Diversity
Bacteria and Archaea
Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,[157] and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory.[158]
Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), a term that has fallen out of use.[159] Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi.[160] Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes,[161] including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores.
The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.
Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin.[162] Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example.[163]
Protists
Eukaryotes are hypothesized to have split from archaea, which was followed by their endosymbioses with bacteria (or symbiogenesis) that gave rise to mitochondria and chloroplasts, both of which are now part of modern-day eukaryotic cells.[164] The major lineages of eukaryotes diversified in the Precambrian about 1.5 billion years ago and can be classified into eight major clades: alveolates, excavates, stramenopiles, plants, rhizarians, amoebozoans, fungi, and animals.[164] Five of these clades are collectively known as protists, which are mostly microscopic eukaryotic organisms that are not plants, fungi, or animals.[164] While it is likely that protists share a common ancestor (the last eukaryotic common ancestor),[165] protists by themselves do not constitute a separate clade as some protists may be more closely related to plants, fungi, or animals than they are to other protists. Like groupings such as algae, invertebrates, or protozoans, the protist grouping is not a formal taxonomic group but is used for convenience.[164][166] Most protists are unicellular, which are also known as microbial eukaryotes.[164]
The alveolates are mostly photosynthetic unicellular protists that possess sacs called alveoli (hence their name alveolates) that are located beneath their cell membrane, providing support for the cell surface.[164] Alveolates comprise several groups such as dinoflagellates, apicomplexans, and ciliates. Dinoflagellates are photosynthetic and can be found in the ocean where they play a role as primary producers of organic matter.[164] Apicomplexans are parasitic alveolates that possess an apical complex, which is a group of organelles located in the apical end of the cell.[164] This complex allows apicomplexans to invade their hosts' tissues. Ciliates are alveolates that possess numerous hair-like structure called cilia. A defining characteristic of ciliates is the presence of two types of nuclei in each ciliate cell. A commonly studied ciliate is the paramecium.[164]
The excavates are groups of protists that began to diversify approximately 1.5 billion years ago shortly after the origin of the eukaryotes.[164] Some excavates do not possess mitochondria, which are thought to have been lost over the course of evolution as these protists still possess nuclear genes that are associated with mitochondria.[164] The excavates comprise several groups such as diplomonads, parabasalids, heteroloboseans, euglenids, and kinetoplastids.[164]
Stramenopiles, most of which can be characterized by the presence of tubular hairs on the longer of their two flagella, include diatoms and brown algae.[164] Diatoms are primary producers and contribute about one-fifth of all photosynthetic carbon fixation, making them a major component of phytoplankton.[164]
Rhizarians are mostly unicellular and aquatic protists that typically contain long, thin pseudopods.[164] The rhizarians comprise three main groups: cercozoans, foraminiferans, and radiolarians.[164]
Amoebozoans are protists with a body form characterized by the presence lobe-shaped pseudopods, which help them to move.[164] They include groups such as loboseans and slime molds (e.g., plasmodial slime mold and cellular slime molds).[164]
Plant diversity
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Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae, which would exclude fungi and some algae. A shared derived trait (or synapomorphy) of Plantae is the primary endosymbiosis of a cyanobacterium into an early eukaryote about one billion years ago, which gave rise to chloroplasts.[167] The first several clades that emerged following primary endosymbiosis were aquatic and most of the aquatic photosynthetic eukaryotic organisms are collectively described as algae, which is a term of convenience as not all algae are closely related.[167] Algae comprise several distinct clades such as glaucophytes, which are microscopic freshwater algae that may have resembled in form to the early unicellular ancestor of Plantae.[167] Unlike glaucophytes, the other algal clades such as red and green algae are multicellular. Green algae comprise three major clades: chlorophytes, coleochaetophytes, and stoneworts.[167]
Land plants (embryophytes) first appeared in terrestrial environments approximately 450 to 500 million years ago.[167] A synapomorphy of land plants is an embryo that develops under the protection of tissues of its parent plant.[167] Land plants comprise ten major clades, seven of which constitute a single clade known as vascular plants (or tracheophytes) as they all have tracheids, which are fluid-conducting cells, and a well-developed system that transports materials throughout their bodies.[167] In contrast, the other three clades are nonvascular plants as they do not have tracheids.[167] They also do not constitute a single clade.[167]
Nonvascular plants include liverworts, mosses, and hornworts. They tend to be found in areas where water is readily available.[167] Most live on soil or even on vascular plants themselves. Some can grow on bare rock, tree trunks that are dead or have fallen, and even buildings.[167] Most nonvascular plants are terrestrial, with a few living in freshwater environments and none living in the oceans.[167]
The seven clades (or divisions) that make up vascular plants include horsetails and ferns, which together can be grouped as a single clade called monilophytes.[167] Seed plants (or spermatophyte) comprise the other five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary as in yew, Torreya, Ginkgo.[168] Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species.[169] Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.
