Modern microbiology: Embracing complexity through integration across scales.

Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.

A microbial future.

Life as we know it began with microbes. Microbes sustain life on Earth, and every now and then, a microbe emerges that threatens the survival of an entire species. The dangers and benefits of microbial life are both enormous, as is their potential to help us live long, healthy, sustainable lives. Microbiology at Cell celebrates 50 years, and we're proud to showcase the marvelous and yet mysterious microbial world in our anniversary focus issue.

Unraveling the functional dark matter through global metagenomics.

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Microbial predators form a new supergroup of eukaryotes.

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.

The History of Microbiology-A Personal Interpretation.

Microbiology began as a unified science using the principles of chemistry to understand living systems. The unified view quickly split into the subdisciplines of medical microbiology, molecular biology, and environmental microbiology. The advent of a universal phylogeny and culture-independent approaches has helped tear down the boundaries separating the subdisciplines. The vision for the future is that the study of the fundamental roles of microbes in ecology and evolution will lead to an integrated biology with no boundary between microbiology and macrobiology.

From virus structure to chromatin: X-ray diffraction to three-dimensional electron microscopy.

Early influences led me first to medical school with a view to microbiology, but I felt the lack of a deeper foundation and changed to chemistry, which in turn led me to physics and mathematics. I moved to the University of Cape Town to work on the X-ray crystallography of some small organic compounds. I developed a new method of using molecular structure factors to solve the crystal structure, which won me a research studentship to Trinity College Cambridge and the Cavendish Laboratory. There I worked on the austenite-pearlite transition in steel. This is governed by the dissipation of latent heat, and I ended up numerically solving partial differential equations. I used the idea of nucleation and growth during the phase change, which had its echo when I later tackled the assembly of Tobacco mosaic virus (TMV) from its constituent RNA and protein subunits. I wanted to move on to X-ray structure analysis of large biological molecules and obtained a Nuffield Fellowship to work in J.D. Bernal's department at Birkbeck College, London. There, I met Rosalind Franklin, who had taken up the study of TMV. I was able to interpret some of Franklin's beautiful X-ray diffraction patterns of the virus particle. From then on, my fate was sealed. After Franklin's untimely death in 1958, I moved in 1962 to the newly built MRC Laboratory of Molecular Biology in Cambridge, which, under Max Perutz, housed the original MRC unit from the Cavendish Laboratory. I was thus privileged to join the Laboratory at an early stage in its expansion and consequently able to take advantage of, and to help build up, its then unique environment of intellectual and technological sophistication. There I have remained ever since.

Transitions in development - an interview with Chin-Min (Kimmy) Ho.

Kimmy Ho is an Assistant Research Fellow at the Institute of Plant and Microbial Biology, Academia Sinica, Taiwan. Her research focuses on leaf epidermal development. We caught up with Kimmy over Zoom to find out about her research, her transition to becoming a group leader and her approach to mentoring students.

Climate-land-use interactions shape tropical mountain biodiversity and ecosystem functions.

Agriculture and the exploitation of natural resources have transformed tropical mountain ecosystems across the world, and the consequences of these transformations for biodiversity and ecosystem functioning are largely unknown1-3. Conclusions that are derived from studies in non-mountainous areas are not suitable for predicting the effects of land-use changes on tropical mountains because the climatic environment rapidly changes with elevation, which may mitigate or amplify the effects of land use4,5. It is of key importance to understand how the interplay of climate and land use constrains biodiversity and ecosystem functions to determine the consequences of global change for mountain ecosystems. Here we show that the interacting effects of climate and land use reshape elevational trends in biodiversity and ecosystem functions on Africa's largest mountain, Mount Kilimanjaro (Tanzania). We find that increasing land-use intensity causes larger losses of plant and animal species richness in the arid lowlands than in humid submontane and montane zones. Increases in land-use intensity are associated with significant changes in the composition of plant, animal and microorganism communities; stronger modifications of plant and animal communities occur in arid and humid ecosystems, respectively. Temperature, precipitation and land use jointly modulate soil properties, nutrient turnover, greenhouse gas emissions, plant biomass and productivity, as well as animal interactions. Our data suggest that the response of ecosystem functions to land-use intensity depends strongly on climate; more-severe changes in ecosystem functioning occur in the arid lowlands and the cold montane zone. Interactions between climate and land use explained-on average-54% of the variation in species richness, species composition and ecosystem functions, whereas only 30% of variation was related to single drivers. Our study reveals that climate can modulate the effects of land use on biodiversity and ecosystem functioning, and points to a lowered resistance of ecosystems in climatically challenging environments to ongoing land-use changes in tropical mountainous regions.

