Ultra-tiny bacteria (Introduction)
by David Turell 
, Tuesday, March 03, 2015, 19:29 (3342 days ago)
By using tiny filtration pores, ultra-tiny bacteria have been found. Their incomplete genomes suggest they depend on other bacteria to complete their metabolism:-http://www.pnas.org/content/early/2015/02/18/1420955112.long-"To concentrate these cells in a sample, they filtered groundwater collected at Rifle, Colorado through successively smaller filters, down to 0.2 microns, which is the size used to sterilize water. The resulting samples were anything but sterile. They were enriched with incredibly tiny microbes, which were flash frozen to -272 degrees Celsius in a first-of-its-kind portable version of a device called a cryo plunger. This ensured the microbes weren't damaged in their journey from the field to the lab.-"The frozen samples were transported to Berkeley Lab, where Luef, with the help of Luis Comolli of Berkeley Lab's Life Sciences Division, characterized the cells' size and internal structure using 2-D and 3-D cryogenic transmission electron microscopy. The images also revealed dividing cells, indicating the bacteria were healthy and not starved to an abnormally small size.-"The bacteria's genomes were sequenced at the Joint Genome Institute, a DOE Office of Science User Facility located in Walnut Creek, California, under the guidance of Susannah Tringe. The genomes were about one million base pairs in length. In addition, metagenomic and other DNA-based analyses of the samples were conducted at UC Berkeley, which found a diverse range of bacteria from WWE3, OP11, and OD1 phyla.-"This combination of innovative fieldwork and state-of-the-art microscopy and genomic analysis yielded the most complete description of ultra-small bacteria to date.-"Among their findings: Some of the bacteria have thread-like appendages, called pili, which could serve as "life support" connections to other microbes. The genomic data indicates the bacteria lack many basic functions, so they likely rely on a community of microbes for critical resources.-"The scientists also discovered just how much there is yet to learn about ultra-small life.-"'We don't know the function of half the genes we found in the organisms from these three phyla," says Banfield."
Ultra-tiny bacteria
by David Turell , Friday, October 20, 2017, 18:57 (2380 days ago) @ David Turell
Found in symbiotic relationship within other bacteria:
https://www.quantamagazine.org/tiny-genomes-may-offer-clues-to-first-plants-and-animals...
"With just 121 protein-coding genes, the diminutive Tremblaya princeps, a symbiotic bacterium that lives inside specialized cells of the sap-eating mealybug, has the smallest known genome of any cellular organism on the planet. Tremblaya helps to supply the mealybug with essential amino acids and likely receives nutrients and other life-sustaining molecules in return. And even as it tests the lower limits of genome size, the Tremblaya genome may still be shedding genes.
"Even more surprisingly, scientists discovered in 2011 that Tremblaya plays host to its own bacterial guest. Called Moranella endobia, the bacterium is smaller in physical size than its host but has more than three times as many genes. Together the three organisms form a complex, co-dependent web; the nested bacteria complement each other and their insect host, creating a genetic patchwork of enzymes needed to produce amino acids lacking in the mealybugs’ sap diet.
***
"Indeed, scientists now know that some organelles evolved from endosymbiont bacteria, raising hopes that studying tiny endosymbionts like Tremblaya could shed light on the evolution of those organelles. “There is no bright line between endosymbionts and organelles,” McCutcheon said. “We might be looking at something pretty darn similar to the endosymbiont-to-organelle transition.”
"In a paper published today in the journal Cell, McCutcheon and collaborators reveal a striking new level of interdependency among the Tremblaya troika. The mealybug genome appears to include genes from other varieties of bacteria distinct from Tremblaya and Moranella, and the two endosymbiont bacteria may use the protein products of these genes to manufacture nutrients and to make their membranes.
***
"The collection of bacteria with tiny genomes is surprisingly diverse, having emerged from an array of bacterial ancestries, and having retained and shed a variety of genes. Thanks to the protected environment of the host cell, these organisms tend to evolve rapidly, with the smallest mutating the fastest. Tremblaya and its counterparts have shed many of the genes involved in DNA repair, further accelerating their rates of evolution. They have also lost genes required to make the protective membranes that enclose them and instead are thought to rely on membrane components from the host cell. The genes these organisms retain tend to be involved in producing nutrients for the host, as well as carrying out so-called information repair, which includes DNA replication and the translation of genes into proteins. (Beneficial endosymbionts, such as Tremblaya, are fairly common in invertebrates, but are rare in humans and other vertebrates.)
