Staphylococcus aureus  bacteria magnified about 10,000x


Euglena mutabilis , a  photosynthetic   flagellate


A tetrad of  Deinococcus radiodurans , a  radioresistant   extremophile  bacterium


The photosynthetic  cyanobacterium   Hyella caespitosa  (round shapes) with fungal hyphae (translucent threads) in the  lichen   Pyrenocollema halodytes


Wastewater treatment plants  rely largely on microorganisms to  oxidise  organic matter.


A laboratory  fermentation  vessel


The  eukaryotic   parasite   Plasmodium falciparum  (spiky blue shapes), a causative agent of  malaria , in human  blood


Clockwise from top right:  Amoeba proteus ,  Actinophrys sol ,  Acanthamoeba  sp.,  Nuclearia thermophila .,  Euglypha acanthophora ,  neutrophil  ingesting bacteria.


The forms of  pseudopodia , from left: polypodial and lobose; monopodial and lobose; filose; conical; reticulose; tapering actinopods; non-tapering actinopods


Amoeba  phagocytosis  of a  bacterium


Foraminifera  have reticulose (net-like) pseudopods, and many species are visible with the naked eye.


Trophozoites  of the pathogenic  Entamoeba histolytica  with ingested  red blood cells


The first illustration of an amoeboid, from Rösel von Rosenhof's  Insecten-Belustigung  (1755)


Neutrophil  (white blood cell) engulfing anthrax bacteria


A. robustus  grown in culture media (Bowen, Benjamin P., etal)


Basic features of an  in vivo  microrobot   [ 2 ]  In a biohybrid approach, all three of these  basic features can be realised either biologically by a microorganism, or artificially by synthetic attachments. Blue indicates biological entities (flagellated or target cells), red indicates artificial structures (attached tubes, helices, particles, or external devices). Arrows in the upper left panel indicate the motile actor, wave lines in the upper right panel indicate signal pathways. The lower panel shows how functionalities can be carried out based on cell-cell interactions or by synthetic cargo (red particles).


Biohybrid  Chlamydomonas reinhardtii  microswimmers   [ 31 ]  Top: Schematics of production steps for biohybrid  C. reinhardtii . Bottom: SEM images of bare microalgae (left) and biohybrid microalgae (right) coated with chitosan-coated iron oxide nanoparticles (CSIONPs). Images were pseudocolored. A darker green color on the right SEM image represents chitosan coating on microalgae cell wall. Orange-colored particles represents CSIONPs.


Robocolith hybrids combining polydopamine and coccoliths   [ 61 ]   EHUX coccolithophores are cultivated for isolation of coccoliths. When coccoliths (asymmetric morphology) are exposed to light, no collective motion is observed. Coccoliths are then mixed gently with dopamine solutions. Thus, polydopamine-coated coccoliths hybrids are obtained as a basis for design of Robocoliths. Light excitation and the asymmetry of Robocoliths generates a thermal flux of heat because of polydopamine's photothermal properties. Coupling of convection from neighboring Robocoliths transforms their movement into an aggregated collective motion. Robocolith functionalization is also proposed to prevent and control nonspecific attachment of biomacromolecules and possible diminution of the aggregation.


Asymmetric architecture of coccolith morphology   [ 61 ]  (A) EHUX coccolithophores were cultivated successfully and visualized by SEM (scale bar, 4 μm).  (B) Following this, we broke and removed the cellular material from EHUX coccolithophores to isolate multiple (top; scale bar, 20 μm) and individual (bottom; scale bar, 1 μm) coccoliths, as visualized by SEM.  (C) AFM image of an individual coccolith. Micrograph size, 4 × 4 μm.  (D) AFM magnification the micrograph of an individual coccolith. Scale bar, 400 nm.  (E) Illustration of a coccolith, depicting its specific morphological parameters.  (F) Typical plotted values of the specific morphological parameters. Data are represented as mean ± SD (n = 55), where n is the number of coccoliths visualized by TEM.


Emiliania huxleyi  protected with asymmetric  coccoliths


Biohybrid bacterial microswimmers   [ 83 ]


Biohybrid diatomite microswimmer drug delivery system  Diatom frustule surface functionalised with photoactivable molecules (orange spheres) linked to vitamin B-12 (red sphere) acting as a tumor-targeting tag. The system can be loaded with chemotherapeutic drugs (light blue spheres), which can be selectively delivered to colorectal cancer cells. In addition, diatomite microparticles can be photoactivated to generate carbon monoxide or free radicals inducing tumor cell apoptosis. [ 84 ] [ 85 ]


Cable bacteria in between two layers of sediment split apart inside a glass cylinder.


Diagram demonstrating cable bacteria metabolism in surface sediment. Hydrogen sulfide (H 2 S) is oxidized in the sulfidic sediment layer, and the resulting electrons (e − ) are conducted up through the cable bacteria filament to the  oxic  layer and used to reduce molecular oxygen (O 2 ).


Figure 1: Major steps of a CyTOF procedure. Isotope chelation, antibody tagging, cellular staining, and aerosol injection into the ICP-MS, and data analysis.


Role of the microbial community in the marine  carbon cycle


Relative sizes of microscopic entities


The range of sizes shown by  prokaryotes  (bacteria and archaea) and  viruses  relative to those of other organisms and  biomolecules


Under a magnifier, a splash of seawater teems with microscopic life


Sea spray containing marine microorganisms can be swept high into the atmosphere where they become  aeroplankton , and can travel the globe before falling back to earth.


Virus-host interactions in the marine ecosystem, including viral infection of bacteria, phytoplankton and fish [ 30 ]


Virions  of different families of  tailed phages


These are  cyanophages , viruses that infect  cyanobacteria  (scale bars indicate 100 nm)


The giant  mimivirus


Largest known virus,  Tupanvirus , named after  Tupã , the Guarani  supreme god of creation


Pelagibacter ubique , the most abundant bacteria in the ocean, plays a major role in the global  carbon cycle .


Vibrio vulnificus , a virulent bacterium found in  estuaries  and along coastal areas


Electron micrograph showing a species of the widespread cyanobacteria  Synechococcus .  Carboxysomes  appear as polyhedral dark structures.


Archaea were initially viewed as  extremophiles  living in harsh environments, such as the yellow archaea pictured here in a  hot spring , but they have since been found in a much broader range of  habitats . [ 78 ]


Lichen  on a rock in a marine  splash zone . Lichens are mutualistic associations between a fungus and an alga or cyanobacterium.


A  sea snail ,  Littoraria irrorata , covered in lichen. This snail farms intertidal  ascomycetous  fungi


Composite image showing the global distribution of photosynthesis, including both oceanic  phytoplankton  and terrestrial  vegetation . Dark red and blue-green indicate regions of high photosynthetic activity in the ocean and on land, respectively.


Plankton are drifting or floating organisms that cannot swim effectively against a current, and include organisms from most areas of life:  bacteria ,  archaea ,  algae ,  protozoa  and  animals .


Phytoplankton – such as this colony of  Chaetoceros socialis  – naturally gives off red fluorescent light which dissipates excess solar energy they cannot consume through photosynthesis. This glow can be detected by satellites as an indicator of how efficiently ocean phytoplankton is photosynthesising. [ 154 ] [ 155 ]


Structure of a centric diatom frustule [ 162 ]


Model of the energy generating mechanism in marine bacteria (1) When sunlight strikes a rhodopsin molecule (2) it changes its configuration so a proton is expelled from the cell (3) the chemical potential causes the proton to flow back to the cell (4) thus generating energy (5) in the form of  adenosine triphosphate . [ 165 ]


Halobacteria  in  salt evaporation ponds  coloured purple by  bacteriorhodopsin [ 167 ]


Stone dagger of  Ötzi the Iceman  who lived during the  Copper Age . The blade is made of  chert  containing radiolarians, calcispheres, calpionellids and a few sponge spicules. The presence of  calpionellids , which are extinct, was used to date this dagger. [ 216 ]


Archaea rock – this deep ocean rock harboured worms that consumed methane-eating archaea


Main types of microbial symbioses  (A) Microbial interactions range from mutually beneficial to harmful for one or more partners. Blue double headed arrows highlight that relationships can move between classifications often influenced by environmental conditions. (B) Host-microbe symbioses should be considered within the context of microbial communities where the host participates in multiple and often different symbiotic relationships. (C) Microbial communities are influenced by a variety of microbe-microbe symbioses ranging from cooperation (e.g., syntrophy or co-metabolism) to competition. Arrows depict generally beneficial (blue) and detrimental (red) outcomes for one (single arrowhead) or both (double arrowhead) members. Note as with host-microbe symbioses these relationships can be viewed as fluid and influenced by environmental conditions. [ 230 ]


Marine  export production


Marine  microbial loop


Roles of fungi in the marine carbon cycle [ 247 ]


The  viral shunt pathway  facilitates the flow of  dissolved organic matter  (DOM) and  particulate organic matter  (POM) through the marine food web


Size and classification of marine particles [ 249 ] Adapted from Simon et al., 2002. [ 250 ]


Fluorescence microscopy of various  picoplankton  in the ocean, much of which cannot be effectively studied because they resist attempts at laboratory culture


Subsurface life environments


These aerobic microorganisms, found deep in organically poor sediments, have been in quasi-suspended animation for maybe 100 million years


Unidentified spherical algal microorganism, part of the  microbial dark matter


Strategies for sampling plankton by size classes and abundance The blue background indicates the filtered volume required to obtain sufficient organism numbers for analysis. Actual volumes from which organisms are sampled are always recorded. [ 277 ]


DNA barcode  alignment and comparison between the two species of marine bacteria pictured above [ 280 ]


Methods used to study phytoplankton  Three different possibilities to process the sample are using raw samples, fixation or preservation, and filtration. For microscopy and flow cytometry raw samples either are measured immediately or have to be fixed for later measurements. Since molecular methods, pigment analysis and detection of molecular tracers usually require concentrated cells, filter residues serve for phytoplankton measurements. Molecular characterization and quantification of trace molecules is performed using  chromatography ,  mass spectrometry , and  nuclear magnetic resonance  spectroscopy. [ 281 ]


DNA sequencing technologies used in marine metagenomics  The discovery process involves marine sampling,  DNA sequencing  and  contig generation . Previously unknown genes, pathways and even whole genomes are being discovered. These genome-editing technologies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable.  Metagenomics  is providing especially valuable information for uncultivable samples. [ 287 ]


Meta-omics data based biogeochemical modeling  [ 293 ]  A schematic conceptual framework for  marine biogeochemical modeling  from environmental, imaging, and meta-omics data. [ 294 ]  A semi-automatic computational pipeline is schematized for combining biomarkers with biogeochemical data  [ 295 ]  that can be incorporated into classic biogeochemical models  [ 296 ]  for creating a next generation of biogeochemical trait-based meta-omics models by considering their respective traits. Such novel meta-omics-enabled approaches aim to improve the monitoring and prediction of ocean processes while respecting the complexity of the planktonic system. [ 297 ] [ 298 ]


Using omics data with marine phytoplankton [ 299 ]  As an example of how omics data can be used with marine phytoplankton to inform  Earth system science ,  metatranscriptome sequences  from natural phytoplankton communities were used to help identify physiological traits (cellular concentration of  ribosomes  and their  rRNAs ) underpinning adaptation to environmental conditions (temperature). A mechanistic phytoplankton cell model was used to test the significance of the identified physiological trait for cellular  stoichiometry . Environmental selection in a trait‐based global marine ecosystem model was then linking emergent growth and cellular allocation strategies to large‐scale patterns in light, nutrients and temperature in the surface marine environment. Global predictions of cellular resource allocation and stoichiometry (N:P ratio) were consistent with patterns in metatranscriptome data [ 300 ]  and latitudinal patterns in the elemental ratios of marine plankton and organic matter. [ 301 ]  The three‐dimensional view of ribosome shows rRNA in dark blue and dark red. Lighter colours represent  ribosomal proteins . Bands above show temperature‐dependent abundance of the  eukaryotic  ribosomal protein S14. [ 300 ]


Microorganisms and climate change in marine and terrestrial biomes [ 6 ]


Diagram above contains clickable links


This timeline contains clickable links


Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes


The range of sizes shown by  prokaryotes  (bacteria and archaea) and  viruses  relative to those of other organisms and  biomolecules


Sea spray  containing  marine microorganisms , including prokaryotes, can be swept high into the atmosphere where they become  aeroplankton , and can travel the globe before falling back to earth.


