Draft genome sequence of Enterobacter sp. strain EA-1, an electrochemically active microorganism isolated from tropical sediment

© 2018 Doyle et al. Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that Enterobacter sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia, forms a distinct clade within the Enterobacter genus

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems

The Complex Genetic Architecture of the Metabolome

Discovering links between the genotype of an organism and its metabolite levels can increase our understanding of metabolism, its controls, and the indirect effects of metabolism on other quantitative traits. Recent technological advances in both DNA sequencing and metabolite profiling allow the use of broad-spectrum, untargeted metabolite profiling to generate phenotypic data for genome-wide association studies that investigate quantitative genetic control of metabolism within species. We conducted a genome-wide association study of natural variation in plant metabolism using the results of untargeted metabolite analyses performed on a collection of wild Arabidopsis thaliana accessions. Testing 327 metabolites against >200,000 single nucleotide polymorphisms identified numerous genotype–metabolite associations distributed non-randomly within the genome. These clusters of genotype–metabolite associations (hotspots) included regions of the A. thaliana genome previously identified as subject to recent strong positive selection (selective sweeps) and regions showing trans-linkage to these putative sweeps, suggesting that these selective forces have impacted genome-wide control of A. thaliana metabolism. Comparing the metabolic variation detected within this collection of wild accessions to a laboratory-derived population of recombinant inbred lines (derived from two of the accessions used in this study) showed that the higher level of genetic variation present within the wild accessions did not correspond to higher variance in metabolic phenotypes, suggesting that evolutionary constraints limit metabolic variation. While a major goal of genome-wide association studies is to develop catalogues of intraspecific variation, the results of multiple independent experiments performed for this study showed that the genotype–metabolite associations identified are sensitive to environmental fluctuations. Thus, studies of intraspecific variation conducted via genome-wide association will require analyses of genotype by environment interaction. Interestingly, the network structure of metabolite linkages was also sensitive to environmental differences, suggesting that key aspects of network architecture are malleable

Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics

10.1142/S0219720021020030Journal of Bioinformatics and Computational Biology1962102003

High dissolved oxygen selection against nitrospira sublineage i in full-scale activated sludge

© 2019 American Chemical Society. A single Nitrospira sublineage I OTU was found to perform nitrite oxidation in full-scale domestic wastewater treatment plants (WWTPs) in the tropics. This taxon had an apparent oxygen affinity constant lower than that of the full-scale domestic activated sludge cohabitating ammonium oxidizing bacteria (AOB) (0.09 ± 0.02 g O2 m-3 versus 0.3 ± 0.03 g O2 m-3). Thus, nitrite oxidizing bacteria (NOB) may in fact thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions selected for and high aeration inhibited the NOB in a long-term lab-scale reactor. The relative abundance of Nitrospira sublineage I gradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. The morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their oxygen affinities. NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to the Nitrosomonas-like AOB clusters, which maintained a porous and nonspherical morphology. In conclusion, the effect of oxygen on AOB/NOB population dynamics depends on which OTU predominates given that oxygen affinities are species-specific, and this should be elucidated when devising operating strategies to achieve mainstream partial nitritation

Using meta-omics of contaminated sediments to monitor changes in pathways relevant to climate regulation

Microbially mediated biogeochemical processes are crucial for climate regulation and may be disrupted by anthropogenic contaminants. To better manage contaminants, we need tools that make real-time causal links between stressors and altered microbial functions, and the potential consequences for ecosystem services such as climate regulation. In a manipulative field experiment, we used metatranscriptomics to investigate the impact of excess organic enrichment and metal contamination on the gene expression of nitrogen and sulfur metabolisms in coastal sediments. Our gene expression data suggest that excess organic enrichment results in (i) higher transcript levels of genes involved in the production of toxic ammonia and hydrogen sulfide and (ii) lower transcript levels associated with the degradation of a greenhouse gas (nitrous oxide). However, metal contamination did not have any significant impact on gene expression. We reveal the genetic mechanisms that may lead to altered productivity and greenhouse gas production in coastal sediments due to anthropogenic contaminants. Our data highlight the applicability of metatranscriptomics as a management tool that provides an immense breadth of information and can identify potentially impacted process measurements that need further investigation