scholarly journals Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Anahit Penesyan ◽  
Ian T. Paulsen ◽  
Staffan Kjelleberg ◽  
Michael R. Gillings
Keyword(s):  
Multicellular Organism ◽  
Main Mode ◽  
Microbial World ◽  
Biofilm Growth ◽  
Microbial Cells ◽  
Microbial Life

AbstractBiofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.

scholarly journals Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World

2018 ◽  
Vol 72 (7) ◽  
pp. 987-1000 ◽  
Author(s):  
Malama Chisanga ◽  
Howbeer Muhamadali ◽  
David I. Ellis ◽  
Royston Goodacre
Keyword(s):  
Raman Scattering ◽  
Surface Enhanced Raman Scattering ◽  
Industrial Applications ◽  
Accurate Identification ◽  
Microbial World ◽  
Microbial Cells ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering ◽  
Ir Instrumentation

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Effects of carbon to nitrogen ratios on amounts and composition of Bacillus subtilis biofilms

2020 ◽  
Author(s):  
Natalia Cortes Osorio ◽  
Robert Endrika ◽  
Karsten Kalbitz ◽  
Cordula Vogel
Keyword(s):  
Bacillus Subtilis ◽  
Extracellular Polymeric Substances ◽  
High Vacuum ◽  
Chemical Properties ◽  
High Ratio ◽  
Natural Environments ◽  
Radial Expansion ◽  
Biofilm Growth ◽  
Microbial Cells ◽  
Biofilm Development

<p>In natural environments, bacteria can be found as multicellular communities exhibiting a high degree of structure, denominated biofilms. Biofilms are composed of microbial cells, often of multiple species, embedded within a matrix of extracellular polymeric substances (EPS). The exact composition, physical and chemical properties, and amounts of these components varies depending on their growth conditions. However, it remains unclear how nutrient availability drives the allocation into cell growth or EPS production, especially under conditions found in soils. Here we aimed to evaluate the effect of various C/N ratios on <em>Bacillus subtilis</em> biofilm growth (spatial expansion and structure) and their EPS composition. We hypothesized that the largest biofilm development and highest EPS production by <em>Bacillus subtilis</em> would be caused by a nutrient imbalance reflected in C/N ratios, especially high C availability. Biofilms were grown on membranes on MSgg agar plates with C/N ratios of 1:1, 10:1, 25:1 and 100:1. Several methods from macroscopic observations over EPS extraction and determination up to various microscopic visualisation techniques were used. The radial expansion of the biofilm was measured, followed by EPS extraction to quantify EPS-proteins and EPS-polysaccharides. Hydrated biofilm samples were studied regarding their biofilm structures by scanning electron microscopy (SEM) within the environmental mode at approximately 97% humidity. Fixed, dehydrated and embedded samples were used to evaluate the biofilm height and internal structure with SEM in high vacuum mode. Low C/N ratio (1:1) resulted in the smallest biofilms in terms of radial expansion and biofilm height, with densely packed layers of cells and low amounts of EPS. Our first results revealed that the highest biofilm productions were observed at C/N ratio of 10:1 and 25:1. The microscopic approaches indicated that biofilms growing at C/N ratios of 100:1 produced the highest amount of EPS. Furthermore, changes in the microscopical features of the biofilms were detected with different structures along the biofilm regions affected by the nutrient conditions. These results suggest that the C/N ratio has a large impact on the biofilm development and structure, with different allocations into microbial cells and EPS. Overall, the results obtained until now allowed us to accept the initial hypothesis, indicating that higher C/N ratios induce a higher EPS production. This suggests that environments containing a high ratio between carbon and the limiting nutrient, often nitrogen, may favour polysaccharide production, probably because energy from the carbon excess is used for polysaccharide biosynthesis.</p>

scholarly journals Flow-induced symmetry breaking in growing bacterial biofilms

2019 ◽  
Author(s):  
Philip Pearce ◽  
Boya Song ◽  
Dominic J. Skinner ◽  
Rachel Mok ◽  
Raimo Hartmann ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Bacterial Biofilms ◽  
Natural Environments ◽  
Bacterial Cells ◽  
Cell Orientation ◽  
Biofilm Growth ◽  
Time Resolved ◽  
Microbial Life ◽  
Biofilm Development ◽  
Life On Earth