Estimates of microbial species counts in the three domains of life  Bacteria are the oldest and most biodiverse group, followed by Archaea and Fungi (the most recent groups). In 1998, before awareness of the extent of microbial life had gotten underway,  Robert M. May [ 49 ]  estimated there were 3 million species of living organisms on the planet. But in 2016, Locey and Lennon  [ 50 ]  estimated the number of microorganism species could be as high as 1 trillion. [ 51 ]


Different bacteria shapes ( cocci ,  rods  and  spirochetes ) and their sizes compared with the width of a human hair. [ 58 ]  A few bacteria are comma-shaped ( vibrio ). Archaea have similar shapes, though the archaeon  Haloquadratum  is flat and square. [ 59 ]     The unit  μm  is a measurement of length, the  micrometer , equal to 1/1,000 of a millimeter


Pelagibacter ubique  of the  SAR11 clade  is the most abundant bacteria in the ocean and plays a major role in the global  carbon cycle .


Scanning electron micrograph of a strain of  Roseobacter , a widespread and important genus of marine bacteria. For scale, the membrane pore size is 0.2   μm in diameter. [ 60 ]


Vibrio vulnificus , a virulent bacterium found in  estuaries  and along coastal areas


Colonies of marine cyanobacteria  Trichodesmium interact with bacteria to acquire iron from dust   a.  The N 2 -fixing  Trichodesmium  spp., which commonly occurs in tropical and sub-tropical waters, is of large environmental significance in fertilizing the ocean with important nutrients. b.   Trichodesmium  can establish massive blooms in nutrient poor ocean regions with high dust deposition, partly due to their unique ability to capture dust, center it, and subsequently dissolve it. c.  Proposed dust-bound Fe acquisition pathway: Bacteria residing within the colonies produce  siderophores  (c-I) that react with the dust particles in the colony core and generate dissolved Fe (c-II). This dissolved Fe, complexed by siderophores, is then acquired by both  Trichodesmium  and its resident bacteria (c-III), resulting in a mutual benefit to both partners of the  consortium . [ 82 ]


The  chloroplasts  of  glaucophytes  have a  peptidoglycan  layer, evidence suggesting their  endosymbiotic  origin from  cyanobacteria . [ 83 ]


Archaea were initially viewed as  extremophiles  living in harsh environments, such as the yellow archaea pictured here in a  hot spring , but they have since been found in a much broader range of  habitats . [ 91 ]


Two  Nanoarchaeum equitans  cells with its larger host  Ignicoccus


A microbial mat encrusted with iron oxide on the flank of a  seamount  can harbour microbial communities dominated by the iron-oxidizing  Zetaproteobacteria


Bacterial flagellum  rotated by a  molecular motor  at its base


Earth's magnetic field


Model of the energy generating mechanism in marine bacteria       (1) When sunlight strikes a rhodopsin molecule       (2) it changes its configuration so a proton is expelled from the cell       (3) the chemical potential causes the proton to flow back to the cell       (4) thus generating energy       (5) in the form of  adenosine triphosphate . [ 152 ]


Halobacteria  in  salt evaporation ponds  coloured purple by  bacteriorhodopsin [ 154 ]


Phylogenetic tree representing bacterial OTUs from  clone libraries  and  next-generation sequencing . OTUs from next-generation sequencing are displayed if the OTU contained more than two sequences in the unrarefied OTU table (3626 OTUs). [ 164 ]


Bacterioplankton and the pelagic marine food web  Solar radiation can have positive (+) or negative (−) effects resulting in increases or decreases in the heterotrophic activity of bacterioplankton. [ 171 ]


Bacteria, sea slicks and satellite remote sensing   Surfactants are capable of dampening the short capillary ocean surface waves and smoothing the sea surface.  Synthetic aperture radar  (SAR) satellite remote sensing can detect areas with concentrated surfactants or sea slicks, which appear as dark areas on the SAR images. [ 174 ]


Export processes in the ocean from remote sensing [ 176 ]


Phylogenetic and symbiogenetic tree of living organisms, showing a schematic view of the central position occupied by the protista (protists)


Schematic view of the eukaryotic  tree of life  with effigies of main marine protist representatives  [ 22 ]


Difference of beating pattern of flagellum and cilium


Marine flagellates from the genera (left to right) Cryptaulax ,  Abollifer ,  Bodo ,  Rhynchomonas ,  Kiitoksia ,  Allas , and  Metromonas   [ 47 ]


Cilia performs powerful forward strokes with a stiffened flagellum followed by relatively slow recovery movement with a relaxed flagellum.


Diatoms come in many shapes and sizes.


Structure of a centric diatom frustule [ 66 ]


The fossil coccolithophore  Braarudosphaera bigelowii  has an unusual shell with a regular dodecahedral structure about 10 micrometers across. [ 74 ]


Conjugation of two  Coleps  sp.  Two similar-looking but sexually distinct partners connected at their front ends exchange genetic material via a plasma bridge.


Yellow-brown zooxanthellae, a photosynthetic algae that lives inside hosts like  radiolarians  and  coral


Planktonic protist interactome   [ 118 ] Bipartite  networks, providing an overview of the interactions represented by a manually curated Protist Interaction DAtabase (PIDA)


Possible ecological interactions between two individuals. The result of the interaction for each member of the pair can be positive, negative or neutral. For example, in predation, one partner obtains the benefits while the other assumes the costs. [ 1 ] [ 2 ]


Main types of microbial symbioses  (A) Microbial interactions range from mutually beneficial to harmful for one or more partners. Blue double headed arrows highlight that relationships can move between classifications often influenced by environmental conditions. (B) Host-microbe symbioses should be considered within the context of microbial communities where the host participates in multiple and often different symbiotic relationships. (C) Microbial communities are influenced by a variety of microbe-microbe symbioses ranging from cooperation (e.g., syntrophy or co-metabolism) to competition. Arrows depict generally beneficial (blue) and detrimental (red) outcomes for one (single arrowhead) or both (double arrowhead) members. Note as with host-microbe symbioses these relationships can be viewed as fluid and influenced by environmental conditions. [ 8 ]


Figure 1 shows  Osedax rubiplumus  with ovisac (red colored projections) which houses symbiont bacteria


Figure 2 shows sagittal section of bobtail squid  Euprymna scolopes . light organ. The crypts house symbiont bacteria  Vibrio fischeri . They emit light during night time to camouflage themselves against the moon and star light coming down the ocean. It helps them to avoid predators.


The sponge holobiont  The sponge  holobiont  is an example of the concept of nested ecosystems. Key functions carried out by the microbiome (coloured arrows) influence holobiont functioning and, through cascading effects, subsequently influence community structure and ecosystem functioning. Environmental factors act at multiple scales to alter microbiome, holobiont, community, and ecosystem scale processes. Thus, factors that alter microbiome functioning can lead to changes at the holobiont, community, or even ecosystem level and vice versa, illustrating the necessity of considering multiple scales when evaluating functioning in nested ecosystems. [ 16 ]   DOM:  dissolved organic matter ; POM:  particulate organic matter ; DIN: dissolved inorganic nitrogen


General steps of methylotrophic metabolism displaying 4 known assimilatory methylotrophic pathways. The general catabolic pathway is also shown. Q denotes a membrane-bound quinone. Methane monooxygenase (MMO) and Formate dehydrogenase (FDH) may be membrane-associated or cytoplasmic while Methanol dehydrogenase (MDH) and Formaldehyde dehydrogenase (FALDH) are always membrane-associated.


RuMP pathway in type I methanotrophs


3-hexulose 6-phosphate (hexulose phosphate)


Microbial consortia naturally formed on the roots of  Arabidopsis thaliana  Scanning electron microscopy pictures of root surfaces from natural A. thaliana populations showing the complex microbial networks formed on roots. a) Overview of an  A. thaliana  root (primary root) with numerous root hairs. b)  Biofilm-forming  bacteria. c)  Fungal  or  oomycete   hyphae  surrounding the root surface. d) Primary root densely covered by  spores  and  protists . e, f)  Protists , most likely belonging to the  Bacillariophyceae  class. g) Bacteria and  bacterial filaments . h, i) Different bacterial individuals showing great varieties of shapes and morphological features. [ 7 ]


Rhizosphere microbial consortia   [ 31 ]


Workflow of enrichment and dilution-to-extinction cultures to select simplified microbial consortia (SMC) for keratin degradation. [ 23 ]


Painting of a cross-section through an  Escherichia coli  bacterium, a   chemoheterotrophic  bacterium often used in synthetic microbial consortia.


Ancient bacteria found in the permafrost possess a remarkable range of antibiotic resistance genes (red). However, their capacity to resist is also generally lower than of modern bacteria from the same area (black). [ 1 ]


Some of the ancient amoeba-eating viruses revived by the research team of Jean-Michel Claverie. Clockwise from the top:  Pandoravirus yedoma ;  Pandoravirus mammoth  and  Megavirus mammoth ;  Cedratvirus lena ;  Pithovirus mammoth ;  Megavirus mammoth ;  Pacmanvirus lupus . [ 13 ]


Topographic map of the Red Sea and the relative location.


Morphologies of varying Caudovirales including  Siphoviridae ,  Myoviridae , and  Podoviridae .


