Marine Microbial Ecology PDF

MARINE MICROBIAL ECOLOGY Chapitre I: Introduction Prepared by : Dr Claude DAOU Faculty of Science - LU  Ecologie Microbienne Marine -Dr DAOU 2 PLAN I. Les fondements de l’Ecologie Microbienne II. Les interactions microbiennes...

MARINE MICROBIAL ECOLOGY Chapitre I: Introduction Prepared by : Dr Claude DAOU Faculty of Science - LU  Ecologie Microbienne Marine -Dr DAOU 2 PLAN I. Les fondements de l’Ecologie Microbienne II. Les interactions microbiennes II.1 Le mutualisme II.2 Le commensalisme II.3 Le parasitisme II.4 Les symbioses III. Les interactions cycliques des elements nutritifs III.1 Le cycle du carbone III.2 Le cycle du soufre III.3 Le cycle de l’azote III.4 Autres cycles IV. L’environnement physique IV.1 Le microorganisme et la niche IV.2 Les biofilms et les tapis microbiens IV.3 Les microorganismes et les ecosystemes IV.4 Les mouvements de microorganisms entre ecosystems IV.5 Le stress et les ecosystems V. Les microorganismes dans les milieux aquatiques  Ecologie Microbienne Marine -Dr DAOU 3 CONCEPTS Marine microbial communities (consisting of bacteria, archaea, protists, fungi and viruses) process about one-half of the global biogeochemical flux of biologically important elements, such as carbon, nitrogen, phosphorus, sulphur and iron. These organisms include phototrophic and chemotrophic primary producers, as well as heterotrophic ‘secondary’ producers, which recycle dissolved organic carbon and nutrients through the microbial loop.  Ecologie Microbienne Marine -Dr DAOU 4 CONCEPTS In recent years, molecular analysis has made great progress in determining the organisms that are present at a given site and how they are distributed over space and time. Most of this information is derived from phylogenetic analyses using a few informative genes, such as the 16S and 18S rRNA genes, but phylogenetic identification alone is insufficient to assess the environmental functions and ecology of the community.  Ecologie Microbienne Marine -Dr DAOU 5 CONCEPTS Although we are learning much about such functions via ‘omics’ : ▫ metagenomic, ▫ metatranscriptomic, ▫ and metabolomic analyses, Such studies alone rarely provide the information that is needed to predict interactions, competition for nutrients, symbioses and other processes that determine the overall roles of the distinct organisms in the sea.  Ecologie Microbienne Marine -Dr DAOU 6 CONCEPTS Traditionally, a microbiome has been defined as a microbial community occupying a reasonably well-defined habitat. One of the most common approaches to studying a microbiome is analyzing its constituent microbial genomes through metagenomics. Metagenomics allows us to investigate the composition of a microbial community. ▫ Genomic studies consider the genetic material of a specific organism, while metagenomics (meta meaning beyond) refers to studies of genetic material of entire communities of organisms. This process usually involves next-generation sequencing (NGS) after the DNA is extracted from the samples.  Ecologie Microbienne Marine -Dr DAOU 7 CONCEPTS Metatranscriptomics By focusing on what genes are expressed by the entire microbial community, metatranscriptomics sheds light on the active functional profile of a microbial community. The metatranscriptome provides a snapshot of the gene expression in a given sample at a given moment and under specific conditions by capturing the total mRNA.  Ecologie Microbienne Marine -Dr DAOU 8 CONCEPTS Metabolomics Metabolomics is the comprehensive analysis by which all metabolites of a sample (small molecules released by the organism into the immediate environment) are identified and quantified. The metabolome is considered the most direct indicator of the health of an environment or of the alterations in homeostases. Variation in the production of signature metabolites are related to changes in activity of metabolic routes, and therefore, metabolomics represent an applicable approach to pathway analysis.  Ecologie Microbienne Marine -Dr DAOU 9 CONCEPTS Therefore, additional information, beyond that which can be derived from omics, is needed to predict community functions and interactions between organisms. Towards this goal, a great deal can be learned by evaluating the dynamics of community composition and the corresponding environmental parameters to determine the extent to which such dynamics follow predictable patterns, and potentially to show which organisms interact and how.  