**3. Chemodiversity explodes with the emergence of life**

### **3.1. "Cool" carbon chemistry**

amino acids and their non-enzymatic condensation into dipeptides or small oligopeptides within the lipid bilayer. In addition, vectorial properties in phospholipidic vesicles are thought to influence the inner pH (making it lower than outer pH) in small vesicles, due to differences

**Figure 3.** A phospholipid vesicle, with a double-layered membrane. Each layer includes a hydrophilic head (dark knobs) and a hydrophobic tail made up of long lipid chains. The aqueous environment inside the vesicle isolates en‐

The total synthesis of a simple cell is possibly the ultimate challenge in synthetic biology. It is experimentally possible to entrap nucleic acids inside self - forming phospholipid vesicles, acting as reaction vessels for e.g. polymerase chain reaction, enzymatic RNA replication and even protein synthesis, as demonstrated by Oberholzer and collaborators (reviewed in [19]). The molecular pump scenario [20], in which peptides were initially synthesized through a molecular engine could also have taken place inside such structures. In nature, the inclusion of clay microparticles acting as catalysts is highly probable. Thus, phospholipid vesicles can be regarded as useful experimental models of proto-cells [21], but many questions still need

*Protobiology* uses a bottom up approach when designing complex and functional protocells

*Synthetic biology* uses a top-down approach to identify the minimal components of living cells that will qualify, in other words to rediscover the basic cell before it underwent the complexities of Darwinian evolution. Thus protocells are of exciting biotechnological interest in the quest

Prebiotic chemistry is certainly more complex than previously thought, and chemodiversity has undergone periods of expansion, especially through stochastic combinations during the

to optimize chemotherapies (cellular target recognition, kinetics of drug delivery).

trapped metabolites, biopolymers and catalysts, the whole structure acting as a reaction vessel.

addressing before considering them as early precursors of living cells.

so-called RNA world, and during the development of proto-cells.

from simple molecules and organic catalysts.

in the behavior of water molecules.

76 Biodiversity - The Dynamic Balance of the Planet

*2.3.3. Vesicles as proto-cells*

Our chemodiversity is usually classified as mineral or organic. Exploitable minerals are solidified in the earth crust or deposited as sediments or conglomerates - geochemical cycles connect the molten inner core of the planet with the biosphere through the displacement of continental plates and volcanic activity. Organic chemodiversity is concentrated in the biosphere, as the result of the present and past metabolic processes of marine and terrestrial organisms. Chemically, organic molecules are carbon atoms and scaffolds of connected carbon atoms, linked to hydrogen and covalently to heteroatoms e.g. oxygen, nitrogen, atoms but also to sulfur, phosphorus and halogens or metal complexes (*coordination chemistry*) to form functional groups. Larger organic molecules often adopt three-dimensional architectures that confer them with the exquisite specificity required for recognition and binding to a defined molecular target. Organic natural products are by far the largest contributors to marine and terrestrial chemodiversity, and also the most labile in the face of anthropic and natural influences that affect the stability of our ecosystems.

#### **3.2. "Cool" oxygen biochemistry**

The chemistry of our oceans has evolved considerably [22], especially with the gradual production of oxygen, which initially oxidized mantle rocks and dissolved reduced metals such as iron then tended to precipitate, as evidenced by red strata in ancient sediment beds. Free oxygen then started to rise in atmospheric concentrations, some of which was split by cosmic radiations to form the protective ozone layer. Respiration became possible and some life forms moved out of the oceans, and both aquatic and terrestrial species diversification started, and with it, organic chemodiversity. It should be emphasized that combustion occurs at oxygen levels only above 15% and organic matter would spontaneously burn at 25% concentrations - which explains that life is possible only if the present level (21%) is maintained around 20% and if genotoxic radiations can be efficiently filtered out. Oxygen is also toxic at the cellular level, if the production of (or exposure to) reactive oxygen species (ROS) or oxygen radicals cannot be counterbalanced by antioxidants or if the resulting damages cannot be repaired. When involved in regular intracellular signaling, ROS can be involved in the activation of defense metabolic pathways, and contribute to the enrichment of the metabolic repertoire of planktonic and benthic organisms.

#### **3.3. Biochemistry operates under very specific conditions**

With the exception of very few extremophiles that can live under elevated temperatures (above 80°C) and hyper acidic environments pH < 2), most microorganisms are not tolerant to conditions found outside the biosphere. The biosphere represents a very narrow region less than one thousand times thinner than the globe's diameter, and comparable conditions have not been found on any other planet so far. This does not mean that dormant bacterial spores could not withstand intersidereal journeys - lichens have successfully resisted prolonged exposures in outer space during space craft experimentations. High biodiversity environments are usually found in warm, stable environments where nutrient cycling is efficient (without accumulation of wastes) - this is at least true for tropical rainforests and shallow water coral reefs.

such changes in microbial life or on the putative role microbial associates had on the *reinven‐ tion* (understand: adaptive evolution) of new species. As Falkowski [25] puts it, animals and plants are merely new incarnations of ancient metabolic processes, but the ultimate key to biodiversity may be held by bacteria ferrying the set of core genes that are necessary for life