Modern  stromatolites  in Shark Bay, Western Australia. It can take a century for a stromatolite to grow 5 cm. [ 10 ]


Bacteria in a capule


A bottom-dwelling community found deep in the European Arctic. [ 18 ]


Paramecium tetraurelia , a ciliate, with oral groove visible


A scanning electron microscope image of a  diatom


Transmission electron microscope image of budding  Ogataea polymorpha


FMIB 50036 Vibrion Babuette (Muller), magnified


Porosome


An illustration depicting diversity in the architecture of protein secretion systems found in  diderm bacteria [ 1 ]


T1SS schematic


T2SS schematic


T3SS schematic


T4SS schematic


T5SS schematic


ESX-5: type VII secretion system, Mycobacterium xenopi


Type IX secretion system schematic diagram [ 38 ]


Earwax in ear


Dry-type human earwax


World map of the distribution of the A allele of the single nucleotide polymorphism rs17822931 in the  ABCC11  gene associated with dry-type earwax. The proportion of A alleles (dry-type earwax) in each population is represented by the white area in each circle.


An ear-cleaner, attending to a man's ear. Gouache painting, Delhi, 1825.


Photograph of a male  red deer  ( Cervus elaphus ), taken during the  mating season . The prominent preorbital gland is  enlarged  and dilated.


A male  Père David's deer  ( Elaphurus davidianus ). Note the large preorbital gland extending from just below the  orbit .


A male  sambar  ( Rusa unicolor ) in  Pench National Park ,  Madhya Pradesh , India. These animals are often referred to as "four-eyed deer", due to their large preorbital glands. [ 9 ]


Hirola  ( Beatragus hunteri ) are often referred to as the "four-eyed antelope", due to their large preorbital glands [ 13 ]


Circadian and ultradian rhythms of thyrotropin (TSH) concentration. Simulated time series created with  SimThyr .


Insulin release from the islet of Langerhans is pulsatile with a period of 3–6 minutes. [ 21 ]


Conditions of sebaceous glands


Figure 1 Schematic diagram of the basic Trimeric Autotransporter Adhesin structure


Figure 2  The C-terminal membrane anchor domain can clearly be seen on the right in blue. The stalk domain can be seen in red.


Figure 3 The protein domain arrangement of the Trimeric Autotransporter Adhesin, BadA [ 1 ]  This figure shows the head, stalk and anchor domains. It shows the YadA-like head in grey. The stalk contains repeats coloured in green and the membrane anchor in red. The sequence below shows colouring according to domain arrangement and protease cleavage sites red (trypsin) and blue (chymotrypsin). (Figure used from open access journal, in the public domain, Public Library of Science (PLoS) Pathogen


Figure 4 Comparison of Head domains in different Trimeric Autotransporter Adhesins [ 10 ]  (Figure used from open access journal, in the public domain, Public Library of Science (PLoS) Pathogen)


Figure 5 A schematic diagram illustrating the Trimeric Autotransporter Adhesins in Type V  Secretion  System.


Diagram showing the type II secretion system


Type IV Secretion system


A  transmission electron microscope  image of isolated T3SS needle complexes from  Salmonella  Typhimurium


Diagram of individual substructures of the needle complex from  Salmonella typhimurium


The topology and organization of the  Salmonella  needle complex. [ 21 ]


Flagellum of Gram-negative bacteria. The rings of the base are very similar to needle-complex rings, although the existence of a C-ring in the needle complex has not been proven. The flagellar hook is homologous to the T3SS needle


Structure of a Type VI  secretion system


An oligomer formed by one of proteins from Type VI secretion system in  Burkholderia pseudomallei .


The antibacterial mechanism in  P. aeruginosa .  P. aeruginosa  have self-immunity to their own effector toxins: Tsi proteins bind and stabilise Tse toxins, preventing cell senescence and peptidoglycan cell wall lysis.


Currently identified secretion systems


Architecture of Yip1 domain family proteins


Localization of Yip1 domain family members


The magneto-mechano-chemical synthesis (1) is accompanied by splitting of electron energy levels (SEELs) and electron transfer in magnetic field (2) from nanoparticles Fe3O4 to doxorubicin. The concentration of paramagnetic centers (free radicals) is increased in the magneto-sensitive complex (MNC) (3). The local combined action of constant magnetic and electromagnetic fields and MNC in tumor (4) initiated SEELs, free radicals, leading to  oxidative stress ,  electron-  and  proton-transport  deregulation in the mitochondrion and changes in mechanochemical tumor heterogeneity (5). Magnetic nanotherapy has more effectively inhibited the synthesis of ATP in mitochondria of tumor cell and induced the death of tumor cells compared to conventional doxorubicin.


Schematic of a cylindrical superconducting MR scanner. Top: cross section of the cylinder with primary coil, gradient coils and RF transmit coils. Bottom: longitudinal section of the cylinder and table, showing the same coils and the RF receive coil.


A mobile MRI unit


Effects of TR and TE on MR signal


Examples of T1-weighted, T2-weighted and  PD-weighted  MRI scans


Diagram of changing magnetization and spin orientations throughout spin-lattice relaxation experiment


Patient being positioned for MR study of the head and abdomen


Radiologist  interpreting MRI images of head and neck


MRI diffusion tensor imaging of  white matter  tracts


MR angiogram in congenital heart disease


Magnetic resonance angiography


Motion artifact (T1 coronal study of cervical vertebrae) [ 142 ]


The process of magnetofection. Magnet concentrates nanoparticles with gene vectors to cells for transfection.


Neural stem cells growing in culture.


Bruker 700 MHz nuclear magnetic resonance (NMR) spectrometer.


Splitting of nuclei spin energies in an external magnetic field


An intuitive model. Nuclei with spin have  magnetic moments  ( spin magnetic moments ). By itself, there is no energetic difference for any particular orientation of the nuclear magnet (only one energy state, on the left), but in an external magnetic field there is a high-energy state and a low-energy state depending on the relative orientation of the magnet to the external field, and in thermal equilibrium, the low-energy orientation is preferred. The average orientation of the magnetic moment will  precess  around the field. The external field can be supplied by a large magnet and also by electrons and other nuclei in the vicinity.


A  Hahn echo  decay experiment measuring dephasing time.


900 MHz, 21.2  T  NMR Magnet at HWB-NMR, Birmingham, UK


Medical MRI


Schematic of in situ NMR


A collage of different bacteria viewed under a microscope.


Tanmay Bharat at the  MRC Laboratory of Molecular Biology


Dr Mina Bizic at Soapbox Science in Berlin 2020


Mireille Dosso (2011)


Grave of David Gruby,  Saint-Vincent Cemetery ,  Montmartre


Four photographs of a series of underwater fresh water springs found in the Dead Sea, approximately 1.8 km west of Mitzpe Shalem, in 2010 by Danny Ionescu


Irina Ivshina


Memorial at Münster zoo. The medallion was made by sculptor August Schmiemann and unveiled in 1903 by zoo director  Hermann Landois .


1878 engraving


Vilém Dušan Lambl


Vilém Dušan Lambl photographed as a young man


Professor Ogbadu


Rebecca Vega Thurber sampling in Curaçao


Eugène Wollman, circa 1910


Arturo Zychlinsky discovered  Neutrophil Extracellular Traps  (NETs) together with Volker Brinkmann. This scanning electron image shows a NET (green), ejected by a neutrophil (yellow) to capture bacteria (purple). A red blood cell (orange) is also trapped in the NET.


The BCCM collections contain more than 269.000 different resources.


Building where the Culture Collection University of Gothenburg (CCUG) is located.


Headquarters of the National Institute of Molecular Biology and Biotechnology in Los Baños, Laguna


University of Santander


Chlorophyll d


A  bioreactor  containing the anammox bacterium  Kuenenia stuttgartiensis


C17-C20 ladderane lipids from anammox bacteria containing either three linearly  fused  cyclobutane rings and one cyclohexane or five cyclobutane rings. Fatty acids are esterified with methanol or the glycerol backbone, and the ladderane alcohols are ether-linked with glycerol, all in different combinations. [ 7 ]


Figure 2. The biological nitrogen cycle, with  dissimilatory nitrate reduction to ammonium


Figure 3. Possible biochemical pathway and cellular localization of the enzyme systems involved in anammox reaction.


Figure 4. Hypothetical metabolic pathways and reversed electron transport in the anammoxosome. (a) Anammox catabolism that uses nitrite as the electron acceptor for the creation of a proton motive force over the anammoxosomal membrane. (b) Proton motive force- driven reversed electron transport combines central catabolism with nitrate reductase (NAR) to generate ferredoxin for carbon dioxide reduction in the acetyl-CoA pathway. HAO,  hydrazine oxidoreductase ; HD, hydrazine dehydrogenase; HH, hydrazine hydrolase; NIR, nitrite oxidoreductase; Q, quinine. Light blue diamonds, cytochromes; blue arrows, reductions; pink arrows, oxidations.


Wastewater


The Laboratory of Microbiology in  Delft , where Beijerinck worked from 1897 to 1921.


Beijerinck working in his laboratory


General structure of a PCB


Global distribution of  A. thalassa [ 13 ]


Mechanism of Ammonium Oxidation


Cavanaugh's analyses of bacterial symbioses involving  giant tube worms  and other  deep sea   invertebrateshas  led to her being described as a "scientific  Captain Nemo ." [ 3 ] [ third-party source needed ]


Ruth Turner  and Cavanaugh dissecting  Alvin -retrieved clams from the deep sea in 1992


Leica  confocal microscope systems


Anaerobic experiment station


CBE Industrial Associates as of Nov. 1, 2021.


Venenivibrio stagnispumantis  gains energy by oxidizing hydrogen gas.


Giant tube worms ( Riftia pachyptila ) have an organ containing chemosynthetic bacteria instead of a gut.


Figure 1. Steps of Terminal Restriction Fragment Length Polymorphism analysis for a single microbial community with 3 phylotypes


Figure 2. The microbial fingerprinting technique called Denaturing Gradient Gel Electrophoresis. The diagram demonstrates how samples from different microbial communities can be compared.


Figure 3. The microbial fingerprinting technique called (Automated) Ribosomal Intergenic Spacer Analysis. The diagram shows the output of both Automated RISA (Pathway 1) or RISA (Pathway 2).


The Great Sippewissett Salt Marsh


Nitrogen cycle.


Leguminous plants used to fertilize an abandoned land


Escherichia coli , one of the many species of  bacteria  present in the human gut


Composition and distribution of gut microbiota in human body


Candida albicans , a dimorphic fungus that grows as a yeast in the gut


Illustration showing the developmental colonization of gut microbiota


Microfold cells  transfer antigens (Ag) from the lumen of the gut to  gut-associated lymphoid tissue  (GALT) via  transcytosis  and present them to different innate and adaptive immune cells.


Gut–brain axis overview [ 1 ]


Gut-brain communication


Bifidobacterium adolescentis


Lactobacillus  sp 01


Graphic depicting the human  skin microbiota , with relative prevalences of various classes of bacteria


Flowchart illustrating how the human microbiome is studied on the DNA level.