Ecologie Microbienne Marine -Dr DAOU 10 CONCEPTS the term Dynamics is used to refer to changes in the abundance of various members (or populations) in a community, but not necessarily changes in the physiological state of these members; the term Community is used here to refer to the types of microorganisms present and their relative proportions.  Ecologie Microbienne Marine -Dr DAOU 11 CONCEPTS Marine microbial communities are : – dynamic (in a constant state of flux) – but also resilient, which means that their behaviours are broadly predictable in terms of typical features of daily, seasonal and interannual variation in community composition. This implies that despite external forces that alter the community (such as temperature, nutrient supply and physical mixing), there are internal feedback mechanisms, including competition, viral infection and predator–prey interactions, that help to maintain a remarkably steady ‘average’ community year after year, even in seasonally changing habitats.  Ecologie Microbienne Marine -Dr DAOU 12 What processes drive dynamics at different scales? Microorganisms change over multiple timescales and in response to different forces, including both biological and non-biological properties of the environment that drive changes in microbial community composition. As the typical average generation times of marine plankton are approximately a day in surface waters, and longer in deep waters, substantial changes in community composition in less than a few hours are not expected; therefore, changes over timescales of hours and longer are considered here.  Ecologie Microbienne Marine -Dr DAOU 13 What processes drive dynamics at different scales? Timescales of hours : Candidates for change on this timescale are copiotrophic organisms: ▫ often Gammaproteobacteria, Flavobacteriia, certain Alphaproteobacteria and others) that can grow rapidly, and although these taxa are usu- ally rare in seawater, they can quickly become abun- dant under suitable conditions  Ecologie Microbienne Marine -Dr DAOU 14 What processes drive dynamics at different scales? Timescales of « daily to weekly »: In the offshore surface ocean, estimated whole- community biomass turnover times range from less than a day to about a week. Therefore, this timescale is suitable for the observation of microbial variation in response to environmental variation. The forces that vary substantially on this scale include: ▫ weather, ▫ meso-scale oceanographic processes interactions with larger organisms (from protists to fish), ▫ food-web cascade effects ▫ and microbial interactions involving all types of viruses, bacteria, archaea and protists.  Ecologie Microbienne Marine -Dr DAOU 15 What processes drive dynamics at different scales? Timescales of « daily to weekly »: Appropriate for studying dynamics associated with phytoplankton blooms, which have a direct influence on the composition of bacterial and archaeal communities via : ▫ cross-feeding interactions and the effects of toxins or other allelopathic substances, ▫ as well as an indirect influence through oxygen depletion and injury or death of larger organisms (if the bloom is toxic). Few copiotrophic bacterial lineages have been repeatedly shown to be involved: Flavobacteriia, Rhodobacter spp. and Gammaproteobacteria  Ecologie Microbienne Marine -Dr DAOU 16 What processes drive dynamics at different scales? Timescales of « Monthly to seasonal »: Forcing functions that vary at this scale include : ▫ changes in solar angle (including associated changes in light intensity and ultraviolet penetration of the ocean), ▫ seasonal weather patterns (such as winds and storm frequencies), ▫ seasonal upwelling and the associated changes in nutrient availability, ▫ and stratification. Other forcing factors include : ▫ changes in temperature and day length; ▫ seasonal variation in land runoff and atmospheric deposition; ▫ and interactions with larger organisms and other microbial species, which can all be influenced by the same pervasive environmental factors.  Ecologie Microbienne Marine -Dr DAOU 17 What processes drive dynamics at different scales? Long-term time series Is the most straightforward approach to observe the dynamics of marine microbial communities. There are a few long-term studies at major time-series sites and many small-scale studies, all of which typically examine the underlying physical and/or chemical oceanographic features, such as temperature, salinity, and chlorophyll and nutrient concentrations, which have a strong influence on microbial dynamics.  