Appunti di Biodiversity

Biodiversity Exam Overview

Presentation Requirements

The biodiversity exam will be oral, starting with a PowerPoint presentation related to a scientific paper (more recent than 2013) regarding biodiversity. The presentation should last 10 minutes.

Introduction to Biodiversity

It is difficult to define what is biodiversity. Diversity defines whatever is different. It is a word that can be used in many scopes. Biodiversity refers to the number and variety of species. It refers to the diversity of life, which can be summarized by using the number of species. We divide organisms into three different domains: Bacteria, Archaea, and Eukarya. Variety can also relate to different metabolisms or communication methods (e.g., range of colors with different meanings, such as poison symbols, even in our species there are groups of people that never get in contact with us).

Marine Biodiversity

Marine biodiversity is now gaining popularity. Nowadays, we classify the ocean into five different oceans, all connected with each other. Water of the ocean comes from space, probably during the formation of the solar system, from asteroids (different hypotheses). Another hypothesis proposes that water can come from the deep mantle. The water covers approximately 1.3 billion square km. It is not much when compared to the dimensions of other planets (like Jupiter).

Importance of Biodiversity Papers

One of the most important papers related to biodiversity starts the introduction with a very interesting story: alien species can be potentially present in our universe, and if aliens were real, they would probably not be aggressive, just curious. They conclude the introduction speculating on the landing of these aliens on our Earth and what would be their first question. That question would be: How many distinct life form species does your planet have? We don’t know the answer.

Challenges in Estimating Biodiversity

There are many reasons why we can’t answer this question:

• Labor force is inefficiently distributed: 1/3 of taxonomists work on vertebrates (1% of the total number of species, in terms of biodiversity they are not so much relevant), 1/3 on plants (10%), 1/3 on invertebrates (comprising at least 90%).

The answer is one of the most challenging questions. On land, it is simpler to investigate the number of species, but this is not the same for the ocean: in the ocean, we can find different habitats along the water column. Moreover, this huge column of water dominates our planet and its average depth is 3600 meters. Only 10% is mapped, about 90% is yet unexplored. Scuba diving is a recent activity and we can’t reach many depths. The deeper part of the ocean is the most extended habitat of our planet. The water column is not empty; it is colonized by species. Even sediments in the ocean are rich in life. The most studied part of our ocean is the one present in the first 200 m (epipelagic domain, 3% of the total volume of water). It is easier to study and more accessible. The same is true for the continental shelf, which represents 6% of the total area of the seafloor. Only 5-10% can be considered explored. The real biodiversity should be amazingly higher than previously thought.

Dominant Phyla and New Discoveries

The dominant phylum of the earth is Arthropoda, the most diffused in the terrestrial environment. However, this phylum is not so dominant in the ocean where there are 8 principal different phyla. There are 35 total phyla in the ocean, 14 of which can be found exclusively in the ocean. (By contrast, only one can be found exclusively in the terrestrial environment).

It is not rare to find new phyla in the ocean:

• Loricifera, discovered in 1983, live in the unconsolidated sediment at any depth.
• Cycliophora, discovered in 1995, live in the mouthparts for several species of lobster, exhibits a very strange life cycle.
• Dendrogramma balenoptera oumurai, a new genus previously considered a new phylum by mistake.
• Discovery of a new species of whale in 2003.

Differences Between Marine and Terrestrial Habitats

The marine habitat is different from the terrestrial because of:

• Tridimensionality: Marine habitat is 3D (1-10 km in the sediment), whereas in the terrestrial we may have life just above 100m in the sediment; otherwise, it can be considered a 2D environment. This huge mass of water colonized by organisms increases the available habitat for species: it is like a fractal-like object. It provides 300 times the habitat provided by the terrestrial environment.
• Evolutive history: It seems that marine organisms had more time to make differences than terrestrial organisms (e.g., stromatolites, first form of life, way older than terrestrial organisms).
• Primary production: Trees on the land, microalgae in the ocean (photosynthesis until 200 m) and cyanobacteria (probably the most abundant organism present on our earth).
• Dimensional rankling: This refers to the range of size (from the biggest to the smallest). In the ocean, this ranking is higher (2-20 microns to 35 meters of whales).
• Trophic levels number: Higher in the marine environments thanks to the small dimension of the primary producers.
• Environmental condition: In the marine environment, conditions are more stable than in the terrestrial ones. The thermic range is less, and also the chemical and physical variations, especially in its deepest part. Environmental stability hypothesis: a stable habitat may reduce the rate of extinction, because species could persist at smaller population sizes. Because of the great age of the deep sea, species may accumulate over time (also because there is a low extinction rate). Deep sea species have also reduced dispersal mechanisms, which led to isolation, a very helpful way for speciation.
• Chemical composition of organisms: Water provides technical support and allows the evolution of simple organisms.
• Connectivity: All of the oceans are connected (not like the terrestrial environment, which has many barriers) thanks to the global ocean conveyor belt and it could act against the genetic segregation of their populations. But we may have different barriers like salinity, depth, temperature, and distance; again, deep sea species may have reduced dispersal mechanisms, as stated above.

