function of bacterial community in river and fish pond sediments after a phenol spill

Phenol is widely used in industrial processes and has microbial toxicity. However, the effects of a phenol spill on the microbial community are not clear. The present study explored the changes of bacterial communities in river and fish pond sediments after a phenol spill. The bacterial richness and diversity in river sediments were lower on day 30 (36 days after the spill) than on day 0, while they increased in fish pond sediments. The structures and functions of bacterial communities in both river and fish pond sediments were changed, and a more dramatical variation was detected in fish pond sediments. In river sediments, Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Nitrospirae were the major bacterial phyla, and Chloroflexi was enriched. In fish pond sediments, genera Brevibacillus dominated bacterial communities initially, and bacterial composition showed a dramatic change on day 30. Most predicted metabolism functions, as well as genetic information processing functions of translation, replication, and repair, were enhanced in both river and fish pond sediments, while they showed an opposite change trend for xenobiotic degradation function. This work could strengthen our understanding of the effects of phenol spills on sediment bacterial communities in both lotic and lentic ecosystems.

Anaerobic biodegradation of phenol in wastewater treatment: achievements and limits

Anaerobic biodegradation of toxic compounds found in industrial wastewater is an attractive solution allowing the recovery of energy and resources but it is still challenging due to the low kinetics making the anaerobic process not competitive against the aerobic one. In this review, we summarise the present state of knowledge on the anaerobic biodegradation process for phenol, a typical target compound employed in toxicity studies on industrial wastewater treatment. The objective of this article is to provide an overview on the microbiological and technological aspects of anaerobic phenol degradation and on the research needs to fill the gaps still hindering the diffusion of the anaerobic process. The first part is focused on the microbiology and extensively presents and characterises phenol-degrading bacteria and biodegradation pathways. In the second part, dedicated to process feasibility, anaerobic and aerobic biodegradation kinetics are analysed and compared, and strategies to enhance process performance, i.e. advanced technologies, bioaugmentation, and biostimulation, are critically analysed and discussed. The final section provides a summary of the research needs. Literature data analysis shows the feasibility of anaerobic phenol biodegradation at laboratory and pilot scale, but there is still a consistent gap between achieved aerobic and anaerobic performance. This is why current research demand is mainly related to the development and optimisation of powerful technologies and effective operation strategies able to enhance the competitiveness of the anaerobic process. Research efforts are strongly justified because the anaerobic process is a step forward to a more sustainable approach in wastewater treatment.Key points• Review of phenol-degraders bacteria and biodegradation pathways.• Anaerobic phenol biodegradation kinetics for metabolic and co-metabolic processes.• Microbial and technological strategies to enhance process performance.

Anaerobic Conversion of Saline Phenol-Containing Wastewater Under Thermophilic Conditions in a Membrane Bioreactor