Ecologie Microbienne Marine -Dr DAOU 18 Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease doi:10.3389/fmars.2015.00062 White Plague Disease (WPD) is implicated in coral reef decline in the Caribbean and is characterized by microbial community shifts in coral mucus and tissue. Studies thus far have focused on assessing microbial communities or the identification of specific pathogens, yet few have addressed holobiont response across metaorganism compartments in coral disease. Here, we report on the first metatranscriptomic assessment of the coral host, algal symbiont, and microbial compartment in order to survey holobiont structure and function in healthy and diseased samples from Orbicella faveolata collected at reef sites off Puerto Rico. Our data indicate holobiont-wide as well as compartment-specific responses to WPD. Gene expression changes in the diseased coral host involved proteins playing a role in innate immunity, cytoskeletal integrity, cell adhesion, oxidative stress, chemical defense, and retroelements. In contrast, the algal symbiont showed comparatively few expression changes, but of large magnitude, of genes related to stress, photosynthesis, and metal transport. Concordant with the coral host response, the bacterial compartment showed increased abundance of heat shock proteins, genes related to oxidative stress, DNA repair, and potential retroelement activity. Importantly, analysis of the expressed bacterial gene functions establishes the participation of multiple bacterial families in WPD pathogenesis and also suggests a possible involvement of viruses and/or phages in structuring the bacterial assemblage. In this study, we implement an experimental approach to partition the coral holobiont and resolve compartment- and taxa-specific responses in order to understand metaorganism function in coral disease.  Ecologie Microbienne Marine -Dr DAOU 19 Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease doi:10.3389/fmars.2015.00062  Ecologie Microbienne Marine -Dr DAOU 20 Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease doi:10.3389/fmars.2015.00062  Ecologie Microbienne Marine -Dr DAOU 21 Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease doi:10.3389/fmars.2015.00062  Ecologie Microbienne Marine -Dr DAOU 22 Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease doi:10.3389/fmars.2015.00062  Ecologie Microbienne Marine -Dr DAOU 23 CONCEPTS The term symbiosis or “life in common” express : ▫ Numerous interactions between microorganisms, ▫ as well as microbial interactions with higher organisms (plants, animals). These interactions could be positives ou negatives.  Ecologie Microbienne Marine -Dr DAOU 24 CONCEPTS The microbial ecology is the science that studies the interactions existing between microorganisms and their environment, between microorganisms themselves and between microorganisms and higher organisms (animal and plant)  Ecologie Microbienne Marine -Dr DAOU 25 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 26 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 27 CONCEPTS Microbial ecology is the study of the behavior and microbial activities in their natural environments (micro-environments) Environmental microbiology, in comparaison, refers mainly to the global microbial processes occurring in water, soil or food.  Ecologie Microbienne Marine -Dr DAOU 28 CONCEPTS Positive interactions : 1. Mutualism 2. Protocooperation 3. Commensalism Negative interactions : 1. Parasitism 2. Predation 3. Amensalism 4. Competition These interactions are important in natural processes and the onset of diseases. They may vary according to the environment and the changes in the organisms involved.  Ecologie Microbienne Marine -Dr DAOU 29 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 30 CONCEPTS Microorganisms, when interacting, can form complex physical assemblies, often described as biofilms. These biofilms appear on living or inert surfaces and have a major impact on microbial survival and disease outbreaks. Microorganisms also interact by using molecules as chemical signals (increase in population density) – Quorum perception controlling a wide variety of microbial properties.  Ecologie Microbienne Marine -Dr DAOU 31 CONCEPTS Energy, electrons and nutrients must be available in a suitable physical environment for microorganisms to live. These interact with their environment to obtain energy (light or chemical source), electrons and nutrients Biogeochemical recycling Microorganisms alter the physical state and mobility of many nutrients, using them in their growth processes.  Ecologie Microbienne Marine -Dr DAOU 32 CONCEPTS CYCLE DU CARBONE  Ecologie Microbienne Marine -Dr DAOU 33 CONCEPTS Microorganisms are an important part of ecosystems. They play a major role in the succession of predictable changes that occur in ecosystems when disturbed. The methods used to study these interactions are microscopic, chemical, enzymatic and molecular techniques.  