[meteorite-list] First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit

[Ron Baalke]

http://newscenter.lbl.gov/2015/02/27/ultra-small-bacteria/

News Center

First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit 
of Life

Berkeley Lab research provides comprehensive description of ultra-small 
bacteria

News Release 
Dan Krotz 510-486-4019 - February 27, 2015

[Image]
This cryo-electron tomography image reveals the internal structure of 
an ultra-small bacteria cell like never before. The cell has a very dense 
interior compartment and a complex cell wall. The darker spots at each 
end of the cell are most likely ribosomes. The image was obtained from 
a 3-D reconstruction. The scale bar is 100 nanometers. (Credit: Berkeley 
Lab)

Scientists have captured the first detailed microscopy images of ultra-small 
bacteria that are believed to be about as small as life can get. The research 
was led by scientists from the U.S. Department of Energy's Lawrence Berkeley 
National Laboratory and the University of California, Berkeley. The existence 
of ultra-small bacteria has been debated for two decades, but there hasn't 
been a comprehensive electron microscopy and DNA-based description of 
the microbes until now.

The cells have an average volume of 0.009 cubic microns (one micron is 
one millionth of a meter). About 150 of these bacteria could fit inside 
an Escherichia coli cell and more than 150,000 cells could fit onto the 
tip of a human hair.

The scientists report their findings Friday, Feb. 27, in the journal Nature 
Communications.

The diverse bacteria were found in groundwater and are thought to be quite 
common. They're also quite odd, which isn't a surprise given the cells 
are close to and in some cases smaller than several estimates for the 
lower size limit of life. This is the smallest a cell can be and still 
accommodate enough material to sustain life. The bacterial cells have 
densely packed spirals that are probably DNA, a very small number of ribosomes, 
hair-like appendages, and a stripped-down metabolism that likely requires 
them to rely on other bacteria for many of life's necessities.

The bacteria are from three microbial phyla that are poorly understood. 
Learning more about the organisms from these phyla could shed light on 
the role of microbes in the planet's climate, our food and water supply, 
and other key processes.

[Image]
A lifeline to other cells? Cryo-transmission electron microscopy captured 
numerous hairlike appendages radiating from the surface of this ultra-small 
bacteria cell. The scientists theorize the pili-like structures enable 
the cell to connect with other microbes and obtain life-giving resources. 
The scale bar is 100 nanometers. (Credit: Berkeley Lab)

"These newly described ultra-small bacteria are an example of a subset 
of the microbial life on earth that we know almost nothing about," says 
Jill Banfield, a Senior Faculty Scientist in Berkeley Lab's Earth Sciences 
Division and a UC Berkeley professor in the departments of Earth and Planetary 
Science and Environmental Science, Policy and Management.

"They're enigmatic. These bacteria are detected in many environments and 
they probably play important roles in microbial communities and ecosystems. 
But we don't yet fully understand what these ultra-small bacteria do,"
says Banfield.

Banfield is a co-corresponding author of the Nature Communications paper 
with Birgit Luef, a former postdoctoral researcher in Banfield's group 
who is now at the Norwegian University of Science and Technology, Trondheim.

"There isn't a consensus over how small a free-living organism can be, 
and what the space optimization strategies may be for a cell at the lower 
size limit for life. Our research is a significant step in  characterizing 
the size, shape, and internal structure of ultra-small cells," says Luef.

The scientists set out to study bacteria from phyla that lack cultivated 
representatives. Some of these bacteria have very small genomes, so the 
scientists surmised the bacteria themselves might also be very small.

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.

The scientists also used the Advanced Light Source, a DOE Office of Science 
User Facility located at Berkeley Lab, where Hoi-Ying Holman of the Earth 
Sciences Division helped determine the majority of the cells in the samples 
were bacteria, not Archaea.

The research is a significant contribution to what's known about ultra-small 
organisms. Recently, scientists estimated the cell volume of a marine 
bacterium at 0.013 cubic microns, but they used a technique that didn't 
directly measure the cell diameter. There are also prior electron microscopy 
images of a lineage of Archaea with cell volumes as small as 0.009 cubic 
microns, similar to these bacteria, including results from some of the 
same researchers. Together, the findings highlight the existence of small 
cells with unusual and fairly restricted metabolic capacities from two 
of the three major branches of the tree of life.

The research was supported by the Department of Energy's Office of Science.

 ###

Lawrence Berkeley National Laboratory addresses the world's most urgent 
scientific challenges by advancing sustainable energy, protecting human 
health, creating new materials, and revealing the origin and fate of the 
universe. Founded in 1931, Berkeley Lab's scientific expertise has been 
recognized with 13 Nobel prizes. The University of California manages 
Berkeley Lab for the U.S. Department of Energy's Office of Science. For 
more, visit www.lbl.gov.

DOE's Office of Science is the single largest supporter of basic research 
in the physical sciences in the United States, and is working to address 
some of the most pressing challenges of our time. For more information, 
please visit the Office of Science website at science.energy.gov/ .

Additional information:

	o  The paper, "Diverse uncultivated ultra-small bacterial cells 
in groundwater," is published in Nature Communications on Feb. 27, 2015.