Rare biosphere
Encyclopedia
Changes in the biodiversity
of an ecosystem
, whether marine or terrestrial, may affect its efficiency and function. Disruption due to climate change
, or other anthropogenic
perturbations can result in decreased productivity
and in some cases lead to disruptions in global biogeochemical cycles. The possible ramifications of changes in ecosystem biodiversity are not well characterized or understood, and it may be possible that disruption, up to a point, will have little to no effect given the redundancy within an ecosystem. This is particularly troubling in the context of microbial ecosystems. The dynamics of microbial ecosystems are tightly coupled to biogeochemical processes, and any perturbation within this system in particular could result in dramatic changes (Kirchman, 2008). For example, the microbial loop
within the marine context is responsible for the decomposition of organics and recycling of nutrients back into the ecosystem. This allows for other organisms, such as phytoplankton
, to reuse essential nutrients, like nitrogen, and continue production (Kirchman 2008). Without this recycled nitrogen, phytoplankton would be highly limited in their production rates, in turn limiting the growth of grazers. The effects of such an occurrence would reverberate throughout the food web, and nitrogen cycle. It is important to establish a base line of microbial diversity within ecosystems in order to gauge possible change due to climate change and the possible outcomes.
Recent use of high-throughput sequencing
techniques has broadened the scope of biodiversity, with the discovery of what has been titled the “Rare Biosphere” (Sogin et al., 2006). Previous attempts to characterize in situ abundance have been made through pure culture and molecular techniques (Fuhrman, 2009). Pure culture providing a very narrow picture of some of the rarer species present, <1-5% of bacteria present (Fuhrman, 2009). Molecular techniques, such as Sanger sequencing, resulting in a much broader scope but highlighting the more abundant species present (Heidelberg et al., 2010)(Pedros-Alio, 2007). Neither technique captures all of the diversity present. Alternatively high throughput sequencing, “tag sequencing”, divides unique rRNA tag sequences into operational taxonomic units (OTUs) based upon similarities in mitochondrial-encoded cytochrome oxidases (Sogin et al., 2006). Both Sanger, shot gun sequencing, and tag sequencing organize sequences into OTUs (Heidelberg et al., 2010). However, it is the resolution that tag sequencing provides that sets it apart, resulting from the increased efficiency in serial analysis (Heidelberg et al., 2010). This efficiency increase is made possible through the use of internal primer sequences resulting in restriction-digest overhanging sequences (Heidelberg et al., 2010). Though OTUs provide a means of distinguishing the possible number of phylogenetic groups, it is not possible to deduce phylogenetic relationships based upon OTU’s. Tags associated with OTUs must be cross-referenced with gene bank
s, in order for tags to be phylotyped and relationships established (Sogin et al., 2006).
The result of tag sequencing has been to produce orders of magnitude larger estimates of OTUs present in ecosystems, producing a long tail on species abundance curves (Patterson, 2009)(Pedrós-Alío, 2007). This long tail accounts for less than .1% of the abundant species in a particular ecosystem. At the same time it represents thousands of populations accounting for most of the phylogenetic diversity in an ecosystem. This low-abundance high-diversity group is what is now called the “Rare Biosphere”. Using this method, Sogin et al.’s study of microbial diversity in North Atlantic deep water produced an estimate of 5266 different taxa (Sogin et al., 2006). This is particularly dramatic considering that previous studies employing more traditional PCR cloning techniques have resulted in estimates of up to 500 (Pedrós-Alío, 2007).
, is unlikely (Pedrós-Alío, 2007). Viruses depend on high concentrations of hosts to persist. Additionally being less abundant implies limited growth, and on the smaller end of the cell size spectrum (Pedrós-Alío, 2007). This limits the likelihood of death by ingestion, as grazers prefer larger more active microbes. As well it is important to note that just because these taxa are “rare” now does not mean that under previous conditions in our planet’s history they were “rare” (Sogin et al., 2006). These taxa could be have been episodically abundant, resulting in global changes in biogeochemical cycles (Sogin et al., 2006). Essentially this requires microbial ecologists to change their perspective on how microbial interactions function on evolutionary time scales (Sogin et al., 2006).