Commensals vs pathogens mechanism. Mechanisms underlying the inflammation in COPD. Airway epithelium has complex structure: consists of at least seven diverse cell types interacting with each other by means of tight junctions. Moreover, epithelial calls can deliver the signals into the underlying tissues taking part in the mechanisms of innate and adaptive immune defence.  The key transmitters of the signals are dendritic cells.  Once pathogenic bacterium (e.g., S. pneumoniae, P. aeruginosa) has activated particular pattern recognition receptors on/in epithelial cells, the proinflammatory signaling pathways are activated.  This results mainly in IL-1, IL-6 and IL-8 production.  These cytokines induce the chemotaxis to the site of infection in its target cells (e.g., neutrophils, dendritic cells and macrophages). On the other hand, representatives of standard microbiota cause only weak signaling preventing the inflammation.  The mechanism of distinguishing between harmless and harmful bacteria on the molecular as well as on physiological levels is not completely understood.


Microbiome-based interventions to modulate gut ecology and the immune system [ 127 ]


Depiction of prevalences of various classes of bacteria at selected sites on human skin


Biofilms in marine environments  Various biofilm components (including bacteria, algae, and fungi) are embedded in a matrix of extracellular polymeric substances.


Stages of biofilm development    1) Initial Attachment 2) Irreversible Attachment 3) Maturation I 4) Maturation II 5) Dispersion.


Scanning electron micrograph of mixed-culture biofilm, showing the arrangement of bacterial cells and extracellular polymeric substances


Various types of interactions within the biofilm (1) Communication through quorum sensing (2) Adaptations to varying conditions such as light


Nutrient cycling in the marine environment


In metagenomics, the genetic materials ( DNA ,  C ) are  extracted  directly from samples taken from the environment (e.g. soil, sea water, human gut,  A ) after filtering ( B ), and are  sequenced  ( E ) after multiplication by  cloning  ( D ) in an approach called  shotgun sequencing . These short sequences can then be put together again using  assembly methods  ( F ) to deduce the individual genomes or parts of genomes that constitute the original environmental sample. This information can then be used to study the  species diversity  and functional potential of the microbial community of the environment. [ 1 ]


Flow diagram of a typical metagenome project [ 19 ]


Schematic representation of the main steps necessary for the analysis of whole metagenome shotgun sequencing-derived data. [ 27 ]  The software related to each step is shown in italics.


Metagenomics allows the study of microbial communities like those present in this stream receiving acid drainage from surface coal mining.


General overview of microbial biodegradation of petroleum oil by microbial communities. Some microorganisms, such as  A. borkumensis , are able to use hydrocarbons as their source for carbon in metabolism. They are able to oxidize the environmentally harmful hydrocarbons while producing harmless products, following the general equation C n H n  + O 2  → H 2 O + CO 2 . In the figure, carbon is represented as yellow circles, oxygen as pink circles, and hydrogen as blue circles. This type of special metabolism allows these microbes to thrive in areas affected by oil spills and are important in the elimination of environmental pollutants.


Decomposing  pig  showing signs of bloat and discoloration, a result of microbial proliferation within the   body.


Proposed evolution of microorganisms within the body during decomposition. As oxygen is available at the beginning of decomposition, aerobic microorganisms flourish and quickly deplete the oxygen. Anaerobic bacteria can then proliferate in the body. Later in the decomposition process, fungi and bacteria from the environment will also become involved in the process.


Skeletonized pig carcass showing the production of a cadaver decomposition island surrounding the remains as a result of leaching of decomposition fluids into the surrounding environment.


Fungal mycelia (white) on hoof of a deceased pig


The nutrient cycles in and around the oxygen minimum zone


Methanogenesis cycle with intermediates


Sulfate reduction pathway


(A) Detection frequencies of the 504 trace substances. Red line is detection frequency of 25%. (B) Maximum concentrations (cmax) of all compounds with cmax > 1 µg/L. (C) Detection frequencies of 96 compounds detected in more than 25% of the samples. The number next to each bar represents the mean concentration (cmed) in µg/L. (D) Maximum concentrations (cmax > 1 µg/L) of compounds detected in more than 25% of the samples. The number next to each bar represents the maximum concentration (cmax) in µg/L. Pesticides and biocides are shown in green, pharmaceuticals in blue and other chemicals in purple.


Block diagram of a so-called Ulm process with powdered activated carbon (PAC)


Phototrophic biofilm cultivated in a lab


Cross-section of a  microbial mat


Crateriform structures. (A) Crateriform structures from the outside of the cell (B–E) Micrographs of crateriform structures, perpendicular to the membrane outer membrane (OM), inner membrane (IM), cytoplasm (C), and periplasm (P). Scale bars, 50 nm [ 16 ]


Representation of cell division modes in the last PVC common ancestor and in current the PVC superphylum: Outer membranes are represented by thick lines, and inner membranes are represented by thin lines. The peptidoglycan layer is displayed in dotted lines, and FtsZ proteins are displayed as a ring of gray circles. [ 26 ]


Transmission electron micrographs of dividing cells displaying different cell division modes in the PVC superphylum. (a)  Gemmata obscuriglobus  (b)  Chthoniobacter flavus  (c)  Lentisphaera araneosa  (d)  Phycisphaera mikurensis  and (e)  Chlamydia trachomatis . Scale bars, 0.5 μm. [ 26 ]


Ecklonia radiata ,  a species of kelp in the phylum  Ochrophyta


Laminaria hyperborea ,  a species of kelp in the phylum Ochrophyta


Labeled diagram of an anammox cell.


Diagram of the anammox mechanisms


Schematic of the microbial loop.


A photo of sewage fungus found in the River Crane (London, England)


Three examples of the triangle inequality for triangles with sides of lengths  x ,  y ,  z . The top example shows a case where  z  is much less than the sum  x  +  y  of the other two sides,  and the bottom example shows a case where the side  z  is only slightly less than  x  +  y .


Environmental Shotgun Sequencing (ESS)           (A) Sampling from habitat           (B) filtering particles, typically by size           (C) Lysis and DNA extraction           (D) cloning and library construction           (E) sequencing the clones           (F) sequence assembly into contigs and scaffolds


This picture depicts the initial appearance of three different Winogradsky columns.  They are soil and water samples from a river, the later two columns have been modified with phosphate, nitrate, sulfur and oxygen additives. These additions promote the growth of various bacteria specific to the anaerobic and aerobic regions of the column.


Shown above as a result of a 7-week period where the columns have been allowed to grow  algae , cyanobacteria and other bacterial colonies.  Of specific interest are the red regions of the middle column, indicative of purple non-sulfur bacteria (e.g.  Rhodospirillaceae ). Also, in column three, the red growth along the side of the column: a purple sulfur bacterium,  Chromatium .


Nitrogen cycle


Main staining types when using  hematoxylin and eosin (H&E) , where acidophile cells stain eosinophilic


Anaerobic  bacteria  can be identified by growing them in test tubes of  thioglycollate broth :   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.   5:  Aerotolerant organisms  do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen.  They can be found evenly spread throughout the test tube.


Alginite


Staphylococcus  growth in Baird-Parker (BP) agar.


After 24 hours of growth, this image depicts four different agar media culture plates that had been inoculated with Shigella sp., Escherichia sp., and Proteus sp. bacteria, (clockwise: MacConkey, Shigella-Salmonella, Bismuth Sulfite, and Brilliant Green agars).


First known science-based boil-water advisory (1866)


P. aeruginosa  with yellow-green pycocyanin-pigment on cetrimid agar-agar


Chocolate agar showing  Francisella tularensis  colonies


Comparison of two culture media types used to grow  Neisseria gonorrhoeae  bacteria. Known as overgrowth,  the nonselective chocolate agar medium on the left, due to its composition, allowed for the growth of organismal colonies other than those of  N. gonorrhoeae , while the selective  Thayer–Martin medium  on the right, containing antimicrobials that inhibit the growth of organisms other than  N. gonorrhoeae , shows no overgrowth, but is positive for  N. gonorrhoeae  bacteria. (Enlarge image to see  N. gonorrhoeae  colonies)


Botryococcus braunii


Multiwell culture plates


Penicillium  mold colonies in a Petri dish


Aspergillus tubingensis  growing on Czapek medium


Aspergillus bertholletius  on Czapek agar


Aspergillus fumigatus  on Czapek agar


Blacksmoker  thermal vent


Endo agar


French depiction of gongylidia and staphylae in different sizes


Photograph of gongylidia (G) and staphylae (S) in a fungal garden taken care of by  Acromyrmex echinatior


Dr. Kerstin Voigt, head of the Jena Microbial Resource Collection


The fungus  Lichtheimia corymbifera


The fungus  Mucor mucedo


Kinyoun stain on organism  Mycobacterium smegmatis


Photograph of a fungus (unidentified) mounted using a Lactofuchsin mount.


Fusarium oxysporum   conidiophores  stained by lactophenol cotton blue


LIA used in test


An MSA plate with  Micrococcus  sp. (1),  Staphylococcus epidermidis  (2) and  S. aureus  colonies (3).


Methylmalonyl-CoA pathway


Endospore made visible with a stain


MRC-5 cell


Adelchi Negri


Negri's tomb in the Monumental Cemetery in Pavia


Escherichia coli  is a neutrophilic organism. [ 1 ]


Streak plates  of several bacterial species on nutrient agar plates


Aerobic and anaerobic  bacteria  can be identified by growing them in test tubes of  thioglycollate broth :   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.   5:  Aerotolerant organisms  do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen.  They can be found evenly spread throughout the test tube.


Toxoplasma gondii in a bar-shouldered dove, lung. Two  tachyzoites  enclosed in a parasitophorous vacuolar membrane (pvm). Note conoid (co), micronemes (mn), rhoptries (ro) with honey-combed contents, and a nucleus (nu) in each tachyzoite. The parasitophorous vacuole has membranous tubules. Transmission electron microscopy.


An isolate of  Erythropsidinium . The arrow indicates the piston; the double arrowhead indicates the  ocelloid . Scale bar 20 μm. [ 1 ]


Alataspora solomoni , a  myxosporean  parasite of Atlantic horse mackerel, showing the arrangement of the polar capsules on either side of the sutural line.


Aspergillus  sp.  growing in potato dextrose agar


Risk assessment relative to the other activities of risk analysis1


Bottom view of a Sabouraud agar plate with a colony of  Trichophyton rubrum  var.  rodhaini


Sporothrix schenckii  in Sabouraud agar


Candida albicans  in Sabouraud agar


Trichophyton  terrestre  in Sabouraud agar


A stained preparation of  Bacillus subtilis  showing endospores as green and the vegetative cell as red


Albomycin δ2, a sideromycin, bound to iron


Simmons' citrate agar (not planted yet)


Comparison of two culture media types used to grow  Neisseria gonorrhoeae  bacteria. Known as overgrowth, note that the non-selective  chocolate agar  medium on the left, due to its composition, allowed for the growth of organismal colonies other than those of  Neisseria gonorrhoeae , while the selective Thayer–Martin medium on the right, containing antimicrobials that inhibit the growth of organisms other than  N. gonorrhoeae , shows no overgrowth, but is positive for  N. gonorrhoeae  bacteria.


