[naturenews] from [nature.com]
[naturenews]
Published online 23 December 2009 | Nature |
News
Microbial encyclopaedia guided by evolution
Sequencing project reveals microbial cache of protein families.
Brendan Borrell
Sequencing neglected microbes could accelerate the discovery of new protein families and biological traits, a study published today suggests.
Genome sequencers have tended to gravitate towards microbes with special traits, such as deadly pathogens or deep-sea extremophiles, but as a result sequencing efforts have been piecemeal and have left blank large portions of the microbial tree of life. In this week's issue of Nature, Jonathan Eisen at the University of California, Davis, and his co-authors analyse the complete sequences of 56 bacterial and archaeal species1 that were selected to help fill those gaps.
{{Sequencing shows that the bacterium Haliangium ochraceum appears to have stolen a textbook gene from eukaryotes.}
M. Rohde/Helmholtz Centre for Infection Research, Braunschweig}
The approach nets an average of 1,000 protein families for each genome sequenced, and so far the researchers have identified 1,768 protein families that seem to be new to science. Discovering novel enzymes that can be used in industrial processes such as bioremediation or biofuel production is one of the main practical goals of microbial genomics.
Donald Bryant, a microbial physiologist at Pennsylvania State University in University Park who was not involved in the research, says that this evolutionarily guided strategy "has the potential to direct people toward new discoveries".
Sequencing history
The study represents the first publication of the Genomic Encyclopedia of Bacteria and Archaea, launched in 2007 by the Joint Genome Institute (JGI) in Walnut Creek, California, where Eisen holds an adjunct appointment. The project developed after he completed eight microbial genome sequences and realized — with some disappointment — that the deepest branches of the microbial tree of life were still murky. JGI director Eddy Rubin suggested starting up a large-scale sequencing project to rectify the situation, but only if Eisen and his collaborators could demonstrate the practical benefits of this basic research.
Now Eisen believes he has made his case. The team examined a microbial family tree that had been assembled on the basis of the gene encoding the RNA that forms the small subunit of the bacterial ribosome, and chose 200 lineages whose members had never been sequenced. Collaborators at the German Collection of Microorganisms and Cell Cultures in Braunschweig then grew enough of the microbes to begin the sequencing; the team prioritized work on ones that would be easiest to obtain sufficient quantities of DNA. Compared with a random selection of microbes, Eisen says, evolutionarily guided sequencing can net more proteins and improve the reconstruction of the tree of life.
One species, called Haliangium ochraceum, which lives in coastal saltwater environments, has a gene similar to those that make actin proteins in eukaryotes — organisms whose cells contain complex membrane-bound structures, such as fungi, plants and animals. This is the first time that a version of this 'textbook' eukaryotic gene has been discovered in bacteria. Eisen suspects that the bacterium stole the gene from a eukaryote, and may use it to disrupt the growth of eukaryotic prey or competitors such as fungi. "This is just an emblematic reason to do unbiased sampling," Eisen says. "Nobody would have sequenced the genome of this organism other than for phylogenetic reasons."
He believes that sequencing just 1,520 microbial strains selected to fill in the microbial tree of life could encompass half of the diversity of the bacteria and archaea that can be cultured in a laboratory. Ultimately, Eisen hopes that this study will convince funding agencies to support the sequencing of not only those organisms, but thousands more that have never been cultured.
But not everyone is enamored of the strategy. "We all agree that many more microbial genomes are needed, but it does not really matter in what order these will be sequenced," says Stephan Schuster of Pennsylvania State University. For Schuster, the most important thing is that genomes are finished and annotated rather than being reported as "laundry lists of novel features".
References
1. Wu, D. et al. Nature 462, 1056-1060 (2009).
[naturenews]
Published online 23 December 2009 | Nature |
News
Fish tanks 'threaten Sunshine State sea creatures'
Florida invertebrate fishery could be heading for collapse, scientists warn.