Fungi
Fungi are eukaryotic organisms that digest foods outside of their bodies.[170] They do so through a process called absorptive heterotrophy whereby they would first secrete digestive enzymes that break down large food molecules before absorbing them through their cell membranes. Many fungi are also saprobes as they are able to take in nutrients from dead organic matter and are hence, the principal decomposers in ecological systems.[170] Some fungi are parasites by absorbing nutrients from living hosts while others are mutualists.[170] Fungi, along with two other lineages, choanoflagellates and animals, can be grouped as opisthokonts. A synapomorphy that distinguishes fungi from other two opisthokonts is the presence of chitin in their cell walls.[170]
Most fungi are multicellular but some are unicellular such as yeasts, which live in liquid or moist environments and are able to absorb nutrients directly into their cell surfaces.[170] Multicellular fungi, on the other hand, have a body called mycelium, which is composed of a mass of individual tubular filaments called hyphae that allows for nutrient absorption to occur.[170]
Fungi can be divided into six major groups based on their life cycles: microsporidia, chytrids, zygospore fungi (Zygomycota), arbuscular mycorrhizal fungi (Glomeromycota), sac fungi (Ascomycota), and club fungi (Basidiomycota).[170] Fungi are classified by the particular processes of sexual reproduction they use. The usual cellular products of meiosis during sexual reproduction are spores that are adapted to survive inclement times and to spread. A principal adaptive benefit of meiosis during sexual reproduction in the Ascomycota and Basidiomycota was proposed to be the repair of DNA damage through meiotic recombination.[171]
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species.[172] Of these, only about 148,000 have been described,[173] with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans.[174]
Animal diversity
Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.
Animals can be distinguished into two groups based on their developmental characteristics.[175] For instance, embryos of diploblastic animals such as ctenophores, placeozoans, and cnidarians have two cell layers (ectoderm and endoderm) whereas the embryos of triploblastic animals have three tissue layers (ectoderm, mesoderm, and endoderm), which is a synapomorphy of these animals.[175] Triploblastic animals can be further divided into two major clades based on based on the pattern of gastrulation, whereby a cavity called a blastopore is formed from the indentation of a blastula. In protostomes, the blastopore gives rise to the mouth, which is then followed by the formation of the anus.[175] In deuterostomes, the blastopore gives rise to the anus, followed by the formation of the mouth.[175]
Animals can also be differentiated based on their body plan, specifically with respect to four key features: symmetry, body cavity, segmentation, and appendages.[175] The bodies of most animals are symmetrical, with symmetry being either radial or bilateral.[175] Triploblastic animals can be divided into three types based on their body cavity: acoelomate, pseudocoelomate, and coelomate.[175] Segmentation can be observed in the bodies of many animals, which allows for specialization of different parts of the body as well as allowing the animal to change the shape of its body to control its movements.[175] Finally, animals can be distinguished based on the type and location of their appendages such as antennae for sensing the environment or claws for capturing prey.[175]
Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the diploblasts.[176][177][178][179][180] They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.
