PALAIOS, 2012, v. 27, p. 206–219
Research Article
DOI: 10.2110/palo.2011.p11-088r
INFLUENCE OF GAS PRODUCTION AND FILAMENT ORIENTATION ON
STROMATOLITE MICROFABRIC
SCOTT A. MATA,1* CARA L. HARWOOD,2 FRANK A. CORSETTI,1 NATALIE J. STORK,3 KATHRYN EILERS,4
WILLIAM M. BERELSON,1 and JOHN R. SPEAR 5
1Department
of Earth Sciences, University of Southern California, Los Angeles, California 90089-0740, USA, scottmat@usc.edu, fcorsett@usc.edu, berelson@usc.edu;
Department, University of California, Davis, Davis, California 95616, USA, clharwood@ucdavis.edu; 3Center for Integrative Geosciences, University of
Connecticut, Storrs, Connecticut 06269, USA, njstork@gmail.com; 4Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder,
Colorado 80309-0216, USA, kateilers@gmail.com; 5Environmental Science and Engineering Division, Colorado School of Mines, Golden, Colorado 80401, USA,
jspear@mines.edu
2Geology
ABSTRACT
* Corresponding author.
This repeated pattern of thick light laminae and thin dark laminae is
preserved in many ancient stromatolites, although in many instances
filaments are typically not preserved (e.g., Grotzinger and Knoll, 1999).
In rare instances, filamentous microfossils are preserved in silicified
stromatolites (e.g., Barghoorn and Tyler, 1965; Cloud, 1965; Awramik,
1976; Awramik and Semikhatov, 1979), although a clear pattern of
alternating vertical-horizontal filament microstructures is not always
apparent (e.g., Zhongying, 1986; Seong-Joo and Golubic, 1998, 1999).
Alternatively, some ancient stromatolites exhibit alternations of light
laminae containing filamentous microfossils and dark laminae containing coccoid forms (Hofmann, 1975). Although some ancient stromatolites do preserve microfossils, the majority do not. With varying
degrees of microfossil preservation in the rock record, interpreting the
activity and organization of the microbial communities from ancient
stromatolites requires a modern analogue that can provide insight into
what features will actually be preserved.
Modern marine stromatolites have limited utility as analogues for
ancient stromatolites, especially for Precambrian stromatolites (e.g.,
Awramik and Riding, 1988; Fairchild, 1991; Grotzinger and Knoll,
1999) because most modern marine stromatolites form through the
trapping, binding, and cementation of sand-sized sediment grains and
have a crude, coarse lamination (Logan, 1961; Dravis, 1983; Dill et al.,
1986; Macintyre et al., 2000; Reid et al., 2000; Dupraz and Visscher,
2005). Ancient marine forms, however, show a larger preference for
in situ precipitation of minerals with lesser contributions from the
accretion of sediment. This in situ precipitation results in a fine-scale,
well-defined lamination that contrasts with that found in modern forms
(Fairchild, 1991; Grotzinger and Knoll, 1999). While it would seem that
modern marine stromatolites should form the base for the interpretation of ancient marine stromatolites, it appears that stromatolites from
modern lake and hot spring environments may actually be better
textural analogues for these ancient forms, even though they are not
of a marine origin. This is because they form primarily by in situ
precipitation of minerals, being calcareous or siliceous, and contain low
levels of detrital material. They commonly exhibit a submillimeter-scale
lamination, and stromatolite microstructure is mediated by mineral
precipitation mechanisms (e.g., Walter et al., 1976; Osborne et al., 1982;
Jones et al., 2000; Petryshyn and Corsetti, 2011).
Stromatolites from a silica hot spring, Obsidian Pool Prime (Spear
et al., 2005; Shock et al., 2005), in Yellowstone National Park,
Wyoming (Fig. 2) exhibit light-dark lamina couplets (Fig. 3) that occur
beneath a surface mat consisting of cyanobacteria (Pepe-Ranney et al.,
2010, 2012). These couplets are characterized by the alternation of open
networks of filaments within light laminae and dense networks of
filaments within dark laminae (Fig. 4). These structures are excellent
microstructural analogues for many ancient stromatolites, despite
differences in mineralogy, because of their fine-scale lamination and
lack of trapped and bound sediment grains. Rounded pores occur
Published Online: April 2012
Copyright G 2012, SEPM (Society for Sedimentary Geology)
0883-1351/12/0027-0206/$3.00
Alternating light-dark laminae within stromatolites have been attributed
to a phototactic response of the constituent microbial communities,
whereby filaments orient vertically during the day and recline at night.
