‘Space profoundly alters microbes’

During microbial tracking missions on the International Space Station in 2015-16, US space agency NASA found that the spacecraft’s microbial population included 13 strains of Enterobacter bugandensis—a pathogenic bacterium that had been first detected on Earth only in 2009 and designated a separate species in February 2016. A study on the 13 strains, published in Microbiome in March 2024, found them to be distinct from their terrestrial counterparts. Karthik Raman, professor; Pratyay Sengupta, scholar under Prime Minister’s Research Fellows scheme; and Shobhan Karthick, undergraduate student, Department of Biotechnology, Indian Institute of Technology, Madras, authored the study in collaboration with Jet Propulsion Laboratory, NASA. In an interview with Aditya Misra, they say that evolutionary pressure exerted by space conditions drives microbes to develop new strategies for survival and potentially increases their pathogenicity. Excerpts:

Is there information on how Enterobacter bugandensis (E bugandensis) reached ISS? What are our learnings from the incident?

E bugandensis likely reached ISS via astronauts, new equipment, supplies, or onboard experiments, as ISS is a hermetically sealed spacecraft where microorganisms can only be introduced through such vectors.

The study of E bugandensis on ISS reveals significant insights into microbial adaptation and persistence in extreme environments. It highlights the unique genomic alterations and resistance mechanisms of this multidrug-resistant bacterium, distinct from terrestrial strains. The research provides valuable information on the prevalence, distribution, and colonisation patterns of microbes in closed environments, emphasising the importance of advanced analytical techniques like metabolic modelling to understand microbial interactions. By identifying genes specific to ISS and antibiotic resistance genes, the study aids in developing targeted antimicrobial treatments and strategies for microbial management in both space and healthcare settings.

How do extreme environments (microgravity, radiation and increase in carbon dioxide levels) affect microbial behaviour, biology?

Extreme environments such as microgravity, elevated radiation and increased levels of carbon dioxide profoundly affect microbial behaviour and biology, driving adaptation and evolution in unique ways. In microgravity, microbes experience changes in gene expression, virulence and biofilm formation, which can enhance their resistance to stress and antibiotics. Elevated radiation levels on ISS induce DNA damage, leading to the activation of SOS response systems. Genes like LexA, which are rare on Earth but prevalent in space strains, regulate this response, helping bacteria like E bugandensis repair DNA damage and survive. Additionally, toxin-antitoxin systems are more prominent in space, playing critical roles in stress response, plasmid maintenance and biofilm production, thereby increasing bacterial resilience and virulence.

Microbes also evolve unique genetic adaptations to survive the harsh conditions of space. For example, the BvgAS two-component regulatory system, a master virulence regulator in Bordetella species, and the Colicin-E2 immunity protein in E coli enhance bacterial defence mechanisms in space. Specific genes such as the inner membrane protein YbjJ in Bacillus cereus and ATP-dependent zinc metalloprotease FtsH-4 in Acinetobacter pittii are exclusively found in ISS strains, suggesting they provide an adaptive advantage in the space environment. These genetic changes underscore the significant evolutionary pressure exerted by space conditions, driving microbes to develop new strategies for survival and potentially increasing their pathogenic potential. Understanding these adaptations is crucial for developing countermeasures to protect astronaut health during long-term space missions.

How is astronauts’ immune system altered during space voyages?

Astronauts’ immune systems undergo significant alterations due to several factors. Disrupted sleep patterns and altered circadian rhythms negatively impact immune function. Exposure to space radiation directly damages immune cells and increases stress hormones, further suppressing immune responses. The microgravity environment alters the distribution and function of immune cells and impairs lymphopoiesis [production of white blood cells], leading to changes in acquired immunity. These combined effects result in astronauts being immunocompromised, making them more susceptible to infections and illnesses.

What is the microbial landscape on ISS?

The microbial landscape on ISS and other spacecraft is diverse and dynamic, comprising millions of bacteria and fungi present on surfaces and in the air. These microorganisms originate from various sources, including the crew, cargo and the environment. Commonly identified microorganisms on ISS include Staphylococcus species, such as Staphylo-coccus aureus, which can cause human infections, and Malassezia species, which are prevalent fungi. Other notable bacteria include Pantoea spp, which are generally harmless, as well as Klebsiella species like K aerogenes, K pneumoniae and K quasipneumoniae, which are associated with human infections. Serratia marcescens, an opportunistic human pathogen, has also been found on ISS and the Mir spacecraft. These microorganisms can contaminate equipment and surfaces, posing potential health risks to the crew and affecting spacecraft systems.

Your study says E bugandensis coexisted and helped other microorganisms survive on ISS.

E bugandensis coexisted with and supported the survival of many microorganisms on ISS through complex metabolic interactions. To explore these interactions, we constructed 47 genome-scale metabolic models and simulated them in relevant media. We used the Metabolic Support Index (MSI), a measure that predicts the metabolic benefit a microorganism gains when in a community compared to being in isolation, to assess the interactions among 957 identified microbial communities. Our findings revealed that E bugandensis provided notable metabolic benefits (in terms of MSI) to several Gram-positive microorganisms, including Staphylococcus saprophyticus, S hominis and S epidermidis during several flights. Interestingly, E bugandensis did not derive significant metabolic benefits from any coexisting organisms, suggesting it maintains metabolic competitiveness and potentially acts as a metabolic support hub within these communities. This dynamic underscores the interdependence among microorganisms on ISS and E bugandensis’s role in fostering a viable microbial ecosystem in the unique environment of space.

This was first published in the 1-15 July 2024 print edition of Down To Earth