Ecologie Microbienne Marine -Dr DAOU 34 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 35 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 36 CONCEPTS  Ecologie Microbienne Marine -Dr DAOU 37 CONCEPTS Prokaryotes (Bacteria) Eubacter "True" bacteria ▫ human pathogens ▫ clinical or environmental ▫ one kingdom Archaea ▫ Environmental organisms ▫ second kingdom Eukaryotes ▫ Other cell-based life e.g. – Protists – plants – fungi – animals  Ecologie Microbienne Marine -Dr DAOU 38 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 39 II. A connaître The essential needs of the organisms to survive Elements Energie chimiques Organismes  Ecologie Microbienne Marine -Dr DAOU 40 II. A connaître Energy aspects The energy needs of microorganisms can be met by two mechanisms: 1) Photosynthesis, in which light is used as a source of energy. 2) The oxidation of chemical substances, also called energetic substrates  Ecologie Microbienne Marine -Dr DAOU 41 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 42 II. A connaître Photosynthesis (photophosphorylation) Occurs in photosynthetic cells that contain chlorophyll. Organic molecules are synthesized by light energy. Photophosphorylation begins this process by converting light energy into chemical energy into ATP and NADPH, which, in turn, are used to synthesize organic molecules.  Ecologie Microbienne Marine -Dr DAOU 43 II. A connaître Photosynthesis (photophosphorylation) ECOLOGIE MICROBIENNE 44  Ecologie Microbienne Marine -Dr DAOU 45 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 46 II. A connaître Respiration (aerobic and anaerobic)  Ecologie Microbienne Marine -Dr DAOU 47 II. A connaître Aerobic respiration  Ecologie Microbienne Marine -Dr DAOU 48 II. A connaître Anaerobic respiration p Functions like aerobic respiration except it utilizes oxygen containing ions, rather than free oxygen, as the final electron acceptor (facultative anaerob: E. coli, Pseudomonas, Bacillus,…) n Nitrate (NO3-) and nitrite (NO2-) p Most obligate anaerobes use the H+ generated during glycolysis and TCA to reduce some compound other than O2. Methanogens: reduce CO2 -> CH4 Sulfate Bacteria: reduce SO42- -> H2S Some bacteria use metals or organic compounds as H+ acceptor  Ecologie Microbienne Marine -Dr DAOU 49 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 50 II. A connaître Fermentation  Ecologie Microbienne Marine -Dr DAOU 51 II. A connaître Fermentation Uses glycolysis but does not use TCA cycle or Electron Transport Chain Free of the energy of sugars or other organic molecules but produces only 2 ATP of each glucose Do not use O2 or inorganic electron acceptors Uses an organic molecule as the ultimate electron acceptor Produces only a small amount of ATP and most of the energy remains in the final products of fermentation  Ecologie Microbienne Marine -Dr DAOU 52 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 53 II. A connaître Two major "trophic" categories of organisms (troph=nutrient): Autotrophs: synthesize organic substances essential for their survival, from mineral elements contained in water or soil, and carbon dioxide (CO2). Heterotrophs: require, for their trophic needs, the presence of organic matter and are therefore dependent on autotrophs.  Ecologie Microbienne Marine -Dr DAOU 54 II. A connaître Heterotrophs are divided into consumers and decomposers. Consumers may be herbivores or carnivores or parasites. Decomposers are essentially bacteria and fungi. Their physiological activity ensures the recycling of organic waste produced by producers and consumers. This waste once returned to the mineral state is reused by the producers.  Ecologie Microbienne Marine -Dr DAOU 55 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 56 II. A connaître Terminology (“trophs”) in microbial metabolism Energy source Carbon source Chemo= chem bonds Hetero- = organic Organo = organic Auto- = inorganic Litho= inorganic Photo= sunlight e- acceptor Aerobic = oxygen Anaerobic= not O2  Ecologie Microbienne Marine -Dr DAOU 57 II. A connaître ¢ Inorganic nutrients– atom or molecule that contains a combination of atoms other than carbon and hydrogen l metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate), gases (oxygen, carbon dioxide) and water ¢ Organic nutrients- contain carbon and hydrogen atoms and are usually the products of living things l methane (CH4), carbohydrates, lipids, proteins, and nucleic acids  Ecologie Microbienne Marine -Dr DAOU 58 