Biodiversity and Microbial Biodiversity

BIODIVERSITY and Microbial biodiversityMajid Mohiuddin

The Origins of LifeOur Planet was Lifeless.Based on radioisotopicdating associated with fossils (mainly Uranium to lead decay).The Oldest macrofossils of plants and animals are only 0.6-0.7 billion years old. If these were the remains of the original living organisms, the planet would have been lifeless for almost 4 billion years.

Now evidence that microbial life existed more than 3.85 billion years ago (Mojzsis et al. 1996).1 billion after the formation of earth and 3 billions years before the appearance of macroscopic plants and animals. (Nisbet 1980).Microscopic fossils of procaryotic cells (primitive microorganisms) have been identified in 3.5 billion year old rocks.Rocks that are 3.85 billion years old have been found to contain organic matter rich in 12C.

The geochemical evidence indicates that living organisms were assimilating carbon into organic molecules from atmospheric methane and carbondioxide.Data also suggest that this process was changing the chemical composition of Earth within 1 billion years of Earth’s formation.

Comparison of atmospheric and temperature conditions

Life exist on Earth and That Microorganisms had influence in shaping its currently prevailing Physicochemcial conditions.

Today Earth provides a favorable environment for the proliferation of life.It took millions of years after formation of Earth for conditions to develop that permitted life to evolve and survive.It is true that Earth was favored by a sufficient mass and gravitational pull to retain most atmospheric gases and by a distance from the sun that allowed most of its water to remain in the liquid state.All conditions will not favorable to predate life.

What is the role of Life?The role of life in forming the physicochemical environment of our planet and it is maintaining the environment in its current state (Gaia Hypothesis) (by James Lovelock – 1979).

Chemical EvolutionPrebiotic Earth Chemical Evolution (by Russian Scientist Alexander IvanovichOparin and British Scientist John B.S. Haldane) between 1925 and 1930.Premitiveprebiotic Earth had an anaerobic atmosphere consisting largely of Carbondioxidenitrogen, hydrogen and water vapor with smaller amounts of ammonia, carbon monoxide, and hydrogen sulfide.In such chemical mixture, organic compounds would have formed with relatively small inputs of energy.Oxygen was absent or present only in trace amounts.Lack of an ozone.Temperature extremes (both geographical and seasonal)Large amount of abiotically formed organic matter apparently present mainly in dissolved or suspended forms, from which Life could evolve.

Radiant, geothermal electric discharge and radioactive decay energy fueled the slow chemical evolution of this organic matter toward ever more complex and polymeric forms.The resulting macromolecules were endowed with an inherent tendency to aggregate and form membrane like interface toward the surrounding liquid, foreshadowing a cellular organization.In an environment free of oxygen and microbial decomposers, this chemical evolution could proceed uninterrupted for millions of years.(Stanley L. Miller and Harold C. Urey Experiments)Oparin Haldane theory of Chemical evolution is the best known and accepted one. This theory suggests that life began on Earth’s surface in areas where organic chemicals accumulated.An alternative hypothesis is that life on Earth began at deep ocean thermal vents. – mixture of chemicals and catalysts needed for formation of life.

First living organisms based on surface catalysis (German Scientist GuntherWachtershauser 1988).The first form of “Life” visualized by this theory is an acellular organic film, which is anionically attached to positively charged mineral surfaces and grows chemoautotraphically in an anaerobic thermal environment.Initially RNA formed.

Cellular EvolutionOparin and his coworkers performed studies on the properties of microspheres that form spontaneously in the colloidal solution of two different polymeric substances such as GUM ARABIC and HISTONE.

These microspheres, which Oparin called COACERVATES, develop spontaneously when the two polymers are added to water.Coacervates behaves as semipermeable membranes and vacuoles.

Physiological DiversityWhen Life evolved on Earth,Organic compounds (formed abiotically) served as initial substrates for growth.Cells degrade these compounds and derive energy.Cells growth and maintaned.