This study examines the orientation of cyanobacterial filaments within a
laminated siliceous stromatolite from a Yellowstone National Park hot
spring to identify the controls on microfabric development and whether
phototaxis plays a role. Results indicate that filament orientation is
predominantly perpendicular or parallel to lamination, even when laminae
are steeply inclined. Thus, phototaxis is not a significant control of
microfabric development in these stromatolites. Vertical aspects of the
fabric are dominated by hourglass-shaped filament bundles (hourglass
structures) adjacent to rounded pores, rather than being defined by
individual filaments. The rounded pores likely represent oxygen-rich
bubbles generated during photosynthesis. Upon stabilization by filaments,
upward buoyancy of the bubbles rotated the bundles toward a vertical
orientation. Thus, vertical aspects of the fabric in this stromatolite result
from buoyancy forces rather than phototaxis. Examples from the
Neoproterozoic Beck Spring Dolomite reveal that similar subvertical
hourglass structures are present in the rock record and may be better
preserved than individual filaments. The presence of rounded pores
(fenestrae) and hourglass structures in ancient microbialites, here termed
the hourglass-associated fenestral fabric, can serve as an indication of
biogenic influence in stromatolites, especially in the absence of preserved
filaments, and may be an indication of oxygenic photosynthesis.
INTRODUCTION
The notion that photosynthetic filamentous microbes (e.g., cyanobacteria) orient toward the light is a basic tenet of microbialite studies
(Monty, 1967; Gebelein, 1969; Golubic, 1973; Walter et al., 1972, 1976;
Golubic and Focke, 1978) and finds support in the microstructure of
some stromatolites. Modern hot spring and marine stromatolites can
exhibit alternations of vertically and horizontally oriented filaments,
with the interpretation that the filaments are oriented vertically under
daylight conditions and horizontally at night (Monty, 1967; Gebelein,
1969; Golubic, 1973; Walter et al., 1972, 1976; Golubic and Focke,
1978). The vertical orientation of microbial filaments is attributed to a
phototactic response in which the filaments orient themselves toward a
light source, with the long axis of the filament orienting with the
incident angle of incoming light (Fig. 1, Golubic, 1973; Kim et al.,
2005). At the meso-scale, the alternation of filament orientation
appears as alternating light-dark laminae, with the vertical filaments
forming thicker light laminae and the horizontal filaments forming
thinner dark laminae (Fig. 1, Golubic, 1973; Golubic and Focke, 1978).
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FIGURE 1—Proposed relationship between filament orientation and lamination in
stromatolites for microbial communities that are orienting with light (phototaxis). All
filaments are vertically oriented, even on steeply dipping laminae (modified from
Golubic, 1973).
within open filament networks and resemble fenestrae similar to those
generated from gas production during breakdown of organic matter
(e.g., Choquette and Pray, 1970) or photosynthesis (Tebbutt et al.,
1965; Von der Borch et al., 1977), and these rounded pores are bounded
by hourglass-shaped filament bundles. Exceptional preservation and
mineralization of microbial filaments within the stromatolites, in the
absence of significant diagenesis or detrital input, allow for highresolution petrographic analysis.
This study quantitatively characterizes the orientation of filament
fabrics at the microfacies scale within these stromatolites to examine
FIGURE 2—Map showing the location of Obsidian Pool Prime within Yellowstone
National Park in Wyoming, United States, and the location of the Beck Spring
Dolomite in southeastern California (specific localities of Harwood and
Sumner, 2011).
whether filaments within the laminae show a preferred vertical or subvertical orientation, which would be predicted if the fabric dominantly
reflects a photic response by the surface cyanobacterial mat, or if the
filament orientation is responding to other factors (e.g., nutrient diffusion, Petroff et al., 2010). In addition, this study examines the unique
fenestral fabric of the stromatolite—consisting of hourglass-shaped
FIGURE 3—Thin section of the stromatolite from Obsidian Pool Prime, Yellowstone National Park, United States, used in this study. The six boxes mark portions of the
stromatolite that were examined in detail for fabric and filament orientation. Numbers in boxes correspond to numbers utilized in the text when referring to portions of
the stromatolite.
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FIGURE 4—Photomicrographs of the microfacies and structural components of the stromatolite from Obsidian Pool Prime, Yellowstone National Park, United States.