Closing water loops in chemical industries result in hot and highly saline residual streams, often characterized by high strength and the presence of refractory or toxic compounds. These streams are attractive for anaerobic technologies, provided the chemical compounds are biodegradable. However, under such harsh conditions, effective biomass immobilization is difficult, limiting the use of the commonly applied sludge bed reactors. In this study, we assessed the long-term phenol conversion capacity of a lab-scale anaerobic membrane bioreactor (AnMBR) operated at 55°C, and high salinity (18 gNa^+.L^–1). Over 388 days, bioreactor performance and microbial community dynamics were monitored using specific methanogenic activity (SMA) assays, phenol conversion rate assays, volatile fatty acids permeate characterization and Illumina MiSeq analysis of 16S rRNA gene sequences. Phenol accumulation to concentrations exceeding 600 mgPh^.L^–1 in the reactor significantly reduced methanogenesis at different phases of operation, while applying a phenol volumetric loading rate of 0.12 gPh^.L^–1.d^–1. Stable AnMBR reactor performance could be attained by applying a sludge phenol loading rate of about 20 mgPh^.gVSS^–1.d^–1. In situ maximum phenol conversion rates of 21.3 mgPh^.gVSS^–1.d^–1 were achieved, whereas conversion rates of 32.8 mgPh^.gVSS^–1.d^–1 were assessed in ex situ batch tests at the end of the operation. The absence of caproate as intermediate inferred that the phenol conversion pathway likely occurred via carboxylation to benzoate. Strikingly, the hydrogenotrophic SMA of 0.34 gCOD-CH₄^.gVSS^–1.d^–1 of the AnMBR biomass significantly exceeded the acetotrophic SMA, which only reached 0.15 gCOD-CH₄^.gVSS^–1.d^–1. Our results indicated that during the course of the experiment, acetate conversion gradually changed from acetoclastic methanogenesis to acetate oxidation coupled to hydrogenotrophic methanogenesis. Correspondingly, hydrogenotrophic methanogens of the class Methanomicrobia, together with Synergistia, Thermotogae, and Clostridia classes, dominated the microbial community and were enriched during the three phases of operation, while the aceticlastic Methanosaeta species remarkably decreased. Our findings clearly showed that highly saline phenolic wastewaters could be satisfactorily treated in a thermophilic AnMBR and that the specific phenol conversion capacity was limiting the treatment process. The possibility of efficient chemical wastewater treatment under the challenging studied conditions would represent a major breakthrough for the widespread application of AnMBR technology.

Effects of Sludge Retention Time on the Performance of Anaerobic Ceramic Membrane Bioreactor Treating High-Strength Phenol Wastewater

Anaerobic ceramic membrane bioreactor (AnCMBR) is an attractive alternative for the treatment of high-strength phenol wastewater, but the effects of sludge retention time (SRT) on the performance and membrane fouling are still unclear. The results indicated that the AnCMBR was successfully employed to treat high-strength wastewater containing 5 g phenol L⁻¹. The removal efficiencies of phenol and chemical oxygen demand (COD) reached over 99.5% and 99%, respectively, with long SRT and short SRT. SRT had no obvious effect on the performance of the AnCMBR treating high-strength phenol wastewater with long time operation. The strong performance robustness of AnCMBR benefited from the enrichment of hydrogenotrophic methanogens and syntrophic phenol-degrading bacteria. However, the decline of SRT led to a more severe membrane fouling in the AnCMBR, which was caused by the small size of sludge flocs and high concentration of protein in the biopolymers. Therefore, this work presented a comprehensive insight to the feasibility and robustness of the AnCMBR for treating high-strength phenol wastewater.

Correlations between microbial population dynamics, bamA gene abundance and performance of anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol

The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L^-1). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L^-1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR.

Influence of organic loading rate on purified terephthalic acid wastewater treatment in a temperature staged anaerobic treatment (TSAT) system: Performance and metagenomic characteristics

In this study, a temperature staged anaerobic treatment (TSAT) system featured by thermophilic reactor (R1)-mesophilic reactor (R2) co-digestion was introduced to treat PTA wastewater. The process was successively conducted at three organic loading rates (OLRs): 3.34, 4.45, 6.68 kg COD/(m³·d), respectively (OLRs were R1 basis). The results indicated that TSAT system was highly efficient in PTA wastewater treatment at OLR lower than 4.45 kg COD/(m³·d). Miseq sequencing analysis demonstrated that R1 and R2 were predominated by hydrogenotrophic Methanolinea and acetotrophic Methanosaeta, separately. In addition, TA06, Caldisericia and Acetothermia associated groups were highly abundant in R1, whereas Chlorobiaceae and Syntrophobacteraceae were largely observed in R2. Tax4Fun analysis suggested that the important functional capabilities were significantly different between R1 and R2 (P < 0.05). The pathways related to aromatic compounds degradation mainly occurred in mesophilic stage, while the biosynthesis and metabolism pathways were more favored in thermophilic stage.

