Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray

Exploring the potential of biofiltration for mitigating harmful gaseous emissions from small or old landfills: a review

Landfills are widely employed as the primary means of solid waste disposal. However, this practice generates landfill gas (LFG) which contains methane (CH4), a potent greenhouse gas, as well as various volatile organic compounds and volatile inorganic compounds. These emissions from landfills contribute to approximately 25% of the total atmospheric CH4, indicating the imperative need to valorize or treat LFG prior to its release into the atmosphere. This review first aims to outline landfills, waste disposal and valorization, conventional gas treatment techniques commonly employed for LFG treatment, such as flares and thermal oxidation. Furthermore, it explores biotechnological approaches as more technically and economically feasible alternatives for mitigating LFG emissions, especially in the case of small and aged landfills where CH4 concentrations are often below 3% v/v. Finally, this review highlights biofilters as the most suitable biotechnological solution for LFG treatment and discusses several advantages and challenges associated with their implementation in the landfill environment.

Microbial ecology of biofiltration used for producing safe drinking water

Abstract

Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application.

Key points

• Biofilters are composed of complex microbiomes, primarily shaped by water quality.

• Conventional biofilters contribute to address safety challenges in drinking water.

• Studies may underestimate the active/functional role of microbiomes in biofilters.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12013-x.

Use of methanotrophically activated biochar in novel biogeochemical cover system for carbon sequestration: Microbial characterization

Biochar-amended soils have been explored to enhance microbial methane (CH₄) oxidation in landfill cover systems. Recently, research priorities have expanded to include the mitigation of other components of landfill gas such as carbon dioxide (CO₂) and hydrogen sulfide (H₂S) along with CH₄. In this study, column tests were performed to simulate the newly proposed biogeochemical cover systems, which incorporate biochar-amended soil for CH₄ oxidation and basic oxygen furnace (BOF) slag for CO₂ and H₂S mitigation, to evaluate the effect of cover configuration on microbial CH₄ oxidation and community composition. Biogeochemical covers included a biochar-amended soil (10% w/w), and methanotroph-enriched activated biochar amended soil (5% or 10% w/w) as a biocover layer or CH₄ oxidation layer. The primary outcome measures of interest were CH₄ oxidation rates and the structure and abundance of methane-oxidation bacteria in the covers. All column reactors were active in CH₄ oxidation, but columns containing activated biochar-amended soils had higher CH₄ oxidation rates (133 to 143 μg CH₄ g^-1 day^-1) than those containing non-activated biochar-amended soil (50 μg CH₄ g^-1 day^-1) and no-biochar soil or control soil (43 μg CH₄ g^-1 day^-1). All treatments showed significant increases in the relative abundance of methanotrophs from an average relative abundance of 5.6% before incubation to a maximum of 45% following incubation. In activated biochar, the abundance of Type II methanotrophs, primarily Methylocystis and Methylosinus, was greater than that of Type I methanotrophs (Methylobacter) due to which activated biochar-amended soils also showed higher abundance of Type II methanotrophs. Overall, biogeochemical cover profiles showed promising potential for CH₄ oxidation without any adverse effect on microbial community composition and methane oxidation. Biochar activation led to an alteration of the dominant methanotrophic communities and increased CH₄ oxidation.

Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations

Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic CH4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil samples. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis-Menten kinetics of CH4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH4 source such as landfill cover soils. The rate constant of CH4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH4 concentrations and suggest a higher functional diversity within this group than previously recognised.

Methanobactin from methanotrophs: genetics, structure, function and potential applications

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Simultaneous biodegradation of methane and styrene in biofilters packed with inorganic supports: Experimental and macrokinetic study

Four upflow 0.018 m³ biofilters (3 beds), B-ME, B-200, B-500 and B-700, all packed with inorganic materials, were operated at a constant air flow rate of 0.18 m³ h^-1 to eliminate methane (CH₄), a harmful greenhouse gas (GHG), and styrene (C₈H₈), a carcinogenic volatile organic compound (VOC). The biofilters were irrigated with 0.001 m³ of recycled nutrient solution (NS) every day (flow rate of 60 × 10^-3 m³ h^-1). Styrene inlet load (IL) was kept constant in each biofilter. Different CH₄-ILs varying in the range of 7-60 gCH₄ m^-3 h^-1 were examined in B-ME (IL of 0 gC₈H₈ m^-3 h^-1), B-200 (IL of 9 gC₈H₈ m^-3 h^-1), B-500 (IL of 22 gC₈H₈ m^-3 h^-1) and B-700 (IL of 32 gC₈H₈ m^-3 h^-1). Finally, the effect of C₈H₈ on the macrokinetic parameters of CH₄ biofiltration was studied based on the Michaelis-Menten model. Average C₈H₈ removal efficiencies (RE) varying between 64 and 100% were obtained at CH₄-ILs increasing from 7 to 60 gCH₄ m^-3 h^-1 and for C₈H₈-ILs range of 0-32 gC₈H₈ m^-3 h^-1. More than 90% of C₈H₈ was removed in the bottom and middle beds of the biofilters. By increasing C₈H₈-IL from 0 to 32 gC₈H₈ m^-3 h^-1, maximal EC in Michaelis-Menten model and macrokinetic saturation constant declined from 311 to 39 g m^-3 h^-1 and from 19 to 2.3 g m^-3, respectively, which confirmed that an uncompetitive inhibition occurred during CH₄ biofiltration in the presence of C₈H₈.