Filament network types are labeled as I, II, and III. A) Two successive laminae within the rounded pore microfacies. The upper lamina consists of an open filament network that
surrounds rounded pores. Between adjacent pores are found hourglass-shaped filament bundles. Individual laminae can show an upward increase in filament density (bottom of
photomicrograph), and rounded pores are typically concentrated near the base of laminae where filament density is the lowest. B) Scanning electron micrograph of the rounded
pore microfacies showing that the rounded pore spaces are three-dimensional spherical features that are contoured by filaments. C) The grading laminae microfacies is defined
by the gradual upward increase in filament density within each lamina. Filament density increases from bottom-left to top-right within each dipping lamina in this example. D)
The nongrading laminae microfacies showing no distinct changes in filament density within the light laminae consisting of an open filament network. E) The ultraporous
laminae microfacies containing a poorly silicified open filament network in which dark laminae are weakly defined by faint increases in filament density. F) The dense laminae
microfacies showing a general lack of an open filament network and consisting primarily of densely packed filaments alternating with heavily silica-encrusted horizons.
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209
filament bundles and rounded pores—and compares it to similar fabrics
from the Neoproterozoic Beck Spring Dolomite to explore its utility for
the interpretation of phototaxis and oxygenic photosynthesis in the
rock record.
OBSIDIAN POOL PRIME STROMATOLITE LOCALITY
Obsidian Pool Prime (OPP) is a siliceous hot spring located within
Yellowstone National Park, Wyoming, in the Hayden Valley area
(Fig. 2). It derives its name from the adjacent Obsidian Pool Hot Spring
(Hugenholtz et al., 1998; Spear et al., 2005; Shock et al., 2005), and
receives a portion of inflow from it. The pool waters cool from ,75 uC
near the vent to ,45 uC near the outflow of the pool (Shock et al., 2005;
Berelson et al., 2011). The dissolved silica in OPP waters averages 5.7 mM,
which exceeds the 2 mM concentration found in the adjacent Obsidian
Pool, and the pH is 5.7 (Berelson et al., 2011; Pepe-Ranney et al., 2012).
Stromatolites sampled from OPP are located along the northern and
western rim of the pool. The growth rate and morphology (Berelson
et al., 2012), as well as the constructing microbial communities are well
documented (Pepe-Ranney et al., 2012). Surface communities of OPP
stromatolites consist primarily of cyanobacteria (Pepe-Ranney et al.,
2012). The stromatolites grow through the upward accretion of
cyanobacterial filaments, which then become encrusted with silica and
preserved as a microstructure of silicified tubes (Berelson et al., 2011).
The mats generate laminae on the scale of days (Berelson et al., 2011).
A single couplet of light and dark laminae forms approximately every
1.75 days (Berelson et al., 2011). This is consistent with previous
estimates from stromatolites found at Column Spouter Spring, Fairy
Creek Meadows, Yellowstone National Park, that suggest that lamina
couplets form on the order of 1–2 days (Walter et al., 1976).
MATERIALS AND METHODS
Stromatolites were collected from Obsidian Pool Prime in Yellowstone National Park, United States (Fig. 2). Samples were slabbed,
impregnated with blue epoxy to highlight porosity, and thin-sectioned
to examine the meso- and microstructure. Multiple stromatolite
samples were examined to define microfacies, although the same
microfacies were recognized to varying degrees in all examined
stromatolites. One representative stromatolite was chosen to examine
in detail with regard to filament orientation. Five microfacies are
recognized within these siliceous stromatolites: (1) rounded pore; (2)
grading laminae; (3) nongrading laminae; (4) ultraporous laminae; and
(5) dense laminae. These microfacies are based on filament density,
filament structure, and porosity, and are defined below.
Six regions of the stromatolite (,3 3 2 mm) were chosen that
represent different growth periods of the stromatolite, as well as
anterior (i.e., facing the center of the pool), central, and posterior (i.e.,
facing the pool rim) positions (Fig. 3). Image processing software
(ImageJ, http://imagej.nih.gov/) was used to measure the orientation of
filaments and filament bundles within these six regions. Each region of
the stromatolite was divided into a 2.2 3 1.6 mm grid of 9 3 12 boxes
to examine filament fabrics in detail. Within light laminae, filament
fabrics were examined in a total of 648 squares in the six selected
‹
FIGURE 5—Examples of filament orientation scores, with a score of 1 representing
the highest possible degree of orientation and 5 representing no orientation.
