Microbial Adaptation to Extreme Environments PDF

Microbial Adaptation to Extreme Environments Schmidt Ocean Institute  By the end of this lecture, you should understand/ be able to: describe microbial adaptations Intended to different environmental Learning niches, and be ab...

Microbial Adaptation to Extreme Environments Schmidt Ocean Institute  By the end of this lecture, you should understand/ be able to: describe microbial adaptations Intended to different environmental Learning niches, and be able to provide example species for the Outcomes different environments; and understand the relationships between different organisms, in terms of predation and metabolic adaptations.  Structure of today’s lecture This lecture will be delivered in two parts. 1. Focus on cellular adaptations to a range of what we refer to as extreme habitats. 2. Examples of organism relationships between different species (e.g. metabolic dependency or predation)  Fun facts! Hottest environment: Juan de Fuca ridge, 121C Geogemma barossii NSF Deepest organisms: Crypto- endoliths (3.2km under- ground) researchgate Part 1 - Cellular adaptations to a range of “extreme habitats”.  What are “extreme” environments? Examples of extreme environments can include: 1. Acidic environments 2. High saline environments (plus others!) We will use examples to illustrate some of the adaptations that difference species have made to survive in these habitats. Anthropogenic acid tolerance volcano.si.edu  Anthropogenic acid tolerance Pyrite (FeS2), when in contact with air, is oxidised by Thiobacillus ferroxidans to H2SO4 In acid mine drainage, the effluent can reach ~pH3; this empties into lakes to create environments unable to support most other life volcano.si.edu OXIDATION Fe2+ H2SO4 -2 +6 8e- to acceptor  Anthropogenic acid-tolerance At normal pH, a slow, spontaneous oxidation of FeS 2 (Fe2+) occurs by atmospheric oxygen (abiogenic oxidation) 2FeS2 + 7O2 + 2H2O 2Fe2+ + 4SO42- + 4H+ donor acceptor liberated increased acidity iron (a pH decrease) As the metabolic reactions continue, the pH falls, and the Fe 3+ ions predominates as the electron acceptor… 8e- a further decrease in pH Fe2+ AND Fe3+ an increase in Fe2+  Anthropogenic acid-tolerance Acidophiles oxidise Fe 2+ , allowing it to act as an electron acceptor However, acid effluent interacts with mineral compounds and reduces the availability of key trace elements to environmental organisms; e.g. aluminium Al3+ + H2SO4 Al(SO4)3 + 3H2  Iron as an electron donor Iron is an energetically unfavourable electron donor to make ATP (NAD is much more favourable). Acid-tolerant microbes let H+ in through proton motive force (PMF). But the H+ must be neutralised in order to prevent a pH drop in the cytoplasm, which would kill the cell. Iron acts to perform this function. H+ e- Fe2+ Fe2+ + H+ H2 O Fe3+  Anthropogenic acid tolerance Most lakes and streams have a pH between 6 and 8, although some lakes are naturally acidic even without the effects of acid rain. Acid rain primarily affects sensitive bodies of water, which are located in watersheds whose soils have a limited ability to neutralize acidic compounds (called “buffering capacity”). Lakes and streams become acidic when the water itself and its surrounding soil cannot buffer the acid rain enough to neutralize it. In areas where buffering capacity is low, acid rain releases aluminum from soils into lakes and streams; aluminum is highly toxic to many species of aquatic organisms.  The effect of acidity on selected life forms Species pH 6.5 6 5.5 5 4.5 4 Trout Bass Perch Frogs Salaman- ders Clams Crayfish Snails Mayfly  Case study: Scottish lakes Many lakes and rivers in Northern Europe and America were in bad shape after decades of industrial pollution and acid rain. Fish stocks collapsed and ecosystems were damaged. The EU limited emissions of sulphur to control the problem, and the situation has been improving since. Long-term monitoring shows that some lakes are indeed becoming less acidic and that a chemical recovery is underway, but what about the fish, the algae and the small invertebrates? Have the ecosystems recovered as well? http: //plane te arth.nerc.ac.uk/news /story.aspx?id= 682  Case study: Scottish lakes 'As the lake becomes less and less acidic, we'll see an increase of algal production.‘ In 2006, Lochnagar's food network had 45 nodes, with the diatoms at the bottom of the food chain and the trout as the lake's top predator. The lake's invertebrate population is dominated by generalist feeders and species with good tolerance of acidic conditions. They found that the food web has changed through time, 'but not how you would expect from a progressive decrease in acidity'. The number of species in Lochnagar is still low mostly because the lake is not very productive: the algae aren't producing much oxygen. The trout are rare, relatively small, and not in good condition. http://planetearth.nerc.ac.uk/news/s tory.aspx?id=682 Figure 1 Low temperature adaptations Psychrophiles produce enzymes with lower temperature optima. They often denature at room temperatures. Psychrophiles have higher unsaturated fatty acids plus short-chain membrane lipids: keeps membranes fluid at lower temperatures. Example species: Desulfofaba gelida (bottom) Psychromonas ingrahamii (top) Optimal temperatures of Eubacterial psychrophile species ˚C Species Minimum Maximum growth growth temperature temperature -8 25 Micrococcus cryophilus -14 25 Vibrio marinus 0 40 Xanthomonas pharmicola 0 40 Pseudomonas avenae 7 41 Escherichia coli Vibrio marinus  Reminder - Membrane fluidity! Membranes adapted to high temperatures will not survive at low temperatures. This is where the membrane structure becomes important. (Archaea possess ether linkages & Eubacteria posses ester links) The individual Archael bilayers are held together by hydrophobic bonds. These forces plus the ether bonds and hydrocarbon branching increases the heat tolerance of the Archael membranes.  