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What defines a microbial species?

What defines a microbial species?



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I know that microbes are not capable of sexual reproduction, thus sorting them into species according to "groups that can interbreed and generate fertile offspring" should not apply.


Your question is relative to the species concept that you are using. Mayr's biological species concept (BSC) is based on the ability to interbreed; a process-based definition. Most biologists use it, but most taxonomists, who are the people who actually describe species, use some variation of the phylogenetic species concept. The phylogenetic species concept is not based on process, but on fixed differences. Fixed differences are evidence of a lack of interbreeding, but the concept is not explicitly based on reproduction. Fixed morphological differences have been used to classify microbes, most often in culture. But currently, microbes are most often classified with a combination of morphological and genetic characters. The small subunit rRNA is sequenced and put through an algorithm for estimating species based on genetic distances. In short, your question depends a lot on which species concept you are using, and whether you would accept a distance-based DNA definition. But species need not be defined reproductively.


This question actually does not have an easy answer. As indicated in a previous answer, the 16S rRNA gene is used by many scientists. Since this is a fairly conserved genetic region, mutations in this region can differentiate species phylogenetically, but it is not a foolproof method. For example, several species of Shigella can yield nearly identical 16S sequences to those of Escherichia coli and debates rage as to whether they in fact should be classified as the same species. Some scientists even deny that there are such things as microbial species, or if there are, that being able to group microbes into taxonomical units is not worthwhile or informative (although these scientists are still in the minority). If you would like to know more about that viewpoint, you can check out the work of W.F. Doolittle. This one is a fun read:

Doolittle, W., & Zhaxybayeva, O. (2009). On the origin of prokaryotic species. Genome Research, 19(5), 744-756. http://dx.doi.org/10.1101/gr.086645.108


  • Bacteria vary from species to species, thus assigning many common traits to bacteria is difficult. Bacterial species are typified by their diversity.
  • There are three notable common traits of bacteria, 1) lack of membrane-bound organelles, 2) unicellular and 3) small (usually microscopic) size.
  • Not all prokaryotes are bacteria, some are archaea, which although they share common physicals features to bacteria, are ancestrally different from bacteria.
  • archaea: a taxonomic domain of single-celled organisms lacking nuclei, formerly called archaebacteria but now known to differ fundamentally from bacteria.
  • binary fission: a form of asexual reproduction and cell division used by all prokaryotes, (bacteria and archaebacteria)

Bacteria constitute a large domain of prokaryotic microorganisms. Bacteria were among the first life forms to appear on Earth, and are present in most habitats on the planet. Bacteria grow in soil, acidic hot springs, radioactive waste, water, and deep in the Earth&rsquos crust. In addition, they grow in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites, and cockroaches.

But what defines a bacteria? Bacteria as prokaryotes share many common features, such as:

  1. A lack of membrane-bound organelles
  2. Unicellularity and thus division by binary-fission
  3. Generally small size

Bacteria do not tend to have membrane-bound organelles in their cytoplasm and thus contain few large intracellular structures. They consequently lack a true nucleus, mitochondria, chloroplasts, and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum. Bacteria were once seen as simple bags of cytoplasm, but elements such as prokaryotic cytoskeleton, and the localization of proteins to specific locations within the cytoplasm have been found to show levels of complexity. These subcellular compartments have been called &ldquobacterial hyperstructures&rdquo.

Figure: Bacterial structures: Cell structure of a Gram-positive prokaryote.

Unlike in multicellular organisms, increases in cell size (cell growth and reproduction by cell division) are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.

Figure: Binary fission: Many bacteria reproduce through binary fission.

Perhaps the most obvious structural characteristic of bacteria is (with some exceptions) their small size. For example, Escherichia coli cells, an &ldquoaverage&rdquo sized bacterium, are about 2 micrometres (&mum) long and 0.5 &mum in diameter. Small size is extremely important because it allows for a large surface area-to-volume ratio which allows for rapid uptake and intracellular distribution of nutrients and excretion of wastes.