AbstractBacterial biofilms represent a major form of microbial life on Earth and serve as a model active nematic system, in which activity results from growth of the rod-shaped bacterial cells. In their natural environments, ranging from human organs to industrial pipelines, biofilms have evolved to grow robustly under significant fluid shear. Despite intense practical and theoretical interest, it is unclear how strong fluid flow alters the local and global architectures of biofilms. Here, we combine highly time-resolved single-cell live imaging with 3D multi-scale modeling to investigate the mechanisms by which flow affects the dynamics of all individual cells in growing biofilms. Our experiments and cell-based simulations reveal three quantitatively different growth phases in strong external flow, and the transitions between them. In the initial stages of biofilm development, flow induces a downstream gradient in cell orientation, causing asymmetrical droplet-like biofilm shapes. In the later developmental stages, when the majority of cells are sheltered from the flow by the surrounding extracellular matrix, buckling-induced cell verticalization in the biofilm core restores radially symmetric biofilm growth, in agreement with predictions of a 3D continuum model.

scholarly journals The Compressed Vocabulary of Microbial Life

2021 ◽  
Vol 12 ◽  
Author(s):  
Gustavo Caetano-Anollés
Keyword(s):  
Evolutionary Strategies ◽  
Module Structure ◽  
Microbial World ◽  
Scale Free ◽  
Microbial Life ◽  
Size Dependent ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Evolutionary Genomic ◽  
The Impact

Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf’s law, a special case of the scale-free distribution, the Heaps’ law describing sublinear growth typical of economies of scales, and the Menzerath–Altmann’s law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a “triangle of persistence” describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A “causal” word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.

The possibility of alternative microbial life on Earth

2005 ◽  
Vol 4 (3-4) ◽  
pp. 165-173 ◽  
Author(s):  
Carol E. Cleland ◽  
Shelley D. Copley
Keyword(s):  
Pcr Amplification ◽  
Morphological Diversity ◽  
Life Forms ◽  
Rrna Genes ◽  
Molecular Architecture ◽  
Dapi Staining ◽  
Microbial World ◽  
Modern Biology ◽  
Microbial Life ◽  
Life On Earth

Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary Earth contains as yet unrecognized alternative forms of microbial life. The possibility that more than one form of life arose on Earth is consistent with our current understanding of conditions on the early Earth and the biochemical and molecular possibilities for life. Arguments that microbial descendents of an alternative origin of life could not co-exist with familiar life are belied by what we know of the complexity and diversity of microbial communities. Furthermore, the tools that are currently used to explore the microbial world – microscopy (with the aid of techniques such as DAPI staining and fluorescence in situ hybridization), cultivation and PCR amplification of rRNA genes – could not detect such organisms if they existed. Thus, the fact that we have not discovered any alternative life forms cannot be taken as evidence that they do not exist.

scholarly journals Optical Sensing of Microbial Life on Surfaces

2015 ◽  
Vol 82 (5) ◽  
pp. 1362-1371 ◽  
Author(s):  
M. Fischer ◽  
G. J. Triggs ◽  
T. F. Krauss
Keyword(s):  
Basic Research ◽  
High Sensitivity ◽  
Natural Environments ◽  
Label Free ◽  
Biofilm Growth ◽  
Microbial Cells ◽  
Industrial Facilities ◽  
Label Free Detection ◽  
Sensitivity And Selectivity ◽  
The Many

ABSTRACTThe label-free detection of microbial cells attached to a surface is an active field of research. The field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. Despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. We believe that among the many different technologies available for monitoring biofilm growth, optical techniques are the most promising, as they afford direct imaging and offer high sensitivity and specificity. Furthermore, as each technique offers different insights into the biofilm growth mechanism, our analysis allows us to provide an overview of the biological processes at play. In addition, we use a set of key parameters to compare state-of-the-art techniques in the field, including a critical assessment of each method, to identify the most promising types of sensors. We highlight the challenges that need to be overcome to improve the characteristics of current biofilm sensor technologies and indicate where further developments are required. In addition, we provide guidelines for selecting a suitable sensor for detecting microbial cells on a surface.