Turf soil enhances treatment efficiency and performance of phenolic wastewater in an up-flow anaerobic sludge blanket reactor

Phenols are industrially generated intermediate chemicals found in wastewaters that are considered a class of environmental priority pollutants. Up-flow anaerobic sludge blanket (UASB) reactors are used for phenolic wastewater treatment and exhibit high volume loading capability, favorable granule settling, and tolerance to impact loads. Use of support materials can promote biological productivity and accelerate start-up period of UASB. In the present study, turf soil was used as a support material in a mesophilic UASB reactor for the removal of phenols in wastewater. During sludge acclimatization (45-96 days), COD and phenols in the treatments were both reduced by 97%, whereas these contents in the controls were decreased by 81% and 75%, respectively. The phenol load threshold for the turf soil UASB reactor was greater (1200 mg/L, the equivalent of COD 3000 mg/L) in comparison with the control UASB reactor (900 mg/L, the equivalent of COD 2250 mg/L) and the turf soil UASB reactor was also more resistant to shock loading. Improved sludge settling, shear resistance, and higher biological activity occurred with the turf soil UASB reactor due to the formation of large granular sludge (0.6 mm or larger) in higher relative percentages. Granular sludge size was further enhanced by the colonization of filamentous bacteria on the irregular surface of the turf soil.

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics

BACKGROUND

Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information.

RESULTS

Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors. Comparative genomic evidence suggests that temperature difference leads to the colonization of two distinct cooperative sub-communities that can respire sulfate/sulfite/sulfur or nitrate/nitrite compounds and compete for uptake of methanogenic substrates (e.g., acetate and hydrogen). This competition may differentiate methanogenesis. The uncultured ε-Proteobacterium G1, whose close relatives have broad ecological niches including the deep-sea vents, aquifers, sediment, limestone caves, spring, and anaerobic digesters, is implicated as a Sulfurovum-like facultative anaerobic diazotroph with metabolic versatility and remarkable environmental adaptability. We provide first genomic evidence for butyrate, alcohol, and carbohydrate utilization by a Chloroflexi T78 clade bacterium, and phenol carboxylation and assimilatory sulfite reduction in a Cryptanaerobacter bacterium.

CONCLUSION

Genome-resolved metagenomics enriches our view on the differentiation of microbial community composition, metabolic pathways, and ecological interactions in temperature-differentiated methanogenic phenol-degrading bioreactors. These findings suggest optimization strategies for methanogenesis on phenol, such as temperature control, protection from light, feed desulfurization, and hydrogen sulfide removal from bioreactors. Moreover, decoding genome-borne properties (e.g., antibiotic, arsenic, and heavy metal resistance) of uncultured bacteria help to bring up alternative schemes to isolate them.

Novel Mass Bio System (MBS) and its potential application in advanced treatment of coal gasification wastewater

A Novel Mass Bio System (MBS), a suspended biologically activated carbon granular carrier cubic particle with 2–5 mm side length and 1.02–1.08 specific gravity was developed for advanced treatment of coal gasification wastewater.

Influence of upflow velocity on performance and biofilm characteristics of Anaerobic Fluidized Bed Reactor (AFBR) in treating high-strength wastewater

One of the key parameters in Fluidized Bed reactors is the control of biofilm thickness and configuration. The effect of upflow velocity on performance and biofilm characteristics of an Anaerobic Fluidized Bed Reactor was studied in treating Currant wastewater at various loading rates. The reactor used this study was made of a plexiglass column being 60 mm diameter, 140 cm height, and a volume of 3.95 L. The results demonstrated that the AFBR system is capable of handling an exceptionally high organic loading rate. At organic loading rates of 9.4 to 24.2 (kg COD m(-3)) at steady state, reactor performances with upflow velocities of 0.5, 0.75 and 1 (m min(-1)) were 89.3- 63.4, 96.9 - 79.6 and 95 - 73.4 percent, respectively. The average biomass concentration per unit volume of the AFBR (as gVSSatt L(-1) expended bed) decreased with the increase of upflow velocity in the range of 0.5-1 m min(-1) at all applied organic loading rates. The total biomass in the reactor increased with increases in the organic loading rate. The peak biomass concentration per unit volume (as gVSSatt L(-1) expended bed) was observed at the bottom part of the reactor, then it droped off slowly towards the top. The biofilm thickness increased from the bottom to the top of the reactor representing a stratification of the media in the AFBR. The bed porosity increased from the bottom to the top of the reactor.