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 59 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 60 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 61 II. A connaître Ecologie Microbienne Marine -Dr DAOU 62  Ecologie Microbienne Marine -Dr DAOU 63 II. A connaître Nitrogen, phosphorus and sulfur requirements Nitrogen is needed for the synthesis of amino acids, purines, pyrimidines, certain carbohydrates and lipids, enzymatic cofactors and other substances. Most phototrophs and many non-photosynthetic microorganisms reduce nitrates to ammonia, so they incorporate ammonia by anabolic reduction of nitrate. Some bacteria (cyanobacteria and Rhizobium) reduce and assimilate atmospheric nitrogen through the nitrogenase system.  Ecologie Microbienne Marine -Dr DAOU 64 II. A connaître Nitrogen, phosphorus and sulfur requirements Phosphorus in nucleic acids, phospholipids, nucleotides such as ATP, some cofactors, some proteins and other cellular components. Almost all bacteria use inorganic phosphate as a source of phosphorus and incorporate it directly. When the inorganic phosphate is outside the bacterium, it passes through the outer membrane, through a porin channel. If [Pi] is strong, Pit is active If [Pi] is low, TSP (Specific phosphate transport) system is active.  Ecologie Microbienne Marine -Dr DAOU 65 II. A connaître  Ecologie Microbienne Marine -Dr DAOU 66 II. A connaître Nitrogen, phosphorus and sulfur requirements Sulfur is necessary for the synthesis of substances such as cysteine and methionine which are amino acids, some carbohydrates, biotin and thiamine. Microorganisms for the most part use sulphate as a source of sulfur and reduce it, so they assimilate it by anabolic reduction of sulphate; Some require a reduced form of sulfur, for example, cysteine.  Ecologie Microbienne Marine -Dr DAOU 67 III. Microbial interactions Microorganisms can be associated with other organisms in many ways: Ectosymbiote: An organism that can settle on the surface of another that is larger in size. Consortium: dissimilar organisms of similar size that are in physical contact. Endosymbiote: an organism that can move to another organism. Ecto / endosymbiosis: where the microorganism lives at the same time inside and outside another organism. 68  Ecologie Microbienne Marine -Dr DAOU 69 III. Microbial interactions  Ecologie Microbienne Marine -Dr DAOU 70 III. Microbial interactions Microbial consortia of bacteria and fungi with focus on the lichen symbiosis, Martin GRUBE, Gabriele BERG, fungal biology reviews 23 (2009) 72 – 85. The term symbiosis was coined in 1879 by Heinrich Anton de Bary, a German mycologist, who defined it as: ‘‘the living together of unequally named organisms’’. In this broad sense, symbiosis includes all kinds of close biological relationships. This researcher gave the broadest definition of symbiosis by studying microscopically the stages of growth and reproduction of lichens and their adaptability that makes their survival possible during the winter.  Ecologie Microbienne Marine -Dr DAOU 71 III. Microbial interactions These associations may be intermittent and cyclical or permanent. (Exemple : listeriose, malaria, legionellose, etc.) These interactions might be positive : Mutualism Protocooperation Commensalism or negative Predation Parasitism Amensalism Competition  Ecologie Microbienne Marine -Dr DAOU 72 III. Microbial interactions  Ecologie Microbienne Marine -Dr DAOU 73 III. Microbial interactions Mutualism defines the relationship in which a certain reciprocal benefit to both partners. This is a mandatory relationship, where the mutualist and the guest metabolically depend on each other. Examples: 1. Protozoan-termite relationship Flagellate protozoa live in the termites gut. They degrade cellulose acetate, termites absorb acetate. If we increase the pressure of O2 in the laboratory, the flagellates die, the termites continue to eat wood but die of hunger.  Ecologie Microbienne Marine -Dr DAOU 74 III. Microbial interactions Mutualism 2. Lichens are an association between photoautotrophic organism (cyanobacteria or algae) and a mushroom. In a lichen, the fungal partner is called mycobiotic, and the alga or cyanobacterium is called phycobiotic.  Ecologie Microbienne Marine -Dr DAOU 75 III. Microbial interactions Mutualism 2. Lichens are an association between photoautotrophic organism (cyanobacteria) and a mushroom. The fungus obtains organic C from the seaweed through photosynthesis. The mushroom provides water to the seaweed and protects it from light by giving it shape and rigidity. Lichens are extremely sensitive to 2 pollutants: ozone and sulfur dioxide. 