The term &ldquobacteria&rdquo was traditionally applied to all microscopic, single-cell prokaryotes, having the similar traits outlined above. However, molecular systematics show prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. The archaea and eukaryotes are more closely related to each other than either is to the bacteria. It should be noted that Bacteria and Archaea are similar physically, but have different ancestral origins as determined by DNA of the genomes that encode different prokaryotes.

Figure: Archaea and other domains: Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue.


Biology Notes on Microbial Diversity | Microbiology

The below mentioned article provides notes on microbial diversity.

The term ‘microbial diversity’ or biodiversity has become so well known that a public servant is also aware about it. Microbial diversity is defined as the variability among living organisms. The main key of microbial diversity on earth is due to evolution. The structural and functional diversity of any cell represents its evolutionary event which occurred through Darwinian Theory of natural selection.

Natural selection and survival of fittest theory is involved on the microorganisms. This includes diversity within species, between species and of ecosystems. This was first used in the title of a scientific meeting in Washington, D.C. in 1986.

The current list of the world’s biodiversity is quite incomplete (Table 2.1) and that of viruses, microorganisms, and invertebrates is especially deficient. The fungal diversity indicates the total number of species in a particular taxonomic group. The estimates of 1.5 million fungal species is based principally on a ratio of vascular plants of fungi to about 1:6 (Fig. 2.1).

Fig. 2.1 : The number of known species of microorganisms in the world.

Attempts to estimate total numbers of bacteria, archaea, and viruses even more problematical because of difficulties such as detection and recovery from the environment, incomplete knowledge of obligate microbial associations e.g. incomplete knowledge of Symbiobacterium thermophilum, and the problem of species concept in these groups.

Take the case of mycoplasmas, which are prokaryotes having obligate associations with eukaryotic organisms, frequently have tradi­tional nutritional requirements or are mono-culturable and appear to have remarkable diversity. On the other hand, there is one group Spiro plasma, which was discovered in 1972, may be the largest genus on earth.

Spiro plasma species are prin­cipally associated with insects, and the overall rate of new species isolation from such sources of 6% annually indicates species richness. Similarly, marine ecosystems likely support a luxuriant microbial diversity. Further, microbial diversity can be seen on cell size, morphology, metabolism, motility, cell division, developmental biology, adaptation to extreme conditions, etc.

The microbial diversity, therefore, appears in large measure to reflect obligate or facultative associations with higher organisms and to be determined by the spatiotemporal diversity of their hosts or associates.

1. Revealing Microbial Diversity:

The perception of microbial diversity is being radically altered by DNA techniques such as DNA-DNA hy­bridization, nucleic acid fingerprinting and methods of assessing the outcome of DNA probing, and perhaps most important at present, is 16S rRNA sequencing.

The 16S rRNA has radically changed the classification of microbes into 3 domains, the Bacteria, Archaea and Eukarya. While DNA-based analysis (DNA fingerprinting by restriction fragment length polymor­phism i.e. RFLP analysis) is another accepted technique for evaluation of re­lationships between organisms, especially if they are closely related. Holben (1988) detected Brady-rhizobium japonicum selectively at densities as low as 4.3 х 10 3 organisms/gram dry soils.

2. The Concept of Microbial Species:

Biological diversity or biodiversity is actually evolved as part of the evolution of organisms, and the smallest unit of microbial diversity is a species. Bacteria, due to lack of sexuality, fossil records etc., are defined as a group of similar strains distinguished sufficiently from other similar groups of strains by genotypic, phenotypic, and ecological characteristics.

The adhoc committee on (he reconciliation of approach to international committee on systematic bacteriology (ICSB) recommended in 1987 that bacterial species would include strains with approximately 70% or more DNA-DNA relatedness and with 5% or less in thermal stability.

Hence, a bacterial species is a genomic species based on DNA-DNA relatedness and the modern concept of bacterial species differs from those of other organisms. To date, more than 69,000 species in 5100 genera of fungi and about 4,760 species of about 700 genera of bacteria have been described in the literature as given in Table 2.1.

