Meaninglessness run amok!
Intelligent design NOT!
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MICROBIOLOGY: ON MICROBIAL DIVERSITY
ScienceWeek http://scienceweek.com
The following points are made by T.P. Curtis and W.T. Sloan
(Science 2005 309:1331):
1) Exploring microbial diversity is becoming more like exploring
outer space with soil representing a "final frontier" that
harbors a largely unknown microbial universe. There are more than
10^(16) prokaryotes in a ton of soil compared to a mere 10^(11)
stars in our Galaxy. Astronomers have wisely inferred the
population of celestial objects by mathematical inference. Now
microbiologists are following suit, adopting a similar strategy
to estimate the number of prokaryote taxa in soil. According to
new work[1], the inferred diversity is staggering -- higher than
previously thought by almost three orders of magnitude.
2) The extent of prokaryote diversity has been hotly debated and
rightly so. Microbial communities are central to health,
sustainable cities, agriculture, and most of the planet's
geochemical cycles. Prokaryote communities are also reservoirs
for the discovery of new drugs and metabolic processes. As with
any reservoir, its size is important. Measuring the reservoir of
prokaryotic diversity is not a trivial task. There is broad
agreement that the key is to eschew the organisms themselves and
to focus instead on their DNA. If DNA from a single organism is
purified and heated, the strands of the double helix separate or
"melt." If you then slowly cool the DNA, the strands will
reassociate or reanneal, and the rate at which this happens is
affected by the size and complexity of the DNA. Big and complex
DNA reanneals slowly.
3) This fact has been used for the past four decades to estimate
the size and complexity of genomes from individual organisms.
Around 15 years ago, Torsvik et al. [2] reasoned that pooled
genomic DNA from a microbial community might reanneal like the
DNA from a large genome. Indeed, they showed that DNA extracted
from soil reassociated slowly -- so slowly that it resembled a
genome that was 7000 times as large as the genome of a single
bacterium. It follows that there could have been at least 7000
different prokaryote taxa in the sample of soil that they
analyzed. At the time, this was considered a mind-boggling
number. Even ecologist E.O. Wilson speculated that "microbial
diversity was beyond practical calculation" [3].
4) There is, however, another way to estimate prokaryotic
diversity in the environment. A biological community has a
characteristic abundance distribution of its member species. The
observation and contemplation of these distributions have a rich
literature in conventional ecology that is helping rescue
microbial ecology from the conundrum of how to estimate
diversity. In principle, if you know the shape of the taxa
abundance distribution curve, you know the diversity. But there
is a catch: Typically, for large organisms, species abundance
distributions have been determined by assessing the abundance of
almost all of the species in a sample, which means that you must
already know the number of species.
5) In the absence of such information, one still can draw upon
certain theoretical considerations [4], assume that a particular
species distribution pertains, and then make an estimate [5].
Alternatively, you can fit a curve to the data you have to make
an estimate. The latter approach has great merit, but gathering
enough data to make a sensible decision about the underlying
species distribution pattern is problematic. At present, most
microbiologists attempt to estimate diversity by looking at a
gene that occurs in all cellular life forms. They infer diversity
from the number of different variants that can be cloned from a
sample of environmental DNA. Unfortunately, the number of clones
analyzed is typically small (tens to hundreds) compared to the
number of individual microbes being analyzed (billions or
trillions). This is like randomly sampling a bus load of people
and then trying to infer the diversity of all people in the
world. You would not expect to find many Lithuanians.
6) Gans et al (1) and others realized that the pattern of DNA
reassociation kinetics reflects the underlying distribution of
similar sequences, and hence likely reflects genomic diversity.
However, the authors have gone further and show that there is
probably enough data in published DNA reassociation curves for
bacterial communities to allow discrimination between different
possible species abundance curves. By applying new mathematical
treatment of data, the authors generate abundance curves, the
most plausible of which suggests that there could be 10^(7)
distinct prokaryote taxa in 10 grams of pristine (free of
chemical contaminants) soil. Moreover, rare organisms comprise
most of this diversity. They further determine that most of these
rare organisms could be wiped out by heavy metal pollution of the
soil.