Daniel Cressey
{{The blue-legged hermit crab is one of the species that might be under threat.}
RevolverOcelot/Wikipedia}
A growing trend towards fancier fish tanks threatens the future of Florida's invertebrate fishery, researchers warned this week.
While some question the scientists' bleak conclusion, data on crabs, anemones, starfish, snails and the like collected off the coasts of the Sunshine State, show a huge increase in catches for aquaria since 1994.
"The invertebrate ornamental fishery in the State of Florida, with increasing catches over a more diverse array of species, is poised for collapse," warns a paper in PLoS ONE1.
The problem, says lead author of the paper Andrew Rhyne, is a trend away from simple fish-only display tanks towards having entire coral ecosystems in your living room. To create these miniature reefs, invertebrates are harvested from the wild, either to adorn a tank or to provide a useful role, such as keeping algae under control.
Florida hosts the world's third largest ornamental fishery, behind only Indonesia and the Philippines. Rhyne, a marine biologist at the New England Aquarium in Boston, Massachusetts, and Roger Williams University in Bristol, Rhode Island, and his colleagues looked at how fishing in the state has changed. For this, they used the Florida Marine Life Fishery (FMLF) database, which records details of fisheries products caught in the state.
{{“We're not saying the system is totally destroyed or that this is a terrible fishery that shouldn't be occurring. We're saying there should be a different management system.”}
Andrew Rhyne
New England Aquarium}
They found that, each year between 1994 and 2007, the number of invertebrates taken from Florida waters increased by 13.3%, or half a million individual animals. Nine million individuals were collected in 2007, with the most popular including the blue-legged hermit crab (Clibanarius tricolor), the five-holed keyhole sand dollar (Mellita tenuis) and the star snail (Lithopoma americanum).
Worryingly, there has also been a shift towards collecting grazing species. These are prized by aquarium keepers as they keep algae under control. But they perform a similar function in the wild, and their removal may hasten what some researchers have dubbed the "slippery slope to slime", in which coral is killed off by algae.
The FMLF fishery, Rhyne et al write, "appears to be crawling to collapse".
"We're not saying the system is totally destroyed or that this is a terrible fishery that shouldn't be occurring," Rhyne told Nature. "We're saying there should be a different management system."
Downturn hopes
The difficulty, says Rhyne, is that there are no real baseline data for many of these species. Simply put, no one knows what a sustainable level of take for many of these animals might be.
With the aquarium industry quick to respond to new trends, Rhyne worries that some animals might become imperilled under the current management system if demand suddenly increases.
At present, most of the invertebrates in question are caught under 'multi-species' licences that allow collectors to take any species except some corals and endangered animals.
In their paper, the researchers suggest that a predicted — although probably temporary — decline in demand for relatively exotic aquarium species owing to the current economic downturn presents a real opportunity to change the management of these animals. Rhyne suggests individually managing the most popular species or reducing the number of licences granted.
The researchers also note that there is legislation under discussion in the US that could ban trade in non-native wildlife. If laws are enacted banning the import of species from outside the US this could "dramatically increase" the pressure on Florida.
Sherry Larkin, a researcher in marine resource management at the University of Florida, says there is a lot of good work in the paper, including information about types of species gathered and exploration of the potential implications of a trade ban.
"I'm less thrilled about the general categorization of the worldwide problem and how the Florida data supports statements that the fishery is headed for collapse," says Larkin. "The regulations for the Florida commercial industry are extensive but the article gives the impression that the effort by the current restricted fishermen is a run-away train that will be solely responsible for a collapse."
Lee Schlesinger, a spokesman for the Florida Fish and Wildlife Conservation Commission in Tallahassee, denied that there was a problem with the management of Florida's marine resources.
"Our fisheries are well managed and have been for years. The resources are considered to be fairly healthy and abundant," he says. "Five hundred-plus species are collected for the aquarium trade. It is a highly regulated fishery here in Florida."