On that note, rare today does not mean rare tomorrow. Given the persistence of these taxa under the right conditions they have the potential to dominate, and become the more abundant taxa (Sogin et al., 2006). The occurrence of such conditions may occur on many temporal scales. It may be possible that some rare taxa dominate only during anomalous years, such as during El Niño (Fuhrman, 2009). While, a four-year study by Brown et al. in species abundance in a single marine ecosystem found that some taxa were undetectable during some months and accounted for a couple percent of the total abundance other months (Brown et al., 2009). Indicating that a change in abundance may occur on a seasonal scale. Recent global climate change may provide some of these rare taxa with the conditions necessary to increase in abundance.
Even in their low abundance taxa belonging to the “Rare Biosphere” may be affecting global biogeochemical cycles. For example, most of nitrogen fixation was attributed to Trichodesmium and abundant cyanobacterium. However, more recent evidence implicates that the rare minority may be responsible for fixing more cumulative Nitrogen than the abundant majority (Furhman, 2009).
A subtle and less direct manner these populations may be affecting ecosystems, in terms of biodiversity and biogeochemical cycles, is by acting as an unlimited source of genetic diversity and material (Furhman, 2009)(Sogin et al., 2006). How microbial communities present resilience after environmental perturbation or catastrophe and how closely a closely related species may present unique and novel genetic attributes compared to near relatives, are topics of much discussion and investigation (Sogin et al., 2006). The rare biosphere could be a seed bank, transferring genes resulting in fitter recombinants that rise to become the dominant majority (Sogin et al., 2006). Until now this group has been overlooked entirely, and may be the answer to many longstanding questions concerning microbial ecology and genetics.
Biodiversity
Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...
of an ecosystem
Ecosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....
, whether marine or terrestrial, may affect its efficiency and function. Disruption due to climate change
Climate change
Climate change is a significant and lasting change in the statistical distribution of weather patterns over periods ranging from decades to millions of years. It may be a change in average weather conditions or the distribution of events around that average...
, or other anthropogenic
Anthropogenic
Human impact on the environment or anthropogenic impact on the environment includes impacts on biophysical environments, biodiversity and other resources. The term anthropogenic designates an effect or object resulting from human activity. The term was first used in the technical sense by Russian...
perturbations can result in decreased productivity
Productivity
Productivity is a measure of the efficiency of production. Productivity is a ratio of what is produced to what is required to produce it. Usually this ratio is in the form of an average, expressing the total output divided by the total input...
and in some cases lead to disruptions in global biogeochemical cycles. The possible ramifications of changes in ecosystem biodiversity are not well characterized or understood, and it may be possible that disruption, up to a point, will have little to no effect given the redundancy within an ecosystem. This is particularly troubling in the context of microbial ecosystems. The dynamics of microbial ecosystems are tightly coupled to biogeochemical processes, and any perturbation within this system in particular could result in dramatic changes (Kirchman, 2008). For example, the microbial loop
Microbial loop
The microbial loop describes a trophic pathway in the marine microbial food web where dissolved organic carbon is returned to higher trophic levels via the incorporation into bacterial biomass, and coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. The term microbial...
within the marine context is responsible for the decomposition of organics and recycling of nutrients back into the ecosystem. This allows for other organisms, such as phytoplankton
Phytoplankton
Phytoplankton are the autotrophic component of the plankton community. The name comes from the Greek words φυτόν , meaning "plant", and πλαγκτός , meaning "wanderer" or "drifter". Most phytoplankton are too small to be individually seen with the unaided eye...
, to reuse essential nutrients, like nitrogen, and continue production (Kirchman 2008). Without this recycled nitrogen, phytoplankton would be highly limited in their production rates, in turn limiting the growth of grazers. The effects of such an occurrence would reverberate throughout the food web, and nitrogen cycle. It is important to establish a base line of microbial diversity within ecosystems in order to gauge possible change due to climate change and the possible outcomes.
Recent use of high-throughput sequencing
Gene sequencing
Gene Sequencing may refer to:* DNA sequencing* or a comprehensive variant of it: Full genome sequencing...