Orientation score 1 (not shown): All filaments in the same orientation. This is an
idealized orientation that was not observed in any samples, so is not pictured. A)
Orientation score 2: Almost all filaments in the same orientation with few filaments in
different orientations. B) Orientation score 3: Most filaments in the same orientation
with more than a few in different orientations; orientation still easily recognizable. C)
Orientation score 4: Dominant orientation just recognizable, with many other
filaments in different orientations. D) Orientation score 5: No recognizable orientation.
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TABLE 1—Microfacies of the stromatolites from Obsidian Pool Prime, Yellowstone National Park, Wyoming, United States.
Microfacies
Rounded pore
Laminae couplet
thickness (mm)
Components
160–290
I) Open filament network;
II) dense filament network;
III) brown siliceous cap
Grading laminae
80–240
I) Open filament network;
II) dense filament network;
III) brown siliceous cap
Non-grading laminae
90–370
I) Open filament network;
II) dense filament network;
III) brown siliceous cap
150–400
I) Open filament network;
II) dense filament network
60–170
II) Dense filament network;
III) brown siliceous cap
Ultraporous
Dense
Description
Porosity
Thick light laminae and thin dark laminae
couplet; filaments are arranged into
hourglass-shaped bundles that contour
rounded pore spaces.
Thick light laminae and thin dark laminae
couplet; couplet shows a general upwarddensening succession defined by increasing
filament density and contact between
light and dark laminae is gradational.
Thick light laminae and thin dark laminae
couplet; couplet shows no distinct trend
for filament density within the couplet
and contact between light and dark
laminae is sharp.
Thick light laminae with weakly developed
dark laminae couplet; dark laminae
generally defined by deflections and
crooks in filaments that part light
laminae; filaments are poorly silicified.
Defined by the general absence of an open
filament network; laminae are
predominantly dark and alternate with
brown, more silicified, horizons.
regions of the stromatolite. A semi-quantitative score was assigned to
each box depending upon the degree to which filaments showed a
preferred orientation. A score of 1 represents the highest degree of
orientation, while a score of 5 represents no recognizable orientation
(Fig. 5). These scores were then averaged for each microfacies.
For boxes in which a preferred filament fabric orientation could be
readily recognized (orientation score 1–3), the angle of this orientation
was measured relative to horizontal and relative to the lamination. No
orientation data is presented for the dense laminae microfacies because
only a small number of boxes were recorded with a high degree of
orientation. Orientation data were eliminated for laminae dipping +/2
10u from horizontal or +/2 10u from vertical to avoid redundancy. This is
because surface normal (i.e., perpendicular to lamination) and vertical
filaments would generate similar values for low-angle laminae, and
surface parallel filaments would be indistinguishable from vertical
filaments for steep laminae angles. Of the 648 squares generated, 217
met these criteria. Orientation measurements were placed into 10u bins.
Resulting graphs highlight zones that reflect +/2 10u from absolute
horizontal and absolute vertical filament orientations, as well as zones
+/2 10u from surface parallel and surface normal orientations. Surface
parallel refers to orientations that parallel the angle of the underlying
lamination, while surface normal refers to orientations that are
perpendicular to the angle of the underlying lamination.
The orientation of filament bundles and the individual filaments that
comprise them were measured relative to horizontal and relative to
lamination within the rounded pore microfacies for regions 1, 3, and 5.
Regions 2, 4, and 6 lacked hourglass-shaped bundles in the rounded pore
microfacies. Within regions 1, 3, and 5, the orientation of every bundle
that was hourglass-shaped and spanned the vertical extent of the light
laminae was measured. For each bundle orientation that was measured,
40 individual filaments were measured. Measurements were taken only
from portions of the microfacies containing an open filament network
and were focused on filament bundles that surround pore spaces. Due to
a limited dataset, no lamination angles were excluded from this analysis.
Orientation measurements were then placed into 10u bins.
Examples of similar textures and features found within the OPP
stromatolite occur within stromatolitic facies of the Neoproterozoic
Beck Spring Dolomite of southeastern California, United States
(Harwood and Sumner, 2011). Silicified stromatolites within the
Lateral continuity
High within pores;
low within bundles
Low
High at base of couplet;
low at top
Moderate
Moderate
Moderate-high
Very high
Low-moderate
Very low
High
formation yield filamentous and coccoid microfossils, suggesting a
probable biogenic origin for these stromatolites (Licari, 1978). Samples
were slabbed and examined in hand sample and in polished thick
sections (,80 mm) for comparison with the Obsidian Pool Prime
stromatolite. Folk’s white card technique was used in some cases to
highlight dark pigmented areas in the carbonate (Folk, 1987). All
samples are petrographically well-preserved with minimal recrystallization, despite pervasive mimetic dolomitization (e.g., Zempolich et al.,
1988, 1989). Recrystallization was evaluated based on standard
interpretations of crystal size and shape distributions, crystal boundary
geometries, and the distribution of pigments relative to crystals.