References
1. Rhyne, A. et al. PLoS ONE 4, e8413 (2009).
[naturenews]
Published online 23 December 2009 | Nature |
News
Microbial encyclopaedia guided by evolution
Sequencing project reveals microbial cache of protein families.
Brendan Borrell
Sequencing neglected microbes could accelerate the discovery of new protein families and biological traits, a study published today suggests.
Genome sequencers have tended to gravitate towards microbes with special traits, such as deadly pathogens or deep-sea extremophiles, but as a result sequencing efforts have been piecemeal and have left blank large portions of the microbial tree of life. In this week's issue of Nature, Jonathan Eisen at the University of California, Davis, and his co-authors analyse the complete sequences of 56 bacterial and archaeal species1 that were selected to help fill those gaps.
{{Sequencing shows that the bacterium Haliangium ochraceum appears to have stolen a textbook gene from eukaryotes.}
M. Rohde/Helmholtz Centre for Infection Research, Braunschweig}
The approach nets an average of 1,000 protein families for each genome sequenced, and so far the researchers have identified 1,768 protein families that seem to be new to science. Discovering novel enzymes that can be used in industrial processes such as bioremediation or biofuel production is one of the main practical goals of microbial genomics.
Donald Bryant, a microbial physiologist at Pennsylvania State University in University Park who was not involved in the research, says that this evolutionarily guided strategy "has the potential to direct people toward new discoveries".
Sequencing history
The study represents the first publication of the Genomic Encyclopedia of Bacteria and Archaea, launched in 2007 by the Joint Genome Institute (JGI) in Walnut Creek, California, where Eisen holds an adjunct appointment. The project developed after he completed eight microbial genome sequences and realized — with some disappointment — that the deepest branches of the microbial tree of life were still murky. JGI director Eddy Rubin suggested starting up a large-scale sequencing project to rectify the situation, but only if Eisen and his collaborators could demonstrate the practical benefits of this basic research.
Now Eisen believes he has made his case. The team examined a microbial family tree that had been assembled on the basis of the gene encoding the RNA that forms the small subunit of the bacterial ribosome, and chose 200 lineages whose members had never been sequenced. Collaborators at the German Collection of Microorganisms and Cell Cultures in Braunschweig then grew enough of the microbes to begin the sequencing; the team prioritized work on ones that would be easiest to obtain sufficient quantities of DNA. Compared with a random selection of microbes, Eisen says, evolutionarily guided sequencing can net more proteins and improve the reconstruction of the tree of life.
One species, called Haliangium ochraceum, which lives in coastal saltwater environments, has a gene similar to those that make actin proteins in eukaryotes — organisms whose cells contain complex membrane-bound structures, such as fungi, plants and animals. This is the first time that a version of this 'textbook' eukaryotic gene has been discovered in bacteria. Eisen suspects that the bacterium stole the gene from a eukaryote, and may use it to disrupt the growth of eukaryotic prey or competitors such as fungi. "This is just an emblematic reason to do unbiased sampling," Eisen says. "Nobody would have sequenced the genome of this organism other than for phylogenetic reasons."
He believes that sequencing just 1,520 microbial strains selected to fill in the microbial tree of life could encompass half of the diversity of the bacteria and archaea that can be cultured in a laboratory. Ultimately, Eisen hopes that this study will convince funding agencies to support the sequencing of not only those organisms, but thousands more that have never been cultured.
But not everyone is enamored of the strategy. "We all agree that many more microbial genomes are needed, but it does not really matter in what order these will be sequenced," says Stephan Schuster of Pennsylvania State University. For Schuster, the most important thing is that genomes are finished and annotated rather than being reported as "laundry lists of novel features".
References
1. Wu, D. et al. Nature 462, 1056-1060 (2009).
[naturenews]
Published online 23 December 2009 | Nature |
News
Fish tanks 'threaten Sunshine State sea creatures'
Florida invertebrate fishery could be heading for collapse, scientists warn.