Aerobic and anaerobic  bacteria  can be identified by growing them in test tubes of thioglycolate broth:   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube, but not the very top.   5:  Aerotolerant organisms  do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes, though, they are not poisoned by oxygen.  They can be found evenly spread throughout the test tube.


Thioglycollate broth medium is recommended to isolate strict  anaerobes  should an anaerobic infection be suspected. [ 2 ]


Principle of transcriptional memory. A pulse of an inducer (priming) results in expression of target genes, which subsides upon withdrawal. During a window of no induction (window of memory), some genes maintain a poised but transcriptionally silent state that results in a stronger gene activation upon a second challenge.


Paramecium tetraurelia,  a ciliate, with discharged trichocysts (artificially colored in blue).


Colonies of Micrococcus luteus on Tryptic Soy Agar. Cultivation 48 hours, 37°C.


An  agar plate  containing tryptone supporting growth of a micro-organism.


Helicobacter pylori  colonized on the surface of regenerative epithelium, stained with the Warthin–Starry method.


Clusters of  bacteria  (arrow) shown on Warthin–Starry stain.


Blood smear taken from a patient with bubonic plague. Note the safety pin appearance of  Yersinia pestis . Magnification ×1000. Wayson stain.


Salmonella growing on XLD agar


YPD medium bottle and YPD agar plate


An  agar plate  streaked with  microorganisms


Avicenna  postulated the existence of microorganisms.


Antonie van Leeuwenhoek  (1632–1723)


Statue of  Robert Koch , one of the founders of microbiology, [ 13 ]  in Berlin


Martinus Beijerinck  is often considered a  founder of virology .


Innovative  laboratory glassware  and experimental methods developed by  Louis Pasteur  and other biologists contributed to the young field of bacteriology in the late 19th century.


A university food microbiology laboratory


Fermenting tanks with  yeast  being used to  brew   beer


Aerobic and anaerobic  bacteria  can be identified by growing them in test tubes of  thioglycollate broth :   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.   5:  Aerotolerant organisms  do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen.  They can be found evenly spread throughout the test tube.


Some common air-borne spores


A puffball mushroom ejecting its spores.


Illustration depicting inflammation associated with allergic rhinitis.


Map of precipitation change at +2 °C of global warming


Steps of Alkaline lysis. Created in  https://BioRender.com


'The All-Species Living Tree' Project logo


The  heterolobosean  pathogen  Naegleria fowleri  can behave as an amoeba (center) or as a flagellate (right).


The  choanoflagellate   Salpingoeca rosetta  can switch between a swimming ( flagellate ) stage and a crawling ( amoeboid ) stage when subjected to a confined space. [ 3 ]


Spinoloricus cinziae , a metazoan that metabolises with hydrogen, lacking  mitochondria  and instead using  hydrogenosomes .


Aerobic and anaerobic  bacteria  can be differentiated by culturing them in test tubes of  thioglycollate broth :  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest. Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest. Facultative anaerobes  can grow with or without oxygen because they can metabolize energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more  adenosine triphosphate  (ATP) than either fermentation or anaerobic respiration. Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top. Aerotolerant organisms do not require oxygen as they metabolize energy anaerobically. Unlike obligate anaerobes, however, they are not poisoned by  oxygen . They can/will be evenly distributed throughout the test tube.


Example of a workup algorithm of possible bacterial infection in cases with no specifically requested targets (non-bacteria, mycobacteria etc.), with most common situations and agents seen in a New England community hospital setting. Multiple anaerobic growth media are mentioned among agar plate cultures. Anaerobes may also be identified by  MALDI-TOF  as shown at bottom right.


Depiction of a once water covered Mars


Anabaena  flosaquae , a cyanobacterium that would thrive on Mars


Prototypal diagram of Mars bioreactor


Cyanobacteria  such as these carry out  photosynthesis .  Their emergence foreshadowed the evolution of many photosynthetic plants and  oxygenated Earth's atmosphere .


Graphic showing net annual amounts of CO 2  fixation by land and sea-based organisms.


Overview of the six known biological carbon fixation cycles


Overview of the Calvin Cycle


Reverse Krebs Cycle


The reductive acetyl-CoA pathway


Part 1


Part 2


Borgs features including tandem, direct, and inverted repeats.


Food microbiology laboratory at the  Faculty of Food Technology ,  Latvia University of Life Sciences and Technologies .


Salmonella  bacteria (red) invade cultured human cells


S. aureus  uses coagulase to form a fibrin coat from fibrinogen present in the bloodstream. This helps the bacteria evade detection and phagocytosis by the immune system.


A fibrin clot formed in a test tube by the  coagulase reaction


This clinic uses  negative room pressure  to prevent disease transmission


Fungi acting as decomposers of a fallen tree branch


Sample of penicillin mould presented by Alexander Fleming to Douglas Macleod in 1935


Alexander Fleming in his laboratory at  St Mary's Hospital , London


St Mary's Hospital showing Fleming's lab and Praed Street


Fleming at work in his laboratory at St Mary's Hospital, London, during the Second World War


Nobel Prize in Physiology or Medicine  medal awarded to  Sir  Alexander Fleming , on display at the  National Museum of Scotland


Cuvettes for in-vitro electroporation. These are  plastic  with aluminium  electrodes  and a blue lid. They hold a maximum of 400  μl .


Schematic cross-section showing the theoretical arrangement of lipids in a hydrophobic pore (top) and a hydrophilic pore (bottom).


This figure shows that exotoxins are secreted by bacterial cells,  Clostridium botulinum  for example, and are toxic to somatic cells. Somatic cells have  antibodies  on the cell wall to target exotoxins and bind to them, preventing the invasion of somatic cells. The binding of the exotoxin and antibody forms an antigen-antibody interaction and the exotoxins are targeted for destruction by the immune system. If this interaction does not happen, the exotoxins bind to the  exotoxin receptors  that are on the cell surface and causes death of the host cell by inhibiting protein synthesis. This figure also shows that the application of heat or chemicals to exotoxins can result in the deactivation of exotoxins. The deactivated exotoxins are called toxoids and they are not harmful to somatic cells.


Louis Pasteur , Archives Photographiques


Process of  Fermentation


A fermentation lock, an example of a curved neck apparatus used in brewing today


Burton Union fermentation system, Coors Visitor Centre


A  Bacillus cereus  cell that has undergone filamentation following antibacterial treatment (upper electron micrograph; top right) and regularly sized cells of untreated  B. cereus  (lower electron micrograph)


"Flagellata" from  Ernst Haeckel 's  Artforms of Nature , 1904


Parasitic  Excavata  ( Giardia lamblia )


Green algae  ( Chlamydomonas )


"Flagellata" from  Encyclopædia Britannica


Cultivated shiitake mushrooms


A merchant selling oyster mushrooms that have been grown indoors


Home-cultivated  shiitake  developing over approximately 24 hours


Harvesting  Pleurotus ostreatus , cultivated using  spawns  embedded in  sawdust  mixture placed in plastic containers


Details of the gill structure of the edible oyster mushroom  Pleurotus ostreatus [ 27 ]


Scanning electron microscope  image of  Vibrio cholerae ,  the  bacterium  that causes  cholera


A representation by  Robert Seymour  of the cholera epidemic depicts the spread of the disease in the form of poisonous air.


Louis Pasteur's  spontaneous generation  experiment illustrates that liquid nutrients are spoiled by particles in the air rather than the air itself. These results of these experiments supported the germ theory of disease.


Griffith's experiment discovering the "transforming principle" in  Streptococcus pneumoniae (pneumococcal) bacteria.


Glass phial of British Standard penicillin


Penicillium  mould on an orange


Penicillium mould


Alexander Fleming in his laboratory at  St Mary's Hospital , London


St Mary's Hospital showing Fleming's lab and Praed Street


Howard Florey  in his office in 1944


The  Sir William Dunn School of Pathology  in Oxford


Ernst Chain  in his laboratory


Thousands of glass fermentation vessels like this one were used in laboratories to produce penicillin. The mould was grown on the surface of a liquid filled with nutrients. The stopper kept contaminants out while allowing the mould to get fresh air.


A laboratory worker sprays a solution containing penicillin mould into flasks of  corn steep liquor  medium, to encourage further penicillin growth.


Mary Hunt, believed to be on the left, with a fellow worker inside the USDA Northern Regional Research Laboratory,  c.  1943


The USDA's penicillin research team. Back row, left to right: Dorothy Fennell Alexander, H. T. Herrick, F. H. Stodola,  Kenneth B. Raper , Robert Coghill, George Ward and  Andrew J. Moyer


A notebook page signed by Dorothy Fennell Alexander. The circled strain, PS46 (later known as NRRL 1951), was the top performer.


A 1957 fermentor used to grow Penicillium mould in the  Science Museum, London


Mould being strained at the harvest table during the manufacture of penicillin at the  Commonwealth Serum Laboratories  in  Parkville, Victoria .


Penicillin production at the Royal Navy Medical School in  Clevedon , Somerset, in 1944


Construction workers are exhorted to complete work on penicillin plants


Poster touting the value penicillin to inspire workers


1945 molecular model of Penicillin by  Dorothy Hodgkin


Nobel Prize in Physiology or Medicine  medal awarded to  Sir  Alexander Fleming , on display at the  National Museum of Scotland


Amoxicillin


Antibiotic-resistance is a growing public health concern.


Antibiotic use in livestock


Unbleached and bleached coral


Green Vegetable Bug ( Nezara viridula ) in  Fronton , France


Neo-Lamarckian  inheritance of hologenome


Pea aphids extracting sap from the stem and leaves of garden peas


Some representative hopanoids: A. Diploptene, also called 22(29)-hopene  B. Diplopterol, also called hopan-22-ol, the hydrated cyclomer of diploptene  C. Bacteriohopanetetrol (BHT), a common extended hopanoid  D. Hopane, the diagenetic product of A and B that results from reducing conditions during deposition and persists in the rock record. The diagenetic product of C would be an extended C 35  hopane.


Active site of the squalene-hopene cyclase from  Methylococcus capsulatus  engaging the substrate, squalene, shown in gold. The cyclase is depicted as a monomer.


Alpha barrel structure of the squalene-hopene cyclase from  Methylococcus capsulatus . Alpha helices are shown in blue, loop regions in green, and beta sheets in red.


Structure of a 2-α-methylhopane with the carbons of the base hopane structure numbered according to convention. The methyl group at the C 2  position is indicated in red.


Electron micrograph of  Caenorhabditis elegans


Imbalance between our knowledge of  C. elegans  biology gained by laboratory discoveries versus  C. elegans  natural ecology


Pseudomonas


Caenorhabditis elegans  intestine infected with  Bacillus thuringiensis


Calendar from a Medieval  book of hours : the month of December, showing a  baker  putting  bread  into the oven. c. 1490–1500


A 16th-century brewery, engraved by  Jost Amman


An early  Penicillin  bioreactor, from 1957, now in the  Science Museum, London


Scientists working with Class III cabinets at the U.S. Biological Warfare Laboratories, Camp Detrick, Maryland, in the 1940s


Jack London 's 1912  The Scarlet Plague  was reprinted in the February 1949 issue of  Famous Fantastic Mysteries , the cover illustrated by  Lawrence Sterne Stevens .