Methanogenicarchae used hydrogen and Co2. generate cellular energy.The central molecule of Biological Energy Transformation – ATP.Gradually, organized sequences for enzymatically catalyzed degradation reactions (catabolic pathways) evolved that permitted cells to use the chemical energy of organic substrates to generate ATP more efficiently.Archae – Entner-Doudoroffpathyway (halophilic and thermophilicarchae)

Bacterial and archaeal cells developed ability to utilize sulfur compounds.(early form of anaerobic respiration)Sulfate hydrogen sulfide. 2.7 billion years Rocks.Most of the hyperthermophilicarchae and bacteria are obligate or facultative autotrophs that use molecular hydrogen and reduce elemental sulfur, carbondioxide, or oxygen. (reductive acetyl-CoA pathway or reductive citric acid cycle) not Calvin cycle for Co2 assimilation.Chemoautotrophy predated photoautotrophy.

It was limited pool of nutritional resources.There was selective pressure for more direct utilization of the radiant sun energy to fuel life processes – to generate ATP.They used hydrogen sulfide, which was present in the Oceans, as a source of electrons for the reduction of carbon dioxide.

Early photosynthesis was anoxygenic (non oxygen producing) type found today in the Rhodospirillaceae,Chromatiaceae and Chlorobiaceae, the anaerobic photosynthetic bacteria.Lack Photosystem II and unable to use the Hydrogen in water for the reduction of carbon dioxide.

Early cyanobacteria did not posses Photosystem II.Under anoxic, H2S rich conditions, some contemporarycyanobacteria revert to anoxygenic photosynthesis and use only their photosystem I (Cohen et al. 1986).Important Evolutionary step – use of Chemiosmosis for ATP generation – it improved the efficiency of generating ATP.

The Evolution of Oxygenic (oxygen producing) photosynthesis in cyanobacteria is evidenced by the appearance of heterocyst like structures and banded iron formation approximately 2.0 – 2.5 billion years ago.Heterocysts – separating the oxygen sensitive nitrogen fixation system from oxygen evolving photosynthesis.

The dating of the development of oxygen producing metabolism is based upon the observation that about 2.5 billion years ago virtually all iron disappeared from the oceans.A few million years – oxidized iron was deposited in sediments.Prior to this period, all iron deposits were reduced.

This record indicates that about 2 billion years ago the originally reducing atmosphere of our planet changed to an oxidizing one.Oxygen accumulated in the atmosphere.And some cells developed the capacity of nitrogen fixation.

The geologic evidence – oxygenic photosynthetic microorganisms – 2 billion years ago.Some fix atmospheric nitrogen.Oxygen accumulation in the atmosphere haled abiotic generation of organic compounds – (strictly anaerobic conditions).

Ozone formed from molecular oxygen reduced the influx of ultaviolet radiation – (perticularly less than 200 nm) was major energy.

The Evolution of photosystem II in cyanobacteria - source of reducing power in the form of water.More solar energy is required to split the Strong H-O-H than H-S-H.Oxygen evolved in this type of photsynthesis was toxic to most existing forms of anaerobic life.There became extinct or were restricted to specific environments that still live obligatory anaerobic.Nitrogen fixing cells develop adaptations to protect nitrogenase enzyme.

Great physiological diversification - efficient modes of substrate utilization.Some cells developed chemoautotrophic metabolic capabilities in which inorganic molecules are used to generate ATP.Other generate ATP from Organic substrates.

MICROBIAL BIODIVERSITYNew species of microorganisms evolved through the interactions of their genomes with the environment giving rise to great microbial diversity and altered ecosystem functions. (Allsopp et al. 1995).3 billion years of microbial evolution involved very limited changes in size and morphology, compare to multicellular organisms.Gradual evolution of biochemical pathways and regulatory mechanisms.

Darwinian Principles: Mutations, genetic recombination and natural selection all played roles in the evolution of new microbial species.As evolution proceeded, new kinds of microorganisms appeared so that the diversity of the microbial world increased.New and diverse microorganisms represent new species (Latin Spec = look or behold the kind, appearance, or form of something)

The biodiversification of microorganisms has been occurring for over 3.85 billions years compared to only 600 million years for macroorganisms.Great biodiversity of Microbial world has yet to be discovered.Bacterial BiodiversityArchaeal BiodiversityEucaryal Biodiversity

Bacterial BiodiversityAquificales (Aquifex and Hydrogenobacter lineage) – oldest evolutionary branch within the Bacterial domain. – show about early bacterial ecology and physiology. Use H2, S2O32- (thiosulfate) and S0 (sulfur) as electron donors to reduce oxygen to water.Aquifex = water makerWater was metabolic waste product.Aquifex pyrophilus – extreme thermophile – from hydrothermal vent in Iceland – 85o C and also 950C.