Survival & death at extreme temperature Below the optimal temperature, microbial activity decreases (basis for the refrigeration of food). In natural soil & water, microbes generally present slower metabolic activity in winter due to a decrease in ambient temperature; above usually kills the organism. Some bacterial species produce endospores, or fungi produce sclerotia.  In addition to affecting survival and growth, temperature influences the metabolic activities of microbes. Effect of In general, higher temperatures which temperature do not kill the cells result in higher on metabolic activities- e.g. increased O2 microbial consumption occurs as temperature increases. activity This increased respiration indicates an increase in enzyme activity almost up until the point where the stability of the enzyme fails (protein denaturation).  Q10 values (relative) Enzyme Q10 Catalase 2.2 (10- The Q10 value is where a 10°C 20°C) increase results in an increase in enzyme activity. For most organisms, Maltase 1.9 (10- this is approximately 2 20°C) Succinic 2.0 (30- i.e. a 10°C increase results in a Oxidase 40°C) doubling of enzyme activity Urease 1.82 (20- 30°C) Not always- some sulphate reducers have a Q10 + 3.5 (very temperature sensitive)  Halophiles exist where there is a high level of dissolved ions; consequentially this means that there is a reduced water availability High salt for the cells to utilise for respiration. environments: HALOPHILES NB- water availability can be influenced by agriculture; e.g. irrigation and aeration alters soil profile.  Water availability In hypertonic environments, non-halophiles become dehydrated. In addition to affecting osmotic pressure, high salt concentrations act to denature proteins. Halophiles effectively act to exclude the sodium ion at concentrations where it could become toxic. – E.g. The halophilic alga Dunaliella lacks a rigid cell wall & builds up a high internal glycerol concentration – E.g. Halobacterium uses a different strategy: it accumulates potassium ions  Halophile adaptations Example genus- Halobacterium. These organisms are aerobic, heterotrophic Archaea. They require at least 0.3 M NaCl to grow. Some strains possess bacteriorhodopsin in their membranes that function as light-driven proton pumps, thus generating electrical potential, thus acting to drive ATP synthesis through Proton Motive Force (PMF). Max Planck Institute  One of the key adaptations of halophiles ifsthe inclusion of bacteriorhodopsin in to their membranes, allowing them to utilise light energy. Halophiles and Halobacteria use light to generate PMF, and therefore light utilisation to provide: motility ATP Na+ pump uptake of pre-formed organic nutrients  Bacterial rhodopsin This is a 26 kDa pigmented protein Seen as purple patches on the cell membrane that act as a H+ pump http://dx.doi.org/10.13140/RG.2.1.4382.9281  Summary Points Organisms adapt to survive by two key points: – Firstly, to prevent entry of toxic compounds in to the cell cytoplasm or to destroy the membrane; – Secondly, to utilise the environment to their benefit. Examples could be where acidophiles use H+ ions to power PMF, or where halophiles utilise light-harvesting pigments (membrane proteins) such as rhodopsin to utilise light energy. Part 1 - Cellular adaptations to a range of “extreme habitats”. Part 2 - Examples of relationships between different organisms in “extreme” environments.  So what is a hydrothermal vent? The vents range in diameter from less than an inch to more than six feet. They are usually found at least a mile deep long the mid- ocean ridges. So far, several dozen vent fields have been discovered. The cold seawater is heated by hot magma and re-emerges to form the vents. Seawater in hydrothermal vents may reach temperatures of over 340°C. Hot seawater in hydrothermal vents does not boil because of the extreme pressure at the depths where the vents are formed. This means there is liquid water present, plus a heat source.  How can life exist away from the sun? Water coming out of a vent is rich in dissolved minerals but also in chemosynthetic bacteria. These bacteria are capable of utilizing sulphur compounds to produce organic material through the process of chemosynthesis. The bacteria are autotrophs that oxidize hydrogen sulphide in vent water to obtain energy, which is used to produce organic material. Chemosynthetic bacteria are the primary producers and form the base of vent food webs. All vent animals ultimately depend on the bacteria for food. Max Planck Institute How does a hydrothermal community develop in such harsh conditions? The first organisms to populate the vents are bacteria, then other microorganisms, including amphipods and copepods appear. These are followed by limpets (snails), shrimp, crabs, tube worms, fish, and octopi. Sometime late, acorn worms, and species of shrimp and tube worms add to the expanding community.  