Ultra-small bacteria — reportedly from three bacterial phyla — discovered in Rifle (Colorado) groundwater

© 2015 Peter Free

Citation — to study

Birgit Luef, Kyle R. Frischkorn, Kelly C. Wrighton, Hoi-Ying N. Holman, Giovanni Birarda, Brian C. Thomas, Andrea Singh, Kenneth H. Williams, Cristina E. Siegerist, Susannah G. Tringe, Kenneth H. Downing, Luis R. Comolli, and Jillian F. Banfield, Diverse uncultivated ultra-small bacterial cells in groundwater, Nature Communications 6: 6372, DOI:10.1038/ncomms7372 (27 February 2015)

Citation — to press release

Dan Krotz, First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life, Lawrence Berkeley National Laboratory – US Department of Energy (27 February 2015)

Method and findings

Using 0.2 micron-porous filters (supposedly creating sterile water), scientists found ultra-small bacteria left behind in Rifle (Colorado) ground water samples. Genetic analysis indicated that these bacteria belong to three different bacterial phyla.

Note

According to Wikipedia, there are 29 bacterial phyla that have been cultured and another 23 (or more) that have not been.

These ultra-small bacteria are about 150 times tinier than E. coli cells:

Cryogenic transmission electron microscopy [see here] demonstrates that, despite morphological variation, cells consistently have small cell size (0.009±0.002 μm3).

© 2015 Birgit Luef, Kyle R. Frischkorn, Kelly C. Wrighton, Hoi-Ying N. Holman, Giovanni Birarda, Brian C. Thomas, Andrea Singh, Kenneth H. Williams, Cristina E. Siegerist, Susannah G. Tringe, Kenneth H. Downing, Luis R. Comolli, and Jillian F. Banfield, Diverse uncultivated ultra-small bacterial cells in groundwater, Nature Communications 6: 6372, DOI:10.1038/ncomms7372 (27 February 2015) (at Abstract)

In American lay language, this dimension is 0.009 cubic microns (micrometres).

The team used cryogenic transmission electron microscopy to investigate the bacteria’s structure

From the press release:

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 images also revealed dividing cells, indicating the bacteria were healthy and not starved to an abnormally small size.

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.

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.

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 . . . .

Together, the findings highlight the existence of small cells with unusual and fairly restricted metabolic capacities from two of the three major branches [— meaning the domains: Archaea, Bacteria and Eukarya] of the tree of life.

© 2015 Dan Krotz, First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life, Lawrence Berkeley National Laboratory – US Department of Energy (27 February 2015) (extracts)

The moral? — A new world to explore

These little “guys” have almost certainly been here all along, without us knowing.

Expanding agricultural production in Africa — looks as if it may be substantially increasing crop associated populations of plague-carrying rodents

© 2015 Peter Free

Citation — to study

Douglas J. McCauley, Daniel J. Salkeld, Hillary S. Young, Rhodes Makundi, Rodolfo Dirzo, Ralph P. Eckerlin, Eric F. Lambin, Lynne Gaffikin, Michele Barry, and Kristofer M. Helgen, Effects of Land Use on Plague (Yersinia pestis) Activity in Rodents in Tanzania, American Journal of Tropical Medicine and Hygiene, DOI: 10.4269/ajtmh.14-0504 (accepted for publication, 23 February 2015)

Citation — to press release

Burness Communications, Agriculture expansion in Tanzania may greatly increase human plague risk, ScienceDaily (24 February 2015)

Solve one problem — create another

From the informative press release:

Researchers studied rodents in northern Tanzania, where over the last few decades croplands have expanded by 70 percent. They found that in areas where maize production has been introduced, the number of rodents infested with plague-carrying fleas that can cause human infections nearly doubled compared to numbers in neighboring wilderness areas.

Scientists also linked the maize fields to a 20-fold increase in the population of the African rat (Mastomys natalensis) that is a major conduit for plague and a number of other diseases, including deadly Lassa fever . . . that has become a growing concern in West Africa.

Plague is an ancient disease caused by the bacterium Yersinia pestis that continues to sicken and kill people even in the 21st century. Since 2000, most of the outbreaks of plague have occurred in Africa, particularly the Democratic Republic of Congo and Madagascar. . . .