References (abridged):
1. J. Gans et al., Science 309, 1387 (2005)
2. V. Torsvik et al., Appl. Environ. Microbiol. 56, 782 (1990)
3. E. O.Wilson, The Diversity of Life (Penguin, London, UK) 1993
4. R. M. May, in Ecology and Evolution of Communities, M. L.
Cody, J. M. Diamond, Eds. (Harvard Univ. Press, Cambridge, MA,
1974), p. 81
5. T. P. Curtis et al., Proc. Natl. Acad. Sci. U.S.A. 99, 10494
(2002)
Science http://www.sciencemag.org
--------------------------------
Related Material:
VIROLOGY: ON VIRUS DIVERSITY
The following points are made by Paul Ahlquist (Current Biology
2005 15:R465):
1) Viruses are exceptionally diverse in morphology, replication
strategies, genetic organization and many other characteristics.
Such differences raise significant questions about the diversity
of virus origins and the possible extent of functional and
evolutionary relationships among existing viruses. These issues
are important for increasing our basic biological understanding
and for practical applications, since underlying similarities
linking virus classes could provide a basis for antiviral
approaches that have a broader spectrum. Recent findings,
including a new structural study of birnaviruses [1], reveal
structural, functional and likely evolutionary links between
positive-strand RNA and double-stranded (ds) RNA viruses at
multiple levels, and in some cases extend these to reverse
transcribing viruses [2-5].
2) Most viruses store and replicate their genomes solely via RNA
intermediates. The infectious virion particles of such viruses
may contain the genome either as positive-strand (i.e. mRNA-
sense) single-stranded (ss) RNA, or as negative-strand (i.e.
mRNA-antisense) ssRNA, or as dsRNA. These different genome forms
are associated with significant differences in viral replication
and transcription strategies:for example, virions of dsRNA
viruses contain all the necessary machinery to transcribe the
enclosed genomic dsRNA into mRNAs, while positive-strand ssRNA
viruses encapsidate only RNA and form separate RNA synthesis
complexes.
3) The protein capsids of many positive-strand RNA viruses and
all known dsRNA viruses embody extensions of icosahedral
symmetry. These quasi-icosahedral capsids contain 60 copies of a
capsid protein multimer, with the number of subunits per multimer
matching the allowable values of a triangulation number T. For
integers h and k, the increasing values of T = h2 + hk + k2
define ways to assemble capsids that are progressively larger
than a perfect isosahedron (T = 1), using subunit-subunit
interactions that are nearly equivalent (quasi-equivalent) rather
than perfectly equivalent throughout the capsid. dsRNA viruses in
the Reoviridae and Cystoviridae families consist of one or more
T=13 outer capsid shells surrounding an inner, transcriptionally
active T=2 core. The dsRNA Totiviridae, which may be primitive or
degenerate relatives of the Reoviridae and Cystoviridae, also
have a T=2 transcriptionally active core but lack an outer capsid
shell and the ability to transmit infection extracellularly.
4) The dsRNA birnaviruses, like Reoviridae and Cystoviridae,
possess a T=13 outer capsid shell, composed of 60T=780 copies of
viral capsid protein VP2 [1]. These birnavirus virions are also
transcriptionally competent, but lack an icosahedrally ordered
inner core. Instead, the outer capsid encloses the viral dsRNA,
the polymerase VP1, and many copies of the birnaviral protein VP3
in a complex whose order has not been well determined but is
recoverable from virions as a ribonucleoprotein filament.
References (abridged):
1. Coulibaly, F., Chevalier, C., Gutsche, I., Pous, J., Navaza,
J., Bressanelli, S., Delmas, B., and Rey, F.A. (2005). The
Birnavirus crystal structure reveals structural relationships
among icosahedral viruses. Cell 120, 761-772
2. Paul, A.V., Rieder, E., Kim, D.W., van Boom, J.H., and Wimmer,
E. (2000). Identification of an RNA hairpin in poliovirus RNA
that serves as the primary template in the in vitro uridylylation
of VPg. J. Virol. 74, 10359-10370
3. Gorbalenya, A.E., Pringle, F.M., Zeddam, J.L., Luke, B.T.,
Cameron, C.E., Kalmakoff, J., Hanzlik, T.N., Gordon, K.H., and
Ward, V.K. (2002). The palm subdomain-based active site is
internally permuted in viral RNA-dependent RNA polymerases of an
ancient lineage. J. Mol. Biol. 324, 47-62
4. Magyar, G., Chung, H.K., and Dobos, P. (1998). Conversion of
VP1 to VPg in cells infected by infectious pancreatic necrosis
virus. Virology 245, 142-150
5. Schwartz, M., Chen, J., Janda, M., Sullivan, M., den Boon, J.,
and Ahlquist, P. (2002). A positive-strand RNA virus replication
complex parallels form and function of retrovirus capsids. Mol.