Semper Augustus Tulip , 17th century, owed its pattern to  a virus .


A photomicrograph of a stool that has shigella dysentery. This bacteria typically causes foodborne illness.


Two pinworms next to a ruler, measuring in 6 millimeters in length


Magnified 100X and stained. This photomicrograph of the brain tissue shows the presence of the prominent spongiotic changes in the cortex, with the loss of neurons in a case of a variant of Creutzfeldt-Jakob disease (vCJD)


Chemosynthetic   microbial mats  at the junction between  hydrothermal vent  and  coral reef  communities


A cloud of effluent being violently expelled by a hydrothermal vent.


A diagram showing the process of how seawater becomes a part of the hydrothermal effluent including the elements that are added and precipitated.


The sulfur cycle processes relevant to hydrothermal vent microbial communities with examples of phyla/genera.


Processes of the nitrogen cycle relevant to microbial communities at hydrothermal vents, including names of pyla/genera. Adapted from Gruber et al. (2008)


Black smoker  in the High Rise portion of the  Endeavour Hydrothermal Vents .


Lysogenic Cycle: 1. The prokaryotic cell is shown with its DNA, in green. 2. The bacteriophage attaches and releases its DNA, shown in red, into the prokaryotic cell. 3. The phage DNA then moves through the cell to the host's DNA. 4. The phage DNA integrates itself into the host cell's DNA, creating prophage. 5. The prophage then remains dormant until the host cell divides. 6. After the host cell has duplicated, the phage DNA in the daughter cells activate, and the phage DNA begins to express itself. Some of the cells containing the prophage go on to create new phages which will move on to infect other cells.


Figure 1: Equivalent electrical circuit to model a couple of electrodes in direct contact with a liquid medium


Figure 2: R s  curve and bacterial concentration curve as function of time


Figure 3: R s  curves for samples featuring different bacterial concentration as function of time


IMViC Results


In Situ Bioremediation


Synthesis and general structure of polychlorinated byphenyls.


Rickettsia rickettsii  (stained red) within tick haemolymph cells.


Bacteria extracted from soil sample.


Example of gram staining on a gram positive rod.


Collage depicting the Franco-Prussian war.


Robert Koch was a German physician. He was awarded the Nobel Prize in Physiology or Medicine for his tuberculosis findings in 1905. He is considered one of the founders of microbiology.


Louis Pasteur [1822 - 1895], microbiologist and chemist Description.


Cholera bacteria under a microscope.


Candida albicans


Gram stain of lactobacilli and squamous epithelial cells in vaginal swab


Bacteroides


Fusobacterium


Staphylococcus epidermidis 01


Enterococcus faecalis


Escherichia coli (257 06) Gramnegative rods


Candida albicans  ( Gram stain )


An example of what prehistoric Microbial matgrounds may have looked like. The wrinkled "elephant skin" texture is seen throughout most Precambrian sediments.


Microbes and men: scientists working with Class III cabinets at the U.S.  Biological Warfare  Laboratories, Camp Detrick, Maryland, in the 1940s


Beach scene with bacterial strains expressing different kinds of  fluorescent protein , from the laboratory of the  Nobel Prize –winning biochemist  Roger Tsien


Cell to Cell , winner of 2015  ASM  Agar Art Competition (by Mehmet Berkmen and Maria Peñil)


Cyst stage of  Entamoeba histolytica


Cyst of  Artemia salina


Life cycle of  Giardia


Cryptosporidium  life cycle


Cryptosporidium  under a microscope.


Bacteria are classified by their shape.


Taq polymerase which is used in Polymerase Chain Reaction(PCR)


The  cyanobacterial   algal mat , salty lake on the  White Sea  seaside


Stromatolites  are formed by some microbial mats as the microbes slowly move upwards to avoid being smothered by sediment.


Wrinkled Kinneyia-type fossil sedimentary structures formed beneath cohesive microbial mats in  peritidal zones . [ 11 ]  The image shows the location, in the  Burgsvik beds  of  Sweden , where the texture was first identified as evidence of a fossil microbial mat. [ 12 ]


Fossil  Kinneyia -like structure in the Grimsby Formation (Silurian) exposed in Niagara Gorge, New York


Blister-like fossil microbial mat on ripple-marked surface of a  Cambrian  tidal flat at  Blackberry Hill , Wisconsin


Diverse microbial communities of characteristic microbiota are part of  plant microbiomes , and are found on the outside surfaces and in the internal tissues of the host plant, as well as in the surrounding soil. [ 1 ]


The predominant species of  bacteria  on  human skin


Pathogenic  microbiota causing  inflammation  in the lung


Routes of colonization of potato tubers by bacteria [ 45 ]


Light micrograph of a cross section of a coralloid root of a cycad, showing the layer that hosts symbiotic cyanobacteria


Bleached branching coral (foreground) and normal branching coral (background). Keppel Islands,  Great Barrier Reef .


Smear from solid medium and liquid medium


Tissue processing - Embedding station


Tissue processing - Tissue sections on slides are stained on an automated stainer


Paraffin wax


Microtome-knife-profile


Christian Gottfried Ehrenberg


Ernst Marcus  - 1943


A mixotrophic plant using mycorrhizal fungi to obtain photosynthesis products from other plants


Traditional classification of mixotrophic protists  In this diagram, types in open boxes as proposed by Stoecker  [ 18 ]  have been aligned against groups in grey boxes as proposed by Jones. [ 19 ] [ 20 ]                                DIN = dissolved inorganic nutrients


A variety of different bacteria - testing for antimicrobial resistance


Structures found in the  ALH84001 meteorite  are similar to the structures found in nanobes


Necrobiome on pig cadaver


Aerobic and anaerobic  bacteria  can be identified by growing them in test tubes of  thioglycollate broth :   1:  Obligate aerobes  need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.   2:  Obligate anaerobes  are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.   3:  Facultative anaerobes  can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.   4:  Microaerophiles  need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.   5:  Aerotolerant organisms  do not require oxygen and cannot utilise it even if present; they metabolise energy anaerobically. Unlike obligate anaerobes, however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.  Both facultative anaerobes and aerotolerant organisms will undergo fermentation in the absence of oxygen, but the facultative anaerobes will switch to aerobic metabolism when oxygen is present (a phenomenon known as the  Pasteur effect ). The Pasteur effect is sometimes used to distinguish between facultative anaerobes and aerotolerant organisms, in the lab.


Thrush, a common condition caused by overgrowth of the fungus Candida albicans. Cases are characterized by growth of matted, yellow-white patches of fungus in the mouth.


Oral Microbiology Lab Analysis Report. [ 10 ]


Systemic effects of human oral microbiome. [ 34 ]


Pangenome analysis of  Streptococcus agalactiae  genomes made with Anvi'o  [ 1 ]  software whose development is led by  A. Murat Eren . Genomes obtained from Tettelin et al. (2005). [ 2 ]  Each circle corresponds to one genome and each radius represent a gene family. At the bottom and at right are localized the core genome families. Some families in the core may have more than one homologous gene per genome. In the middle, at the left of the figure the shell genome is observed. At the top left are shown families from the dispensable genome and singletons.


In the pangenome, we can identify three sets of genes: Core, Shell, and Cloud genome. The Core genome comprises the genes that are present in all genomes analyzed. To avoid dismissing families due to sequencing artifacts some authors consider the softcore (>95% occurrence). The Shell genome consists of the genes shared by the majority of genomes (10-95% occurrence). The gene families present in only one genome or <10% occurrence are described as Dispensable or Cloud genome.


a) Closed pangenomes are characterized by large core genomes and small accessory genomes. b) Open pangenomes tend to have small core genomes and large accessory genomes. c) The size of open pangenomes tends to increase with every added genome, meanwhile closed pangenome's size tends to be asymptotic despite adding more genomes. Due to this characteristic, complete pangenome size for closed pangenomes can be predicted.


The supergenome is defined as all genes accessible for a certain species, the pangenome if sequencing of all genomes of one species was available. Metapangenome is the pangenome analysis applied to metagenomic samples, where the union of genes of several species is evaluated for a given habitat.


The  S. pneumoniae  pan-genome. (a) Number of new genes as a function of the number of sequenced genomes. The predicted number of new  genes  drops sharply to zero when the number of genomes exceeds 50. (b) Number of core genes as a function of the number of sequenced genomes. The number of core genes converges to 1,647 for number of genomes n→∞. From Donati et al. [ 36 ]


Pangenome analysis of genomes of  Streptococcus agalactiae . [ 2 ]  Example of phylogenies made with BPGA software. This software allows us to generate phylogenies based on the clustering of the core genome or pangenome. Core and pan phylogenetic reconstructions are not necessarily matching.


Pangenome graph of 3 117  Acinetobacter baumannii  genomes generated with PPanGGOLiN software. Edges correspond to genomic colocalization and nodes correspond to genes. The thickness of the edges is proportional to the number of genomes sharing that link. The edges between persistent (similar to core genes), shell and cloud nodes are colored in orange, green and blue, respectively.


Example of possible outputs of BPGA software. Pangenome analysis of genomes of  Streptococcus agalactiae . At the left, the distribution of Go terms by core/dispensable/unique genome is shown. In this example, the category replication, recombination, and repair are enriched on unique gene families. On the right, a typical pan/core plot is shown, when more genomes have added the size of the core is decreasing, and on the contrary the size of the pangenome increases. [ 2 ]


A photomicrograph of a stool that has shigella dysentery. These bacteria typically cause foodborne illness.


Magnified 100× and stained. This photomicrograph of the brain tissue shows the presence of the prominent spongiotic changes in the cortex, with the loss of neurons in a case of a variant of Creutzfeldt-Jakob disease (vCJD)


Two pinworms next to a ruler, measuring 6 millimeters in length


Brown rot fungal disease on an apple. Brown rot typically target a variety of top-fruits.


A structure of Doxycycline a tetracycline-class antibiotic


Summary of dynamic genomics events


Pan-genome overview


Staphylococcus aureus biofilm


Summary of host-microbe project goals in the Pathogenomics European Research Agenda [ 9 ]


Baby receiving immunizations


Bacterial black spot of mango caused by  Xanthomonas citri  pv.  mangiferaeindicae


Bacterial leaf blight of common panax ( Polyscias guilfoylei ) caused by  Xanthomonas campestris  pv.  hederae


Phage display cycle. 1) fusion proteins for a viral coat protein + the gene to be evolved (typically an antibody fragment) are expressed in bacteriophage. 2) the library of phage are washed over an immobilised target. 3) the remaining high-affinity binders are used to infect bacteria. 4) the genes encoding the high-affinity binders are isolated. 5) those genes may have random mutations introduced and used to perform another round of evolution. The selection and amplification steps can be performed multiple times at greater stringency to isolate higher-affinity binders.