techniques has broadened the scope of biodiversity, with the discovery of what has been titled the “Rare Biosphere” (Sogin et al., 2006). Previous attempts to characterize in situ abundance have been made through pure culture and molecular techniques (Fuhrman, 2009). Pure culture providing a very narrow picture of some of the rarer species present, <1-5% of bacteria present (Fuhrman, 2009). Molecular techniques, such as Sanger sequencing, resulting in a much broader scope but highlighting the more abundant species present (Heidelberg et al., 2010)(Pedros-Alio, 2007). Neither technique captures all of the diversity present. Alternatively high throughput sequencing, “tag sequencing”, divides unique rRNA tag sequences into operational taxonomic units (OTUs) based upon similarities in mitochondrial-encoded cytochrome oxidases (Sogin et al., 2006). Both Sanger, shot gun sequencing, and tag sequencing organize sequences into OTUs (Heidelberg et al., 2010). However, it is the resolution that tag sequencing provides that sets it apart, resulting from the increased efficiency in serial analysis (Heidelberg et al., 2010). This efficiency increase is made possible through the use of internal primer sequences resulting in restriction-digest overhanging sequences (Heidelberg et al., 2010). Though OTUs provide a means of distinguishing the possible number of phylogenetic groups, it is not possible to deduce phylogenetic relationships based upon OTU’s. Tags associated with OTUs must be cross-referenced with gene bank
Gene bank
Gene banks help preserve genetic material, be it plant or animal. In plants, this could be by freezing cuts from the plant, or stocking the seeds. In animals, this is the freezing of sperm and eggs in zoological freezers until further need. With corals, fragments are taken which are stored in water...
s, in order for tags to be phylotyped and relationships established (Sogin et al., 2006).
The result of tag sequencing has been to produce orders of magnitude larger estimates of OTUs present in ecosystems, producing a long tail on species abundance curves (Patterson, 2009)(Pedrós-Alío, 2007). This long tail accounts for less than .1% of the abundant species in a particular ecosystem. At the same time it represents thousands of populations accounting for most of the phylogenetic diversity in an ecosystem. This low-abundance high-diversity group is what is now called the “Rare Biosphere”. Using this method, Sogin et al.’s study of microbial diversity in North Atlantic deep water produced an estimate of 5266 different taxa (Sogin et al., 2006). This is particularly dramatic considering that previous studies employing more traditional PCR cloning techniques have resulted in estimates of up to 500 (Pedrós-Alío, 2007).
Marine context
Considering their low abundance, members of the rare biosphere may represent ancient and persistent taxa (Sogin et al., 2006). As these less abundant species are limited in number viral infection, and ultimately death by lysisLysis
Lysis refers to the breaking down of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a "lysate"....
, is unlikely (Pedrós-Alío, 2007). Viruses depend on high concentrations of hosts to persist. Additionally being less abundant implies limited growth, and on the smaller end of the cell size spectrum (Pedrós-Alío, 2007). This limits the likelihood of death by ingestion, as grazers prefer larger more active microbes. As well it is important to note that just because these taxa are “rare” now does not mean that under previous conditions in our planet’s history they were “rare” (Sogin et al., 2006). These taxa could be have been episodically abundant, resulting in global changes in biogeochemical cycles (Sogin et al., 2006). Essentially this requires microbial ecologists to change their perspective on how microbial interactions function on evolutionary time scales (Sogin et al., 2006).
On that note, rare today does not mean rare tomorrow. Given the persistence of these taxa under the right conditions they have the potential to dominate, and become the more abundant taxa (Sogin et al., 2006). The occurrence of such conditions may occur on many temporal scales. It may be possible that some rare taxa dominate only during anomalous years, such as during El Niño (Fuhrman, 2009). While, a four-year study by Brown et al. in species abundance in a single marine ecosystem found that some taxa were undetectable during some months and accounted for a couple percent of the total abundance other months (Brown et al., 2009). Indicating that a change in abundance may occur on a seasonal scale. Recent global climate change may provide some of these rare taxa with the conditions necessary to increase in abundance.
Even in their low abundance taxa belonging to the “Rare Biosphere” may be affecting global biogeochemical cycles. For example, most of nitrogen fixation was attributed to Trichodesmium and abundant cyanobacterium. However, more recent evidence implicates that the rare minority may be responsible for fixing more cumulative Nitrogen than the abundant majority (Furhman, 2009).
A subtle and less direct manner these populations may be affecting ecosystems, in terms of biodiversity and biogeochemical cycles, is by acting as an unlimited source of genetic diversity and material (Furhman, 2009)(Sogin et al., 2006). How microbial communities present resilience after environmental perturbation or catastrophe and how closely a closely related species may present unique and novel genetic attributes compared to near relatives, are topics of much discussion and investigation (Sogin et al., 2006). The rare biosphere could be a seed bank, transferring genes resulting in fitter recombinants that rise to become the dominant majority (Sogin et al., 2006). Until now this group has been overlooked entirely, and may be the answer to many longstanding questions concerning microbial ecology and genetics.