3. Significance of Study of Microbial Diversity:

As quoted by American Society of Microbiology under Microbial Diversity Research Priority, “microbial diversity encompasses the spectrum of variability among all types of microorganisms in the natural world and as altered by human intervention”. The role of microorganisms both on land and water, including being the first colonizer, have ameliorating effects of naturally occurring and man-made disturbed environments.

Current evidence suggests there exist perhaps 3 lakh to 10 lakh species of prokaryotes on earth but only 3100 bacteria are described in Bergey’s Manual. More and more information’s are required and will be of value because microorganisms are important sources of knowledge about strategies and limits of life.

There are resources for new genes and organisms of value to biotechnology, there diversity patterns can be used for monitoring and predicting environmental change. Microorganisms play role in conservation and restoration biology of higher organisms. The microbial communities are excellent model for understanding biological interactions and evolutionary history.

Molecular microbiological methods involving DNA-DNA hybridization and 16S rRNA sequencing, etc. now more helpful in establishing microbial diversity. Data bases are becoming more widely available as a source of molecular and macromolecular information on microorganisms. New- technologies are being developed that are based on diverse organisms from diagnostics to biosensors and to biocatalysts.

In the year 1990s’ microbial diversity has burst forward in a new and exciting form due to efforts of environmental microbiologists, who kept the diversity flame alive during the paradigm organism years.

The molecular revolution that has been sweeping through environmental microbiol­ogy has shown how diverse microbes really are. It has also leashed new waves of creativity in the from of RNA sequence analysis to prove the metabolic activities and gene regulation of microbes in situ.

The gainful advantages may occur by enriching microbial diversity. Microbial genomes can be used for recombinant DNA technology and genetic engineering of organisms with environmental and energy related applications. Emergence of new human pathogen such as SARS is becoming quite important due to threat to public health can be solved by analyzing the genomes of such pathogen.

Culture collections can play a vital role in preserving the genetic diversity of microorganisms. Microbial information’s including molecular, phenotypic, chemical, taxonomic, metabolic, and ecological information can be deposited on databases. A large number of yet unexplored microorganisms may lead to beneficial information’s.

This can be further strengthened by multidisciplinary involvement of experts. There is a compelling need for discovery and identification of microbial bio-control agents, an assessment of their efficacy etc.

The mo­lecular nature of genomes of some important pathogens is necessary to understand the pathogenesis, bio-control, and bioremediation of pollution etc., besides helping in rapid de­tection and diagnosis and in identification of genes for transfer of desirable properties.

Microorganisms are sensitive indicators of envi­ronmental quality. Thus, microbial diversity may be helpful in determining the environmen­tal state of a given habitat of ecosystem. The diverse microorganisms can cause disease and could potentially be used as biological weap­ons. Knowing what is likely to be present can help in rapid diagnosis and treatment.

Biodegradation and bioremediation are potentially important to clean-up and destruction of unwanted materials. Microbial diversity of marine microorganisms is equally important. Sometimes, it is helpful to solve the contamination of sea­food by pathogenic microorganisms e.g. Vibrio vulnificus contaminated oysters. Blue green algae and cyanophages are another dangerous organisms to aquaculture industries.

4. Microbial Evolution:

The microbial evolution has entered a new era with the use of molecular phylogenies to determine relatedness. Certainly this type of phylogenetic analysis remains controversial, but it has opened up possibility of comparing very diverse microbes with a single yardstick and attempting to deduce their history.

Some scientists have opined that the ‘failure’ of molecular methods of find a single unambiguous evolutionary progression from a single ancestor to the present panoply of microorganisms.

The increasing appreciation of the ubiquity and frequency of gene transfer events open the possibility of learning quite essential prokaryotes is by establishing a central core of genes that has not participated in the general orgy of gene transfer. The increasing number of genome sequences may also contribute to a better understanding of the evolutionary history of microbe.


Types of Microbial Interaction

There are two types of interaction based on positive and negative affect.