'Queer in Microbiology': a Microbiology Society members' endeavour for creating a safe and inclusive environment for LGBTQIA+ microbiologists.

The past decade has seen growing awareness of the challenges faced by LGBTQIA+ scientists, including discrimination in the workplace and the lack of representation. Initiatives such as 500 Queer Scientists, Pride in STEM and the Microbiology Society's LGBTQIA+ events have been instrumental in promoting inclusivity in science, technology, engineering, mathematics and medicine (STEMM). The Microbiology Society and its members have played a pivotal role in these efforts and summarized here are their initiatives towards safer and more inclusive scientific and research environments. Starting with a series of interviews and blog posts about the experiences of LGBTQIA+ microbiologists in research, the Society has promoted the organization of networking and social events and developed guidelines for creating more inclusive scientific conferences. These initiatives have not only improved the representation and visibility of LGBTQIA+ individuals in microbiology, but have also served as a blueprint for similar efforts in other scientific areas. Nevertheless, despite improvements in some areas, full inclusion of LGBTQIA+ scientists is still hindered by societal and institutional policies around the world. Here, we propose novel measures to support and empower LGBTQIA+ microbiological communities within learned societies.

Biodiversity increases and decreases ecosystem stability.

Losses and gains in species diversity affect ecological stability1-7 and the sustainability of ecosystem functions and services8-13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience2,3,6,11,12,14. How these stability components covary remains poorly understood15. Similarly, the effects of diversity on overall ecosystem stability16, which is conceptually akin to ecosystem multifunctionality17,18, remain unknown. Here we studied communities of aquatic ciliates to understand how temporal variability, resistance and overall ecosystem stability responded to diversity (that is, species richness) in a large experiment involving 690 micro-ecosystems sampled 19 times over 40 days, resulting in 12,939 samplings. Species richness increased temporal stability but decreased resistance to warming. Thus, two stability components covaried negatively along the diversity gradient. Previous biodiversity manipulation studies rarely reported such negative covariation despite general predictions of the negative effects of diversity on individual stability components3. Integrating our findings with the ecosystem multifunctionality concept revealed hump- and U-shaped effects of diversity on overall ecosystem stability. That is, biodiversity can increase overall ecosystem stability when biodiversity is low, and decrease it when biodiversity is high, or the opposite with a U-shaped relationship. The effects of diversity on ecosystem multifunctionality would also be hump- or U-shaped if diversity had positive effects on some functions and negative effects on others. Linking the ecosystem multifunctionality concept and ecosystem stability can transform the perceived effects of diversity on ecological stability and may help to translate this science into policy-relevant information.

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms.

Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.

A social life for discerning microbes.

Microbes are not only extremely social but also extremely discerning about whom they socialize with. Recent research has uncovered some of the evolutionary explanations behind these feats of social sophistication in bacteria (Ackermann et al., 2008; Diggle et al., 2007) and, most recently, has provided insights into the molecular mechanisms of discrimination in yeast (Smukalla et al., 2008).

Lasker-Koshland Award to 21st century microbe master.

The 2008 Lasker-Koshland Award will be presented to Stanley Falkow, one of the legendary figures in the history of microbiology research. Falkow's many contributions remade the way we think about bacterial pathogens, antibiotic resistance, and infectious disease.

Antoni van Leeuwenhoek 1723-2023: a review to commemorate Van Leeuwenhoek's death, 300 years ago : For submission to Antonie van Leeuwenhoek journal of microbiology.

In the 300 years since Van Leeuwenhoek died, some of the details around his life and his work have provided material for discussion or dispute. As archives and libraries are being scanned and technology improves, information is becoming more readily available. This review therefore aims to take a new look at some of those discussions, and Van Leeuwenhoek's possible experimental methods. Digital photography has made it possible to show exactly what can be seen through his simple microscopes, and how he could have obtained his results by, for example, modifying his microscopes and lighting. Equally, the completion of the series known as the Collected Letters, begun in 1931 with volume 1 published in 1939 and to be completed in 2023, allows researchers to see complete letters in English and modern Dutch. Theories about experimental methods can be tested and the results recorded photographically. Additionally, new, non-destructive techniques such as neutron tomography have improved the evaluation of the authenticity of surviving microscopes.