scholarly journals The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life

2022 ◽  
Vol 9 (1) ◽  
Author(s):  
Sunanda Sharma ◽  
Vera Meyer
Keyword(s):  
Model Organism ◽  
Time Lapse ◽  
Environment Interaction ◽  
Microbial World ◽  
Functional Roles ◽  
Microbial Life ◽  
Multiple Products ◽  
Science And Art ◽  
Interdisciplinary Practice ◽  
Fungal Pigments

Abstract Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.

scholarly journals Corona and Other Virus: Their Useful and Harmful Aspects

2020 ◽  
pp. 1-11
Author(s):  
Birhanu Gizaw ◽  
Keyword(s):  
Genetic Resource ◽  
Human Life ◽  
Physical World ◽  
Culture Collection ◽  
Conservation Strategy ◽  
Microbial Culture ◽  
Symbiotic Relationship ◽  
Biotechnological Application ◽  
Microbial World ◽  
Microbial Life

How the single virus is forceful and shakes the world is eye witness during this contemporary COVID19 pandemic time. People primarily think of viruses such as HIV, Ebola, Zika, Influenza, Tobacco mosaic virus or whatever new outbreak like SARS, Corona are all viruses worst and non-beneficial. However, not all viruses are detrimental and influential to human, animal and plant health. In fact some viruses have beneficial properties for their hosts in a symbiotic relationship and scientific research in many disciplines. Understanding the microbial world is very critical and crucial thing that they are driving force and governing the physical world and biosphere at all. The virus and other microbial life those of bacteria, fungi, prion, viroid, viron are requiring great attention and research to enhance their utilization from majority of useful aspects of microbial genetic resource. The secret behind of every industry, agriculture, health and environment are the application of microbes and their products are too high for human being and environment. Without microbes all life would be cease on earth. However some microbes are very dangerous like Corona virus, HIV, Ebola, Mycobacterium and others that destroy human life, but majority of microorganisms are too useful to promote development. Through building and strengthening microbial culture collection centers and through strong conservation strategy, it is possible to exploit more from the unseen microbial genetic resource. This paper will review the harmful and use full aspect of virus in respect with health, environment, agriculture and biotechnological application during this Covid19 pandemic time to raise awareness about virus at all.

Hydrothermal preparation of TiO2-Ag nanoparticles and its antimicrobial performance against human pathogenic microbial cells in water

BIOCELL ◽  
2018 ◽  
Vol 42 (3) ◽  
pp. 93-97 ◽  
Author(s):  
Mahmoud MOUSTAFA ◽  
Saad ALAMRI ◽  
Mohamed ELNOUBY ◽  
Tarek TAHA ◽  
M. A. ABU-SAIED ◽  
...  
Keyword(s):  
Ag Nanoparticles ◽  
Hydrothermal Preparation ◽  
Microbial Cells ◽  
Antimicrobial Performance

"Marketocentric" Economics Is Obsolete

2004 ◽  
pp. 36-49 ◽  
Author(s):  
A. Buzgalin ◽  
A. Kolganov
Keyword(s):  
Economic Theory ◽  
Middle Ages ◽  
Modern Science ◽  
Economic Systems ◽  
Main Mode ◽  
Post Market ◽  
Market Relations ◽  
Post Industrial ◽  
The 19Th Century ◽  
The Universe

The "marketocentric" economic theory is now dominating in modern science (similar to Ptolemeus geocentric model of the Universe in the Middle Ages). But market economy is only one of different types of economic systems which became the main mode of resources allocation and motivation only in the end of the 19th century. Authors point to the necessity of the analysis of both pre-market and post-market relations. Transition towards the post-industrial neoeconomy requires "Copernical revolution" in economic theory, rejection of marketocentric orientation, which has become now not only less fruitful, but also dogmatically dangerous, leading to the conservation and reproduction of "market fundamentalism".

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