The majority (~97%) of animal species are invertebrates,[181] which are animals that do not have a vertebral column (or backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include sponges, cnidarians (hydras, jellyfishes, sea anemones, and corals), mollusks (chitons, snail, bivalves, squids, and octopuses), annelids (earthworms and leeches), and arthropods (insects, arachnids, crustaceans, and myriapods). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata.[182]
In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata, which are chordates with vertebral columns. These animals have four key features, which are an anterior skull with a brain, a rigid internal skeleton supported by a vertebral column that encloses a spinal cord, internal organs suspended in a coelom, and a well-developed circulatory system driven by a single large heart.[175] Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.[183] Vertebrates comprise different major groups that include jawless fishes (not including hagfishes), jawed vertebrates such as cartilaginous fishes (sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds, and mammals.[175]
The two remaining groups of jawless fishes that have survived beyond the Devonian period are hagfishes and lamprey, which are collectively known as cyclostomes (for circled mouths).[175] Both groups of animals have elongated eel-like bodies with no paired fins.[175] However, because hagfishes have a weak circulatory system with three accessory hearts, a partial skull with no cerebellum, no jaws or stomach, and no jointed vertebrae, some biologists do not classify them as vertebrates but instead as a sister group of vertebrates.[175] In contrast, lampreys have a complete skull and a distinct vertebrae that is cartilaginous.[175]
Mammals have four key features that distinguish them from other animals such as sweat glands, mammary glands, hair, and a four-chambered heart.[175] Small and medium-sized mammals used to co-exist with large dinosaurs in much of the Mesozoic era but soon radiated following the mass extinction of dinosaurs at the end of the Cretaceous period.[175] There are approximately 57,000 mammal species, which can be divided into two primary groups: prototherians and therians. Prototherians do not possess nipples on their mammary but instead secrete milk onto their skin, allowing their offspring to lap if off their furs.[175] They also lack a placenta, lays eggs, and have sprawling legs. Currently, there only five known species of prototherians (platypus and four species of echidnas).[175] The therian clade is viviparous and can be further divided into two groups: marsupials and eutherians.[175] Marsupial females have a ventral pouch to carry and feed their offspring. Eutherians form the majority of mammals and include major groups such as rodents, bats, even-toed ungulates and cetaceans, shrews and moles, primates, carnivores, rabbits, African insectivores, spiny insectivores, armadillos, treeshrews, odd-toed ungulates, long-nosed insectivores, anteaters and sloths, pangolins, hyraxes, sirenians, elephants, colugos, and aardvark.[175]
A split in the primate lineage occurred approximately 90 million years ago during the Cretaceous, which brought about two major clades: prosimians and anthropoids.[175] The prosimians include lemurs, lorises, and galagos whereas the anthropoids comprise tarsiers, New World monkeys, Old World monkeys, and apes.[175] Apes separated from Old World monkeys about 35 million years ago, with various species living in Africa, Europe, and Asia between 22 and 5.5 million years ago.[175] The modern descendants of these animals include chimpanzees and gorillas in Africa, gibbons and orangutans in Asia, and humans worldwide. A split in the ape lineage occurred about six million years ago in Africa, which resulted in the emergence of chimpanzees as one group and a hominid clade as another group that includes humans and their extinct relatives.[175] Bipedalism emerged in the earliest protohominids known as ardipithecines. As an adaptation, bipedalism conferred three advantages. First, it enabled the ardipithecines to use their forelimbs to manipulate and carry objects while working.[175] Second, it elevated the animal's eyes to spot preys or predators over tall vegetation.[175] Finally, bipedalism is more energetically efficient than quadrupedal locomotion.[175]
Viruses
Viruses are submicroscopic infectious agents that replicate inside the cells of organisms.[184] Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.[185][186] More than 6,000 virus species have been described in detail.[187] Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.[188][189]
When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material (DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.
The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.[190] Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life",[191] and as self-replicators.[192]
Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids; and viruses in animals can be carried by blood-sucking insects. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.
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