Positive Microbial Interaction

It is the type of interaction, where both the individuals interact or cooperate to establish a positive relationship for each other’s mutual benefit. In positive interaction, the organisms of two different population can build a consistent, transitory and obligatory relationship. There are three types of positive interaction as we can see in the image:

Mutualism

It is a positive interaction where both the microbial population are interdependent for mutual benefit. The effect of mutualism is positive for both the population. Both the interacting individuals in mutualism are termed symbionts. Thus, mutualism is a type of symbiotic relationship, in which the two organisms closely live together. Therefore, the effect of mutualism is +/+, as a result of an interaction.

  1. The interaction between gut flora and humans: Some microbes reside within the digestive tracts of humans and are considered gut microflora or gut microbiota. The intestinal microflora includes some bacteria, archaea and fungi those live symbiotically in the human’s gut. The gut microflora benefits by harnessing the energy stored in the human body and also provide benefit to the host (human) by providing resistance against the colonization of exogenous microbes, promotes vitamin synthesis, helps in digestion and develops a competent immune system.
  2. An interaction between Trichonympha and Termites: Trichonympha is a protozoan that helps in degrading the complex carbohydrate (cellulose) present in the wood into simple sugars, which is utilized by the termites. The Trichonympha lives symbiotically in the termite’s gut and benefits by getting shelter and constant food supply through the termites’ chewing action.
  3. Chlorella’s interaction with Paramecium: Paramecium bursaria (ciliated protist) harbours the algal cells of Chlorella species. The Chlorella sp. resides within the cytoplasm of P. bursaria and both functions as a host for each other. P. bursaria supplies carbon dioxide and protects the thousands of algal cells. At the same time, Chlorella sp. (endosymbiont) helps P. bursaria to survive in anaerobic conditions and provides maltose as a source of energy.

Protocooperation

It is very similar to mutualism. Unlike mutualism, the two interacting species in protocooperation are not dependent on each other, i.e. they only interact for the benefit they will get. The organisms involved in protocooperation do not share an obligatory relationship, i.e. the organisms are not closely dependent on each other. Therefore, the effect of proto-cooperation is +/+, as a result of an interaction.

  • The interaction between Desulfovibrio and Chromatium: Both Desulfovibrio and Chromatium cooperate and participate in the carbon and sulphur cycle.
  • The interaction between nitrogen-fixing bacteria and Cellulomonas: Both nitrogen-fixing bacteria and Cellulomonas cooperate in the nitrogen cycle.

Commensalism

It is the third type of positive interaction. In commensalism, the one organism associated with the other is benefitted called commensal, while the other organism is neither benefitted nor harmed. Therefore, the effect of commensalism is +/0, as a result of an interaction.

  • The interaction between Flavobacterium and Legionella pneumophila: Flavobacterium secretes cystine that helps in the survival of Legionella pneumophila in the aquatic habitat. Legionella pneumophila thrives in an aquatic habitat.
  • Nitrosomonas and Nitrobacter’s interaction: The Nitrosomonas oxidize ammonia to nitrite and Nitrobacter uses nitrite to get energy and oxidizes it into nitrate.

Negative Microbial Interaction

It is the type of interaction between the two microbial populations, in which the one population of the microorganisms is benefitted, while the other is affected. One organism either attacks or inhibits the other organisms for the survival and food source in a negative interaction.
There are four types of negative interaction, as we can see in the picture:

Competition

It is a type of negative interaction, where two different organisms compete with each other for the same resources. Due to competition for the same resources, there is a limitation of resources by which both the organisms are adversely affected. The competition between the same species’ organisms is called intraspecific competition and the competition between the organisms of different species is known as Interspecific competition. Therefore the effect of the competition is -/-, as a result of an interaction.

  • The interaction between Paramecium cadatum and Paramecium aurelia: Paramecium cadatum and Paramecium aurelia compete for the same bacteria as a food source. P. aurelia outcompetes P. cadatum to survive.