76  Ecologie Microbienne Marine -Dr DAOU 77 Marine biodiversity At the end of the summer of 2005, water temperatures abnormally high resulted in striking discoloration of coral reefs in the northeastern part of the Caribbean. The algae that had lived until there in perfect harmony (symbiosis) with the corallaries (polyps) were squeezed out and what remained thereafter was than large areas of coral reef white and discolored. During the twelve months who followed the increase in temperature, corals have also been heavily affected by diseases. In two years, up to 50% of certain parts had died. What is the precise link between the temperature, discoloration, illness and the death of coral? Superficial mucus houses a lot of types of bacteria who in normal circumstances, are able to guarantee the 'health’ of corals. Many of these bacteria produce antibiotics that help repel attacks of all kinds pathogens. But when the coral is under pressure - for example when the temperature rises - drastic changes occur in the bacteria community. The species 'Usual' decreases in number and pathogens take their place.  Ecologie Microbienne Marine -Dr DAOU 78 III. Microbial interactions Syntrophy Is an association where the growth of an organism depends on or is enhanced by growth factors, foods or substrates, provided by another organism growing nearby. Sometimes both organisms benefit from it. This type of mutualism is also called cross feed or satellite phenomenon. Example: in methanogenic ecosystems, such as anaerobic sediments in freshwater and flooded soils.  Ecologie Microbienne Marine -Dr DAOU 79 III. Microbial interactions Syntrophy In these environments, fatty acids can be degraded to produce hydrogen and methane through the interaction of two different bacterial groups. Methan production by methanogens depends on an interspecific transfer of gaseous hydrogen. A fermentative bacterium produces gaseous hydrogen and the methanogen rapidly uses it as a substrate for the production of methane gas.  Ecologie Microbienne Marine -Dr DAOU 80 Figure 2 Schematic drawing of ‘classical’ syntrophy depending on the environmental conditions (methanogenic or... FEMS Microbiol Rev, Volume 37, Issue 3, May 2013, Pages 384–406, https://doi.org/10.1111/1574-6976.12019 The content of this slide may be subject to copyright: please see the slide notes for details.  Ecologie Microbienne Marine -Dr DAOU 81 FEMS Microbiol Rev, Volume 37, Issue 3, May 2013, Pages 384–406, https://doi.org/10.1111/1574-6976.12019 In this review, they define syntrophy simply as ‘obligately mutualistic metabolism’. This definition of syntrophy continues to focus on the set of chemical reactions that occur from the microbial cooperation (i.e. the metabolism), but is expanded to include information about the ecology of the interdependence. The mutualism that occurs during syntrophy can most often be defined as a resource-service type, with one partner providing a chemical compound that is consumed by the other in exchange for a reward.  Ecologie Microbienne Marine -Dr DAOU Figure 3 Schematic drawing visualizing the different possibilities of extracellular electron transfer. In all cases, syntrophic activity produces a set of chemical outcomes that are different from what could occur when each microbe acts separately, and the benefits of this metabolic interaction often come at the cost of low energetic yields and slower growth rates. FEMS Microbiol Rev, Volume 37, Issue 3, May 2013, Pages 384–406, https://doi.org/10.1111/1574-6976.12019 The content of this slide may be subject to copyright: please see the slide notes for details.  Ecologie Microbienne Marine -Dr DAOU 83 III. Microbial interactions Protocooperation Is a mutually beneficial relationship, similar to those of mutualism. In the protocooperation however, this relationship is not mandatory. Beneficial supplemental resources are provided by each of the matched microorganisms. The microorganisms involved in this type of relationship can be separated, and if the resources offered by the complementing organism are provided by the growth medium, each of the microorganisms will function independently.  Ecologie Microbienne Marine -Dr DAOU 84 III. Microbial interactions Protocooperation Examples: 1. Association between Desulfovibrio and Chromatium in which carbon and sulfur cycles are linked. 