RESULTS
Stromatolite Microfacies
Microfacies, and their constituent laminae within the Obsidian Pool
Prime stromatolite, are comprised of three distinct filament networks:
(I) open networks of filaments with a high porosity (40–330 mm thick);
(II) dense networks of filaments with low porosity (30–50 mm thick);
and (III) brown, densely packed silica-encrusted filament networks,
with essentially no porosity, that mark the uppermost surface of II (20–
60 mm thick). The presence, absence, or combination of these filament
networks, in addition to the volume and distribution of internal
porosity, define the microfacies found within the stromatolites
(Table 1): (1) rounded pore (I, II, and III); (2) grading laminae (I, II,
and III); (3) nongrading laminae (I and III); (4) ultraporous laminae (I
and II); and (5) dense laminae (II and III). Filaments that comprise
each microfacies are observed to be 3–5 mm in diameter and up to
230 mm in length in the observed sample.
The rounded pore microfacies consists of thick lamina couplets (160–
290 mm thick) comprised of a thicker light lamina and a thinner dark
lamina (Fig. 4A). The internal structure of light laminae consists of
open filament networks with bundled filaments that contour around
circular, horizontal ellipsoid, and vertically elongate pore spaces that
are 40–200 mm in diameter in their longest dimension. Pore spaces
typically span the entire thickness of the light laminae. Filament
bundles pinch upward around flat-topped pores and form symmetrical
hourglass shapes, termed hourglass structures, around circular pore
spaces. The central taper of these hourglass-shaped bundles may be as
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thin as a few filaments, and is usually 10–60 mm wide. Bundle length is
100–180 mm, roughly the same scale of adjacent pores. Scanning
electron microscopy (SEM) of circular pore spaces reveals that they are
spherical three-dimensional features (Fig. 4B). Laminae within the
rounded pore microfacies exhibit limited lateral continuity and have
high levels of porosity. Unlike all other microfacies, which occur at
nearly all lamina dip angles, the rounded pore microfacies is rare on
laminae dipping more than approximately 60u.
The grading laminae microfacies is comprised of thin to thick lamina
couplets (80–240 mm thick) that show a gradual upward increase (i.e.,
grading) in filament density. This is capped by a brown silica-encrusted
horizon (Fig. 4C). A sharp contact exists between underlying dense
filament networks and overlying open networks, while the transition
between underlying open networks and overlying dense networks is
gradational. Lamina couplets exhibit moderate levels of lateral
continuity and have high porosity at the base of a couplet and low
porosity at the top of a couplet.
The nongrading laminae microfacies is defined as thin to thick
lamina couplets (90–370 mm thick) in which the thicker light laminae
are characterized by an open filament network that shows a density
structure that does not change from its base to top (i.e., nongrading)
(Fig. 4D). Dark, thinner laminae are commonly more highly silicified
than lighter laminae and usually contain a dense network of filaments.
Laminae show moderate to high levels of lateral continuity and have
high porosity in the open filament networks and low porosity in the
dense, silica-encrusted networks.
The ultraporous laminae microfacies consists of very loosely packed
filamentous laminae with an open filament network coupled with
thinner, slightly denser laminae to comprise light-dark couplets (150–
400 mm thick) (Fig. 4E). Thinner, denser laminae appear to be defined
by minor surface-parallel crooks and deflections in surface normal
filaments. These laminae appear short-lived and are poorly established.
Dense, silica-encrusted laminae—as found in all other microfacies—are
conspicuously absent, and the majority of filaments within this
microfacies are poorly silicified and therefore poorly preserved. This
is the most porous of all the microfacies. Lamina couplets exhibit
limited to moderate lateral continuity.
The dense laminae microfacies is defined by the general absence of an
open filament network, with a concomitant decrease in porosity and
increase in density relative to other microfacies (Fig. 4F). Lamina
couplets within this microfacies consist of a dense network of filaments
capped by a more silicified horizon and range in thickness from 60 to
170 mm. Subtle changes in filament density and silicification define light
and dark laminae.
