Save the microbes to save the planet: A call to action

Over recent decades, an increased awareness of the human impact on planet Earth has begun to mobilize populations around the world. Clearly our generation is taking from our planet more resources than it can sustainably deliver, and this has an impact on climate, biodiversity and ecosystems which in turn impact human health and wellbeing. We are in search of solutions that could decrease carbon dioxide emissions, containing a global temperature rise to below 2 C° by 2100 and so limiting the impacts of climate change.

We are also beginning to recognize the impact of human activities on living organisms and biodiversity, with 705 vertebrate species and 571 plant species having already been pushed to extinction in the past five centuries. A further one million species of animals and plants are currently threatened with extinction, including large terrestrial animals, marine mammals, animal pollinators, marine corals, and fish stocks.

Moreover, increased consumption of limited resources and intensified industrial processes are degrading ecosystems and biodiversity with declining indicators of the status of Nature, leading to a deterioration of the fabric of life itself. However, we are not yet paying attention to the consequences of human impact on microorganisms. This impact on microbial species is happening quietly, below the radar of most scientists, politicians, and the public, but it should not be underestimated because microorganisms are at the origin of life and sustain all life forms.

Microorganisms were the first form of life to appear on our planet 3.8 billion years ago. Two and half billion years ago they were instrumental in the emergence of the first eukaryotic cell from which all animals and plants, including humans, were derived. About forty trillion (10¹²) microbes live in the gut of every human, with an increasing number of studies highlighting the key role they play in our physiology: from providing essential metabolic functions to influencing our own immune responses. Indeed, they play important roles in the survival and functioning of every form of life. Today our planet is populated by about a trillion species of microorganisms. They include bacteria – the vast majority – but also viruses, fungi, and unicellular microorganisms.

At any one time there are roughly five million trillion trillion (10³⁰) living bacteria and 10³¹ phages (viruses that infect bacteria) that attack them, killing 40% of them every day. Microorganisms are the essence of life, and the driving force of evolution. They evolve at a speed that would require 10,000 years of experiments in the laboratory just to match 1 day of natural evolution. High biodiversity and fluctuation of microbial communities are critically important for species interaction and function.

A minority of them (1415 species, 217 viruses or prions, 538 bacteria, 307 fungi, 66 protozoa, and 287 helminths) are also responsible for causing infectious disease with few having shaped human history and its evolution over time by killing hundreds of millions of people. The remaining 999 billion species of microorganisms are useful and essential to the life on our planet. They are present in the water, soil, air, in harsh environments such as deep-sea vents and hot springs with boiling water, in obscure caves where they get their nutrients from sulfur, and they can resist radiation better than any other living organism.

We rely on them to make food (bread, wine, beer), to treat wastes (sewage treatment plants), and to make essential medicines such as antibiotics. During the 3.8 billion years on our planet, they evolved genes that can perform many of the functions we depend on. They can make chemical reactions and material transformations at room temperature that we can only perform at extremely high temperatures with heavily polluting industrial plants. We engineer them in our laboratories to produce biological molecules, drugs, and enzymes. The application of microbes can also help in finding sustainable solutions to most of the critical problems that face our planet such as climate change, environmental degradation, health and energy needs, provided that we learn how to use them wisely and we stop destroying them either inadvertently or by our ambition to sterilize the environment that surrounds us.

In summary, life on our planet is fully dependent on microbes and the almost limitless functions performed by them. Microbial diversity is essential to maintaining the functions that support life on the planet and therefore it is important to monitor and preserve that diversity. Below are some of the challenges facing the microbial world today and possible ways to overcome them.

Microbes are present everywhere, and they make the planet habitable. The oceans probably carry a large part of the microbial mass of the planet. Indeed, microbes represent from 50 to 90% of the biomass of the oceans. The number of microbial cells in the waters of the planet has been calculated to be in the range of 10³⁰ with a mass equal to the weight of 240 billion African elephants. In 2004, Craig Venter identified 1800 genomic species and 148 previously unknown bacterial phylotypes by sequencing the genome of microorganisms collected by filtering 200 l of water from the Sargasso sea. On dry land, one gram of surface soil can contain more than 10⁹ bacterial and archaeal cells, trillions of viruses, tens of thousands of protists and 200 m of fungal hyphae. Microorganisms colonize all living organisms and, as previously mentioned, about 40 trillion microbes reside in the gut of every human. Since we estimate that the number of human cells that make up our body are around 30 trillion, this means that we are as much microbes as we are human.

Their presence, in addition to providing vitamins, helps the digestion by breaking down fibers and starch, supports endocrine metabolism, and is essential for the formation and maintenance of our immune system. Mice born without exposure to microbes – germ free mice – have fewer and smaller Peyer’s patches and mesenteric lymph nodes and show extensive defects in the development of gut-associated lymphoid tissues and antibody production. Immune dysfunctions are also observed when mice are treated with antibiotics early in life, revealing the key role of microbial colonization on immune maturation. Recent studies have shown that the ability of our immune system to fight tumors, infections, and chronic inflammation is heavily dependent on the presence of a healthy microbiome. Interestingly, supplementation of microbes can also help restore a healthy microbiota, with clear therapeutic opportunities that are currently being pursued.

Microbes also support many industrial activities, starting from traditional fermentation of bread, cheese, beer, wine, to the production of chemicals, energy sources, enzymes, pharmaceuticals, and to waste treatment and pollution control where we use their ability to degrade virtually any product, including fossil oils and plastics. Finally, we should not forget that microorganisms provide an important function in supporting agricultural productivity, by fixing atmospheric nitrogen and favoring the growth of high yielding crops, thus avoiding the pollution caused by use of synthetic nitrogen fertilizers.

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