Parasitism

It is a negative interaction, where one organism closely depends and lives upon the other to invade all the nutrients is called a parasite. The parasite that attacks the other organism is called a host. In parasitism, the host-parasite relationship is an obligatory interaction where a parasite strongly needs a long interaction for its growth and multiplication.

The parasites living outside the host cell are called ectoparasites. The parasites living inside the host cell are called endoparasite. In parasitism, one organism (parasite) will be benefitted, and the host cell will be destroyed. Therefore, the effect of parasitism is +/-, as a result of an interaction.

  • The interaction between virus and bacteria: The bacteriophages are the viruses that hunt bacteria. They infect bacteria by penetrating their viral genome into the host cell’s cytoplasm where the genome replicates and translates structural proteins for the assembly of the parasites (bacteriophages). Thus, the bacteriophages hijack the bacterial cell machinery to increase their own population.
  • Bdellavibrio and gram-negative bacteria interaction: Bdellavibriobacteriovorus acts as a parasite for some of the gram-negative bacteria. Bdellavibriobacteriovorus penetrates the gram-negative bacterial cell and resides in the periplasmic space for a short period of time. Later, Bdellavibriobacteriovorus degrades the peptidoglycan layer and ruptures the host cell via hydrolytic enzymes to release its progenies.

Ammensalism

It is also called Antagonism. It is a type of negative interaction where one organism produces inhibitory substance for the other. One population is either unaffected or benefitted, and the other is inhibited in the ammensalism. It is a type of chemical inhibition. Therefore, the effect of predation is 0/-, as a result of an interaction.

  • The vaginal tract produces lactic acid, which inhibits the pathogenic species like Candida albicans.
  • Skin microflora produces fatty acids that restrict the growth of pathogenic bacteria of the skin.
  • Penicillium is a fungus that secretes penicillin, which acts as an inhibitory substance for bacteria’s growth.
  • Thiobacillus thiooxidant produces sulphuric acid, which inhibits most of the bacteria’s growth by lowering culture media’s pH.

Predation

It is a type of negative interaction, where one organism engulfs or attacks the other organism is called a predator. The predator that attacks the other organism is called prey. One organism (predator) is benefitted in predation, and the other (prey) is killed. Therefore, the effect of predation is +/-, as a result of an interaction.

Example:
Bdellavibrio and some protozoans are the predators that attack the other bacteria.

Conclusion

Therefore, we can conclude that all the biotic components like plants, animals, and microorganisms somehow relate to each other for the food, resources, and survival in the ecosystem. The interaction can occur either between the organisms of the same species or different species. Hence, some organisms cooperate for mutual benefit, and some compete with each other. The interaction between the two microbial population will definitely produce an effect which can be in one way or reciprocal.


What are Bacterial Species?

AbstractBacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion divergence between different species is irreversible and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.


Extremophile

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Extremophile, an organism that is tolerant to environmental extremes and that has evolved to grow optimally under one or more of these extreme conditions, hence the suffix phile, meaning “one who loves.”

Extremophilic organisms are primarily prokaryotic (archaea and bacteria), with few eukaryotic examples. Extremophiles are defined by the environmental conditions in which they grow optimally. The organisms may be described as acidophilic (optimal growth between pH 1 and pH 5) alkaliphilic (optimal growth above pH 9) halophilic (optimal growth in environments with high concentrations of salt) thermophilic (optimal growth between 60 and 80 °C [140 and 176 °F]) hyperthermophilic (optimal growth above 80 °C [176 °F]) psychrophilic (optimal growth at 15 °C [60 °F] or lower, with a maximum tolerant temperature of 20 °C [68 °F] and minimal growth at or below 0 °C [32 °F]) piezophilic, or barophilic (optimal growth at high hydrostatic pressure) oligotrophic (growth in nutritionally limited environments) endolithic (growth within rock or within pores of mineral grains) and xerophilic (growth in dry conditions, with low water availability). Some extremophiles are adapted simultaneously to multiple stresses ( polyextremophile) common examples include thermoacidophiles and haloalkaliphiles.