Biofiltration of methane

The on-going annual increase in global methane (CH₄) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH₄ emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH₄ concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH₄ biofiltration studies that have been performed in the last decades.

Odor mitigation and bacterial community dynamics in on-site biocovers at a sanitary landfill in South Korea

Unpleasant odors emitted from landfills have been caused environmental and societal problems. For odor abatement, two pilot-scale biocovers were installed at a sanitary landfill site in South Korea. Biocovers PBC1 and PBC2 comprised a soil mixture with different ratios of earthworm casts as an inoculum source and were operated for 240 days. Their odor removal efficiencies were evaluated, and their bacterial community structures were characterized using pyrosequencing. In addition, the correlation between odor removability and bacterial community dynamics was assessed using network analysis. The removal efficiency of complex odor intensity in the two biocovers ranged from 81.1% to 97.8%. Removal efficiencies of sulfur-containing odors (hydrogen sulfide, methanethiol, dimethyl sulfide, and dimethyl disulfide), which contributed most to complex odor intensity, were greater than 91% in both biocovers. Despite the fluctuations in ambient temperature (-8.2 to 31.3 °C) and inlet complex odor intensity (10,000-42,748 of odor dilution ratio), biocovers PBC1 and PBC2 displayed stable deodorizing performance. A high ratio of earthworm casts as an inoculum source led to high odor removability during the first 25 days of operation, but different mixing ratios of earthworm casts did not significantly affect overall odor removability. A bacterial community analysis showed that Methylobacter, Arthrobacter, Acinetobacter, Rhodanobacter, and Pedobacter were the dominant genera in both biocovers. Network analysis results indicated that Steroidobacter, Cystobacter, Methylosarcina, Solirubrobacter, and Pseudoxanthomonas increased in relative abundance with time and were major contributors to odor removal, although these bacteria had a relatively low abundance compared to the overall bacterial community. These data contribute to a more comprehensive understanding of the relationship between bacterial community dynamics and deodorizing performance in biocovers.

Assessing the Performance of Floating Biofilters for Oxidation of Methane from Dairy Effluent Ponds

Mitigating methane (CH) emissions from New Zealand dairy effluent ponds using volcanic pumice soil biofilters has been found to be a promising technology. Because the soil column biofilter prototype previously used was cumbersome, here we assess the effectiveness of volcanic pumice soil-perlite biofilter media in a floating system to remove high concentrations of CH emitted from a dairy effluent pond and simultaneously in a laboratory setting. We measured the CH removal over a period of 11 mo and determined methanotroph population dynamics using molecular techniques to understand the role of methanotroph population abundance and diversity in CH removal. Irrespective of the season, the pond-floating biofilters removed 66.7 ± 5.7% CH throughout the study period and removed up to 101.5 g CH m h. By contrast, the laboratory-based floating biofilters experienced more biological disturbances, with both low (∼34%) and high (∼99%) CH removal phases during the study period and an average of 58% of the CH oxidized. These disturbances could be attributed to the measured lower abundance of type II methanotroph population compared with the pond biofilters. Despite the acidity of the pond biofilters increasing significantly by the end of the study period, the biofilter encouraged the growth of both type I ( and ) and type II ( and ) methanotrophs. This study demonstrated the potential of the floating biofilters to mitigate dairy effluent ponds emissions efficiently and indicated methanotroph abundance as a key factor controlling CH oxidation in the biofilter.