***
"The findings provide a more detailed understanding of the symbionts’ differences and similarities to organelles. Tremblaya hasn’t transferred genes to its host, a defining property of organelles. But, like mitochondria, McCutcheon’s findings suggest, Tremblaya coopts some host-derived proteins that originally came from other types of bacteria. “This is a murky gray area; the host encodes genes the symbiont needs to survive, which suggests the hosts target proteins to the organism,” said Patrick Keeling, a biologist at the University of British Columbia, who was not involved in the Cell study. “That’s something organelles do but not usually endosymbionts.”
"Not everyone agrees that understanding Tremblaya may help illuminate the evolution of organelles. William Martin, a biologist at the University of Düsseldorf in Germany, wrote in an email that Tremblaya is instead “a beautiful contrast to organelles.” He noted, for example, that organelles import the vast majority of proteins from the host. Tremblaya also seems to import some proteins, but “it’s a far cry from the protein import apparatus of chloroplasts and mitochondria,” he wrote.
***
"The intracellular parasites that Keeling studies, which also have reduced genomes and are unable to produce their own source of energy or survive without their hosts, are typically thought of as organisms. “But no one refers to mitochondria as an organism because it’s so integrated with its host,” he said.
"The difference is that Keeling’s parasites steal energy, in the form of a molecule called adenosine triphosphate or ATP, from their hosts, but they possess the necessary genes to replicate DNA. An organelle, on the other hand, relies on proteins provided by the host to replicate its DNA. “We have arbitrarily decided that stealing ATP from a host constitutes an organism and stealing proteins does not,” said Keeling. “It’s truly just a matter of degrees.'”
Comment: These findings indirectly support Margulies theory about mitochondria. This is a strange branch of the tree of life, but these organisms are not fully independent organisms, but do represent the experimentation that goes on within evolution. I am unsure about God's role here. Does God allow these guys to play together on their own or does He take control? I don't think this advances evolution but it does support balance of nature. The arrangement of mitochondria is only tangentially related, and I suspect He controlled that advancement in complexity.
Ultra-tiny bacteria; bacteria added by 50%
by David Turell , Friday, April 27, 2018, 19:20 (2191 days ago) @ David Turell
By using ultra fine filters the branch of bacteria is enlarged by 50%:
https://www.quantamagazine.org/newfound-bacteria-expand-tree-of-life-20150728/
"A team of microbiologists based at the University of California, Berkeley, recently figured out one such new way of detecting life. At a stroke, their work expanded the number of known types — or phyla — of bacteria by nearly 50 percent, a dramatic change that indicates just how many forms of life on earth have escaped our notice so far.
“'Some of the branches in the tree of life had been noted before,” said Chris Brown, a student in the lab of Jill Banfield and lead author of the paper. “With this study we were able to fill in many gaps.”
"As an organizational tool, the tree of life has been around for a long time. Lamarck had his version. Darwin had another. The basic structure of the current tree goes back 40 years to the microbiologist Carl Woese, who divided life into three domains: eukaryotes, which include all plants and animals; bacteria; and archaea, single-celled microorganisms with their own distinct features. After a point, discovery came to hinge on finding new ways of searching.
***
"DNA sequencing is at the heart of this current study, though the researchers’ success also owes a debt to more basic technology. The team gathered water samples from a research site on the Colorado River near the town of Rifle, Colo. Before doing any sequencing, they passed the water through a pair of increasingly fine filters — with pores 0.2 and 0.1 microns wide — and then analyzed the cells captured by the filters. At this point they already had undiscovered life on their hands, for the simple reason that scientists had not thought to look on such a tiny scale before.
***
"The discovery of new organisms is fairly cut and dried: Either you’ve found one or you haven’t. Cataloging organisms, fitting them into the tree of life, involves more judgment calls.
"The researchers divided the 789 organisms into 35 phyla — 28 of which were newly discovered — within the domain bacteria. They based the sorting on the organisms’ evolutionary history and on similarities in the code on the organisms’ 16S rRNA genes — those with at least 75 percent of their code in common went into the same phylum.
"With these new additions, there are now roughly 90 identified bacterial phyla. This is a lot more than there were a year ago, but also far fewer than the 1,300 to 1,500 phyla that microbiologists estimate we’ll have once a complete accounting is finished.
***
“'Looking at things from a different angle may offer that possibility of a fourth domain,” he said — an equal partner to bacteria, archaea and eukaryotes. “There will always be novel stuff that will teach us foundational info about how life operates.'”
Comment: Life started with bacteria and they are still successfully the biggest biomass. why should there be anything else? My reason is God.