Extremophiles are of biotechnological interest, as they produce extremozymes, defined as enzymes that are functional under extreme conditions. Extremozymes are useful in industrial production procedures and research applications because of their ability to remain active under the severe conditions (e.g., high temperature, pressure, and pH) typically employed in these processes.

The study of extremophiles provides an understanding of the physicochemical parameters defining life on Earth and may provide insight into how life on Earth originated. The postulations that extreme environmental conditions existed on primitive Earth and that life arose in hot environments have led to the theory that extremophiles are vestiges of primordial organisms and thus are models of ancient life.

Extremophiles are also of research importance in the field of astrobiology. Extremophiles that are active at cold temperatures are of particular interest in this field, as the majority of the bodies in the solar system are frozen. The discovery of microorganisms with unusual biochemical properties, such as the ability to use arsenic rather than phosphorus for their growth, are also of interest to astrobiology, since extraterrestrial environments may favour life-forms that use or are built from elements not typically found in life on Earth (see shadow biosphere). Thus, understanding the limits of life on Earth provides scientists with information about the possible existence of extraterrestrial life and provides clues about where and how to search for life on other solar bodies.


Endemic Disease

While Lyme disease and relapsing fever are endemic to these areas, they are not endemic to say, Australia. If there were even a few cases of Lyme disease in Australia, the disease would be considered epidemic, because the normal level of Lyme disease in Australia is zero.


Electrically Conductive Filaments Found in Many Microbial Species

Microfilaments that are capable of conducting electricity, termed nanowires, were discovered in the bacterium Geobacter several years ago by the team of Derek Lovley at the University of Massachusetts Amherst. Now those scientists have found these interesting structures in many other species this work is likely to expand the field studying nanowires. Reporting in the International Society of Microbial Ecology Journal, this research could have many applications in so-called green energy production, now that many more bacteria have been found to be capable of harboring filaments that conduct electricity.

"Geobacter have evolved these special filaments with a very short basic subunit called a pilin that assembles to form long chains that resemble a twisted rope. Most bacteria have a basic subunit that is two to three times longer. Having electrically conducting pili or e-pili is a recent evolutionary event in Geobacter, so the working hypothesis was that this ability would only be found in its close relatives,&rdquo explained Lovley, who began to publish work on Geobacter 30 years ago.

"It was surprising to us, and I think many people will be surprised to learn, that the concept that microbes need the short pilin subunit to produce e-pili is wrong. We have found that some much larger pilins can also yield e-pili and that the ability to express e-pili has arisen independently multiple times in the evolution of diverse microbial groups." He and co-authors added that "e-pili can have an important role in the biogeochemical cycling of carbon and metals and have potential applications as 'green' electronic materials."

"This is a great development, because now the field will widen. Microbiologists now know that they can work with other microbes to investigate electrically conductive filaments. We've found a broad range of microbes that have this,&rdquo noted Lovley. &ldquoOne interesting thing we already can report is that some of the new bacteria we've identified have filaments up to 10 nanometers in diameter. Geobacter's filament[s] are very thin, just three nanometers in diameter. For building electronic devices like nanowire sensors, it is a lot easier to manipulate fatter wires. It will also be more straightforward to elucidate the structural features that confer conductivity with the thicker wires because it is easier to solve their structure."

The researchers are hopeful that the discovery of many more electrically conducting protein nanowires will help in a sustainability revolution. "Our current system of using considerable energy and rare resources to produce electronics, then throwing them away in toxic waste dumps overseas, is not sustainable," Lovley said. Creating microbes that synthesize electronic biologics can eliminate the use of harsh chemicals and requires lower energy inputs, he noted. "And the microbes eat cheaply. In the case of Geobacter, we basically feed them vinegar."

The scientists found bacterial strains that produced high current densities due to pilin genes. They determined that e-pili are conductive because of aromatic amino acids in pilin subunits. That identifying characteristic has made pilin genes easier to identify - they have a high density of aromatic acids with few gaps in pilin chains.

The researchers went a step further, and removed native pilin genes from Geobacter, then replaced them with genes from another conductive microbial strain. In several cases, conductivity was maintained.