So now we can answer that question above: if we don’t know anything, we can state that, with the topics discussed above, the marine environment should have many more species because many factors led us to this conviction. But this is not actually true: we know today 250,000 species living in the ocean and 1.4 million species living in the terrestrial environment. However, this number is far from reality.

Definition and Importance of Biodiversity

Diversity is a feature of each living system and is present at each level. The history of this term starts in 1968, when we began to talk about biological diversity. Many other terms followed it and the first time that biodiversity was used was in a forum. After that, in 1992, during a convention, this term started to be accepted and used under a specific definition: “the variability among living organisms from all sources, including, 'inter alia', terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part: this includes diversity within species, between species and of ecosystems.”

This is the most classical definition but is not complete. Clearly, the meaning of the term is not just the number of species but it also includes diversity among organisms. It is a multivariate concept. At the moment, we can’t live or predict the quality of our life without knowing much about nature because we are part of it.

Components of Biodiversity

Biodiversity components we can depict are:

• Species diversity or biological diversity, describes the variety of species or other taxonomic groups within an ecosystem and represents the key identifiable units that determine the complexity and resilience of habitats. The number of species is a parameter we can use. More species we have the richer is the habitat (richness). But this parameter isn’t the best because it simplifies the question. Rare species are excluded and it doesn’t consider the number of individuals for each species. We can use alpha and beta diversity: alpha is the biodiversity within a particular community or sample, usually expressed as an average of species plot. Beta diversity is a bit more complicated; it is the ratio between gamma and alpha diversity, but there are different formulas, it indicates differences between communities. Evenness instead measures the relative abundance of the different species. The number of species may be the same but some species may dominate the habitat. There are some indexes to use to measure the evenness: Simpson index (measures the probability that two individuals randomly selected from a sample will belong to the same species (or some category other than species)), this may be referred to as dominance index; Shannon index (accounts for both abundance and evenness of the species present. The proportion of species i relative to the total number of species (pi) is calculated, and then multiplied by the natural logarithm of this proportion (lnpi).)
• Genetic diversity: differences within the species, describes how species are able to recover from perturbations; diversity increases the robustness of the species itself, helping during environmental changes. Genetic diversity can be within population, among population, and within individuals; we have different metrics. The higher the genetic diversity among individuals, the more chances the population will have to survive. This weakness of the species is not always visible at first; it may be visible only when it is too late. This loss reduces the ability of the species to perform its inherent role in the whole ecosystem. The risk of extinction will be higher. Variability within the species increases the ability to resist.
• Ecosystem diversity: the range of biological communities and the dynamics and nature of their interdependence and interactions with the environment. We have many different ecosystems on our planet, unique combinations of organisms of different origins and their non-living physical characteristics interacting as a functional unit. Communities with more species are more stable, show resistance or resilience to occasional disturbances, and are resistant to invasion by alien species. Stable communities do not show too much variation in productivity from year to year.
• Functional diversity: it may be more important than the three above. It is not present in the classical definition. It includes the array of biological processes, functions, or characteristics of a specific ecosystem. It is the range of functions that are performed by organisms in a system. Any living species does something different from the others. Functional diversity is important because we may have a very biodiverse ecosystem but species doing the same thing can represent redundancy. Losing some species will not change so much our ecosystem, but losing a species in an ecosystem where every organism is doing something different would be terrible because it would also result in the loss of a function happening in the ecosystem. It is possible to measure functional richness and functional evenness. Answering this question would help us to exploit natural resources in a sustainable way.

The number of species predicted to be alive on earth may vary from 3 million to approximately 1 billion! See the paper posted on e-learning. To discover all the biodiversity of our planet, we need approximately 1200 years! However, this calculation does not include the extinction rate, which is currently high.

Benthos, Plankton, and Nekton

The traditional way of classifying species is not very correct. DNA is an important tool for classification. We are not going to classify in a specific way, but rather discuss how organisms relate to the environment. We can divide organisms into three different categories: Plankton, Nekton, and Benthos.

Benthos

Benthos means deep depth in ancient Greek. It refers to all the organisms that are associated with the seafloor. These associations can be very strict or less intimate but with a deep relation.

