Understanding ecological functioning of urban freshwater ecosystems, with an emphasis on complex microbial communities
Background
The pressures on urban water resources in megacities have led to a growing interest in engineering ecologically friendly urban waterways that allow and enhance microbial community-derived services. These ecological services are critical to self-cleaning capacities of waterways. In megacities, ecological approaches for such purposes face challenges arising from complex interactions within microbial communities, densely interspersed land-use patterns and anthropogenic influences, despite having best practices to manage levels of physicochemical parameters and flooding risks. Therefore, in order to inform and develop such ecological approaches, it is necessary to gain an understanding of the interactions between microbial communities and urbanised environments at various scales, ranging from sediments to large catchments and regions. These are being investigated using a combination of multiple culture-independent, meta-omics, and data-intensive computational approaches.
In the tropics, rain-events are a major source of disturbance, that introduces sediments of different types, complex mixtures of inorganic and organic molecules/nutrients and microbial communities associated with sediment and water phases. The characteristics of rain events and hydrodynamics in the stormwater canals which in turn, is based on the canal design influence the extent of disturbance and the ensuing changes or succession in the canal system. Microbial communities develop biofilms both on biotic (plant roots) and abiotic surfaces (sediments and other engineering structures). We have identified sedimentary biofilms to be the major sources of microbial load, as well as biodiversity, that provide multiple ecosystem services in the waterway system. In order to combine observational and hypothesis-driven studies, we have been conducting field based investigations, combined with development and use of novel experimental tools. These approaches have allowed us to investigate sediment microbial communities, their functions and their environmental drivers across different spatial and temporal scales.
![Picture 1 Figure 1. Research framework to understand the ecological functioning of microbial communities in urban waterways](https://nus.edu.sg/neri/wp-content/uploads/2024/08/Picture-1.jpg)
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.
Our results show three major phases in biogeochemical successions after rain event, which are acclimatization, reductive and oxidative phase. Most number of parameters changed during the acclimatization phase, including metals groups. Second phase, reductive, appeared with high levels of nutrients (nitrogen and/or sulfur species) and metals combinations. Finally, the oxidative phase showed emergence of some metals, oxidised nutrients, such as, sulfates, ORP and cell counts.
Future Directions
We identified the taxa groups and selected functions leading these coupled nitrogen-sulfur-metals transformations. We now plan to understand the underlying mechanism leading to the coupling of metals with these transformations through controlled manipulative experiments. We will test the hypothesis that metals mediate the nitrogen and sulfur transformations by enriching the taxa-groups involved in these transformations and thus are responsible for community successions. We will use manipulative experiments to enrich the nitrogen and sulfur transforming taxa groups using step increase in metals concentrations. An enrichment of the taxa-groups involved in actively assimilating the nutrients will likely prove our hypothesis. We will then identify the underlying mechanism of metals-nutrients coupling in the enriched taxa-groups using SIP-RNA-Seq.
Our previous studies have revealed a deeper understanding of change in microbial community composition succession over rain events in sediments. We are interested in investigating the spatial contribution of land cover types (geochemical and microbial load contribution) to waterways in Singapore using a model naturalised park i.e. Bishan Ang-Mo Kio Park. This work has been recently published in Science of the Total Environment.
The Government of Singapore has embarked on an ambitious “Singapore Green Plan 2030” to target achieving long-term sustainability goals such as net zero emission by 2030. One of the key pillars of the plan is the greening of Singapore aptly called “City in Nature”. By 2030, the government targets to increase nature parks’ land area by over 50% from 2020 baseline as well as planting over 1 million trees in Singapore. At an island scale this will lead to an increased contribution of organics through run off on to the waterways. As such studying the effects of different functional groups of organics on microbial community structure and function will be investigated using coupled spectroscopy techniques such as mIRage-FTIR (Fourier transform infrared). We also want to look at changes in the bioavailability of metal ions to microbes as these processes determine key biogeochemical pathways e.g. those linked to greenhouse gas emissions.
Researchers involved:
Lead Principal Investigator: A/P Sanjay Swarup
Research Team:
Prof. Stefan Wuertz
Prof. Staffan Kjelleberg
Dr. Gourvendu Saxena
Dr. Aditya Bandla
Dr. Rajat Mishra
Dr. Ezequiel Marzenelli
Dr. Canh Tien Trinh Nguyen
Dr. Ooi Qi En
Dr. Andrew Elohim Laloo
Dr. Abhishek Gupta.
Publications
- Saxena, G., Marzinelli, E. M., Naing, N. N., He, Z., Liang, Y., Tom, L., Ping, H., Josh, U.M., Reuben, S., Mynampati, K.C., Mishra, S., Umashankar, S., Mitra, S., Andersen, G., Kjelleberg, S., & Swarup, S. (2015). Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environmental Science and Technology, 49(3), 1462–1471 [Abstract]
- Saxena, G., Mitra, S., Marzinelli, E. M., Xie, C., Wei, T.J., Steinberg, P.D., Williams, R.B.H., Kjelleberg, S., Lauro, F. M., & Swarup, S. (2018). Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway. MSystems, 3(3) [Abstract].
- Fazi, S., Bandla, A., Pizzetti, I., & Swarup, S. (2016). Microbial biofilms as one of the key elements in modulating ecohydrological processes in both natural and urban water corridors. Ecohydrology and Hydrobiology, 16(1), 33–38. 2015[Abstract].
- Bandla, A., Saxena, G., Mishra, R., & Swarup, S. (2019). A Framework to Address the Food, Energy and Water Nexus among Indian Megacities and Their Rapidly Expanding Peripheries. Dialogue – Science. Scientists. Society, Indian Academy of Sciences.10.29195/DSSS.02.01.0019 [Abstract].
- Rachelle, E.B., Bandla, A., Swarup, S., & Krassimira, H. (2020). Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance from Agricultural Land Runoff. Frontiers in Microbiology. 11, 2552 [Abstract].
- Mishra, R., Koay, T.B., Chitre, M., Swarup, S. (2021) Multi-USV Adaptive Exploration Using Kernel Information and Residual Variance. Front Robot AI. 28 (8), 572243 . [Abstract]
- Ooi, Q.E., Nguyen, C.T.T., Laloo, A.E., Koh,Y.Y., Swarup, S. (2024) Soil-sediment connectivity through Bayesian source tracking in an urban naturalised waterway via microbial and isotopic markers, Science of The Total Environment, Volume 949, 175152. [Abstract]