Over the years, Geobacter's unique features have led to may &lsquofirsts&rsquo in microbiology. "Now Geobacter has drawn us into electronics. I am excited to find out if these new electrically conductive protein nanowires from other bacteria might function even better than the Geobacter wires for applications such as biomedical sensors. The simple screening method described in our paper is identifying genes for conductive wires in diverse microorganisms that may rely on electrical signaling for unique functions of biomedical and environmental significance,&rdquo said Lovley.


Biologists Estimate that Earth is Inhabited by One Trillion Microbial Species

This colorized scanning electron micrograph shows Mycobacterium tuberculosis, gram-positive bacteria that cause tuberculosis. Image credit: Ray Butler / Centers for Disease Control and Prevention.

Dr. Kenneth Locey and Dr. Jay Lennon, both from the Indiana University’s Department of Biology, combined microbial, plant and animal community datasets from different sources, resulting in the largest compilation of its kind.

Altogether, these data represent over 5.6 million microscopic and nonmicroscopic species from 35,000 locations across all the world’s oceans and continents, except Antarctica.

“Our study combines the largest available datasets with ecological models and new ecological rules for how biodiversity relates to abundance,” Dr. Lennon said.

“This gave us a new and rigorous estimate for the number of microbial species on Earth.”

According to the team, older estimates were based on efforts that dramatically under-sampled the diversity of microorganisms.

“Before high-throughput sequencing, scientists would characterize diversity based on 100 individuals, when we know that a gram of soil contains up to a billion organisms, and the total number on Earth is over 20 orders of magnitude greater,” Dr. Lennon said.

The realization that microorganisms were significantly under-sampled caused an explosion in new microbial sampling efforts over the past several years.

“A massive amount of data has been collected from these new surveys. Yet few have actually tried to pull together all the data to test big questions,” Dr. Locey said. “We suspected that aspects of biodiversity, like the number of species on Earth, would scale with the abundance of individual organisms.”

“After analyzing a massive amount of data, we observed simple but powerful trends in how biodiversity changes across scales of abundance,” the scientists said.

“One of these trends is among the most expansive patterns in biology, holding across all magnitudes of abundance in nature.”

The study results, published in the Proceedings of the National Academy of Sciences, also suggest that actually identifying every microbial species on Earth is a huge challenge.

“The Earth Microbiome Project — a global multidisciplinary project to identify microscope organisms — has so far cataloged less than 10 million species. Of those cataloged species, only about 10,000 have ever been grown in a lab, and fewer than 100,000 have classified sequences,” Dr. Lennon said.

“Our results show that this leaves 100,000 times more microorganisms awaiting discovery — and 100 million to be fully explored. Microbial biodiversity, it appears, is greater than ever imagined.”

Kenneth J. Locey & Jay T. Lennon. Scaling laws predict global microbial diversity. PNAS, published online May 2, 2016 doi: 10.1073/pnas.1521291113


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The definition of a species is not so clear cut

A koala bear isn’t actually a bear, it’s a marsupial. Whales aren’t fish, they’re mammals. Tomatoes aren’t vegetables, they’re fruit. Almost nothing is actually a nut. Peanuts, brazil nuts, cashews, walnuts, pecans and almonds: none of them are really nuts (for the record, peanuts are legumes, brazils and cashews are seeds, and the others are all drupes). Hazelnuts and chestnuts are the exception: they are the elite, the “true” nuts.

We’ve all heard facts like this before. But they are more than just ammunition for pub conversation. They reflect an area of science known as biological taxonomy, the classification of organisms into different groups. At the core of this area lies the notion of the species. The basic idea is very simple: that certain groups of organisms have a special connection to each other. There is something that you and I have in common – we are both human beings. That is, we are members of the same species.

Biological taxonomy’s core aim is to sort all of the organisms of the world into species. Of course, this job really matters, both inside biology and out. The task of evolutionary biology is to track the evolution and development (and eventual extinction) of species. Outside of biology, conservation programmes routinely put various species on “endangered” lists, and urge us to donate money to stop them dying out. In order for any of this to make sense, we need to know how many species there are, and what a species even is.