Daniel Cressey
{{The blue-legged hermit crab is one of the species that might be under threat.}
RevolverOcelot/Wikipedia}
A growing trend towards fancier fish tanks threatens the future of Florida's invertebrate fishery, researchers warned this week.
While some question the scientists' bleak conclusion, data on crabs, anemones, starfish, snails and the like collected off the coasts of the Sunshine State, show a huge increase in catches for aquaria since 1994.
"The invertebrate ornamental fishery in the State of Florida, with increasing catches over a more diverse array of species, is poised for collapse," warns a paper in PLoS ONE1.
The problem, says lead author of the paper Andrew Rhyne, is a trend away from simple fish-only display tanks towards having entire coral ecosystems in your living room. To create these miniature reefs, invertebrates are harvested from the wild, either to adorn a tank or to provide a useful role, such as keeping algae under control.
Florida hosts the world's third largest ornamental fishery, behind only Indonesia and the Philippines. Rhyne, a marine biologist at the New England Aquarium in Boston, Massachusetts, and Roger Williams University in Bristol, Rhode Island, and his colleagues looked at how fishing in the state has changed. For this, they used the Florida Marine Life Fishery (FMLF) database, which records details of fisheries products caught in the state.
{{“We're not saying the system is totally destroyed or that this is a terrible fishery that shouldn't be occurring. We're saying there should be a different management system.”}
Andrew Rhyne
New England Aquarium}
They found that, each year between 1994 and 2007, the number of invertebrates taken from Florida waters increased by 13.3%, or half a million individual animals. Nine million individuals were collected in 2007, with the most popular including the blue-legged hermit crab (Clibanarius tricolor), the five-holed keyhole sand dollar (Mellita tenuis) and the star snail (Lithopoma americanum).
Worryingly, there has also been a shift towards collecting grazing species. These are prized by aquarium keepers as they keep algae under control. But they perform a similar function in the wild, and their removal may hasten what some researchers have dubbed the "slippery slope to slime", in which coral is killed off by algae.
The FMLF fishery, Rhyne et al write, "appears to be crawling to collapse".
"We're not saying the system is totally destroyed or that this is a terrible fishery that shouldn't be occurring," Rhyne told Nature. "We're saying there should be a different management system."
Downturn hopes
The difficulty, says Rhyne, is that there are no real baseline data for many of these species. Simply put, no one knows what a sustainable level of take for many of these animals might be.
With the aquarium industry quick to respond to new trends, Rhyne worries that some animals might become imperilled under the current management system if demand suddenly increases.
At present, most of the invertebrates in question are caught under 'multi-species' licences that allow collectors to take any species except some corals and endangered animals.
In their paper, the researchers suggest that a predicted — although probably temporary — decline in demand for relatively exotic aquarium species owing to the current economic downturn presents a real opportunity to change the management of these animals. Rhyne suggests individually managing the most popular species or reducing the number of licences granted.
The researchers also note that there is legislation under discussion in the US that could ban trade in non-native wildlife. If laws are enacted banning the import of species from outside the US this could "dramatically increase" the pressure on Florida.
Sherry Larkin, a researcher in marine resource management at the University of Florida, says there is a lot of good work in the paper, including information about types of species gathered and exploration of the potential implications of a trade ban.
"I'm less thrilled about the general categorization of the worldwide problem and how the Florida data supports statements that the fishery is headed for collapse," says Larkin. "The regulations for the Florida commercial industry are extensive but the article gives the impression that the effort by the current restricted fishermen is a run-away train that will be solely responsible for a collapse."
Lee Schlesinger, a spokesman for the Florida Fish and Wildlife Conservation Commission in Tallahassee, denied that there was a problem with the management of Florida's marine resources.
"Our fisheries are well managed and have been for years. The resources are considered to be fairly healthy and abundant," he says. "Five hundred-plus species are collected for the aquarium trade. It is a highly regulated fishery here in Florida."
References
1. Rhyne, A. et al. PLoS ONE 4, e8413 (2009).
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