Responses of methanotrophic activity, community and EPS production to CH4 and O2 concentrations in waste biocover soils

Biocover soils are known to be a good alternative material to mitigate CH4 emissions from landfills to the atmosphere. In this study, 16 treatments with four O2 concentrations (∼0%, 5%, 10% and 21%) and four CH4 concentrations (i.e. 1%, 10%, 20% and 50%) were conducted to estimate extracellular polymeric substances (EPS) production, methanotrophic activity and community in response to CH4 and O2 concentrations in waste biocover soil (WBS). When the CH4 concentration was saturated for CH4 oxidation in the WBS, the continuous exposure of CH4 above the saturated concentrations could not obviously enhance CH4 oxidation activity. In the WBS, extracellular protein (ECP) production was negatively related with the tested CH4 concentrations, while both ECP and extracellular polysaccharides (ECPS) productions were positively related with the tested O2 concentrations. Cloning and terminal restriction fragment length polymorphism analyses showed that type I methanotrophs (Methylocaldum, Methylococcaceae, Methylomicrobium and Methylobacter) and type II methanotrophs (Methylosinus) dominated in the WBS. Among them, Methylocaldum and/or Methylococcaceae were sensitive to low O2 concentrations of ∼0%. Methylobacter had propensity to grow at low O2 concentrations of ∼0% and 5%, while Methylosinus preferred environments with high concentrations of CH4 (⩾10%) and O2 (21%). In the tested five environmental variables of ECPS, O2, EPS, CH4 and ECP, only ECPS and O2 concentrations had significant effect on the methanotrophic communities. These results suggested that O2 concentration in landfill covers should be paid more attention to optimize and sustain CH4 oxidation for mitigating CH4 emission from landfills.

Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

The effect of environmental factors on bacterial and actinobacterial communities was assessed to predict microbial community structure in natural gradients. Bacterial and actinobacterial communities were studied at four sites differing in vegetation and water regime: creek sediment, wet meadow, dry meadow and deciduous forest located in a shallow valley. The vegetation structure was assessed by phytocoenological releves. T-RFLP and quantitative PCR were used to determine community composition and abundances. Significant relationships between bacterial community structure and selected soil traits at sites located relatively close to each other (within 200 m) were demonstrated. Both the quantity and structure of bacterial communities were significantly influenced by organic matter content, soil moisture and pH. Bacterial diversity was higher in summer, while that of actinobacteria increased in winter. The Simpson’s evenness E was significantly correlated with soil organic matter content. Soil pH had the greatest influence on bacterial community structure showing higher within-site variability in summer than in winter.

Assessing the influence of CH4 concentration during culture enrichment on the biodegradation kinetics and population structure

Methanotrophic communities were enriched in three stirred tank reactors continuously supplied with CH4-laden air at 20, 2 and 0.2 gCH4 m(-3) in order to evaluate the influence of CH4 concentration on the biodegradation kinetics, population structure and potential polyhydroxyalkanoate production under sequential nitrogen limitations. The population structure of the enriched cultures, dominated by type I methanotrophs, was influenced by CH4 concentration. No significant correlation between CH4 concentration and the maximum specific degradation rate (qmax) or the half-saturation constant (KS) was recorded, microorganisms enriched at 2 gCH4 m(-3) presenting the highest qmax and those enriched at 20 and 0.2 gCH4 m(-3) exhibiting the lowest KS. Maximum polyhydroxybutyrate (PHB) contents of 1.0% and 12.6% (w/w) were achieved at 20 and 2 g CH4 m(-3), respectively. Polyhydroxyvalerate (PHV) was also detected at PHV:PHB ratios of up to 12:1 and 4:1 in the communities enriched at 20 and 0.2 gCH4 m(-3), respectively.

Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability

Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body.

Microbial community and function of enrichment cultures with methane and toluene

The interaction effect of co-existence of toluene and CH4 on community and activity of methanotrophs and toluene-degrading bacteria was characterized in three consortia enriched with CH4 and toluene (MT), toluene (T), and CH4 (M), respectively, in this study. The CH4 oxidation activity in the enrichment culture of MT was significantly lower than that of M at the end of the experiment (P = 0.001). The toluene degradation rate could be enhanced by continuous addition of CH4 and toluene in the initial days, but it was inhibited in the later days. Phylogenetic analysis of 16S rRNA genes showed that Proteobacteria and Bacteroidetes were dominant in the three enriched consortia, but the community of methanotrophs and toluene-degrading bacteria was significantly affected by the co-existence of CH4 and toluene. Both Methylosinus (91.8 %) and Methylocystis (8.2 %) were detected in the enrichment culture of MT, while only Methylocystis species were detected in M. The toluene-degrading bacteria including Burkholderia, Flavobacteria, Microbacterium, and Azoarcus were all detected in the enrichment culture of T. However, only Azoarcus was found in the enrichment culture of MT. Significantly higher contents of extracellular polymeric substances polysaccharose and protein in the enrichment culture of MT than that of T and M suggested that a higher environmental stress occurred in the enrichment culture of MT.

