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

From: Ron Baalke <baalke_at_meteoritecentral.com>
Date: Fri, 27 Feb 2015 16:36:03 -0800 (PST)
Message-ID: <201502280036.t1S0a33S003118_at_zagami.jpl.nasa.gov>

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.
Received on Fri 27 Feb 2015 07:36:03 PM PST