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey

Anaerobic digestion (AD) processes are known to effectively convert organic waste to CO2 and CH4 , but much of the microbial ecology remains unclear. Specifically, we have limited insights into symbiotic syntroph and methanogen ('syntrophy') acid degradation, although they are essential for preventing process deterioration. Also, we often observed many uncharacterized or uncultivated organisms, but poorly understood their role(s) in relation to syntrophy. To define syntrophy-associated populations, this study enriched methanogenic communities with propionate, butyrate, benzoate, acetate, formate and H2 from two different inocula over 3 years. 16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships. Based on comprehensive re-evaluation of publically available microbial community data for AD, the known syntrophs and methanogens identified were clearly representatives of the AD-associated syntrophs and methanogens. In addition, uncultivated clades related to Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi were ubiquitously found in AD and enrichments. These organisms may be universally involved in AD syntrophic degradation, but only represented <23% of the yet-to-be-cultivated organisms (89 of 390 clades). Thus, the contribution of these uncultured organisms in AD remains unclear and warrants further investigation.

Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing

Methanogenesis from wastewater-borne organics and organic solid wastes (e.g., food residues) can be severely suppressed by the presence of toxic phenols. In this work, ambient (20 °C) and mesophilic (37 °C) methane-producing and phenol-degrading consortia were enriched and characterized using high-throughput sequencing (HTS). 454 Pyrosequencing indicated novel W22 (25.0 % of bacterial sequences) in the WWE1 and Sulfurovum-resembled species (32.0 %) in the family Campylobacterales were the most abundant in mesophilic and ambient reactors, respectively, which challenges previous knowledge that Syntrophorhabdus was the most predominant. Previous findings may underestimate bacterial diversity and low-abundance bacteria, but overestimate abundance of Syntrophorhabdus. Illumina HTS revealed that archaeal populations were doubled in ambient reactor and tripled in mesophilic reactor, respectively, compared to the ∼4.9 % (of the bacteria and archaea sequences) in the seed sludge. Moreover, unlike the dominance of Methanosarcina in seed sludge, acetotrophic Methanosaeta predominated both (71.4-76.5 % of archaeal sequences) ambient and mesophilic enrichments. Noteworthy, this study, for the first time, discovered the co-occurrence of green sulfur bacteria Chlorobia, sulfur-reducing Desulfovibrio, and Sulfurovum-resembling species under ambient condition, which could presumably establish mutualistic relationships to compete with syntrophic bacteria and methanogens, leading to the deterioration of methanogenic activity. Taken together, this HTS-based study unravels the high microbial diversity and complicated bacterial interactions within the biogas-producing and phenol-degrading bioreactors, and the identification of novel bacterial species and dominant methanogens involved in the phenol degradation provides novel insights into the operation of full-scale bioreactors for maximizing biogas generation.

Substrate type drives variation in reactor microbiomes of anaerobic digesters

The goal of this study was to obtain causative information about beta-diversity (differentiation between microbiomes) by comparing sequencing information between studies rather than just knowledge about alpha-diversity (microbiome richness). Here, published sequencing data were merged representing 78 anaerobic digester samples originating from 28 different studies for an overall comparison of beta-diversity (measured using unweighted UniFrac). It was found that digester microbiomes based on bacterial sequences clustered by substrate type, independent of the study of origin, and that this clustering could be attributed to distinct bacterial lineages.