We can classify them by:

• Nature/origin: Two main categories are phytobenthos (vegetal organisms) and zoobenthos (animal organisms).
• Habitat: Hard bottom or soft bottom (unconsolidated substrate, perfect habitat for organisms living in the sediment).
• Position: Epibenthic position (above the bottom, both hard and soft, if we are talking about animals we use the term epifaunal. They can also crawl on the bottom.) and endobenthic position (inside the bottom, infaunal if they are animals. Photosynthetic organisms can’t live completely in an endobenthic way but there are some exceptions like in symbiosis with corals, some algae live in the skeleton of the coral).
• Movement capacity: Epibenthic can be divided into several categories:
• Sessile, not able to move—sponges, an exception is produce specific filaments that can make it move, corals are sessile but there are exceptions like fungi corals, solitary free-living species when they mature, using a bumping of their body they can change position, bryozoans are sessile.
• Sedentary, they apparently do not move but they are able to change their position—limpets, strongly attached to the substrate but can change their position, chiton, (polyplacophora, during their life they can move).
• Vagile, moving but covering small distances, but it depends on the dimension of the organisms—Caprellidae spp., they are crustaceans.
• Pivoting, they move using a particular rotatory movement—Pennatulacea, an order of Anthozoa, pivoting is used as an escape method.
• Swimmers and demersal, they can swim but are in relation to the bottom—cuttlefishes, crustaceans, some fish like rays.
• Endobenthic can be divided into 4 categories:
• Borers, are able to create a hole where the organism lives, thanks to some acids or other compounds—Teredo navalis, a mollusk able to create holes in the wood, heavily colonized boats, some sponges like Cliona sp., they live inside rocks and protrude osculum to expel water.
• Burrowers, live in the soft stable and are able to excavate the soft sediment. They use their body to create space in the soft sediments—clams and polychaetes use mechanical properties of their soft body to excavate the sediments, some of them not only move through the sediments but move by ingesting the sediment: in this way, they feed (and produce pseudofeces, some specific structures on the top part of the bottom, result of this type of movement) and they move. Oxygen diffuses from the water interphase but not much through the sediments, so the presence of O₂ in the sediments also relies on the behavior of this organism that mixes O₂ with sediments.
• Semi-infaunal organisms that live partially below the sediment-water interface but protrude above it.
• Interstitial, they live in the space between the grains of the sediments—foraminifera and copepods (a very biodiverse group); (a soft sediment can be classified based on the size of the particles that compose that sediment: gravel, >2mm, sand, 2-0.6 mm, mud, <0.06 mm. Whenever we find a sediment, it can be mixed. Not every type of sediment can support the same types of organisms. Where we have strong currents, the sediment will have particles with a bigger size, strong currents will reduce the nutrients in the sediment but it can increase the presence of organic matter. In the soft sediments, we can find species living in the sediments or on the sediments).

Size: Smaller the size, the higher the number of organisms

• Femtobenthos 0.02-0.2 micron—viruses (not organisms but biological entities, the most abundant one), they have the highest genetic diversity on Earth, they are the first cause of death in marine organisms, they regulate many microbial loops, viruses manipulate the marine environment thanks to their ability to be used as vectors for genes transfer (ex. On slide paper. Sea slug showing the ability of kleptoplasty, they feed on algae and rob their chloroplasts. They keep functional these chloroplasts—but part of the DNA that can make functional photosynthesis is in the cell, not only in the chloroplasts. Sea slug can exploit the photosynthetic capacity of the chloroplasts because they receive these genes thanks to a transfer operated by viruses).
• Picobenthos 0.2-2 micron—prokaryotes and picoeukaryotes (many bacteria are not able to be cultured, so it is difficult to study the real biodiversity of these organisms, thanks to new genetic approaches it is easier to understand it, like using environmental DNA).
• Nanobenthos 2-20 micron—Bacteria, Protozoa both heterotrophs and autotrophs.
• Microbenthos 20-100 micron protozoa, like loriciphera.
• Meiobenthos 0.1-0.5 mm. In this range, we can distinguish permanent meiofauna (all their life in this range) and temporary meiofauna (only part of their life). More than 24 phyla can have species present in this range, nematoda being the most abundant. IBE is a tool that can use freshwater meiobenthic organisms to measure the health of a habitat.
• Macrobenthos > 0.5 mm

Lifestyle and Feeding Preference

Deposit feeder (one of the most common)—feed on the particulate organic matter present in the sand. They ingest the sediment and use whatever they can find inside. Many types of organisms are deposit feeders. Example: Nereis virens, use this strategy to move in the sediment. Sediments can be more or less sorted, based on how much they are homogeneous or not (poorly sorted). This can also be related to the quantity of oxygen: sediment can be divided into three different layers: the light brown oxidized layer, the gray layer (redox potential discontinuity), and the reduced black layer (there can only live anaerobic organisms). Aerobic life is almost impossible in this layer, but there may be different adaptations like surface tentacles of polychaetes, siphons of bivalve, tentacle feeding bivalve. They can feed in a big variety of ways. Another example is the Spionids polychaetes which is an example. It is a polychaetes that has appendixes, they can also change their habits, by becoming suspension feeders, using their appendixes to catch particles, they extend them. Deposit feeders can be divided into the ones who feed upon the sediment, within the sediment, or at the sediment. Head down deposit feeders feed within the sediment at depth, usually using their body to create space in the sediment.