New frontiers in microbiology

Issue: Why Microbiology Matters

05 May 2020 article

As we have progressed through the 21^st century, we have expanded and developed our understanding of how microbes are related to and interact with each other. This section considers the ever-growing tree of life, how we can study complex microbial communities to gain new insights and the possibility of discovering life on other planets.

The ever-growing tree of life

Bryn McCulloch and Thorsten Allers

Genealogical research can yield some unexpected surprises. The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it had two major branches: prokaryotes and eukaryotes. Then Carl Woese suggested that life could be categorised into three fundamental domains: Eukarya, Bacteria and Archaea. Notably, Archaea and Eukarya are more closely related to each another than to Bacteria.

The discovery of new archaeal groups has included DPANN – archaea with extremely small cell and genome sizes that appear to be obligate symbiotes – and Asgard – a recently cultivated group found at deep sea vents. Including Asgard archaea in phylogenetic analyses has uncovered a strong affiliation with eukaryotes, leading to the proposal for a two-domain Tree of Life: this time, the Eukarya branch originates from within the Archaea. In this scenario, eukaryotic cells originated from a symbiosis between an Asgard-like host cell and a proteobacterium, which later became a mitochondrion.

As with any genealogical research, the two-domain versus three-domain tree has been a topic of debate within the scientific community, but new evidence is making a two-domain tree appear more promising. Tom Williams and colleagues at the University of Bristol analysed more than 3,000 gene families in Archaea and Eukaryotes and consistently found Eukaryotes to have originated from within Archaea and that an Asgard lineage called Heimdallarchaeota is the closest archaeal relative to the Eukarya.

The tree of life continues to expand with the discovery of new life. This could come from previously unexplored environments, such as the growing field of astrobiology, but also from the ability to create synthetic life. Expect plenty more unexpected surprises!

Bryn McCulloch

School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK

[email protected]

Bryn McCulloch graduated with a first class BSc (Hons) in Biology at Edge Hill University, working on extremophiles from salterns in Cabo Verde, and is now completing a master’s in Thorsten Allers’ lab, working on growth conditions of Archaea and the corresponding effects on DNA repair and replication.

Thorsten Allers

School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK

[email protected]

After a PhD at the University of Edinburgh and a postdoctoral fellowship at the National Institutes of Health (NIH), USA, Thorsten Allers was awarded a Royal Society University Research Fellowship to establish his laboratory at the University of Nottingham. His group uses the model species Haloferax volcanii to study the genetics of DNA replication, repair and recombination in Archaea.

Why does microbiology matter?

Thorsten: Microbiology with model species helps us to understand the rules of life and where we come from. We were all microbes once upon a time!

How did you enter this field?

Thorsten: I have always worked on micro-organisms; I did my PhD with the bacterium Escherichia coli, my postdoc with the eukaryote Saccharomyces cerevisiae, and my own research group works on the archaeon Haloferax volcanii.

Microalgae, bacteria and vitamins: three key players in aquatic microbial communities

Andre Holzer, Shelby Newsad, Nhan-An Tran, Ellen Harrison and Alison Smith

Micro-organisms are ubiquitous and form complex communities whenever they inhabit the same environment. Well-known examples of microbial communities include the human gut microbiome, but equally important to life on the planet are those in the aquatic environment. These are made up of photosynthetic algae and bacteria as well as many other protists, and are responsible for 50% of global carbon fixation. However, it is only recently that modern sequencing-based approaches have opened up the possibility of studying these aquatic microbial communities and their metabolic dependencies in exquisite detail.

Evolution of life began in the aquatic environment and so too did the formation of microbial communities. Today, diverse groups of microbes are found in every ocean and continent, ranging from temperate to extreme environments, and encompass members from all kingdoms of life (bacteria, archaea, protists and fungi). Whilst every teaspoon of seawater is filled with millions of these organisms, entangled in complex networks of interactions, from mutualistic to commensal (neutral) to parasitic, each community’s composition is unique to the environment in which it lives. Understanding these microbial communities is of major importance, as they form the base of the ocean’s food web, and their metabolic interplay is responsible for approximately 50% of total global carbon fixation.

What shapes these communities?

