Networks of engineered waterways are critical in meeting the growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. On the basis of PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, this difference was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters from spatial analysis, only three metals, namely potassium, copper and aluminum significantly explained between 7% and 11% of the variation in taxa and functions, based on distance-based linear models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.

Abstract. Tropical peatlands from southeast Asia are undergoing extensive drainage, deforestation and degradation for agriculture and human settlement purposes. This is resulting in biomass loss and subsidence of peat from its oxidation. Molecular profiling approaches were used to understand the relative influences of different land-use patterns, hydrological and physicochemical parameters on the state of degraded tropical peatlands. As microbial communities play a critical role in biogeochemical cascades in the functioning of peatlands, we used microbial and metabolic profiles as surrogates of community structure and functions, respectively. Profiles were generated from 230 bacterial 16 S rDNA fragments and 145 metabolic markers of 46 samples from 10 sites, including those from above and below water table in a contiguous area of 48 km2 covering five land-use types. These were degraded forest, degraded land, oil palm plantation, mixed crop plantation and settlements. Bacterial profiles were most influenced by variations in water table and land-use patterns, followed by age of drainage and peat thickness in that order. Bacterial profiling revealed differences in sites, based on the duration and frequency of water table fluctuations and on oxygen availability. Mixed crop plantations had the most diverse bacterial and metabolic profiles. Metabolic profiling, being closely associated with biogeochemical functions, could distinguish communities not only based on land-use types but also their geographic locations, thus providing a finer resolution than bacterial profiles. Agricultural inputs, such as nitrates, were highly associated with bacterial community structure of oil palm plantations, whereas phosphates and dissolved organic carbon influenced those from mixed crop plantations and settlements. Our results provide a basis for adopting molecular marker-based approaches to classify peatlands and determine relative importance of factors that influence peat functioning. Our findings will be useful in peatland management by providing a basis to focus early efforts on hydrological interventions and improving sustainability of oil palm plantations by adopting mixed cropping practices to increase microbial diversity in the long term.

Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the coexpressing genes we propose an ab initio method that identifies motif families in promoters of target gene groups, map these families to the promoters of all genes in the genome, and determine the best matches of each of the target group gene promoters with all other promoters. When the method was tested in rice starting from a group of co-expressing Late Embryogenesis Abundant (LEA) genes, we obtained a promoter similarity-based network that contained candidate genes that could plausibly complement the function of LEA genes. Importantly, 73.36% of 244 genes predicted by our method were experimentally confirmed to co-express with the LEA genes in maturing rice embryos, making this methodology a promising tool for biological systems analyses. Rice (2008) 1:177-187 DOI 10.1007 Stuart Meier, Chris Gehring, Yue-ie Hsing, and Vladimir Bajic are the first authors.Electronic supplementary material The online version of this article

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Metabolic perturbations by a gain-of-function approach provide a means to alter steady states of metabolites and query network properties, while keeping enzyme complexes intact. A combination of genetic and targeted metabolomics approach was used to understand the network properties of phenylpropanoid secondary metabolism pathways. A novel quercetin oxidoreductase, QuoA, from Pseudomonas putida, which converts quercetin to naringenin, thus effectively reversing the biosynthesis of quercetin through a de novo pathway, was expressed in Arabidopsis thaliana. QuoA transgenic lines selected for low, medium, and high expression levels of QuoA RNA had corresponding levels of QuoA activity and hypocotyl coloration resulting from increased anthocyanin accumulation. Stems of all three QuoA lines had increased tensile strength resulting from increased lignification. Sixteen metabolic intermediates from anthocyanin, lignin, and shikimate pathways had increased accumulation, of which 11 paralleled QuoA expression levels in the transgenic lines. The concomitant upregulation of the above pathways was explained by a significant downregulation of the phenolamide pathway and its precursor, spermidine. In a tt6 mutant line, lignifications as well as levels of the lignin pathway metabolites were much lower than those of QuoA transgenic lines. Unlike QuoA lines, phenolamides and spermidine were not affected in the tt6 line. Taken together, these results suggest that phenolamide pathway plays a major role in directing metabolic intermediates into the lignin pathway. Metabolic perturbations were accompanied by downregulation of five genes associated with branch-point enzymes and upregulation of their corresponding products. These results suggest that gene–metabolite pairs are likely to be co-ordinately regulated at critical branch points. Thus, these perturbations by a gain-of-function approach have uncovered novel properties of the phenylpropanoid metabolic network.