So, what even is a species? The truth is, we don’t really have any idea.

Recommended

What is a species?

The most famous definition of a species comes from the 20th century German-born biologist Ernst Mayr, who emphasised the importance of interbreeding. The idea (roughly) is that two organisms are of the same species if they can breed with one another to produce fertile offspring. That is why a donkey and a horse aren’t the same species: they can breed and produce offspring, but not fertile offspring.

Mayr’s way of thinking about species has some amazing consequences. Recently, due to rising temperatures in the Arctic, polar bears and grizzly bears have been coming into increased contact, and have been producing fertile offspring. The offspring are (adorably) called grolar or pizzly bears. What this suggests is that polars and grizzlies may actually be the same species after all, despite radical differences in size, appearance, hibernation behaviours, diet and so on.

But it wasn’t long before the problems with Mayr’s approach became apparent. The definition makes use of the notion of interbreeding. This is all very well with horses and polar bears, but smaller organisms like bacteria do not interbreed at all. They reproduce entirely asexually, by simply splitting in two. So this definition of species can’t really apply to bacteria. Perhaps when we started thinking about species in terms of interbreeding, we were all just a bit too obsessed with sex.

So maybe we should forget about sex and look for a different approach to species. In the 1960s, another German biologist, Willi Hennig, suggested thinking about species in terms of their ancestry. In simple terms, he suggested that we should find an organism, and then group it together with its children, and its children’s children, and its children’s children’s children. Eventually, you will have the original organism (the ancestor) and all of its descendents. These groups are called clades. Hennig’s insight was to suggest that this is how we should be thinking about species.

But this approach faces its own problems. How far back should you go before you pick the ancestor in question? If you go back in history far enough, you’ll find that pretty much every animal on the planet shares an ancestor. But surely we don’t want to say that every single animal in the world, from the humble sea slug, to top-of-the-range apes like human beings, are all one big single species?

Enough of species?

This is only the tip of a deep and confusing iceberg. There is absolutely no agreement among biologists about how we should understand the species. One 2006 article on the subject listed 26 separate definitions of species, all with their advocates and detractors. Even this list is incomplete.

The mystery surrounding species is well known in biology, and commonly referred to as “the species problem”. Frustration with the idea of a species goes back at least as far as Darwin. In an 1856 letter to his friend Joseph Hooker, he wrote:

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“It is really laughable to see what different ideas are prominent in various naturalists’ minds, when they speak of ‘species’ in some, resemblance is everything and descent of little weight – in some, resemblance seems to go for nothing, and creation the reigning idea – in some, sterility an unfailing test, with others it is not worth a farthing. It all comes, I believe, from trying to define the indefinable.”

Darwin even dreamt of a time when a revolution would come about in biology. He proposed that one day, biologists could pursue their studies without ever worrying about what a species is, or which animals belong to which species. Indeed, some contemporary biologists and philosophers of biology have taken up this idea, and suggested that biology would be much better off if it didn’t think about life in terms of species at all.

Scrapping the idea of a species is an extreme idea: it implies that pretty much all of biology, from Aristotle right up to the modern age, has been thinking about life in completely the wrong way. The upshots of this new approach would be enormous, both for our scientific and philosophical view of life. It suggests that we should give up thinking about life as neatly segmented into discrete groups. Rather, we should think of life as one immense interconnected web. This shift in thinking would fundamentally reorient our approach to a great many questions concerning our relation to the natural world, from the current biodiversity crisis to conservation.

And, in a way, this kind of picture may be a natural progression in biological thought. One of the great discoveries of evolutionary biology is that the human species is not special or privileged in the grand scheme of things, and that humans have the same origins as all the other animals. This approach just takes the next step. It says that there is no such thing as “the human species” at all.

Henry Taylor is a Birmingham fellow in philosophy at the University of Birmingham. This article first appeared on The Conversation