The microbiology of olive mill wastes

Olive mill wastes (OMWs) are high-strength organic effluents, which upon disposal can degrade soil and water quality, negatively affecting aquatic and terrestrial ecosystems. The main purpose of this review paper is to provide an up-to-date knowledge concerning the microbial communities identified over the past 20 years in olive mill wastes using both culture-dependent and independent approaches. A database survey of 16S rRNA gene sequences (585 records in total) obtained from olive mill waste environments revealed the dominance of members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. Independent studies confirmed that OMW microbial communities' structure is cultivar dependent. On the other hand, the detection of fecal bacteria and other potential human pathogens in OMWs is of major concern and deserves further examination. Despite the fact that the degradation and detoxification of the olive mill wastes have been mostly investigated through the application of known bacterial and fungal species originated from other environmental sources, the biotechnological potential of indigenous microbiota should be further exploited in respect to olive mill waste bioremediation and inactivation of plant and human pathogens. The implementation of omic and metagenomic approaches will further elucidate disposal issues of olive mill wastes.

Use of a hierarchical oligonucleotide primer extension approach for multiplexed relative abundance analysis of methanogens in anaerobic digestion systems

In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products.

Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales

A novel mesophilic, hydrogenotrophic methanogen, designated strain TNRT, was isolated from an anaerobic, propionate-degradation enrichment culture that was originally established from a rice field soil sample from Taiwan. Cells were non-motile rods, 2.0–6.5 µm long by 0.3 µm wide. Filamentous (up to about 100 µm) and coccoid (about 1 µm in diameter) cells were also observed in cultures in the late exponential phase of growth. Strain TNRT grew at 20–40 °C (optimally at 37 °C), at pH 6.5–7.4 (optimally at pH 7.0) and in the presence of 0–25 g NaCl l−1 (optimally at 0 g NaCl l−1). The strain utilized H2/CO2 and formate for growth and produced methane. The G+C content of the genomic DNA was 56.4 mol%. Based on sequences of both the 16S rRNA gene and the methanogen-specific marker gene mcrA, strain TNRT was related most closely to Methanolinea tarda NOBI-1T; levels of sequence similarities were 94.8 and 86.4 %, respectively. The 16S rRNA gene sequence similarity indicates that strain TNRT and M. tarda NOBI-1T represent different species within the same genus. This is supported by shared phenotypic properties, including substrate usage and cell morphology, and differences in growth temperature. Based on these genetic and phenotypic properties, strain TNRT is considered to represent a novel species of the genus Methanolinea , for which the name Methanolinea mesophila sp. nov. is proposed; the type strain is TNRT ( = NBRC 105659T = DSM 23604T). In addition, we also suggest family status for the E1/E2 group within the order Methanomicrobiales , for which the name Methanoregulaceae fam. nov. is proposed; the type genus of family is Methanoregula.

Conversion of phenols during anaerobic digestion of organic solid waste--a review of important microorganisms and impact of temperature

During anaerobic digestion of organic waste, both energy-rich biogas and a nutrient-rich digestate are produced. The digestate can be used as a fertiliser in agricultural soils if the levels of hazardous compounds and pathogens are low. This article reviews the main findings about phenols in anaerobic digestion processes degrading organic solid wastes, and examines the effect of process temperature on the anaerobic degradation of phenols, the microbial community and the quality of the digestate. The degradation efficiency of a number of different phenols has been shown to be correlated to the process temperature. Higher degradation efficiency is observed at mesophilic process temperature than at thermophilic temperature. Possible explanations for this variation in the degradation of phenols include differences in diversity, particularly of the phenol-degrading bacteria, and/or the presence of temperature-sensitive enzymes. Chemical analysis of digestate from bioreactors operating at thermophilic temperature detected a higher content of phenols compared to mesophilic bioreactors, verifying the degradation results. Digestate with the highest phenol content has the greatest negative impact on soil microbial activity.

Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.

A great leap forward in microbial ecology

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge

A novel methane-producing archaeon, strain SMSPT, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSPT was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8T (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSPT and Methanoregula boonei 6A8T represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSPT represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSPT (=NBRC 105244T =DSM 22288T).