Open water communities of microbes are shaped by a patchy distribution of nutrients and other abiotic factors such as temperature and salinity. Research into aquatic microbial communities has highlighted the importance of nutrient availability in determining microbial community dynamics in both the freshwater and marine environments. Besides the major inorganic macro- and micro-nutrients such as nitrogen, phosphorus and iron, scientists discovered that the availability of many organic micronutrients, or vitamins, co-limits phytoplankton growth and determines its composition. It has been shown that B-vitamins in particular influence community composition, by favouring the succession of some species over others. In fact, research has revealed that many interactions within aquatic microbial communities are underpinned by the exchange of B-vitamins. This is because vitamin B₁ (thiamine), vitamin B₇ (biotin) and vitamin B₁₂ (cobalamin) are required in different combinations by 60–70% of all microalgae. But what exactly are microalgae and where do algae obtain the vitamins from if they can’t make them themselves?

Microalgae are a diverse group of largely unicellular photosynthetic eukaryotes, and their photosynthetic activity makes them responsible for primary production, which contributes significantly to the carbon fixation capacities of the ocean microbiome. A common misconception about microalgae, however, is that they are completely autotrophic, needing only simple nutrients, sunlight and carbon dioxide (CO₂) for growth. But with over half of all microalgae dependent on vitamin B₁₂, which is synthesised only by bacteria, this underlines the importance of metabolic exchange in defining ecological interactions between micro-organisms.

Images of algae communities from the Antarctic. — © Monika Krolikowski

How can microbial communities be studied?

To gain a mechanistic understanding of interactions, it is necessary to break down complex interaction networks by focusing on single model systems that can be co-cultured under controlled laboratory conditions. Direct demonstration of vitamin exchange came from studies with Ostreococcus tauri, an important picoeukaryotic microalga in oligotrophic waters, which has been shown to require B₁₂and B₁, and the bacterium Dinoroseobacter shibae, which requires vitamins B₃, B₇ and a precursor of B₉ for growth. The microalgae and bacteria can support each other’s growth while in co-culture in the laboratory in a stable mutualism by fulfilling the vitamin requirements of the other species. Other studies of environmental samples looking at 16S rRNA gene sequences found that the Rhodobacteraceae family of bacteria, of which D. shibae is one example, are often found to co-occur with microalgae, suggesting that vitamins shape microbial interactions in the aquatic environment.

Recent advances in next-generation sequencing provide much more extensive possibilities to study interactions within microbial communities by identifying the entire metabolic capability present in an environment. One of the most important large-scale attempts applying such a strategy has been Tara Oceans. “The largest DNA sequencing effort ever done on ocean science” (Patrick Wincker, Genoscope, France) allowed identification of species in various communities and resulted in an extension of the tree of life by more than 30,000 species. With around 40 million mostly novel genes identified in the marine environment, this study provides a key resource that is now available to investigate species interactions in diverse aquatic communities by looking at co-occurrence of organisms in combination with their metabolic abilities.

How can this knowledge be used?

As sequencing data becomes more readily available and species identification of microbial communities improves, it is now possible to infer more complex interactions and further investigate the importance of abiotic factors such as vitamins in regulating communities. Nutrient requirements can be inferred from the genetic or transcriptomic information and interactions can be tested in laboratory settings, experimentally validating co-occurring, metabolically compatible species. Increasingly, gene expression profiles can be generated to look for significant changes in the nutrient dependencies of microbes in different environmental conditions. This will be of great importance as climate change will continue to alter the pattern of nutrients in the ocean and so will change the species that can occur, especially with regards to the formation of harmful algal blooms.

Besides advancing our understanding of aquatic ecology, insights into microbial communities are key for a range of biotechnological applications. Industrial production of microalgae for feed and food applications or production of high-value compounds is often challenged by contamination issues. These may be overcome by the use of designed microbial consortia rather than using monocultures, since the former are likely to be more resistant to contamination. Moreover, vitamins have been shown to repress gene expression in microalgae, by both vitamin-responsive promoters and riboswitches. These genetic elements have the potential to be added to the synthetic biology toolkit, to engineer strains with more targeted production of high-value compounds. In future, we look forward to more breakthroughs, to move on from metabolic fitting to understanding more complex regulatory dynamics in both industrial and natural microbial communities.