These physiological properties suggest that ancestral bacterial progenitor was thermophilic and fix carbon chemoautotrophically (Achenbac-Richter et al. 1987).

Thermotogales are another deeply rooted evolutionary branch within the Bacterial domain.The Thermotogales are extremely thermophilic microorganisms, which supports that hypothesis that the earliest microorganisms. (Many Thermotoga and Thermosipho spp. Isolated from sulfur hot springs).As the Earth cooled, bacteria evolved that grow at low temperatures, including the low temperatures that characterize most of the oceans and the near freezing temperatures of many soils.PhotosynthesisChemolithotrophsPhotosynthetic purple bacteria

The Evolution of Bacteria (eubacteria) – at least 12 lineages (Kingdoms)0.1 Change per nucleotide (nt)BACTERIAProteobacteriaDeinococciCyanobacteriaGram PositivesGreen Nonsulfur BacteriaChlamydiaePlanctomycesBacteroides and relativesThermotogalesAquificalesGreen sulfur bacteriaARCHAEA AND EUCARYASpirochetes

ChlamydiaPlanctomycesFlavobacteriumFlexibacterSynechococcusLeptonemaGloeobacterChlorobiumAgrobacteriumRhodocyclusEscherichia coliDesulfovibrioCloastridiumHeliobacteriumArthrobacterBacillusARCHAEAThermusEUCARYAThermomicrobiumThermotogaHydrogenobacterAquifexNumerous species evolved within the 12 kingdoms0.1 Change per nucleotide (nt)

Archael BiodiversityDistinct physiological propertiesSince Earth was hot and anaerobicCytoplasmic membranes – branched hydrocarbons and ether linkages compared to the straight chain fatty acids and ester linkages found in the membranes of all other organisms.Some form tetraethers and have monolayer membranes instead of the typical bilipids.Instead of peptidoglycan, their cell walls consist of proteins and glycoproteins, some contain pseudomurein.

The metabolic cofactors of the Archaea also differ from those of Bacteria and Eucarya: Coenzymes M (involved in C1 metabolism)Factor F 420 ( involved in electron transport )7-mercaptoheptanoylthreonine phosphate (involved in methanogenesis)Tetrahydromethanopterin (instead of folate)MethanofuranRetinal

The Evolution of the Archaea (based upon rRNA analyses) – 3 kingdoms.HaloferaxEURYARCHAEOTAMethanospirillumThermoplasmaMethanobacteriumCRENARCHAEOTADesulfurococcusSulfolobusMethanothermusPyrodictiumArchaeoglobusThermoproteusMethanococcus vannieliiThermofilumMethanococcus jannaschiipSL50ThermococcuspJP96MethanopyruspSL12BACTERIApSL4pSL 17pSL 22Marine SBAR5pJP27KORARCHAEOTApJP78EUCARYA0.1 Change per nucleotide (nt)

Eucaryal BiodiversityFossils of eukaryotes appear coincides with a decline in stromatolites deposited by bacterial mats.Green algae and fungi. ( 1 billion year old)Nucleated eukaryotic cell, sexual reproduction. (Pace of evolution).PALEOZOIC GEOLOGICAL AGE : Macrofossils of plants and animals appeared.

rRNA analyses reveal that eukaryotes evolved much earlier, shortly after the evolution of the Archaea.Unicellular, anaerobic mesophilic organisms domain.Great diversification – acquisition of mitochondria and chloroplasts through endosymbiosis.Independent analyses of cytochromes, ferredoxins, and rRNA molecules indicate that mitochondria originated from the Proteobacteria (purple bacteria) and the chloroplast came from cyanobacteria.Sexual reproduction within eucaryotes – rapid evolution of new organisms.

