Microbial biogeography

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Microbial biogeography is a subset of biogeography, a field that concerns the distribution of organisms across space and time. [1] Although biogeography traditionally focused on plants and larger animals, recent studies have broadened this field to include distribution patterns of microorganisms. This extension of biogeography to smaller scales—known as "microbial biogeography"—is enabled by ongoing advances in genetic technologies.

Contents

The aim of microbial biogeography is to reveal where microorganisms live, at what abundance, and why. Microbial biogeography can therefore provide insight into the underlying mechanisms that generate and hinder biodiversity. [2] Microbial biogeography also enables predictions of where certain organisms can survive and how they respond to changing environments, making it applicable to several other fields such as climate change research.

History

Schewiakoff (1893) theorized about the cosmopolitan habitat of free-living protozoans. [3] In 1934, Lourens Baas Becking, based on his own research in California's salt lakes, as well as work by others on salt lakes worldwide, [4] concluded that "everything is everywhere, but the environment selects". [5] Baas Becking attributed the first half of this hypothesis to his colleague Martinus Beijerinck (1913). [6] [7]

Baas Becking hypothesis of cosmopolitan microbial distribution would later be challenged by other works. [8] [9] [10] [11]

Microbial vs macro-organism biogeography

The biogeography of macro-organisms (i.e., plants and animals that can be seen with the naked eye) has been studied since the eighteenth century. For macro-organisms, biogeographical patterns (i.e., which organism assemblages appear in specific places and times) appear to arise from both past and current environments. For example, polar bears live in the Arctic but not the Antarctic, while the reverse is true for penguins; although both polar bears and penguins have adapted to cold climates over many generations (the result of past environments), the distance and warmer climates between the north and south poles prevent these species from spreading to the opposite hemisphere (the result of current environments). This demonstrates the biogeographical pattern known as "isolation with geographic distance" by which the limited ability of a species to physically disperse across space (rather than any selective genetic reasons) restricts the geographical range over which it can be found.[ citation needed ]

The biogeography of microorganisms (i.e., organisms that cannot be seen with the naked eye, such as fungi and bacteria) is an emerging field enabled by ongoing advancements in genetic technologies, in particular cheaper DNA sequencing with higher throughput that now allows analysis of global datasets on microbial biology at the molecular level. When scientists began studying microbial biogeography, they anticipated a lack of biogeographic patterns due to the high dispersibility and large population sizes of microbes, which were expected to ultimately render geographical distance irrelevant. Indeed, in microbial ecology the oft-repeated saying by Lourens Baas Becking that "everything is everywhere, but the environment selects" has come to mean that as long as the environment is ecologically appropriate, geological barriers are irrelevant. [12] However, recent studies show clear evidence for biogeographical patterns in microbial life, which challenge this common interpretation: the existence of microbial biogeographic patterns disputes the idea that "everything is everywhere" while also supporting the idea that environmental selection includes geography as well as historical events that can leave lasting signatures on microbial communities. [2]

Microbial biogeographic patterns are often similar to those of macro-organisms. Microbes generally follow well-known patterns such as the distance decay relationship, the abundance-range relationship, and Rapoport's rule. [13] [14] This is surprising given the many disparities between microorganisms and macro-organisms, in particular their size (micrometers vs. meters), time between generations (minutes vs. years), and dispersibility (global vs. local). However, important differences between the biogeographical patterns of microorganism and macro-organism do exist, and likely result from differences in their underlying biogeographic processes (e.g., drift, dispersal, selection, and mutation). For example, dispersal is an important biogeographical process for both microbes and larger organisms, but small microbes can disperse across much greater ranges and at much greater speeds by traveling through the atmosphere (for larger animals dispersal is much more constrained due to their size). [2] As a result, many microbial species can be found in both northern and southern hemispheres, while larger animals are typically found only at one pole rather than both. [15] Furthermore, microorganisms, such as bacteria, are affected by conditions at very small scales that may differ from the scales that are typically considered for macro-organisms. For example, soil bacterial diversity is shaped by the carbon input and connectivity in microscale aqueous habitats. [16]

Distinct patterns

Reversed and non-monotonous latitudinal diversity gradients

Larger organisms tend to exhibit latitudinal gradients in species diversity, with larger biodiversity existing in the tropics and decreasing toward more temperate polar regions. In contrast, studies on indoor fungal communities [14] and global topsoil microbiomes [17] found microbial biodiversity to be significantly higher in temperate zones than in the tropics. Interestingly, different buildings exhibited the same indoor fungal composition in any given location, where similarity increased with proximity. [14] Thus, despite human efforts to control indoor climates, outside environments appear to be the strongest determinant of indoor fungal composition. [14] On the other hand, the strong biogeographical pattern of soil bacteria is typically attributed to changes in environmental factors such as soil pH. [18] [19] However, soil pH may be a biogeographical proxy [18] that is affected by a soils climatic water balance, [20] which mediates carbon inputs and the connectivity of bacterial aqueous habitats. [16] [21]

