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Journal ArticleDOI

The darkest microbiome-a post-human biosphere.

TL;DR: Cavicchioli et al. as mentioned in this paper consider what is likely to happen to the Earth's biosphere if we (and the rest of humanity) fail to rescue it, and they do so with the aim of galvanizing the formulation and implementation of strategic and financial science policy decisions that will maximally stimulate the development of relevant new microbial technologies and maximally exploit available technologies, to repair existing environmental damage and mitigate against future deterioration.
Abstract: Microbial technology is exceptional among human activities and endeavours in its range of applications that benefit humanity, even exceeding those of chemistry. What is more, microbial technologists are among the most creative scientists, and the scope of the field continuously expands as new ideas and applications emerge. Notwithstanding this diversity of applications, given the dire predictions for the fate of the surface biosphere as a result of current trajectories of global warming, the future of microbial biotechnology research must have a single purpose, namely to help secure the future of life on Earth. Everything else will, by comparison, be irrelevant. Crucially, microbes themselves play pivotal roles in climate (Cavicchioli et al., Nature Revs Microbiol 17: 569-586, 2019). To enable realization of their full potential in humanity's effort to survive, development of new and transformative global warming-relevant technologies must become the lynchpin of microbial biotechnology research and development. As a consequence, microbial biotechnologists must consider constraining their usual degree of freedom, and re-orienting their focus towards planetary-biosphere exigences. And they must actively seek alliances and synergies with others to get the job done as fast as humanly possible; they need to enthusiastically embrace and join the global effort, subordinating where necessary individual aspirations to the common good (the amazing speed with which new COVID-19 diagnostics and vaccines were developed and implemented demonstrates what is possible given creativity, singleness of purpose and funding). In terms of priorities, some will be obvious, others less so, with some only becoming revealed after dedicated effort yields new insights/opens new vistas. We therefore refrain from developing a priority list here. Rather, we consider what is likely to happen to the Earth's biosphere if we (and the rest of humanity) fail to rescue it. We do so with the aim of galvanizing the formulation and implementation of strategic and financial science policy decisions that will maximally stimulate the development of relevant new microbial technologies, and maximally exploit available technologies, to repair existing environmental damage and mitigate against future deterioration.
Citations
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Journal ArticleDOI
TL;DR: The importance of thought at each step of the research process, the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most direct and most scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork as discussed by the authors .
Abstract: Practical experiments drive important scientific discoveries in biology, but theory‐based research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we appraise the roles of theory‐based approaches focusing on the experiment‐dominated wet‐biology research areas of microbial growth and survival, cell physiology, host–pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome‐sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most‐direct and most‐scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non‐mainstream; and the importance of theory‐based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more‐recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID‐19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology‐related papers and—although we ourselves are involved in laboratory experiments and practical fieldwork—also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

13 citations

Journal ArticleDOI
TL;DR: Environmental Galenics (EG) encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes to help revitalization of irreversibly lost ecosystems.
Abstract: Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

9 citations

Journal ArticleDOI
TL;DR: In this paper , the authors discuss the implications of some properties of technological life that fundamentally differ from non-technological life in the context of modern astrobiology: it can spread among the stars to many sites, it can be more easily detected at large distances, and it can produce signs that are unambiguously technological.
Abstract: The intuition suggested by the Drake equation implies that technology should be less prevalent than biology in the galaxy. However, it has been appreciated for decades in the SETI community that technosignatures could be more abundant, longer-lived, more detectable, and less ambiguous than biosignatures. We collect the arguments for and against technosignatures’ ubiquity and discuss the implications of some properties of technological life that fundamentally differ from nontechnological life in the context of modern astrobiology: It can spread among the stars to many sites, it can be more easily detected at large distances, and it can produce signs that are unambiguously technological. As an illustration in terms of the Drake equation, we consider two Drake-like equations, for technosignatures (calculating N(tech)) and biosignatures (calculating N(bio)). We argue that Earth and humanity may be poor guides to the longevity term L and that its maximum value could be very large, in that technology can outlive its creators and even its host star. We conclude that while the Drake equation implies that N(bio) ≫ N(tech), it is also plausible that N(tech) ≫ N(bio). As a consequence, as we seek possible indicators of extraterrestrial life, for instance, via characterization of the atmospheres of habitable exoplanets, we should search for both biosignatures and technosignatures. This exercise also illustrates ways in which biosignature and technosignature searches can complement and supplement each other and how methods of technosignature search, including old ideas from SETI, can inform the search for biosignatures and life generally.

9 citations

Journal ArticleDOI
TL;DR: In this paper , the authors highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world.
Abstract: There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self‐interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non‐governmental organisations, to engage – in full partnership – with all relevant stakeholders, to ‘weaponise’ microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.