The Archeozoa – primitive protozoa. ( represent the descendants of early eucaryotes that evolved prior to the endosymbiotic acquisition of mitochondria. They had nucleus, endoplasmic reticulum, rudimentary cytoskeleton, and the 9 + 2 organization of flagella – lack Mitochondria.Metamonada, Microsporidiaand Parabasilia have 70S ribosomes – like those of bacterial and archaeal cells.Metamonanda and Microsporidia also lack hydrogenosomes ( organelles of anaerobic protozoa – involved with energy transformation) and Golgi apparatus (involved in export of materials by exocytosis).

Metamonada – Giardia and Hexamita.Microsporidia - Enterocytozoon and Vairimorpha.Parabasilia - Trichomonas.Giardialamblia – human parasite - attaches to mucosa of the intestine and reproduces there - causing giardiasis. – carries out anaerobic metabolism.( have 2 nuclei and 8 flagella,70S ribosomes with 16S rRNA containing only 1453 nucleotides in the small 30S subunit, rudimentary cytoskeleton.BUT LACK - mitochondria, endoplasmic reticulum, and Golgi apparatus, sexual reproduction.)Deeply rooted animal parasites.

Protozoa ofnext evolution - within Eucaryal domain after Archeozoa– have 80S ribosomes and organelles (mitochondria and in some cases chloroplasts) – Cavalier-Smith 1993.These eucaryotes demonstrate primarily phagotrophic mode of nutrient acquisition.Kinetoplastid protozoa (Trypanosomabrucei) and Euglenoid protozoa ( Euglena gracilis) – 9+2 microtubule arrangement flagella, organelles, tubular mitochondrial cristae (others lamellar cristae).The Entamoebidaeappear to have developed at about the same time as the slime molds through the loss of their mitochondria.

They developed more elaborate genetic organizations.Ciliate protozoa emerged a an evolutionary group more than one billion years ago.By that time, meiosis and fertilization had been established in eucaryotes.Late Protozoa evolution - same time Ciliates evolved, there was nearly simultaneous branching of the animals, fungi, chlorophyte algae, plants and chromophyte algae.

Algae originally considered along with protozoa to compose the protists.Chloroplasts in diatoms and brown algae occur in the lumen of the rough endoplasmic reticulum and are surrounded by a unique periplastic membrane. As such diatoms and brown algae classified as CHROMISTA.The unique membrane surrounding the chloroplasts of Chromista arose from the cytoplasmic membrane of the Photosyntheticprotozoan that was engulfed.

Analyses of 18S rRNAs indicate that the water molds (oomycetes) and net slime molds (Labyrinthula) are closely related to the photosynthetic diatoms and brown algae.Oomycetes – true fungi – tubular mitochondrial cristae - cellulosic cell walls.Kingdom Plantae – Evolution 2 lineages – Green algae (Charophyta and Chlorophyta) along with higher green plants - embryonic developmental stages.Red algae (Rhodophyta).

The Green Algae, Red Algae and plants evolved from a phagotrophic protozoan by the symbiotic acquisition of chloroplasts from photosynthetic bacteria, almost certainly cyanobacteria.Fungi Evolution from protozoa – 400 million years ago – acquisition of rigid chitinous cell walls that eliminated phagotrophic mode of nutrition.Fungi – nutrients by absorption.Fungi evolved diverse reproductive strategies.Early fungi were unicellular yeasts that reproduced by binary fission – later developed buddingAscomycete and basidiomycete fungi evolved – sexual reproduction (major evolutionary lineages of the fungi).Ascomycetes – major group of fungi that form sexual spores (ascospores) with in a specialized sac (ascus).Earliest ascus producing fungi were yeasts that reproduced by fission.Basidiomycetes form sexual spores (basidiospores) on specialized cells (basidia) on fruiting bodies (basidiocarps) that are usually macroscopic structures such as mushrooms.Basidia have complex structures that approach levels of organizational complexity comparable to some plants and animals.These fungi represent the pinnacle of evolution among microorganisms.

CHROMISTAThe Evolution of the EucaryaFUNGICryptomonasCostariaCoprinusAchlyaANIMALSPorphyraBabesiaHomoZeaParameciumTrypanosomaBACTERIAEuglenaEUCARYADictyosteliumPROTOZOAEntamoebaNaegleriaPhysarumARCHAEAEncephalitozoonVairimorphaTritrichomonasGiardiaHexamitaARCHEOZOA0.1 Change per nucleotide (nt)

Biodiversity and Microbial Biodiversity

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