Plague has long been a threat in Tanzania and continues to emerge in sporadic outbreaks. From 1980 to 2011, for example, there were about 8490 cases and 675 deaths reported in the country.

According to the World Health Organization (WHO), plague is treatable with antibiotics and supportive therapy but, left untreated, it is fatal 30 to 60 percent of the time.

One curious finding from the study was that the African rats living in the agriculture areas played host to a larger number of plague-carrying fleas than their relatives in the forest and even carried a species of plague-infected flea that is completely absent in forest rats.

The researchers also noted that the African rat, with its capacity to support large litters–the female of the species can nurse up to 14 pups at a time–is well suited to take advantage of a crop production cycle that offers opportunities for rodent populations to surge as crops mature.

© 2015 Burness Communications, Agriculture expansion in Tanzania may greatly increase human plague risk, ScienceDaily (24 February 2015) (extracts)

The moral? — We indirectly grow our pests

History’s lesson, still operating today.

When plants finally die from increasing aridity — dryness escalates abruptly — a retrospective climate study from sediments at the bottom of Ghana’s Lake Bosumtwi

© 2015 Peter Free

Citation — to study

Timothy M. Shanahan, Nicholas P. McKay, Konrad A. Hughen, Jonathan T. Overpeck, Bette Otto-Bliesner, Clifford W. Heil, John King, Christopher A. Scholz, and John Peck, The time-transgressive termination of the African Humid Period, Nature Geoscience 8(2): 140-144, DOI:10.1038/ngeo2329 (26 January 2015)

Citation — to press release

Northern Arizona University, NAU researcher works to understand forces of abrupt environmental change, NAU News (18 February 2015)

When an ecology shatters due to lack of moisture, aridity can escalate rapidly

In general terms, from the press release:

The isolated lake was formed by a meteor and sits like a bowl on the landscape giving scientists a clear view of environmental changes.

The lake samples were obtained by drilling 1,000 feet to the lake’s bottom and another 1,000 feet into the meteor impact structure. The sediments span 1-million years but the paper focused on the past 20,000 years.

McKay and co-authors describe how Africa changed from a humid environment to the more arid region of today. Earlier studies show the Sahara Desert and other north African regions shifted from lush to dry between 5,000 and 6,000 years ago. Analysis of Lake Bosumtwi reveals humid conditions remained until about 3,000 years ago, providing supportive habitats for humans, animals and plants.

Although the large scale, north-to-south change was gradual, McKay and his team focused on areas where the change happened much quicker than expected. The researchers suggested the anomalies were created by the reactions of soil moisture and plants to the diminishing monsoon.

“The plants do a good job of reinforcing their own existence by making it a little moister and bringing more rain,” McKay said. “But if you cross the moisture threshold where the plants die, then it also stops raining and it sort of snowballs really fast and that is how you can get these really rapid changes,” McKay said.

© 2015 Northern Arizona University, NAU researcher works to understand forces of abrupt environmental change, NAU News (18 February 2015)

In mechanistic context

From the abstract:

During the African Humid Period about 14,800 to 5,500 years ago, changes in incoming solar radiation during Northern Hemisphere summers led to the large-scale expansion and subsequent collapse of the African monsoon. Hydrologic reconstructions from arid North Africa show an abrupt onset and termination of the African Humid Period.

These abrupt transitions have been invoked in arguments that the African monsoon responds rapidly to gradual forcing as a result of nonlinear land surface feedbacks.

Here we present a reconstruction of precipitation in humid tropical West Africa for the past 20,000 years using the hydrogen isotope composition of leaf waxes preserved in sediments from Lake Bosumtwi, Ghana.

We show that over much of tropical and subtropical Africa the monsoon responded synchronously and predictably to glacial reorganizations of overturning circulation in the Atlantic Ocean, but the response to the relatively weaker radiative forcing during the African Humid Period was more spatially and temporally complex.

A synthesis of hydrologic reconstructions from across Africa shows that the termination of the African Humid Period was locally abrupt, but occurred progressively later at lower latitudes.

We propose that this time-transgressive termination of the African Humid Period reflects declining rainfall intensity induced directly by decreasing summer insolation as well as the gradual southward migration of the tropical rainbelt that occurred during this interval.

