Microbial World Research Articles

Predation in a Microbial World: Mechanisms and Trade-Offs of Flagellate Foraging.

Heterotrophic nanoflagellates are the main consumers of bacteria and picophytoplankton in the ocean and thus play a key role in ocean biogeochemistry. They are found in all major branches of the eukaryotic tree of life but are united by all being equipped with one or a few flagella that they use to generate a feeding current. These microbial predators are faced with the challenges that viscosity at this small scale impedes predator-prey contact and that their foraging activity disturbs the ambient water and thus attracts their own flow-sensing predators. Here, I describe some of the diverse adaptations of the flagellum to produce sufficient force to overcome viscosity and of the flagellar arrangement to minimize fluid disturbances, and thus of the various solutions to optimize the foraging-predation risk trade-off. I demonstrate how insights into this trade-off can be used to develop robust trait-based models of microbial food webs.

Microbial Growth under Limiting Conditions-Future Perspectives.

Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.

Chilean biocrusts: an impetus for national park management.

In a world threatened by climate change and biodiversity loss, Chile is one of the leading countries regarding national park management and nature conservation. While there are already protection strategies for plants and animals, it is now the time to include biocrusts, the microbial world at our feet that covers large parts of the soils from the Araucaria forests in the South of Chile to the Atacama Desert in the North.

Ribosomal Protein S12 and its Effects on Specialized Metabolism of Streptomyces Bacteria

Abstract: Species within the actinobacterial genus Streptomyces represent one of the most gifted natural chemists in the microbial world. Their specialized metabolites attract the interest of the pharmaceutical industry as a source of novel drugs. A majority of these molecules pose an insur-mountable challenge for economically justified production via chemical synthesis. Therefore, sub-merged fermentation-based isolation of such molecules often remains the only viable way to obtain them. This in turn fuels interest in process development programs aiming to maximize the yield of specialized metabolite per volume unit of fermentation medium. Along with the optimization of the medium and the fermentation mode itself, strain improvement remains an important part of an over-all process development endeavor. An improved strain can be generated via application of tradition-al approaches of selection for random or induced mutants and genomics-enabled genetic engineer-ing methods. Here I focus on a specific class of mutations with the gene rpsL for ribosomal protein S12, which often confer resistance to streptomycin in bacteria and upregulate specialized metabo-lism in Streptomyces. The review will portray the evolution of our understanding of the mechanisms behind rpsL mutations, as well as how technological advances change the way these mutations are introduced into the genomes of interest.

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon.

Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.

Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs.

Ecological and evolutionary dynamics are intrinsically entwined. On short timescales, ecological interactions determine the fate and impact of new mutants, while on longer timescales evolution shapes the entire community. Here, we study the evolution of large numbers of closely related strains with generalized Lotka Volterra interactions but no niche structure. Host-pathogen-like interactions drive the community into a spatiotemporally chaotic state characterized by continual, spatially-local, blooms and busts. Upon the slow serial introduction of new strains, the community diversifies indefinitely, accommodating an arbitrarily large number of strains in spite of the absence of stabilizing niche interactions. The diversifying phase persists - albeit with gradually slowing diversification - in the presence of general, nonspecific, fitness differences between strains, which break the assumption of tradeoffs inherent in much previous work. Building on a dynamical-mean field-theory analysis of the ecological dynamics, an approximate effective model captures the evolution of the diversity and distributions of key properties. This work establishes a potential scenario for understanding how the interplay between evolution and ecology - in particular coevolution of a bacterial and a generalist phage species - could give rise to the extensive fine-scale diversity that is ubiquitous in the microbial world.

Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth

The exploration of the microbial world in research continues to be fascinating and unending in several aspects of taxonomy, genomics, evolution, and industrial applications [...].