Characterization of a methane-oxidizing biofilm using microarray, and confocal microscopy with image and geostatic analyses

A mixed methane-oxidizing biofilm was characterized, concurrently using a number of advanced techniques. Community analysis results by microarray exhibited that type II members dominated the methanotrophic community, in which Methylocystis was most abundant, followed by Methylosinus. Observation results by fluorescent in situ hybridization and confocal microscopy showed multiple biofilm colonies that were irregular, bell-shaped, with mean thickness of approximately 20 μm. Image analysis results indicated that the relative abundance of methanotrophs peaked at a depth of about 5 μm. Although the biofilm colonies differed in size, methanotrophs accounted for 4-9%. Gaussian and linear regression results between the biofilm volumes and types I (r (2) = 0.86) and II volumes (r (2) = 0.92), respectively, revealed that type I members played a role in the growth of the biofilm but only below a threshold volume, whereas type II members supported the overall growth. Geostatistical analyses results revealed concentration of types I and II methanotrophic individuals with decreasing depth, and randomness between the spatial locations and population levels. Collectively, the methane-oxidizing biofilm was a highly organized system with methanotrophs and their cohabitants.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation.

Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray

Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe the protocol used to develop and validate an MDM method for the semiquantification of a range of functional genes--in this case, particulate methane monooxygenase (pmoA)--and we give an example of its application to the study of the community structure of methanotrophs and functionally related bacteria in the environment. The development and validation of an MDM, following this protocol, takes ∼6 months. The pmoA MDM described in detail comprises 199 probes and addresses ∼50 different species-level clades. An experiment comprising 24 samples can be completed, from DNA extraction to data acquisition, within 3 d (12-13 h bench work).

Methanotrophs and copper

Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.

Spatial and temporal diversity of methanotrophs in a landfill cover soil are differentially related to soil abiotic factors

Methanotrophs present in landfill cover soil can limit methane emissions from landfill sites by oxidizing methane produced in landfill. Understanding the spatial and temporal distribution of populations of methanotrophs and the factors influencing their activity and diversity in landfill cover soil is critical to devise better landfill cover soil management strategies. pmoA-based microarray analyses of methanotroph community structure revealed a temporal shift in methanotroph populations across different seasons. Type II methanotrophs (particularly Methylocystis sp.) were found to be present across all seasons. Minor shifts in type I methanotroph populations were observed. In the case of spatial distribution, only minor differences in methanotroph community structure were observed with no recognizable patterns (both vertical and horizontal) at a 5 m scale. Correlation analysis between soil abiotic parameters (total C, N, NH4 (+) , NO3 (-) and water content) and distribution of methanotrophs revealed a lack of conclusive evidence for any distinct correlation pattern between measured abiotic parameters and methanotroph community structure, suggesting that complex interactions of several physico-chemical parameters shape methanotroph diversity and activity in landfill cover soils.

Activity and structure of methanotrophic communities in landfill cover soils

The composition of the methanotrophic community in soil covers on five landfills in Northern and Eastern Germany was investigated by means of diagnostic microarray and terminal restriction fragment length polymorphism (T-RFLP), both targeting the pmoA gene of methanotrophs. Physical and chemical properties of the 15 sampled soil profiles varied greatly, thus providing for very different environmental conditions. The potential methane oxidation activity, assessed using undisturbed soil cores, varied between 0.2 and 28 µg CH4 gdw (-1)  h(-1) , the latter amounting to 426 g CH4 m(-2)  h(-1) . Total nitrogen was found to be the soil variable correlating most strongly with methanotrophic activity. Explaining close to 50% of the observed variability, this indicates that on the investigated sites activity and thus abundance of methanotrophs may have been nitrogen-limited. Variables that enhance organic matter and thus nitrogen accumulation, such as field capacity, also positively impacted methanotrophic activity. In spite of the great variability of soil properties and different geographic landfill location, both microarray and T-RFLP analysis suggested that the composition of the methanotrophic community on all five sites, in all profiles and across all depths was similar. Methylocystis, Methylobacter and Methylococcus species, including Methylococcus-related uncultivated methanotrophs, were predominantly detected among type II, Ia and Ib methanotrophs, respectively. This indicates that the high methane fluxes typical for landfill environments may be the most influential driver governing the community composition, or other variables not analysed in this study. Principal component analysis suggested that community diversity is most influenced by the site from which the samples were taken and second, from the location on the individual sites, i.e. the soil profile. Landfill and individual profiles reflect the combined impact of all effective variables, including those that were not measured in this study.

Universal ligation-detection-reaction microarray applied for compost microbes

BACKGROUND

Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR) based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones.

RESULTS

Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS) area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array.

CONCLUSION

This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.