© 2015 Timothy M. Shanahan, Nicholas P. McKay, Konrad A. Hughen, Jonathan T. Overpeck, Bette Otto-Bliesner, Clifford W. Heil, John King, Christopher A. Scholz, and John Peck, The time-transgressive termination of the African Humid Period, Nature Geoscience 8(2): 140-144, DOI:10.1038/ngeo2329 (26 January 2015) (at Abstract) (paragraph split)

Relevance

Coming from the US southwest, as I do, the above hypothesis about dying plants abruptly collapsing into desert is relevant. Especially so, given the recently published forecast for likely mega-drought in the region.

See:

Toby R. Ault, Julia E. Cole, Jonathan T. Overpeck, Gregory T. Pederson, and David M. Meko, Assessing the Risk of Persistent Drought Using Climate Model Simulations and Paleoclimate Data, Journal of Climate 27(20): 7529–7549, DOI:10.1175/JCLI-D-12-00282.1 (October 2014)

The moral? — Things can (apparently) change in a hurry

With the obvious caveat that there are a lot of assumptions contained in this retrospective study of Lake Bosumtwi sediments.

Removing cattle from trampled waterway banks — without doing anything else — may be enough to restore the land — a study from south central (arid) Oregon

© 2015 Peter Free

Citation — to study

Jonathan L. Batchelor, William J. Ripple, Todd M. Wilson, and Luke E. Painter, Restoration of Riparian Areas Following the Removal of Cattle in the Northwestern Great Basin, Environmental Management, DOI: 10.1007/s00267-014-0436-2 (online first, 19 February 2015)

Citation — to press release

Springer Science+Business Media, Cattle damage to riverbanks can be undone, ScienceDaily (19 February 2015)

Method and findings

From the press release:

Simply removing cattle may be all that is required to restore many degraded riverside areas in the American West, although this can vary and is dependent on local conditions.

These are the findings of Jonathan Batchelor and William Ripple of Oregon State University . . . .

Their team analyzed photographs to gauge how the removal of grazing cattle more than two decades ago from Hart Mountain National Antelope Refuge [see here] in eastern Oregon has helped to rehabilitate the natural environment.

© 2015 Springer Science+Business Media, Cattle damage to riverbanks can be undone, ScienceDaily (19 February 2015) (paragraph split)

More precisely:

We assessed the effects of the elimination of livestock in riparian systems at Hart Mountain National Antelope Refuge in southeastern Oregon, 23 years after the removal of cattle grazing, using 64 photos taken before grazing was removed compared with later retake photos.

Two methods were used for this assessment: (1) a qualitative visual method comparing seven cover types and processes and (2) a new quantitative method of inserting digital line transects into photos.

Results indicated that channel widths and eroding banks decreased in 64 and 73 % of sites, respectively.

We found a 90 % decrease in the amount of bare soil (P < 0.001) and a 63 % decrease in exposed channel (P < 0.001) as well as a significant increase in the cover of grasses/sedges/forbs (15 % increase, P = 0.037), rushes (389 % increase, P = 0.014), and willow (388 % increase, P < 0.001).

We also assessed the accuracy of the new method of inserting digital line transects into photo pairs. An overall accuracy of 91 % (kappa 83 %) suggests that digital line transects can be a useful tool for quantifying vegetation cover from photos.

Our results indicate that the removal of cattle can result in dramatic changes in riparian vegetation, even in semi-arid landscapes and without replanting or other active restoration efforts.

© 2015 Jonathan L. Batchelor, William J. Ripple, Todd M. Wilson, and Luke E. Painter, Restoration of Riparian Areas Following the Removal of Cattle in the Northwestern Great Basin, Environmental Management, DOI: 10.1007/s00267-014-0436-2 (online first, 19 February 2015) (at Abstract) (paragraph split)

Importance

Two sample pictures attached to the press release show the before and after difference:

The resurgence of riparian vegetation was not ascribed to climate changes, given that the years prior to 1991 were generally less drought-stressed than the years following the removal of the cattle.

“The study at Hart Mountain National Antelope Refuge shows just how much a system can change within only two decades of cattle removal,” said Ripple.

