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1. INTROD
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Fujikawa
994, 1998,
iro 1995;
Dworkin
4; Shapiro
99; Shim-
00; Crespi
J. R. Soc. Interface†
Author for correspondence (ebenjacob@ucsd.edu).bacterial communication; natural self-engineering
UCTION
vation of this article is to present the
ns and the conceptual challenges posed by
ering of bacteria during colonial develop-
eview some of the exciting discoveries about
rative behaviour of bacteria in colonies,
the assumption that they might shed new
foundations and evolution of biocomplexity
The review is aimed at researchers from
sciplines—microbiology, biology, chemistry,
athematics and computer science. To make
tation comprehensible to such a wide
e avoid the use of the specialized terminol-
se different disciplines and limit the exper-
d computational details.
there are an increasing number of strains of
sing bacteria that can resist multiple drugs;
re clearly capable of developing antibiotic
at a higher rate than scientists can develop
(Levy 1998; Liebes et al. 1998; Miller 1998).
o be losing a crucial battle for our health. To
s course of events, we have to outsmart the
taking new avenues of study, which will in
o the development of novel strategies to fight
ris et al. 1999). But for that to happen, we
must first reverse our current notion about b
just simple solitary creatures with limited ca
These most fundamental of all organisms ar
tive beasts that lead complex social lives i
whose populations outnumber that of people
The idea that bacteria act as unsoph
uncommunicative and uncooperative cells s
years of laboratory experiments where the ba
grown in Petri dishes under benign condi
surprisingly, a bacterium that is not under
will strive to reproduce as fast as possible an
worry about complex strategies that require
coordination. However, when these versatile
are exposed to hostile environmental c
namely when the odds are against survival a
uals, they adopt a more complex strategy and
wide range of tactical behaviours to enable
adaptive response. One aspect of these beha
to do with self-engineered spatial organizat
colony (Kuner & Kaiser 1982; Matsushita &
1990; Ohgiwari et al. 1992; Ben-Jacob et al. 1
2000a; 2005; Salmond et al.1995; Shap
Dworkin 1996; Wirth et al. 1996; Shapiro &
1997; Ben Jacob & Levine 1998, 2001, 200
1998; Dunny & Winans 1999; Rosenberg 19
kets 1999; Strassmann 2000; Velicer et al. 20Keywords: biocomplexity; bacterial colonies; self-organization; gene-networks;Self-engineering cap
Eshel Ben-Jacob
1,2,†
1
School of Physics and Astronomy, Raymond
Tel-Aviv University,
2
Center for Theoretical Biological Physics, U
CA 92093
Under natural growth conditions, bacteria c
(e.g. quorum-sensing, chemotactic signalling
(self-organize) complex colonies with ele
collectively engineered according to the en
do not genetically store all the informatio
Instead, additional information is cooperativ
organization to proceed.
We describe how complex colonial forms (
based singular interplay between individual
itself, a biotic autonomous system with its
(storage, processing and assessment of inform
its response to biochemical messages it
broadcasting of messages to initiate alteratio
Hence, new features can collectively emerg
level to the whole colony. The cells thus assu
are not explicitly stored in the genetic informbilities of bacteria
d Herbert Levine
2
d Beverly Sackler, Faculty of Exact Sciences,
978 Tel-Aviv, Israel
versity of California at San Diego, La Jolla,
19, USA
utilize intricate communication capabilities
d plasmid exchange) to cooperatively form
ed adaptability—the colonial pattern is
ntered environmental conditions. Bacteria
equired for creating all possible patterns.
generated as required for the colonial self-
tterns) emerge through the communication-
teria and the colony. Each bacterium is, by
n internal cellular informatics capabilities
ion). These afford the cell plasticity to select
ceives, including self-alteration and the
in other bacteria.
uring self-organization from the intracellular
newly co-generated traits and abilities that
ion of the individuals.
doi:10.1098/rsif.2005.0089
Published onlineBen-Jacob 2003; Velicer 2003; Mok et al. 2003; Xavier &
Received 3 May 2005
Accepted 5 September 2005 1 q 2005 The Royal Society2001; Bassler 2002; Di Franco et al. 2002; Miller 2002;

2. BRANCHING PATTERNS OF LUBRICATING
2 Bacterial self-organization E. Ben-Jacob and H. LevineBassler 2003; Komoto et al. 2003; Ben Jacob et al. 2004;
Levine and Ben Jacob 2004; Ben Jacob & Shapira
2005), with the bacteria forming different patterns as
needed to function. For example, there is evidence that
colony structure can enhance antibiotic survival rate,
allowing enough time for genetic experimentation in
search of resistance; exactly how this works in detail is
only now being elucidated. Some recent findings show
that colony structures are modified in the presence of
antibiotics (Ben Jacob et al. 2000b; Golding & Ben
Jacob 2001; Ron et al. 2003) in ways which might
optimize bacterial survival and that the bacteria might
be using a sort of short-term epigenetic memory which
enables them to keep track of the previous exposure to
antibiotic.