2. Interaction of a nitrogen-fixing microorganism with a cellulolytic Cellulomonas organism such as Cellulomonas. The cellulolytic microorganism releases glucose from the cellulose which can be used by the nitrogen-fixing microorganisms. Azotobacter  Ecologie Microbienne Marine -Dr DAOU 85 III. Microbial interactions Protocooperation Protocooperative relationships, filamentous, autotrophic, sulphide- dependent microorganisms, fix carbon dioxide and synthesize the organic matter that serves as a source of carbon and energy to a heterotrophic organism. Example 1: Pompei worm (Alvinella pompejana). This unusual organism, 10cm length, lives in tunnels, where the water temperature is around 80ºC, in a deep region of the Pacific Ocean. It uses as nutrient source bacteria that oxidize the organic matter and reduce the sulphide compounds. Alvinella pompejana  Ecologie Microbienne Marine -Dr DAOU 86 III. Microbial interactions Protocooperation Example 2: Filamentous sulfide oxidation bacteria grow on the surface of the shrimp Rimicaris exoculata. When they are delocated, the shrimp swallows them.  Ecologie Microbienne Marine -Dr DAOU 87 III. Microbial interactions Protocooperation The shrimp Rimicaris exoculata is about 5 cm long and has the distinction of being devoid of eyes. It is very abundant on the walls of hydrothermal chimneys, forming communities of several tens of thousands of individuals (on average about 2500 individuals/m²). She lives in an environment with a temperature fluctuating between 10 and 30°C, where chemolithotrophic bacteria grow using sulfide as an electron and energy source. The bacteria, which grow on the vent openings and also on the surface of the crustaceans, fix carbon from CO2 in their autotrophic metabolism, and serve as the nutrient for the shrimp.  Ecologie Microbienne Marine -Dr DAOU 88 III. Microbial interactions Protocooperation Example 3: Nematode Eubostrichus parasitiferus living at the aerobic/anaerobic interface in sulphide rich marine sediments. The marine nematode Eubostrichus parasitiferus with bacteria arranged in a characteristic helix pattern These animals are covered with bacteria that oxidize sulphide. Bacteria not only reduce the concentration of toxic sulphide that often surrounds nematodes, but they also serve as food. The chemolithotropbic bacteria attached to the cuticle of the marine nematode Eubostrichus parasitiferus  Ecologie Microbienne Marine -Dr DAOU 89 III. Microbial interactions Protocooperation A kind of protocooperation is also established when a population of similar microorganisms controls its own density. This is the perception of quorum. Microorganisms produce specific self-inducing compounds, and as the population increases and the concentration of these compounds reaches critical levels, specific genes are expressed. Example for association with plants or animals.  Ecologie Microbienne Marine -Dr DAOU 90 III. Microbial interactions  Ecologie Microbienne Marine -Dr DAOU 91 III. Microbial interactions Commensalism Is a relationship in which one organism, the commensal gets an advantage, while the other, the host, is neither affected nor helped. This is a unidirectional process. Often, the host and the commensal "eat at the same table". The spatial proximity of the two partners allows the commensal to feed on substances captured or ingested by the host, and the commensal often provides shelter by living on and in the host.  Ecologie Microbienne Marine -Dr DAOU 92 III. Microbial interactions Commensalism The commensal is not directly dependent on the metabolism of the host and does not cause to the latter any particular damage. When the commensal is experimentally separated from its host, it can survive in the absence of one or more factors provided by the host. Commensal relationships between microorganisms include situations where a waste produced by one microorganism serves as a substrate for another species.  Ecologie Microbienne Marine -Dr DAOU 93 III. Microbial interactions Commensalism Example: Nitrification Oxidation of the ammonium ion to nitrite by microorganisms such as Nitrosomonas, and subsequent oxidation of nitrite to nitrate by Nitrobacter. Nitrobacter benefits from its association with Nitrosomonas since it uses nitrite to obtain the energy necessary for its growth.  Ecologie Microbienne Marine -Dr DAOU 94 III. Microbial interactions Commensalism Commensal association occurs when a microbial group modifies the environment and makes it more conducive to another organism. Example: Escherichia coli creates an anaerobic environment in the gut, which will allow Bacteroides (anaerobe mandatory) to grow in the gut. Escherichia coli does not make any profit.  