Monitoring the viable grapevine microbiome to enhance the quality of wild wines

Grapevines that are used for winemaking host a diverse range of microorganisms that make up their microbiome. The microbes that inhabit the grapevine have been used by winemakers to produce wine for centuries, although modern wine producers often rely on inoculated microorganisms such as Saccharomyces cerevisiae. In the Australian wine industry, there is a movement towards returning to the utilisation of the microbiome for wine fermentation. With the recent increase in the understanding of the role of the grapevine microbiome in grapevine health, fermentation and subsequent wine sensory traits, the microbial world offers a new level of complexity that can be harnessed for winemaking. In order to develop and maintain a desired vineyard micro-biodiversity, extensive microbial monitoring is required. Here we discuss the utilisation of a viability selection dye in order to distinguish between microorganisms that are live and associated with the host, and relic signals generated from non-living sources.

Resetting urban human‐microbial relations in pandemic times

AbstractMicrobes, particularly of the viral kind, are currently preoccupying human activity and concerns due to the COVID‐19 pandemic. Although for a long time there has been fear associated with ‘germs’, notably viruses and bacteria and the diseases they cause, the pandemic has set these fears into overdrive. As serious as this ongoing event is, there are broader interests and important alternative narratives about the microbial world permeating current thinking, based on research that intersects with and includes biopolitical and relational research in geography. In an attempt at balancing the prevailingly negative discourses about microbes and the potential harms they can cause, and to encourage more geographers to contribute to understanding human‐microbial relations, this paper draws together recent research across disciplines to discuss the prevalence and role of microbes in environments and in and on human bodies. Drawing on ideas of more‐than‐human care, the paper shows how geographers and other social scientists can and are already helping reset human‐microbial relations, and where further work can productively be done.

Evaluation of Proteins Released to Medium in Yeast-Bacteria Co-culture System

The natural ecosystem contains an astonishing variety of microbial species. Populations of microorga-nisms exist in a common habitat in terms of access to nutrients and other resources in the environment. Cultivation of microorganisms in ideal laboratory conditions seperates them from their natural ecosystem conditions and isolates them from their microbial world, especially from their competitors. With traditional pure culture-oriented cultuvation techniques used in laboratories, interactions mediated by small molecules are not taken into account, resulting in the precise nature of the interactions being largely unknown. Coculture systems are systems in which two or more different cell populations are grown together. In this way, studies on natural interactions between populations can be made and synthetic interactions that are not observed in nature can be provided. With these systems, natural product discovery, microbial ecology, evolution and pathogenesis studies are carried out. In addition, coculture systems are also used in industrial, environmental and medical studies. In this study, the wild strain of Schizosaccharomyces pombe and the DH5α strain of Escherichia coli were grown in their own specific media, then cultured for 48 hours and 72 hours by cultivating in media containing 0,1% glucose with different cell number, and finally the differentiation in the proteins released by the cells into the medium was observed in SDS polyacrylamide gels. Different from the control conditions, new protein bands that emerged under the co-culture conditions were detected and two of these bands were analyzed by mass spectrometry (MS). While 6 of differentaited proteins were released by S.pombe, 257 proteins matched with E.coli proteom. These proteins are; Various carbohydrate-binding proteins, membrane proteins involved in the identification of various signaling molecules and antibiotics, and other proteins involved in various cellular processes.

Formation and emergent dynamics of spatially organized microbial systems.

Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.

Breakdown of clonal cooperative architecture in multispecies biofilms and the spatial ecology of predation

Biofilm formation, including adherence to surfaces and secretion of extracellular matrix, is common in the microbial world, but we often do not know how interaction at the cellular spatial scale translates to higher-order biofilm community ecology. Here we explore an especially understudied element of biofilm ecology, namely predation by the bacterium Bdellovibrio bacteriovorus. This predator can kill and consume many different Gram-negative bacteria, including Vibrio cholerae and Escherichia coli. V.cholerae can protect itself from predation within densely packed biofilm structures that it creates, whereas E.coli biofilms are highly susceptible to B.bacteriovorus. We explore how predator-prey dynamics change when V.cholerae and E.coli are growing in biofilms together. We find that in dual-species prey biofilms, E.coli survival under B.bacteriovorus predation increases, whereas V.cholerae survival decreases. E.coli benefits from predator protection when it becomes embedded within expanding groups of highly packed V.cholerae. But we also find that the ordered, highly packed, and clonal biofilm structure of V.cholerae can be disrupted if V.cholerae cells are directly adjacent to E.coli cells at the start of biofilm growth. When this occurs, the two species become intermixed, and the resulting disordered cell groups do not block predator entry. Because biofilm cell group structure depends on initial cell distributions at the start of prey biofilm growth, the surface colonization dynamics have a dramatic impact on the eventual multispecies biofilm architecture, which in turn determines to what extent both species survive exposure to B.bacteriovorus.

