TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment

Lake mixing disrupts chemical and physical gradients that structure bacterial communities. A transplant experiment was designed to investigate the influence of post-mixing environmental conditions and biotic interactions on bacterial community composition. The experimental design was 3x2 factorial, where water was incubated from three different sources (epilimnion, hypolimnion, and mixed epilimnion and hypolimnion) at two different locations in the water column (epilimnion or hypolimnion). Three replicate mesocosms of each treatment were removed every day for 5 days for bacterial community profiling, assessed by automated ribosomal intergenic spacer analysis. There were significant treatment effects observed, and temperature was the strongest measured driver of community change (r=-0.66). Epilimnion-incubated communities changed more than hypolimnion-incubated. Across all treatments, we classified generalist, layer-preferential and layer-specialist populations based on occurrence patterns. Most classified populations were generalists that occurred in both strata, suggesting that communities were robust to mixing. In a network analysis of the mixed-inocula treatments, there was correlative evidence of inter-population biotic interactions, where many of these interactions involved generalists. These results reveal differential responses of bacterial populations to lake mixing and highlight the role of generalist taxa in structuring an emergent community-level response.

Development of a solar-powered microbial fuel cell

AIMS

To understand factors that impact solar-powered electricity generation by Rhodobacter sphaeroides in a single-chamber microbial fuel cell (MFC).

METHODS AND RESULTS

The MFC used submerged platinum-coated carbon paper anodes and cathodes of the same material, in contact with atmospheric oxygen. Power was measured by monitoring voltage drop across an external resistance. Biohydrogen production and in situ hydrogen oxidation were identified as the main mechanisms for electron transfer to the MFC circuit. The nitrogen source affected MFC performance, with glutamate and nitrate-enhancing power production over ammonium.

CONCLUSIONS

Power generation depended on the nature of the nitrogen source and on the availability of light. With light, the maximum point power density was 790 mW m(-2) (2.9 W m(-3)). In the dark, power output was less than 0.5 mW m(-2) (0.008 W m(-3)). Also, sustainable electrochemical activity was possible in cultures that did not receive a nitrogen source.

SIGNIFICANCE AND IMPACT OF THE STUDY

We show conditions at which solar energy can serve as an alternative energy source for MFC operation. Power densities obtained with these one-chamber solar-driven MFC were comparable with densities reported in nonphotosynthetic MFC and sustainable for longer times than with previous work on two-chamber systems using photosynthetic bacteria.

Fine-scale differences between Accumulibacter-like bacteria in enhanced biological phosphorus removal activated sludge

A lab-scale sequencing batch reactor (SBR) and six full-scale wastewater treatment plants (WWTPs) performing enhanced biological phosphorus removal (EBPR) were surveyed. The abundance of Accumulibacter-related organisms in the full-scale plants was investigated using fluorescent in situ hybridization. Accumulibacter-related organisms were present in all of the full-scale EBPR plants, at levels ranging from 9% to 24% of total cells. The high percentage of Accumulibacter-related organisms seemed to be associated with configurations which minimize the nitrate recycling to the anaerobic zone and low influent BOD:TP ratios. PCR-based clone libraries were constructed from the community 16S rRNA gene plus the internally transcribed spacer region amplified from the SBR and five of the full-scale WWTPs. Comparative sequence analysis was carried out using Accumulibacter-related clones, providing higher phylogenetic resolution and revealing finer-scale clustering of the sequences retrieved from the SBR and full-scale EBPR

Uranyl precipitation by biomass from an enhanced biological phosphorus removal reactor

Heavy metal and radionuclide contamination presents a significant environmental problem worldwide. Precipitation of heavy metals on membranes of cells that secrete phosphate has been shown to be an effective method of reducing the volume of these wastes, thus reducing the cost of disposal. A consortium of organisms, some of which secrete large quantities of phosphate, was enriched in a laboratory-scale sequencing batch reactor performing Enhanced Biological Phosphorus Removal, a treatment process widely used for removing phosphorus. Organisms collected after the aerobic phase of this process secreted phosphate and precipitated greater than 98% of the uranyl from a 1.5 mM uranyl nitrate solution when supplemented with an organic acid as a carbon source under anaerobic conditions. Transmission electron microscopy, energy dispersive x-ray spectroscopy, and fluorescence spectroscopy were used to identify the precipitate as membrane-associated uranyl phosphate, UO2HPO4.

Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal

The community structure and metabolic function of activated sludge carrying out enhanced biological phosphorus removal have been investigated. Laboratory-scale sequencing batch reactors were operated at several influent COD/P ratios to obtain sludges with a range of phosphorus contents. Molecular microbiological techniques based on small subunit ribosomal RNA were used to characterize the structure of these sludges. The dominant polyphosphate accumulating organism was a close relative of Rhodocyclus tenuis, a member of the beta subclass of the Proteobacteria. Fragments of genes coding for polyphosphate kinase (PPK), thought to be responsible for polyphosphate accumulation, were retrieved from one of the sludges. The relative abundance of PPK gene copies in genomic DNA extracted from sludges was determined to confirm that at least one of the PPK gene sequences was derived from the dominant polyphosphate accumulating organism.

Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--II: Microbial population dynamics

Microbial population dynamics were evaluated in anaerobic codigesters treating municipal solid waste and sewage sludge. Ribosomal RNA based oligonucleotide probes were used to characterize changes in population abundance of syntrophic volatile fatty acid degrading bacteria and methanogens. Changes in community structure were linked to traditional performance parameters during the recovery of previously unstable codigesters induced by a reduction in mixing levels. Methanosarcina spp. were the most abundant aceticlastic methanogens in unstable codigesters with high acetate concentrations, while Methanosaeta concilii was dominant in stable systems with low levels of acetate. Growth of Syntrophobacter wolinii was enhanced during stabilization of a codigester with a well-developed population of Methanobacteriaceae, possibly because the presence of adequate numbers of these hydrogenotrophic methanogens encouraged the syntrophic oxidation of propionate. Mesophilic saturated fatty acid beta-oxidizing syntrophs were most abundant in previously unstable codigesters. One minimally mixed reactor became unstable after switching to continuously mixed conditions. After the switch, total archaeal abundance decreased sharply, though Methanobacteriaceae and Methanosarcina spp. levels increased as the fermentation became unbalanced. Based on the results presented here, mixing appears to inhibit the syntrophic oxidation of volatile fatty acids, possibly by disrupting the spatial juxtaposition of syntrophic bacteria and their methanogenic partners.

Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--I. Digester performance

The feasibility of codigestion of the organic fraction of municipal solid waste, primary sludge, and waste activated sludge was evaluated in mesophilic (37 degrees C), laboratory-scale digesters. In a first experiment, different startup strategies were compared using four digesters, operated under continuously mixed conditions. After two weeks, the experiment was continued under minimally mixed conditions. Results demonstrated that reducing the level of mixing improved digester performance. Therefore, in a second experiment, six digesters were operated to compare performance under continuous mixing and reduced mixing levels at various loading rates and solids levels. The continuously mixed digesters exhibited unstable performance at the higher loading rates, while the minimally mixed digesters performed well for all loading rates evaluated. In a third experiment, it was demonstrated that an unstable, continuously mixed digester was quickly stabilized by reducing the mixing level. These experiments confirmed that continuous mixing was not necessary for good performance and was inhibitory at higher loading rates. In addition, reduction of mixing levels may be used as an operational tool to stabilize unstable digesters.

A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment

Abstract Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro-transcribed and native rRNA indicated that, when in vitro-transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro-transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.

Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids

An aggressive start-up strategy was used to initiate codigestion in two anaerobic, continuously mixed bench-top reactors at mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions. The digesters were inoculated with mesophilic anaerobic sewage sludge and cattle manure and were fed a mixture of simulated municipal solid waste and biosolids in proportions that reflect U.S. production rates. The design organic loading rate was 3.1 kg volatile solids/m3/day and the retention time was 20 days. Ribosomal RNA-targeted oligonucleotide probes were used to determine the methanogenic community structure in the inocula and the digesters. Chemical analyses were performed to evaluate digester performance. The aggressive start-up strategy was successful for the thermophilic reactor, despite the use of a mesophilic inoculum. After a short start-up period (20 days), stable performance was observed with high gas production rates (1.52 m3/m3/day), high levels of methane in the biogas (59%), and substantial volatile solids (54%) and cellulose (58%) removals. In contrast, the mesophilic digester did not respond favorably to the start-up method. The concentrations of volatile fatty acids increased dramatically and pH control was difficult. After several weeks of operation, the mesophilic digester became more stable, but propionate levels remained very high. Methanogenic population dynamics correlated well with performance measures. Large fluctuations were observed in methanogenic population levels during the start-up period as volatile fatty acids accumulated and were subsequently consumed. Methanosaeta species were the most abundant methanogens in the inoculum, but their levels decreased rapidly as acetate built up. The increase in acetate levels was paralleled by an increase in Methanosarcina species abundance (up to 11.6 and 4.8% of total ribosomal RNA consisted of Methanosarcina species ribosomal RNA in mesophilic and thermophilic digesters, respectively). Methanobacteriaceae were the most abundant hydrogenotrophic methanogens in both digesters, but their levels were higher in the thermophilic digester.