7 citations

Journal ArticleDOI
TL;DR: The International Microbiology Literacy Initiative (IMLI) as mentioned in this paper has created a range of teaching resources that will constitute a child-centric school curriculum of societally relevant microbiology.
Abstract: Microbial activities pervasively impact the wellbeing of all organisms, including humans, and the functioning of the planet itself. In order for society to form informed opinions and take effective actions related to its welfare, it must be able to understand the causes of issues of importance and to appreciate the range of possible responses and their likely effectiveness. ABSTRACT Microbial activities pervasively impact the wellbeing of all organisms, including humans, and the functioning of the planet itself. In order for society to form informed opinions and take effective actions related to its welfare, it must be able to understand the causes of issues of importance and to appreciate the range of possible responses and their likely effectiveness. Society must become microbiology literate. The International Microbiology Literacy Initiative is creating a comprehensive range of teaching resources that will constitute a child-centric school curriculum of societally relevant microbiology. The core of the teaching resources, the lessons, are somewhat unusual in that each one is designed to be essentially stand-alone, so courses can be individually structured by teachers according to their perception of what is interesting and important for their charges. Moreover, the lessons deal not only with societally pertinent microbial activities, but also discuss and propose discussion of their relevance to sustainable development, of their impact on policies and decisions (personal, community, and national), and of issues of stewardship and stakeholder responsibilities. The class lessons are complemented by other child-centric teaching resources whose functions are to add value, to stimulate pupil imagination and excitement in discovery, to engage pupil interest and enthusiasm for topics like sustainability, climate change, international cooperation, citizen science, etc., and to empower pupils as stakeholders in their microbiology education and as educators and multiplicators.

2 citations

References
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Journal ArticleDOI
TL;DR: The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g), respectively, which is 60-100% of the estimated total carbon in plants.
Abstract: The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 3 10 30 cells and 350-550 Pg of C (1 Pg 5 10 15 g), respectively. Thus, the total amount of prokaryotic carbon is 60-100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms. In addition, the earth's prokaryotes contain 85-130 Pg of N and 9-14 Pg of P, or about 10-fold more of these nutrients than do plants, and represent the largest pool of these nutrients in living organisms. Most of the earth's prokaryotes occur in the open ocean, in soil, and in oceanic and terrestrial subsurfaces, where the numbers of cells are 1.2 3 10 29 , 2.6 3 10 29 , 3.5 3 10 30 , and 0.25-2.5 3 10 30 , respectively. The numbers of het- erotrophic prokaryotes in the upper 200 m of the open ocean, the ocean below 200 m, and soil are consistent with average turnover times of 6-25 days, 0.8 yr, and 2.5 yr, respectively. Although subject to a great deal of uncertainty, the estimate for the average turnover time of prokaryotes in the subsurface is on the order of 1-2 3 10 3 yr. The cellular production rate for all prokaryotes on earth is estimated at 1.7 3 10 30 cellsyyr and is highest in the open ocean. The large population size and rapid growth of prokaryotes provides an enormous capacity for genetic diversity. Although invisible to the naked eye, prokaryotes are an essential component of the earth's biota. They catalyze unique and indispensable transformations in the biogeochemical cy- cles of the biosphere, produce important components of the earth's atmosphere, and represent a large portion of life's genetic diversity. Although the abundance of prokaryotes has been estimated indirectly (1, 2), the actual number of pro- karyotes and the total amount of their cellular carbon on earth have never been directly assessed. Presumably, prokaryotes' very ubiquity has discouraged investigators, because an esti- mation of the number of prokaryotes would seem to require endless cataloging of numerous habitats. To estimate the number and total carbon of prokaryotes on earth, several representative habitats were first examined. This analysis indicated that most of the prokaryotes reside in three large habitats: seawater, soil, and the sedimentysoil subsur- face. Although many other habitats contain dense populations, their numerical contribution to the total number of pro- karyotes is small. Thus, evaluating the total number and total carbon of prokaryotes on earth becomes a solvable problem. Aquatic Environments. Numerous estimates of cell density, volume, and carbon indicate that prokaryotes are ubiquitous in marine and fresh water (e.g., 3-5). Although a large range of cellular densities has been reported (10 4 -10 7 cellsyml), the

4,405 citations

Journal ArticleDOI
13 Sep 2012-Nature
TL;DR: Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
Abstract: Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time — especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.

3,890 citations

Journal ArticleDOI
20 Jun 2008-Science
TL;DR: It is indicated that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Abstract: Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.

3,072 citations

Journal ArticleDOI
27 Oct 1972-Nature
TL;DR: Chemotaxis toward amino-acids results from the suppression of directional changes which occur spontaneously in isotropic solutions.
Abstract: Chemotaxis toward amino-acids results from the suppression of directional changes which occur spontaneously in isotropic solutions.

2,069 citations

Journal ArticleDOI
14 May 2015-Nature
TL;DR: The discovery of ‘Lokiarchaeota’ is described, a novel candidate archaeal phylum which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eUKaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.
Abstract: The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

967 citations