Integrated molecular approaches for fermented food microbiome research.

Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.

International Microorganism Day: facilitating global outreach events using a decentralized model.

On 17 September 1683, Antonie van Leeuwenhoek, a Dutch merchant who lacked formal education and fortune, wrote a letter to the Royal Society of London describing for the first time a single-celled organism. As a tribute to this revolutionary discovery, the Portuguese Society of Microbiology with the support of the Federation of European Microbiological Societies in 2017, designated this day as International Microorganism Day (IMD), a day aiming to raise awareness about the wonderful world of microbes. Six years after the establishment of IMD, the knowledge of microbiology outreach around this celebration has expanded greatly, with 5 years of in-person and 2 years of online events. The peak of these commemorations was in 2023, with 63 parallel outreach events and more than 5000 attendees, most of which were children, and young adults. While these in-person events were occurring in the month of September, the #InternationalMicroorganismDay hashtag reached nearly 2.3 million people online, reflecting the number of users who have seen a post containing this hashtag on social media. Using a decentralized model to facilitate 63 grass-roots teams to organize events locally, IMD achieved global representation both online and offline. This paper presents details behind the organization and data on the international impact of the IMD 2022 and 2023 events, outlines plans to expand reach to more countries and audiences, and encourages readers to participate with their own events in future IMD editions so that global impact can be expanded even further.

Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.

Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Herewe showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.

Glimpses of weird and wonderful world of microbes

Microorganisms can be seen with the help of microscope. Microorganisms include Bacteria, Archaea, Viruses, Fungi, Protist, Protozoa and algae etc. Microbes are omnipresent in the biosphere and their presence invariably affects the environment in which they grow. The effects of microbes on the environment can be beneficial or harmful or in apparent with regards to human measure or observation. The most significant effect of microbes on the Earth is their ability to recycle the primary elements that make up all living systems, especially carbon, oxygen, nitrogen. This article mainly focuses on beneficial and harmful impact of microbes on environment and their role to maintain quality, health and sustainability of environment. Some microorganisms are beneficial while some are non-beneficial for human beings. Some microbes spread different disease in the world and make the world polluted but some clean the pollution of the World.

A Review on Spoilage Microorganisms in Fresh and Processed Aquatic Food Products

Aquatic food products are greatly perishable owing to their biological compositions. Spoilage is defined as any alteration in food products that lead to unacceptable attributes to the consumers, mainly through sensory perception. Microbial spoilage is a common type of spoilage among seafood products. In this paper, we reviewed and discussed the various spoilage microorganisms (molds, yeasts, and bacteria) in fresh and processed fish and fishery products. Many studies reported that processed fishery products, such as salted, dried, and hot-smoked fish, are commonly spoiled by molds, mainly under the genus of Aspergillus and Penicillium. Yeasts as spoilage agents have been associated with fish and fishery products stored at low temperatures, notably dominated by two genera, Candida and Rhodotorula, while other yeast species have also been linked to heavily-salted fish and fermented aquatic foods. The important genera of spoilage bacteria that have been documented in fresh and processed fish and fishery products were Pseudomonas, Alcaligenes, Aeromonas, Enterobacter, Bacillus, Enterococcus, Psychrobacter, Escherichia coli, Listeria, Brochothrix, and Shewanella species. Microorganisms play an important role in the spoilage of processed and fresh fish/fishery products. Further research should be undertaken to fully understand the microbial world, particularly associated with aquatic food products.

Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix.

Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix.

Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi.

Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.