Remarkably, the bacteria utilize pattern-formation
mechanisms that we have begun to understand only in
last few decades, mostly through the study of the
physics and mathematics of self-organization in non-
living systems (Levine & Ben Jacob 2004). In a real
sense, the bacteria are billions of years ahead of us in
their harnessing of pattern formation. In this article, we
would like to guide the reader through some of the
remarkable patterns that have been discovered in one
class of bacteria, Paenibacillus. These patterns have
been created by mimicking hostile conditions in a
laboratory setting by growing the colony in a Petri dish
containing a very low level of nutrients and/or a hard
surface (high concentration of agar gel) preventing
normal bacterial motion. As opposed to merely being
objects of aesthetic beauty, they are striking evidence of
an ongoing cooperation that enables the bacteria to
achieve a proper balance of individuality and sociality
as they battle for survival. We will try to convey a
feeling for the multiple challenges faced by scientists
when attempting to make sense of this incredibly
diversity of structures. Our language will be that of
nonlinear mathematics, all the while recognizing that
models that focus on specific aspects of the observed
patterns are necessarily incomplete when compared to
the vast richness of the bacterial dynamics.
Compared to pattern formation in non-living
systems (Kessler et al. 1988; Langer 1989; Ben-Jacob
& Garik 1990; Ben-Jacob 1993), bacterial self-organiz-
ation involves an additional inherent degree of plas-
ticity: the building blocks of the colony are themselves
living organisms, each with internal degrees of freedom,
internally stored information and internal assessment
of external chemical messages (Shapiro 1995; Shapiro &
Dworkin 1997; Ben-Jacob et al. 1998, 2000a; Shapiro
1998; Ben-Jacob 2003). These afford each bacterium
plasticity to respond flexibly and even alter itself, by
means of modifying its genetic expression patterns. One
well studied example is the increase of competence (the
ability of a cell to import snippets of DNA) under
colonial stress (Macfadyen et al. 1998; Bdejov 2003). It
would, therefore, be interesting to learn whether
competence and genetic transformation are related to
colony structure (A. Minsky 2005, personal communi-
cation). At the same time, efficient adaptation of the
colony to adverse growth conditions requires self-
organization on all levels—which can only be achieved
via cooperative behaviour of the individual cells.J. R. Soc. InterfaceBACTERIA
To illustrate the ability of bacteria to cope with
conflicting environmental constraints, we begin with
the branching patterns exhibited by the Paenibacillus
dendritiformis lubricating bacteria (Ben-Jacob et al.
1998). This class of bacteria has developed a sophisti-
cated strategy to move on hard surfaces—they collec-
tively excrete specialized chemicals to form a layer of
lubricant (Ben Jacob et al. 2000a). In detail, they create
on top of the agar crust a layer of lubricating fluid with
a well defined envelope within which they can swim,
even on the hard surface, and thus let the colony
expand as we will explain below in greater details. The
exact mechanisms and the chemical agents employed
by the P. dendritiformis bacteria are yet to be
discovered. However, based on accumulated knowledge
from other bacterial species (Harshey 2003; Matsuyama
et al. 1993), it is reasonable to expect that two classes of
chemical agents are used to perform two distinct
functions: (i) extraction of fluid from the substrate
(probably by polysaccharides) and (ii) regulation of the
surface tension and viscosity of the lubricating layer
(probably by surfactants). Microscope observations
reveal that as they swim, they push the layer forward,
paving their own way.
A dilemma arises when, in addition to the motion
difficulty, the available food is not sufficient to sustain a
dense population (Matsuyama et al.1992, 1993;
Matsushita et al. 1998; Kozlovsky et al. 1999; Golding
et al. 1999; Harshey 2003; Ron et al. 2003; JulkowskaThis function is enabled by bacteria communication
that makes use of a broad repertoire of biochemical
agents. At the same time, each bacterium has equally
intricate intracellular communication mechanisms
involving, for example, signal transduction networks
(Ptashne & Gann 2002; Searls 2002; Hellingwerf 2005).
These are used to generate intrinsic adaptive response
to the chemical messages (Ben-Jacob 2003). Biochemi-
cal messages are also used for the exchange of mean-
ingful information across colonies of different species,
and even with other organisms (Kolenbrander et al.
2002). These abilities of bacterial communication are
relevant in many fields from agriculture (communi-
cation with plants) to medicine. For example, bacteria
in our gut can evaluate the state of our own body by
sensing (‘listening’) to our hormones (Ben-Jacob 1997,
2000; Cohen 2001; Lyte 2004).
As we are discovering, bacterial communication-
based cooperation encompasses colony morphogenesis,
which includes coordinated gene expression, regulated
cell differentiation and division of tasks. Collectively,
bacteria can glean latent information from the environ-
ment and from other organisms, process the infor-
mation, develop common knowledge, and thus learn
from past experience (Levine & Ben Jacob 2004). The
colony behaves much like a multi-cellular organism, or
even a social community with elevated complexity and
plasticity that afford better adaptability to whatever
growth conditions might be encountered (Levine & Ben
Jacob 2004).