Marine Biodiversity and Chemodiversity — The Treasure Troves of the Future

http://dx.doi.org/10.5772/57394

79

Water is an extraordinary medium and, in many respects, mysterious. Its outstanding solvation properties are due to the capacity of the water dipoles (H-OH) to dissociate, reorientate and accommodate salts and polar compounds in a monophasic system [27]. Salts are essential to maintain osmotic balance and membrane polarization. Hydration is essential for the catalytic properties of enzymes. Semiotic (communication) substances are usually released as pheromones (intra-specific signaling) or allomones (against defense or predation). In addition, apolar (long chains or cyclic) molecules can be associated with mucus and dispersed. Some chemical cues are surface-adsorbed on dead substratum and serve as transgeneration signaling, e.g. for the settlement of larvae near adult colonies. Fish have extraor‐ dinarily sensitive and selective receptors that allow them to detect specific chemical signatures

Water participates in all life-essential molecular processes, from the most basic (e.g. Miller's experiment) to the most complex enzymatic processes, and it has allowed virtually all types of interatomic and molecular interactions that have resulted in the highly complex and diverse

The mineral world is massively involved in global geochemical processes, and in the compo‐ sition of solutes in the oceans, as salts and inorganic carbon sources. The cycling of elements is both tectonic and biogenic. Metals are essential catalysts of many organic reactions, and salts are actively involved in osmotic balance and membrane polarization. The availability of heteroatoms (P, S, halogens in particular) is (and has been originally) fundamental in the evolution of natural organic chemistry, because of their involvement in life-essential processes.

"Creative" chemistry is the work of living creatures, and Eubacteria and Archaea are probably the best organic chemists ever. Microbes are the drivers of global biogeochemical processes, and their genes have survived the great extinction events [28]. They have set the stage for other organisms to adapt and evolve. The capacity for pioneer organisms to modify their environ‐ ment for the benefit of other life forms is termed metabiosis, and it has been largely docu‐ mented in soil biology [29], but somewhat overlooked in aquatic ecosystems. They can occupy every niche of the biosphere, utilize different carbon and/or energy sources available in order

**4. Marine biodiversity and chemodiversity today**

to express itself ".

that influence their behavior.

chemical diversity observed in our oceans today.

**4.1. Minerals and geochemical cycles**

**4.2. Prokaryotes and prokaryote chemistry**

to generate ATP, the energy currency of all biochemical processes.

#### *Biodiversity explosions and mass extinctions (from [26])*

"Any lasting change in the biogeochemistry of any of the three components (atmosphere, seawater and land) will disrupt the interfacial equilibrium that supports the many thousands of life forms that interact constantly within an ecosystem. This has happened several times in the history of our planet since it became life-supporting. Changes in soil mineral strata indicate the occurrence of biodiversity-modifying events such as occupation by seas or the occurrence of an ice-age. Discrete organic layers may indicate the presence of a tropical rainforest or of a dry land savannah. Datable fossil evidence within these strata, together with paleontological reconstructions, point out the floristic and faunistic peculiarities of the times. Core drills in ice provide datable evidence of biogeoclimatic episodes within the last few millennia, while core drills in massive scleractinian corals give accurate calendar-like records of recurrent or of accidental climatic events affecting their biotope.

Speciation usually goes along with occupation of new territories and new habitats, the first colonizers having acquired the necessary adaptations to cope with evolving external demands – the Cambrian explosion (545 million years ago) being the most dramatic example of such adaptive diversification at all scales.

Along with this, evidences of accidental episodes of massive species extinctions are witnessed by the sudden "disappearance" of terrestrial and of marine life, that are attributable to tectonic, telluric or meteoritic impacts and to their profound and lasting climatologic and geochemical consequences. The most significant mass extinction is undoubtedly the Permian-Triassic Great Dying [23] where a 96% loss of all non-microbial marine life occurred within ten million years. The precise causes of mass extinction events may be in connection with continuous tectonic movements with their telluric and volcan‐ ic outbreaks and their climatic consequences, to collisions with meteoritic bodies, and to a lesser extent to the appearance of dominant predators, parasites or microbial diseases, or to combinations thereof. Common with many extinction events, however, is the massive release of greenhouse and of toxic gases (carbon dioxide, methane, hydrogen sulfide etc.). The water solubility of CO2 being nearly 30 times that of oxygen, water acidification occurs that impacts preferentially all calcifying organisms with low metabolic rates and weak respiratory systems: most coral genera died out during the Great Dying, along with calcareous sponges, calcifying algae, echinoderms, bryozoans etc. [24].

Interestingly, profound taxonomic changes in all major phyla seem to follow extinction events, resulting in a better adapted biodiversity. Nothing is known, however, on the consequence of such changes in microbial life or on the putative role microbial associates had on the *reinven‐ tion* (understand: adaptive evolution) of new species. As Falkowski [25] puts it, animals and plants are merely new incarnations of ancient metabolic processes, but the ultimate key to biodiversity may be held by bacteria ferrying the set of core genes that are necessary for life to express itself ".