Bipolar latitude distributions

Certain microbial populations exist in opposite hemispheres and at complementary latitudes. These 'bipolar' (or 'antitropical') distributions are much rarer in macro-organisms; although macro-organisms exhibit latitude gradients, 'isolation by geographic distance' prevents bipolar distributions (e.g., polar bears are not found at both poles). In contrast, a study on marine surface bacteria [15] showed not only a latitude gradient, but also complementarity distributions with similar populations at both poles, suggesting no "isolation by geographic distance". This is likely due to differences in the underlying biogeographic process, dispersal, as microbes tend to disperse at high rates and far distances by traveling through the atmosphere.[ citation needed ]

Seasonal variations

Microbial diversity can exhibit striking seasonal patterns at a single geographical location. This is largely due to dormancy, a microbial feature not seen in larger animals that allows microbial community composition to fluctuate in relative abundance of persistent species (rather than actual species present). This is known as the "seed-bank hypothesis" [22] and has implications for our understanding of ecological resilience and thresholds to change. [23]

Applications

Directed panspermia

Panspermia suggests that life can be distributed throughout outer space via comets, asteroids, and meteoroids. Panspermia assumes that life can survive the harsh space environment, which features vacuum conditions, intense radiation, extreme temperatures, and a dearth of available nutrients. Many microorganisms are able to evade such stressors by forming spores or entering a state of low-metabolic dormancy. [24] Studies in microbial biogeography have even shown that the ability of microbes to enter and successfully emerge from dormancy when their respective environmental conditions are favorable contributes to the high levels of microbial biodiversity observed in almost all ecosystems. [25] Thus microbial biogeography can be applied to panspermia as it predicts that microbes are able to protect themselves from the harsh space environment, know to emerge when conditions are safe, and also take advantage of their dormancy capability to enhance biodiversity wherever they may land.[ citation needed ]

Directed panspermia is the deliberate transport of microorganisms to colonize another planet. If aiming to colonize an Earth-like environment, microbial biogeography can inform decisions on the biological payload of such a mission. In particular, microbes exhibit latitudinal ranges according to Rapoport's rule, which states that organisms living at lower latitudes (near the equator) are found within smaller latitude ranges than those living at higher latitudes (near the poles). Thus the ideal biological payload would include widespread, higher-latitude microorganisms that can tolerate of a wider range of climates. This is not necessarily the obvious choice, as these widespread organisms are also rare in microbial communities and tend to be weaker competitors when faced with endemic organisms. Still, they can survive in a range of climates and thus would be ideal for inhabiting otherwise lifeless Earth-like planets with uncertain environmental conditions. Extremophiles, although tough enough to withstand the space environment, may not be ideal for directed panspermia as any given extremophile species requires a very specific climate to survive. However, if the target was closer to Earth, such as a planet or moon in our Solar System, it may be possible to select a specific extremophile species for the well-defined target environment.[ citation needed ]

See also

Related Research Articles

<span class="mw-page-title-main">Extremophile</span> Organisms capable of living in extreme environments

An extremophile is an organism that is able to live in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, radiation, salinity, or pH level.

<span class="mw-page-title-main">Microorganism</span> Microscopic living organism

A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

<span class="mw-page-title-main">Microbial ecology</span> Study of the relationship of microorganisms with their environment

Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

<span class="mw-page-title-main">Aeroplankton</span> Tiny lifeforms floating and drifting in the air, carried by the wind

Aeroplankton are tiny lifeforms that float and drift in the air, carried by wind. Most of the living things that make up aeroplankton are very small to microscopic in size, and many can be difficult to identify because of their tiny size. Scientists collect them for study in traps and sweep nets from aircraft, kites or balloons. The study of the dispersion of these particles is called aerobiology.

An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates of metabolism, and generally low population density. Oligotrophic environments are those that offer little to sustain life. These environments include deep oceanic sediments, caves, glacial and polar ice, deep subsurface soil, aquifers, ocean waters, and leached soils.

Soil ecology is the study of the interactions among soil organisms, and between biotic and abiotic aspects of the soil environment. It is particularly concerned with the cycling of nutrients, formation and stabilization of the pore structure, the spread and vitality of pathogens, and the biodiversity of this rich biological community.

<span class="mw-page-title-main">Phyllosphere</span> The plant surface as a habitat for microorganisms

In microbiology, the phyllosphere is the total above-ground surface of a plant when viewed as a habitat for microorganisms. The phyllosphere can be further subdivided into the caulosphere (stems), phylloplane (leaves), anthosphere (flowers), and carposphere (fruits). The below-ground microbial habitats are referred to as the rhizosphere and laimosphere. Most plants host diverse communities of microorganisms including bacteria, fungi, archaea, and protists. Some are beneficial to the plant, while others function as plant pathogens and may damage the host plant or even kill it.

<span class="mw-page-title-main">Microbial loop</span> Trophic pathway in marine microbial ecosystems

The microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

<span class="mw-page-title-main">Microbiology</span> Study of microscopic organisms

Microbiology is the scientific study of microorganisms, those being of unicellular (single-celled), multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology, immunology, and parasitology.

