To understand the interactions between microbiome and the environmental parameters under different landuse pressures, we first conducted a field study to address the influence of pressures from urbanised catchments with mixed and interspersed land-use patterns on composition and functions of sedimentary and suspended microbial communities of these waterways. It was seen that physical separation of same land-use types does not influence the assembly of microbial communities. Differences were apparent between land-use types, both at the level of functional potential and phylogenetic taxa but not at the level of chemical markers. Sediments harbour more diverse and complex communities than do particles suspended in the water. In well-managed urban waterways of Singapore, we found for the first time that where, levels of physicochemical parameters are low, metals such as aluminium, copper and potassium, rather than organics, are the major driver of microbial community composition and potential function.

Having established that sedimentary microbial communities are the dominant form of microbial life within urban waterways and possess the capacity to drive multiple ecosystem services, we next investigated the influence of sediment habitat composition, in terms of particle size, on the structure and function of such communities. Size separation revealed that the sand fraction dominated sediment size composition. Microbial communities on the dominant size fractions (coarse sand fraction: 2000 μm – 500 μm and fine sand fraction: 250 μm – 63 μm) were substantially different. Preferential enrichment of bacterial lineages on either of the two size fractions was apparent, even at broad phylogenetic levels (e.g. class level). High-resolution amplicon denoising analysis showed that fine scale variation in sediment size, likely supports the co-existence of a number of closely related taxa (i.e. <97% sequence identity of the 16S rRNA gene amplicon) through niche partitioning and specialisation.

Gene-centric analysis showed that communities attached to the two size fractions also differed in their capacity to carry out important nutrient transformations. Key marker genes involved in the transformation of inorganic nitrogen and sulfur compounds were partitioned across the size fractions. Key genes involved in the metabolism of aromatic compounds and response to stressors also showed a significant association with particle size fractions establishing association with niche functioning.

To link phylogeny to function, we reconstructed 202 strain-resolved draft genomes from the different size-specific niches. These genomes span both abundant and rare bacterial lineages in the sediment microbiomes. Functional analysis showed that a majority of taxa only possess the ability to carry out singular redox transformations of inorganic nitrogen and sulfur compounds, for energy metabolism.

To determine the effects of land-use (residential versus industrial) and rain perturbations (pre- versus. post-rain) on the microbial communities of the sediments of Singapore’s urban waterways, two representative industrial and residential locations were selected. We tested the hypothesis that changes in microbial community structure and function are triggered by perturbations due to rain and/or differences in land-use types. This represents the first reference metagenome from tropical urban waterways. The analysis of this large dataset using a combination of network and multivariate analyses yielded important insights into the role of land-use and, to a lesser extent, rain perturbations in causing shifts in the abundance of specific microbial populations.

The combined metagenome of benthic microbial communities in urban waterways was composed of 75 phyla and 4,163 species (OTUs). At genus level, the most reads were from Nitrospirae (Nitrospira) and Cyanobacteria (Coleofasciculus). More than to 99% of the mapped reads in the sediments of urban waterways were represented by 23 phyla (~30%). The microbial communities and their functions from the two land-use types separated into two different clusters in neighbor-net networks. The differences in the pre- and post-rain microbial communities were rain-event specific. The distribution of taxa groups (genera) in different samples suggested that the benthic microbial communities in residential land-use were more diverse and dispersed than in industrial sediments. Overall, our study found that the functions of microbial communities were less affected by environmental factors, compared to the structure of microbial communities. This indicates that core microbial functions do not change with changes in taxa composition to survive in challenging environments. With a comparable diversity index to undisturbed natural freshwater, we showed for the first time that urban waterways with low contaminant levels can maintain the microbial diversity closer to the undisturbed freshwater systems

We studied four aspects of post-rain successions of the microbial communities, their functions and its impact in relationship with the water and sediment environment. Using a novel reactor system, which mimics a linear channel flow first, we explained successions in terms of shifts in the metabolically active member of the microbial community compared with the full community. Second, we identified the metals and ions interactions during biogeochemical successions and their associations with microbial communities. Third, we explained the biogeochemical successions through functional successions. And lastly, we identified the members of microbial communities involved in these transformations.