A culture of bacteria infected by bacteriophages, the "holes" are areas where the bacteria have been killed by the virus. The culture is 10cm in diameter.


Transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall


Chart demonstrating variations in the phageome as seen due to age, disease, diet and methodological choices in research.


Placenta and its tissue layers


Sunlight and carbon dioxide from the atmosphere are absorbed by the leaves in the plant and converted to fixed carbon. This carbon travels down into the roots of the plant, where some travels back up to the leaves. The fixed carbon traveling to the root is radiated outward into the surrounding soil where microbes use it as food for growth. In return, microbes attach to the plant root where it improves the roots access to nutrients and its resistance to environmental stress and pathogens. In specific plant/root symbiotic relationships, the plant root secretes flavonoids into the soil which is sensed by microbes, where these microbes release nod factors to the plant root which promotes the infection of the plant root. These unique microbes carry out nitrogen fixation in root nodules, which supplies nutrients to the plant.


Microorganisms reside in saliva


Salivary glands : 1. parotid , 2. submandibular , 3. sublingual .


Two serotypes 1a and 1b with  antigens  2a and 2b on surface, which are recognized by two distinct  antibodies , 3a and 3b, respectively


Agglutination of  HLA-A3  positive  red blood cells  with anti-A3 alloreactive  antisera  containing Anti-A3  IgM


Ribbon diagram  of Shiga toxin (Stx) from  S. dysenteriae . From  PDB :  1R4Q .


SLT2 from  Escherichia coli  O157:H7 . A-subunit is shown above (viridian), with B-subunit  pentamer  below (multicolored). From  PDB :  1R4P .


Lactococcus lactis  micrograph courtesy of Kenneth Todar, PhD.


Wisconsin is a great cheese state.


The  bobtail squid  can be a home for  Aliivibrio fischeri


Aliivibrio fischeri  glowing on a petri dish


Flavobacterium akiavivensis  was discovered in an ʻākia bush.


Saccharomyces cerevisiae  (brewer's yeast) as seen in a scanning electron micrograph.


Beer is a noteworthy product of brewer's yeast, the Official Microbe of Oregon.


Streptomyces griseus  shown in a color-enhanced scanning electron micrograph. Original b&w image used with permission of the Actinomycetes Society of Japan by S. Amano, S. Miyadoh & T. Shomura .


The potent antibiotic streptomycin is produced by Streptomyces griseus.


Penicillium chrysogenum  produces the antibiotic penicillin


Penicillin continues to have a profound effect on infectious disease.


The penicillin G molecule.


Microorganisms growing on an  agar  plate


Joseph Lister , a pioneer of  antiseptic surgery .


Apparatus to sterilize surgical instruments (1914–1918)


Dry heat sterilizer


Chemiclav


Efficiency illustration of the different radiation technologies (electron beam, X-ray, gamma rays)


A  curette  in sterile packaging.


In the theory of symbiogenesis, a merger of an  archaean  and an aerobic bacterium created the eukaryotes, with aerobic  mitochondria ; a second merger added  chloroplasts , creating the green plants. The original theory by  Lynn Margulis  proposed an additional preliminary merger, but this is poorly supported and not now generally believed. [ 1 ]


Konstantin Mereschkowski 's 1905  tree-of-life  diagram, showing the origin of complex life-forms by two episodes of symbiogenesis, the incorporation of  symbiotic   bacteria  to form successively  nuclei  and  chloroplasts [ 4 ]


An  autogenous model  of the origin of eukaryotic cells. Evidence now shows that a mitochondrion-less eukaryote has never existed, i.e. the nucleus was acquired at the same time as the mitochondria. [ 22 ]


Internal symbiont :  mitochondrion  has a  matrix  and membranes, like a free-living  alphaproteobacterial  cell, from which it may derive.


Diagram of endomembrane system in eukaryotic cell


The  human mitochondrial genome  has retained genes encoding 2  rRNAs  (blue), 22  tRNAs  (white), and 13 redox  proteins  (yellow, orange, red).


a  TEM  picture of E. coli, chemoheterotrophic bacteria often used in synthetic microbial consortia.


DNA microarray  used to analyze the expression of human (left) and mouse genes.


Microbiome analysis flowchart


Epstein–Barr virus


Escherichia coli


Candida  sp.


Bar chart demonstrating increased publications focusing on the uterine microbiome.  A search keyword of “uterine microbiome” was used on Web of Science, and this bar chart only included articles and review papers. The date range of this search is from January 1, 2013 to March 26, 2024.


Lactobacilli and a vaginal  squamous  cell


Glycogen is the complex form of sugar present in the  vaginal epithelium  that is metabolized into lactic acid


Gram stain of lactobacilli and squamous epithelial cells in vaginal swab


Gram stain of a vaginal swab showing gonococci (in pairs - arrow) inside polymorphonuclear granulocytes


Vaginal squamous cell with normal vaginal flora versus  bacterial vaginosis  on  Pap stain . Normal vaginal flora (left) is predominantly rod-shaped  Lactobacilli , whereas in bacterial vaginosis (right) there is an overgrowth of bacteria, which can be of various species.


Viability PCR workflow


Halteria  sp. A species capable of virivory


Paramecium bursaria .  A species capable of virivory.


The viral shunt that demonstrates the movement of organic matter from an organism into the dissolved and particulate organic matter pools.


Host cell lysis of a virally infected cell results in the release of both DOM and viral progeny. Viral progeny is taken up by grazers, which are then consumed by organisms of higher trophic levels.


Oxyrrhis marina , a heterotrophic dinoflagellate.


Scenario 1 represents vertical migration of copepods through the water column. Scenario 2 represents the sinking of fecal pellets from the mixed layer.


Negombata magnifica .  A red sea sponge capable of filtering marine viruses. [ 23 ]


Zodleton Spring: sediments under the spring water


Adult  black fly  ( Simulium yahense ) with  Onchocerca volvulus  emerging from the insect's antenna. The parasite is responsible for the disease known as  river blindness  in Africa. Sample was chemically fixed and critical point dried, then observed using conventional scanning electron microscopy. Magnified 100×.


The  Italian   Francesco Redi , considered to be the father of modern parasitology, was the first to recognize and correctly describe details of many important  parasites . [ 2 ]


Cyst and imago of  Giardia lamblia , the protozoan parasite that causes  giardiasis . The species was first observed by  Antonie van Leeuwenhoek  in 1681.


Steer  with bovine trypanosomiasis


Cachectic  dog infested with  T. congolense  after travel in  West Africa


Schistosoma haematobium egg


Capillaria hepatica  eggs from the corpse of an adolescent from the late  Roman  period in France, treated with  petrographic  methods


The capture, captive breeding, and reintroduction of  California condors  into the wild was the most expensive species conservation project in United States history. The bird was saved from extinction but its  ectoparasite , the  louse   Colpocephalum californici , became extinct. [ 1 ]


Ryukyu rabbit tick


IUCN SSC parasite specialist group logo


A  mosquito  shortly after obtaining blood from a human (note the droplet of blood plasma being expelled as the mosquito squeezes out excess water). Mosquitos are a vector for several diseases, including  malaria .


The  deer tick , a vector for  Lyme disease  pathogens


This figure shows how the  Flavivirus  is carried by  mosquitos  in the  West Nile virus  and  Dengue fever . The mosquito would be considered a disease vector.


Public health agencies educate people about many different disease vectors.  This artwork, at the  London School of Hygiene and Tropical Medicine , shows 10 different animal vectors.


When comparing host sister clades we tend to find taxonomically richer parasite fauna on the taxonomically richer group of hosts.


The "F-diagram" ( feces ,  fingers ,  flies ,  fields ,  fluids ,  food ), showing pathways of fecal–oral disease transmission. The vertical blue lines show barriers:  toilets ,  safe water ,  hygiene  and  handwashing .


Villagers during a  community-led total sanitation  (CLTS) triggering exercise go to the place where meals are prepared to observe how flies are attracted to  human feces  and carry diseases by landing on the food (village near Lake Malawi, Malawi)


School children during a CLTS triggering event in West Bengal, India looking at a glass of water and fresh  human feces  where the flies pass from the water to the feces and back. This demonstrates how pathogens can pollute water.


Modified F-diagram including interventions that can block human exposure to animal feces. [ 7 ]


Launcelot Harrison 1880-1928


Schematic diagram of Harrison's rule: small host species harbor small, large host species harbor large parasite species


Schematic diagram of Harrison's rule with Poulin's supplement: small host species harbor small, large host species harbor both small and large (on average: larger) parasite species


Melampsora laricis-populina  life cycle. (a) Biological macrocyclic heteroecious cycle of  M. larici-populina . (b) Vegetative cycle occurring on  poplar  leaves and used as a model for molecular investigations of the poplar- poplar rust  interaction. hpi=hours of postinoculation.


The  black rat  is a  reservoir host  for  bubonic plague . The  rat fleas  that infest the rats are  vectors  for the disease.


Micropredator ,  parasite ,  parasitoid , and  predator   strategies  compared. Their interactions with their hosts form a continuum. Micropredation and parasitoidism are now considered to be  evolutionary strategies  within parasitism. [ 2 ]


Buff ermine  moth  caterpillar , a polyphagous  micropredator


Influenza  virus can change by genetic reassortment as it travels between different hosts in its range.


Mycorrhiza , a  mutualistic interaction  between a plant's roots and a fungus


Cleaning symbiosis :  a  Hawaiian cleaner wrasse  with its client, a  yellowtail wrasse


Nurse shark  playing host to  commensal   remoras , which gain  a free ride  and which may serve as cleaners


Two apicomplexans,  Toxoplasma gondii , within their host cell. Transmission electron microscopy


Great frigatebirds  ( Fregata minor ) chasing a  red-footed booby  ( Sula sula ) to steal its food


Cuckoo bee from the genus  Nomada


Miltogrammine  fly ( Craticulina seriata ) is a kleptoparasite of  sand wasps , depositing its larvae on the food reserved for the larvae of the wasp


Velia caprai  ( Ardennes , Belgium)


Argyrodes flavescens  on the web of  Argiope pulchella


The relative size and location of each segment present on the MSP-1 complex is shown above. SS represents the signal sequence, which is a short sequence present on the N-terminus of new proteins. GA represents the GPI anchor, which is located at the C-terminus of the protein. [ 7 ]


Tachyzoites  of  Toxoplasma gondii ,  transmission electron microscopy . [ 1 ]   Micronemes: mn  (click to enlarge)


Transmission of malaria parasites between mosquito and human.


Laveran's drawing of pigmented parasites and the exflagellation of male gametocytes


The page in Ross' notebook where he recorded the "pigmented bodies" in mosquitoes that he later identified as malaria parasites


Ribonucleoprotein particles (GFP-Imp) in the Drosophila melanogaster egg chamber, being transported from the nurse cells to the oocyte


Saurophthirus , an ectoparasitic Cretaceous insect [ 1 ]


Cysts found in a corpse in a late Roman grave in France, interpreted  [ 5 ]  as signs of probable  hydatidosis  and  capillariasis


Restoration of a  Tyrannosaurus  head with holes possibly caused by a  Trichomonas -like parasite


High parasite load. Lappet moth caterpillar parasited by braconid wasps.


