Wastewater reveals clues about microorganisms, holds promise for future microbiome engineering

 

Studying the dynamics of microbial communities over several microbial generations, a team of Luxembourg researchers have gained insight into the microorganisms that live in biological wastewater treatment plants. This knowledge can ultimately help predict and control microbial communities – including the human microbiome.

Stock image of intestinal bacteria

The roles of viruses, plasmids and CRISPR-immunity: The dynamics of microbiomes – such as those found in a biological wastewater treatment plants – are driven by both environmental and biological factors. Among the biological factors are bacteriophages and plasmids: invasive mobile genetic elements (iMGEs) which move between organisms and can transfer detrimental or beneficial genetic material to their hosts.

Researchers from the University of Luxembourg’s LCSB, led by Prof Dr Paul Wilmes, studied the impact of viruses (bacteriophages) and plasmids on a model microbial community in a wastewater treatment plant by collecting samples over the span of 18 months.

One bacterial immune system received particular attention: a defence mechanism used by microorganisms against invasion by iMGEs. Through this so-called CRISPR-Cas system – nowadays widely used as a genetic engineering tool – bacteria can recognise foreign elements and integrate parts of the mobile genetic material into their own genomes.

The integrated sequences serve as a genetic memory bank and can be used to interfere with future invasions. By elucidating the CRISPR-mediated interactions between the microorganisms and both bacteriophages and plasmids, the scientists were able to understand better how the structure of the microbial community is shaped by these iMGEs.

Interactions play key role in promoting adaptation

The scientists found that plasmids are highly abundant within the community and have a strong impact on its dynamics. These results suggest that plasmids are the main target of the CRISPR systems, allowing bacteria to selectively retain potentially beneficial genetic material, for example antimicrobial resistance genes.

“This is entirely new as it was previously thought that the viruses were targeted predominantly. It is an important finding as these interactions play a key role in promoting adaptation and diversity within microbiomes. The dynamics are also essential to understand the spread of antimicrobial resistance genes which are typically encoded by plasmids.”- Susana Martínez Arbas, PhD student at the LCSB and first author of the corresponding paper published in Nature Microbiology.

Understanding the factors impacting microbial populations is crucial as it can help to both devise measures against detrimental species and predict how the community will evolve over time. Based on the researcher’s observations, iMGEs and CRISPR-based interactions should now be taken into account as their incorporation can provide more comprehensive models of community dynamics.

“This can of course be used to improve the performance of wastewater treatment plants, but it could also be key in maintaining a healthy gut microbiome for example,” concludes Susana Martínez Arbas.

Part 2: Microbiomes’ responses to disturbances

To allow long-term stable operation of biotechnological processes such as wastewater treatment plants or to maintain the balance of the human microbiome, it is also important to understand how microbial ecosystems respond to disturbances. To this end, the researchers specifically studied resistance and resilience within the microbial community, with a particular focus on lipid-accumulating populations as these bacteria have a competitive advantage in fluctuating environments and have compelling potential to be used in circular economic models.

First, the team identified all the ecological niches present in the wastewater treatment plant ecosystem. A niche is the match of a species to a specific environmental condition. Then they showed how, under constant conditions, the complementarity of the microorganisms occupying these different niches, as well as the interspecific competition for certain resources, guarantees the stability of the ecosystem and thus of the biotechnological process.

Some microorganisms quickly adapt to changes in environment

The researchers results show that in case of perturbation, such as a change in the availability of nutrients, the composition of the community shifts temporarily: some microorganisms are able to quickly adapt to variations in the environment by adopting specific strategies.

For example, one microbial species exhibits extensive plasticity in gene expression, meaning that a set of genes within a species can produce more than one phenotype when exposed to different conditions. The ability to adjust their phenotype – the sum of the organism traits – allows the population to be resistant to fluctuations.

“Globally, the study shows that this microbiome’s resistance and resilience – its capacity to recover after a disturbance – are a function of phenotypic plasticity and niche complementarity,” describes Dr Malte Herold, first author of a corresponding article in Nature Communications and former PhD student within the Systems Ecology group.

“Even though a biological wastewater treatment plant is a controlled process, some factors fluctuate. It has an impact on microbial dynamics and then on the process’ efficiency. So, our results are particularly relevant for the development of future ecological engineering efforts and to achieve our linked sustainability goals,” Dr Herold points out.

Setting the scene for engineering of the human microbiome

In addition to providing new insights into the works of microbial ecosystems, the research highlights the potential of integrated meta-omics approaches to study microbiomes. In both studies, they allowed the researchers to identify ecological niches, characterise microbial activity, track gene expression and get an in-depth understanding of the interactions that shape the community’s structure.

“These articles showcase the expertise acquired by the Systems Ecology group over the years. Our team is now developing new methods in this emerging field, with applications far beyond wastewater treatment. These two studies set the scene for many new exciting applications, including in the context of engineering the human microbiome.” – Prof Paul Wilmes

The research was supported by grants from several of the FNR’s funding instruments (AFR; ATTRACT; CORE; INTER; PRIDE)

Publications

Martínez Arbas, S., Narayanasamy, S., Herold, M. et al. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbio (2020).

Herold, M., Martínez Arbas, S., Narayanasamy, S. et al. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nat Commun 11, 5281 (2020).


This feature was adapted from the original text on the website of the University of Luxembourg

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