Ecologie Microbienne Marine -Dr DAOU 95 III. Microbial interactions Commensalism An important commensalism also presides over the colonization of the human body and the exterior of other animals and plants. The microorganisms associated with the skin or the openings of the animal body use as food volatile, soluble and particulate organic compounds emitted by the host. Under most conditions, these microorganisms cause no harm other than possibly contributing to body odor, but can become opportunistic pathogens.  Ecologie Microbienne Marine -Dr DAOU 96 III. Microbial interactions Predation A widespread phenomenon or predator engulfs or attacks prey. The prey may be larger or smaller than the predator, and the normal result is the death of the prey. Examples: Bdellovibrio, Vampirococcus and Daptobacter. - Bdellovibrio perforate the cell wall and multiplies between the wall and the cytoplasmic membrane. - Vampirococcus attaches to the surface of its prey and secretes enzymes that release the cellular contents. - Daptobacter penetrates its host and feeds on the cytoplasmic contents. Ecologie Microbienne Marine -Dr DAOU 97  Ecologie Microbienne Marine -Dr DAOU 98 III. Microbial interactions Predation Digestion, example = the microbial loop Soluble organic material from primary producers is normally used by bacteria, which is particulate food for higher consumers. Flagella and cilia digest the bacteria, making the nutrients they contain, again available for primary production. This will also allow prey growth and renewal to be faster than it would be in the absence of predators.  Ecologie Microbienne Marine -Dr DAOU 99 III. Microbial interactions Predation Retention The bacteria retained in the predator are useful, as in the transformation into harmless methane, of the toxic hydrogen produced by the rumen cells. Similarly, the trapping of chloroplasts by protozoa provides photosynthesis to the predator.  Ecologie Microbienne Marine -Dr DAOU 100 III. Microbial interactions Predation Protection and increase of aptitude Intracellular survival of Legionella, ingested by the ciliates (Mycobacterium avium), protect it from stress like high temperature and chlorination. Ingesting also leads to an increase in pathogenicity, when the prey is returned to the external environment, and this may be necessary for human infection. The predator serves as a reservoir.  Ecologie Microbienne Marine -Dr DAOU 101 III. Microbial interactions  Ecologie Microbienne Marine -Dr DAOU 102 III. Microbial interactions Parasitism Is one of the most complex microbial interactions. It is a relationship where one of the partners benefits from the other, and/or where the host is usually lysed. This may include food consumption from the host, and/or physically colonization in or on the host. In parasitism, parasite and host coexist in association up to a certain degree.  Ecologie Microbienne Marine -Dr DAOU 103 III. Microbial interactions Parasitism According to the equilibrium established between the two organisms, this coexistence can vary and pass from a stable parasite relation to a pathogenic relation which can be considered as a predation. Example: Viruses in the state of prophage in the cell then lytic cycle Any pathogen.  Ecologie Microbienne Marine -Dr DAOU 104 III. Microbial interactions Parasitism  Ecologie Microbienne Marine -Dr DAOU 105 III. Microbial interactions Amensalism Describes the negative effect of one organism on another. It is a unidirectional process, based on the production by one organism, of a specific compound that acts negatively on another organism. Example: production of antibiotics that can inhibit or kill an organism that is sensitive to it.  Ecologie Microbienne Marine -Dr DAOU 106 III. Microbial interactions Amensalism Other types: production of specific organic compounds that cause damages in the cell wall or cytoplasmic membrane. Example: bacteriocins, as food additives. organic acids resulting from fermentation.  Ecologie Microbienne Marine -Dr DAOU 107 III. Microbial interactions Competition Competition occurs when different microorganisms of a population or community seek to appropriate the same resource, or occupy a physical place, or consume a particular limiting food. Principle of competitive exclusion by Gause in 1934: He discovered that if two cilies compete too directly for the same resource, one of the two populations of protozoa was excluded.  Ecologie Microbienne Marine -Dr DAOU 108 III. Microbial interactions It must be underligned that the cited interactions do not exist independently. Whenever a microorganism interacts with other organisms and their environments, it triggers a series of responses by the biological community, that will influence other parts of the ecosystem. Ecologie Microbienne Marine -Dr DAOU 109