Enumeration of  Plasmodium  parasites (blue) in human red blood cells (pink) to quantify relative parasite load.


Schistosoma mansoni , an endoparasite that lives in human tissue


An example of a cost the peacock must bear from having such a large tail. The tail requires a lot of energy as it weighs the peacock down during its flight.


A gazelle stotting to indicate its fitness and ability to outrun a predator


A barn swallow


Crab with egg sac of the parasitic barnacle  Sacculina carcini . The parasite stops reproduction in its host, the crab, and stimulates the female crab to disperse parasite eggs with the same behavior that she would normally use for her own eggs. [ 1 ]


A  fish parasite , the isopod  Cymothoa exigua , replacing the tongue of a  Lithognathus


Head (scolex) of tapeworm  Taenia solium , an  intestinal parasite , has hooks and  suckers  to attach to its  host


The parasitic castrator  Sacculina carcini  (highlighted) attached to  its crab host


Human head-lice  are directly transmitted  obligate  ectoparasites


Clonorchis sinensis , the Chinese liver fluke, is trophically transmitted


The  vector-transmitted  protozoan endoparasite  Trypanosoma  among human  red blood cells


Mosquitoes  are micropredators and important vectors of disease


Life cycle  of  Entamoeba histolytica , an anaerobic parasitic protozoan transmitted by the  fecal–oral route


Cuscuta  (a dodder), a stem  holoparasite , on an  acacia  tree


The honey fungus,  Armillaria mellea , is a parasite of trees, and a  saprophyte  feeding on the trees it has killed.


Borrelia burgdorferi , the bacterium that causes  Lyme disease , is transmitted by  Ixodes  ticks.


Enterobacteria phage T4  is a  bacteriophage  virus. It infects its host,  Escherichia coli , by injecting its DNA through its tail, which attaches to the bacterium's surface.


Restoration of a  Tyrannosaurus  with holes possibly caused by a  Trichomonas -like parasite


Wolbachia  bacteria within an insect cell


Biologists long suspected  cospeciation  of  flamingos  and  ducks  with their parasitic  lice , which were similar in the two families. Cospeciation did occur, but it led to flamingos and  grebes , with a later  host switch  of flamingo lice to ducks.


The protozoan  Toxoplasma gondii  facilitates its transmission by  inducing behavioral changes  in rats through infection of neurons in their  central nervous system .


Trait loss: bedbug  Cimex lectularius  is flightless, like many insect ectoparasites.


The dry  skin  of vertebrates such as the  short-horned lizard  prevents the entry of many parasites.


Leaf spot  on  oak . The spread of the parasitic fungus is limited by defensive chemicals produced by the tree, resulting in circular patches of damaged tissue.


The rescuing from extinction of the  California condor  was a successful and expensive project, but its  ectoparasite , the louse  Colpocephalum californici , was made extinct.


Parasites are  distributed unevenly  among their hosts, most hosts having no parasites, and a few hosts harbouring most of the parasite population. This distribution makes sampling difficult and requires careful use of statistics.


A plate from  Francesco Redi 's  Osservazioni intorno agli animali viventi che si trovano negli animali viventi  (Observations on living animals found inside living animals), 1684


Ronald Ross  won the 1902  Nobel Prize  for showing that the  malaria parasite  is transmitted by mosquitoes. This 1897 notebook page records his first observations of the parasite in mosquitoes.


Encarsia formosa , widely used in  greenhouse  horticulture, was one of the first biological control agents developed. [ 138 ]


"An Old Parasite in a New Form": an 1881  Punch  cartoon by  Edward Linley Sambourne  compares a  crinoletta  bustle to a parasitic insect's  exoskeleton


Fictional parasitism: oil painting  Parasites  by Katrin Alvarez, 2011


A  parasitoid wasp  ( Trioxys complanatus ,  Aphidiinae )  ovipositing  into the body of a spotted alfalfa  aphid  ( Therioaphis maculata ,  Calaphidinae ), a behaviour that is used in  biological pest control [ a ] [ 2 ]


A  hyperparasitoid   chalcidoid wasp  on the cocoons of its host, a  braconid wasp , itself a koinobiont parasitoid of  Lepidoptera


Female  phorid fly   Apocephalus borealis  (centre left)  ovipositing  into the abdomen of a worker  honey bee ,  altering its behaviour


Potter wasp , an idiobiont, building a mud nest; she will  provision it  with paralysed insects, on which she will lay her eggs; she will then seal the nest and provide no further care for her young


The head of a sessile female  strepsipteran  protruding (lower right) from the abdomen of its wasp host; the male (not shown) has wings


Encarsia formosa , an endoparasitic  aphelinid  wasp, bred commercially to control whitefly in  greenhouses


Parasitic wasps  (centre right) with their  garden tiger moth  host, by  Maria Sibylla Merian


A 1990s  gargoyle  at  Paisley Abbey , Scotland, resembling a  Xenomorph [ 69 ]  parasitoid from the film  Alien [ 70 ]


The  screw-worm fly  was the first  pest  successfully eliminated from an area through the sterile insect technique, by the use of an integrated area-wide approach.


Entomologist Edward F. Knipling


The map shows the current (orange) and former (yellow) distribution area and the approximate seasonal spread of the  screw-worm fly .


A  United States Environmental Protection Agency  researcher dragging for ticks.


Transovarial and transstadial transmission of the  Ixodes  tick


Aedes triseriatus  is the most common vector for La Crosse virus, causing La Crosse Encephalitis. This mosquito is also implicated in the transmission of West Nile Virus.


Malaria Lifecycle


Life cycle of  Balantidium coli


1977 Selman A. Waxman Award Medal - Front View


1977 Selman A. Waxman Award Medal - Rear View


Blastocystis  isolated from stool sample of infected patient.


Plasmodium  in erythrocytic cycle


Top: Ant infected with  Ophiocordyceps unilateralis  fungus clinging to underside of leaf with fungus sprouting from its head. Bottom: Detail of Ophiocordyceps unilateralis sprouting from ants head.


API 20NE Detection system after 24 hours incubation.


Example of antibiotic sensitivity testing. Thin paper discs containing an  antibiotic  have been placed on an  agar plate  growing  bacteria . Bacteria are not able to grow around antibiotics to which they are sensitive. This is called "the zone of inhibition".


From left to right: 0.5, 1, and 2  McFarland standards


Example of an  Etest , which uses a plastic strip impregnated with an antibiotic at a range of concentrations


Antibiotic resistance tests : Bacteria are streaked on dishes with white disks, each impregnated with a different antibiotic. Clear rings, such as those on the left, show that bacteria have not grown—indicating that these bacteria are not resistant. The bacteria on the right are fully resistant to all but two of the seven antibiotics tested. [ 33 ]


Hand scrubbing procedure for surgery


William Stewart Halsted


Packaged, sterilized surgical instruments


Medical illustration of Staphylococcus


Oocysts of  Cryptosporidium parvum  stained with the fluorescent auramine–rhodamine stain.


E. coli  culture on a Petri dish


A tanner treating leather in Morocco


Anaerobic, aerobic, and paediatric blood culture bottles


Signs of growth in manual blood culture systems: a) a film of growth ( pellicle ) on the surface; b) bubbles from gas production; c)  turbidity  from microbial growth (in right bottle); d) visible microbial colonies [ 42 ]


Loading a target plate containing microbial samples into a  Bruker  Biotyper, an instrument used for  MALDI-TOF  analysis in microbiology


An early vacuum tube system for blood culture collection, described by C.E. Simon & C.C.W. Judd in 1915 [ 85 ]


This is an example of a positive CAMP test indicated by the formation of dark arrowheads where the Strep group B ( Streptococcus agalactiae ) meets the  Staphylococcus aureus  (light-yellow/golden middle streak with surrounding dark hemolysis).


Example of a workup algorithm of possible bacterial infection in cases with no specifically requested targets (non-bacteria, mycobacteria etc.), with most common situations and agents seen in a New England community hospital setting. CAMP test is shown at bottom left.


The process of colony hybridization: growth of cell colonies, replication on filter, hybridization, and identification of desired colonies.


Conformational changes can elicit the motion of a  protein complex .  Kinesin  walking on a  microtubule  is a molecular   biological machine  using  protein domain dynamics  on  nanoscales


An example of a  solenoid  powered cryogenic grinder.


How cryogenic grinding with a solenoid works


Chemical-etching measured in real-time


Figure 1.  DHM phase shift image of cell details.


Surface finish measurement


Figure 2.  Typical optical setup of DHM.


Figure 3.  Comparison of a DHM phase shift image (left) and a  phase-contrast microscopy  image (right).


Figure 4.  DHM phase shift image of human  red blood cells .


Figure 5.  Time-lapse of unstained, dividing and migrating cells.


Self-healing surface recovering from a scratch : real-time measurement


Ultrasonic Transducers measured at 8 MHz in stroboscopic mode


Automatic measurement of hip prosthesis : surface roughness characterization


In diagnostic laboratories, the disk diffusion test is used to determine the susceptibility of clinical isolates of bacteria to different antibiotics.  An effective antibiotic will produce a large zone of inhibition (disk C), while an ineffective antibiotic may not affect bacterial growth at all (disk A).  Antibiotics to which a bacterial isolate is partially susceptible will produce an intermediate size zone of inhibition (disk B). [ 1 ] [ 2 ]


In drug discovery laboratories, the disk diffusion test is used to screen natural product extracts for antibacterial activity.  Extracts with antibacterial activity, for example the petroleum ether, chloroform, ethanol and acetone extracts above, will produce a zone of inhibition. [ 3 ]


Standard Kirby–Bauer testing: White disks containing antibiotics shown on an agar plate of bacteria.  Circular zones of poor bacterial growth surround some disks, indicating susceptibility to the antibiotic.


Endospore stain on  Bacillus subtilis . The spore is stained green and the vegetative cell is stained a pinkish red color.


Etest being used to determine the susceptibility of  Neisseria gonorrhoeae  to benzylpenicillin.


E-test being used to determine the susceptibility of  Candida albicans  to caspofungin.


The chemical structure of gentamicin


Main types of staining seen on H&E stain.


Retina  (part of the  eye ) stained with  hematoxylin  and  eosin , cell nuclei stained blue-purple and extracellular material stained pink.


Rack of slides being removed from a bath of hematoxylin stain.


Hemagglutination assay of different influenza samples diluted from the left to the right.


Indirect hemagglutination assay for human echinococcosis. Different  serum  samples diluted from the left to the right. Seropositivity was suspected in Sample 179


Indole test positive: appearance of pink layer at top (e.g.  Escherichia coli )


Bacterial  growth curve


Reagents used for Lancefield grouping


A live-cell microscope. Live-cell microscopes are generally  inverted . To keep cells alive during observation, the microscopes are commonly enclosed in a micro  cell incubator  (the transparent box).