© 2015 Springer Science+Business Media, Cattle damage to riverbanks can be undone, ScienceDaily (19 February 2015) (paragraph split)

The moral? — Restoration and subsequent management may be less costly than one would think

Batchelor added, “The removal of cattle can result in dramatic changes in riparian vegetation, even in semi-arid landscapes and without active restoration treatments.”

© 2015 Springer Science+Business Media, Cattle damage to riverbanks can be undone, ScienceDaily (19 February 2015)

A caveat here would include the question of whether these lands were grazed (perhaps by bison) before cattle were introduced.

If so, reasonable management practice would intermittently (rotationally) graze livestock on the restored areas to achieve somewhat the prehistorical ecological effect.

Elliptical galaxy black hole masses — correlate more strongly with galactic halo dark matter mass — than with visible star mass alone

© 2015 Peter Free

Citation — to study

Ákos Bogdán and Andy D. Goulding, Connecting Dark Matter Halos with the Galaxy Center and the Supermassive Black Hole, Astrophysical Journal 800(2): 124, DOI:10.1088/0004-637X/800/2/124 (20 February 2015)

Citation — to press release

Christine Pulliam, Dark Matter Guides Growth of Supermassive Black Holes, Harvard Smithsonian Center for Astrophysics (18 February 2014)

Not surprising

From the abstract:

Based on a study of 3130 elliptical galaxies selected from the Sloan Digital and ROSAT All Sky Surveys we demonstrate that the central stellar velocity dispersion exhibits a significantly tighter correlation with the total gravitating mass, traced by the X-ray luminosity of the hot gas, than with the stellar mass.

This hints that the central stellar velocity dispersion, and hence the central gravitational potential, may be the fundamental property of elliptical galaxies that is most tightly connected to the larger-scale dark matter halo.

© 2015 Ákos Bogdán and Andy D. Goulding, Connecting Dark Matter Halos with the Galaxy Center and the Supermassive Black Hole, Astrophysical Journal 800(2): 124, DOI:10.1088/0004-637X/800/2/124 (20 February 2015) (at Abstract) (paragraph split)

In lay terms

Science writer Christine Pulliam did a nice job of explaining the idea:

“There seems to be a mysterious link between the amount of dark matter a galaxy holds and the size of its central black hole, even though the two operate on vastly different scales,” says lead author Akos Bogdan . . . .

In our universe, dark matter outweighs normal matter – the everyday stuff we see all around us – by a factor of 6 to 1. We know dark matter exists only from its gravitational effects. It holds together galaxies and galaxy clusters. Every galaxy is surrounded by a halo of dark matter that weighs as much as a trillion suns and extends for hundreds of thousands of light-years.

To investigate the link between dark matter halos and supermassive black holes, Bogdan and his colleague Andy Goulding (Princeton University) studied more than 3,000 elliptical galaxies. They used star motions as a tracer to weigh the galaxies’ central black holes. X-ray measurements of hot gas surrounding the galaxies helped weigh the dark matter halo, because the more dark matter a galaxy has, the more hot gas it can hold onto.

They found a distinct relationship between the mass of the dark matter halo and the black hole mass – a relationship stronger than that between a black hole and the galaxy’s stars alone.

This connection is likely to be related to how elliptical galaxies grow. An elliptical galaxy is formed when smaller galaxies merge, their stars and dark matter mingling and mixing together. Because the dark matter outweighs everything else, it molds the newly formed elliptical galaxy and guides the growth of the central black hole.

“In effect, the act of merging creates a gravitational blueprint that the galaxy, the stars and the black hole will follow in order to build themselves,” explains Bogdan.

© 2015 Christine Pulliam, Dark Matter Guides Growth of Supermassive Black Holes, Harvard Smithsonian Center for Astrophysics (18 February 2014)

The moral? — Mass is mass?

I suspect that the distinction between the matter that we can “see” — and that which we cannot —sometimes leads us to erroneous suppositions that then have to be explained by dragging in allegedly “mysterious” means.

It seems to me that the 6:1 ratio of dark to normal matter would have obvious “physics” consequences, even if we do not yet know how those work. Perhaps I am being simple minded.