<span class="mw-page-title-main">Antarctic microorganism</span>

Antarctica is one of the most physically and chemically extreme terrestrial environments to be inhabited by lifeforms. The largest plants are mosses, and the largest animals that do not leave the continent are a few species of insects.

<span class="mw-page-title-main">Soda lake</span> Lake that is strongly alkaline

A soda lake or alkaline lake is a lake on the strongly alkaline side of neutrality, typically with a pH value between 9 and 12. They are characterized by high concentrations of carbonate salts, typically sodium carbonate, giving rise to their alkalinity. In addition, many soda lakes also contain high concentrations of sodium chloride and other dissolved salts, making them saline or hypersaline lakes as well. High pH and salinity often coincide, because of how soda lakes develop. The resulting hypersaline and highly alkalic soda lakes are considered some of the most extreme aquatic environments on Earth.

Rare biosphere refers to a large number of rare species of microbial life, i.e. bacteria, archaea and fungi, that can be found in very low concentrations in an environment.

<span class="mw-page-title-main">Marine microorganisms</span> Any life form too small for the naked human eye to see that lives in a marine environment

Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism is any microscopic living organism or virus, that is too small to see with the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses as microorganisms, but others consider these as non-living.

<span class="mw-page-title-main">Root microbiome</span> Microbe community of plant roots

The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.

<span class="mw-page-title-main">Phycosphere</span> Microscale mucus region that is rich in organic matter surrounding a phytoplankton cel

The phycosphere is a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell. This area is high in nutrients due to extracellular waste from the phytoplankton cell and it has been suggested that bacteria inhabit this area to feed on these nutrients. This high nutrient environment creates a microbiome and a diverse food web for microbes such as bacteria and protists. It has also been suggested that the bacterial assemblages within the phycosphere are species-specific and can vary depending on different environmental factors.

<span class="mw-page-title-main">Microbiome</span> Microbial community assemblage and activity

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.

<span class="mw-page-title-main">Branches of microbiology</span> List of scientific disciplines

The branches of microbiology can be classified into pure and applied sciences. Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines, and certain aspects of these branches can extend beyond the traditional scope of microbiology In general the field of microbiology can be divided in the more fundamental branch and the applied microbiology (biotechnology). In the more fundamental field the organisms are studied as the subject itself on a deeper (theoretical) level. Applied microbiology refers to the fields where the micro-organisms are applied in certain processes such as brewing or fermentation. The organisms itself are often not studied as such, but applied to sustain certain processes.

<span class="mw-page-title-main">Viral shunt</span>

The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.

<span class="mw-page-title-main">Plant microbiome</span>

The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".

Jennifer B. H. Martiny is an American ecologist who is a professor at the University of California, Irvine. Her research considers microbial diversity in marine and terrestrial ecosystems. In 2020 she was elected a Fellow of the American Association for the Advancement of Science.

References

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  2. 1 2 3 Martiny, Jennifer B. Hughes; Bohannan, Brendan J.M.; Brown, James H.; Colwell, Robert K.; Fuhrman, Jed A.; Green, Jessica L.; Horner-Devine, M. Claire; Kane, Matthew; Krumins, Jennifer Adams; Kuske, Cheryl R.; Morin, Peter J.; Naeem, Shahid; Øvreås, Lise; Reysenbach, Anna-Louise; Smith, Val H.; Staley, James T. (February 2006). "Microbial biogeography: putting microorganisms on the map". Nature Reviews Microbiology. 4 (2): 102–112. doi:10.1038/nrmicro1341. PMID   16415926. S2CID   205496270.
  3. ↑ Schewiakoff, W.T. 1893. Über die geographische Verbreitung der Süßwasser-protozoen. Mem. Acad. Imp. Sci. St. Petersb. Ser. VII 41, n. 8, 1-201, BHL.
  4. ↑ Baas-Becking, L.G.M. (1934). Geobiologie of inleiding tot de milieukunde. The Hague, the Netherlands: W.P. Van Stockum & Zoon, . English translation, 2015, .
  5. ↑ Translated from the original Dutch: "Alles is overal: maar het milieu selecteert"
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  17. ↑ Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K.; Anderson, Jennifer L.; Soudzilovskaia, Nadejda A.; Bodegom, Peter M.; Bengtsson-Palme, Johan; Anslan, Sten; Coelho, Luis Pedro; Harend, Helery; Huerta-Cepas, Jaime; Medema, Marnix H.; Maltz, Mia R.; Mundra, Sunil; Olsson, Pål Axel (August 2018). "Structure and function of the global topsoil microbiome". Nature. 560 (7717): 233–237. doi:10.1038/s41586-018-0386-6. hdl: 1887/73861 . ISSN   1476-4687. PMID   30069051. S2CID   51892834.
  18. 1 2 Fierer, Noah; Jackson, Robert B. (2006-01-17). "The diversity and biogeography of soil bacterial communities". Proceedings of the National Academy of Sciences. 103 (3): 626–631. doi: 10.1073/pnas.0507535103 . ISSN   0027-8424. PMC   1334650 . PMID   16407148.
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