Lithoautotrophs Off the coast of California, the genus Beggiatoa was The Тwithphoto granules demonstrates of elemental thesulfur. bacterial The filaments size of thisofbacterium Beggiatoacan leptomitifomis be as long asneotype 100 micron D-402 and even longer identified as a lithoautotrophic bacterium. Beggiatoa reside in sediments above the reduced zone. It oxidises hydrogen sulphide, producing elemental sulphur, which is deposited within the bacterial cell as sulphur granules, and give this filament its opaque appearance. https://atlasofs cience.org/  Biochemistry & metabolism Beggiatoa sp. are capable of the biogenic oxidisation of hydrogen sulphide to elemental sulphur, that is subsequently stored as intracellular sulphur globules. S2- S SO42- (H2S) Through further + 2e + 2O2 metabolism, the sulphur granules can be converted in to sulphate. Note – these bacteria can utilise organic compounds, if available.  What about trace elements? IRON A limiting micronutrient of marine primary production Vent-derived iron was previously thought to rapidly oxidize and precipitate around vents. However, organic matter can bind to and stabilize dissolved and particulate iron in hydrothermal plumes, facilitating its dispersion into the open ocean Pyrite nanoparticles—composed of iron and sulphur—account for up to 10% of the filterable iron in these fluids (particles of less than 200 nm in size)  Other elements Copper, manganese, zinc, sulphur & silicone Uses? Carbon CO2 is fixed using energy from the oxidation of sulphides H2 S S SO42- (S2-) O2 CO2 Cell carbon  Arcobacter species Bacterial Reside within sulphide-rich, high-fluid-flow environments by the production of rigid deposits species as of filamentous mats (composed of elemental sulphur) that resist turbulence. food? laenciclopediagalactica.info/  The Pompeii Worm of sea Bacterial species as food? Alvinella worms (Pompeii worms) Predate upon these microbial mats, and thus the bacteria produce a source of food (e.g. cell carbon, fixed sulphur compounds) for animals to survive. Studytub.com Other animal-microbe interactions Pompeii worms, reside close to the vents. These worms are the most heat-tolerant complex life form on Earth. They can withstand 105°C water! 1 to 5 H2S, Fe2+, FeS2 metres FeS2 Fe2+ + FeS + O2 Fe(OH)3 Particle sedimentation Particle sedimentation H2S, Fe2+, FeS2  Methane cycling & symbioses Methane diffuses up through sediments is utilised by sulphur- metabolisers before it reaches oxic zones. Bacterial genuses identified include Desulfovibrio and Desulfococcus CH4 + SO42- HCO3- + HS- + H2O These bacteria work in metabolic partnership with archaeal species: the methane & sulphate produced by the Archaea is converted to bicarbonate & sulphide by the Eubacteria Archaea-Bacterial Symbioses https://www.nature.com/articles /35036572/figures/2  Anaerobic oxidation of methane in Depth marine sediments below sea floor SO42- HS- H2 CH4 Sea bed acetate acetate SO4 2- Aerobic sediment SO42- HS- HS- CO2 CO2 Anaerobic sediment H2 SO42- HS- Archaea Eubacterium Adapted from Munn, 2012 Vestimentiferan worms MBARI  Vestimentiferan worms Riftia sp. Possesses root-like structures to obtain sufficient H2S from the sediment. L. luymesi has root like structures extending into the sediment from MBARI the base of its tube. These roots absorb sulphide, which is transported in the blood to the trophosome (body cavity). Fig. 6. Interactions with worms  Worm-bacterial symbioses plume The absence of a mouth and vestimentium gut strongly suggest that the Chitinous adult worms rely entirely on tube their bacterial symbionts for coelomic nutrition. cavity These bacteria oxidize reduced trophosome inorganic sulphur compounds to obtain energy and reducing power for autotrophic carbon fixation. Life in the freezer… Micro-organisms living in ice crystals & sub-zero waters  Cellular adaptations to living in ice or cold water environments Organisms capable of living in cold environments are called psychrophiles. The cold Arctic and Antarctic waters are considered to be low-nutrient in comparison to warmer ones. Therefore, microbes must adapt in order to survive in this habitat. Autotrophic microorganisms are present, as can be determined by RNA analysis for genes involved in photosynthesis.  Cellular adaptations to living in ice or cold water environments RNA analysis further indicates that in cold water, aerobes predominate – suggesting that proximity to the surface might be the key to their survival above the epilimnion. However, some, albeit incomplete evidence, indicates the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Chemical analysis of waters suggests that characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected.  Cellular adaptations to the cold Algal and bacterial cells that subsequently colonize and flourish in the ice matrices also synthesize copious amounts of exopolysaccharide. These form a protective ‘shell’ around the cells, and can reduce the effect of the extreme cold. This combination of living cells existing within an extracellular matrix that they have produced is called a biofilm. The ISME Journal (2013) 7, 2206–2213; doi:10.1038/ismej.2013.97  Psychroflexus torquis It has been reported that the salinity in sea-ice form channels within the ice, but that the degree of channel formation varies, depending on localised conditions. Salt concentration (NaCl) has been reported to be between