Cell 9, 505-514
Current Biology http://www.current-biology.com
--------------------------------
Related Material:
ECOLOGY: ON OCEANIC PLANKTON DIVERSITY
The following points are made by P.J. Morin and J.W. Fox (Nature
2004 429:813):
1) Much of what we know about how the diversity of life varies
across environments comes from studies of large, "charismatic"
terrestrial organisms that typically attract the attention of
ecologists(1). These studies show that diversity often peaks at
intermediate levels of productivity, where productivity describes
the rate of energy capture and its transformation into biomass by
organisms. Little is known about whether similar patterns of
diversity and productivity hold for the much smaller organisms
that predominate in the world's oceans, and there are suggestions
that some ecological patterns of single-celled organisms might
differ in important ways from those of larger ones(2).
2) Irigoien et al(3) have reported that the algae --phytoplankton
-- supporting food webs in the oceans, Earth's largest ecological
realm, exhibit a unimodal diversity-productivity pattern similar
to that described for many other systems. Revealing the unimodal
pattern required the compilation and analysis of a database of
algal species composition and biomass (where biomass serves as a
reasonable surrogate for productivity) in more than 350 samples
collected from oceans around the world. Although several other
diversity-productivity patterns exist(1), the unimodal pattern
appears repeatedly for a variety of organisms in different
circumstances. In this respect, ecology exhibits some important
generalities, which can now be extended to the oceans. The
analysis also emphasizes the value of the new field of
"ecoinformatics" in uncovering patterns that emerge only from
extensive data sets collected over large temporal and spatial
scales.
3) Several factors could make phytoplankton diversity reach a
peak at intermediate levels of productivity. Community
history(4), spatial niche differentiation(5) and competition for
multiple resources can all produce unimodal patterns. Community
history refers to the stochastic, sequential arrival of species
at a local site from a surrounding regional pool of potential
community members. The arrival sequence can affect diversity (for
instance, weaker competitors might persist if they arrive and
become established before other species), and can interact with
productivity to produce a variety of diversity-productivity
relationships, including a unimodal pattern(4). Spatial niche
differentiation occurs when local sites contain different
microhabitats (spatial niches), such as a lake surface or water
column, to which species are differentially adapted, and which
vary in their ability to support reproduction.
4) Diversity is maximized in sites that are sufficiently
productive to allow reproduction in all microhabitats but are not
so productive that the species adapted to the best microhabitat
produces sufficient offspring to "swamp" other species(5). The
hypothesis of competition for multiple resources suggests that
shading within dense algal blooms probably increases with
productivity, so that phytoplankton at high-productivity sites
compete more strongly for light than for nutrients. Superior
competitors for nutrients or light would respectively dominate
low- and high-productivity sites, whereas sites of intermediate
productivity would support a diverse mixture of phytoplankton.
References (abridged):
1. Waide, R. B. et al. Annu. Rev. Ecol. Syst. 30, 257-301 (1999)
2. Finlay, B. J. Science 296, 1061-1063 (2002)
3. Irigoien, X., Huisman, J. & Harris, R. P. Nature 429, 863-867
(2004)
4. Fukami, T. & Morin, P. J. Nature 424, 423-426 (2003)
5. Kassen, R., Buckling, A., Bell, G. & Rainey, P. B. Nature 406,
508-512 (2000)
Nature http://www.nature.com/nature
ScienceWeek http://scienceweek.com
--
Best,
Frederick Martin McNeill
Poway, California, United States of America
mmcneill@fuzzysys.com
http://www.fuzzysys.com
http://members.cox.net/fmmcneill
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Phrase of the week :
"Discovery consists of seeing what everybody has
seen and thinking what nobody has thought."
-- Albert Szent-Gyorgyi (1893-1986)
:-))))Snort!)
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