Filament Orientation Score of Microfacies
Orientation score results for each microfacies reveal that the rounded
pore and ultraporous microfacies have the lowest orientation scores,
which indicates that filaments in these microfacies have the highest
degree of orientation (Fig. 6). The average orientation score for the
rounded pore microfacies is 2.61, while the ultraporous laminae
microfacies has an average score of 3.02. Higher average scores belong
to the grading laminae, nongrading laminae, and dense laminae, with
scores of 3.54, 3.75, and 4.44, respectively. At a first approximation,
this data indicates that the rounded pore and ultraporous laminae
microfacies show the highest degree of orientation. These two
microfacies are notably the most porous of the microfacies, and the
open filament networks that comprise them are more loosely packed
than in the other microfacies. A strong contrast to this is the dense
microfacies, which generally lacks an open filament network, has the
lowest porosity, and has the highest average orientation score,
reflecting a very low degree of orientation. While this proxy does
address the degree to which each microfacies shows a preferred
orientation, it does not show what that orientation is.
FIGURE 6—Orientation score for the microfacies: rounded pore, ultraporous,
grading, nongrading, and dense. Scores are arranged from lowest to highest, with the
lowest score marking the highest degree of orientation and the highest score marking
the lowest degree of orientation. Note that the highest degree of orientation is found
in the rounded pore and ultraporous laminae microfacies, which also have the
highest porosity.
Filament Fabric Orientation
Orientations of filaments relative to horizontal, and relative to
lamination, show variability between microfacies (Fig. 7). In all data, a
measurement of 90u to horizontal corresponds to vertical filaments,
while 90u to lamination refers to filaments oriented perpendicular to the
lamination (i.e., surface normal). The rounded pore microfacies shows a
normal distribution with respect to horizontal with a peak in the 90u–
100u bin; with respect to lamination, a prominent surface normal zone
exists between 80u and 100u (Fig. 7A). The grading laminae microfacies
shows no clear trend with respect to horizontal; however, with respect
to the lamination there are elevated values in the zones of surface
normal and surface parallel (Fig. 7B). The orientation of filaments with
respect to horizontal in the nongrading laminae microfacies shows a
normal distribution with a very prominent peak in the 70u–80u bin
(Fig. 7C). Filaments in the nongrading laminae microfacies have two
distinct bell-shaped distributions with respect to lamination centered
around 80u–90u and 10u–20u, which correspond to surface normal and
surface parallel, respectively. The ultraporous laminae microfacies
shows similar bell-shaped orientation distributions relative to horizontal and relative to lamination, centered around 80u–100u (Fig. 7D).
When the filament orientation data is compiled for all microfacies
(except the dense microfacies, see Materials and Methods for why this
was removed), the most prominent zone for filament orientation relative
to horizontal occurs within 70u–100u (Fig. 8). The most prominent zone
for filament orientation relative to the lamination is from 80u to 100u.
Considering the peaks for the bins +/2 10u from 90u (80u–90u and 90u–
100u), 26.2% of all boxes fell within these values when examining filament
orientation relative to horizontal. By contrast, 38.0% of filament fabrics
are +/2 10u from 90u relative to the lamination, indicating that a higher
percentage of filaments are oriented perpendicular to the lamination than
absolutely vertical. When expanded to +/2 20u from 90u (70u–90u and
90u–110u), 50.9% of all measured filament fabric angles fell within these
values when examined relative to horizontal. Filament fabric relative to
the lamination occurs within these values for 66.7.0% of all boxes.
Therefore, there is a higher preference for filaments to be oriented
perpendicular to the lamination, rather than oriented vertically.
Rounded Pore Microfacies Filaments and Filament Bundles
The orientation of the long axes of individual filaments within
hourglass-shaped bundles of the rounded pore microfacies are normally
distributed with respect to horizontal and to the lamination, and both
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FIGURE 7—Binned orientation angles, relative to horizontal and relative to lamination, for the filament fabrics within the A) rounded pore microfacies; B) grading laminae
microfacies; C) nongrading laminae microfacies; and D) ultraporous laminae microfacies.
exhibit a distinct saddle located around 90u (Fig. 9A). This distribution
spans all bins from 0u to 180u, with filament abundance decreasing
toward angles approaching parallel to horizontal or parallel to the
underlying lamination. Relative to horizontal, filaments exhibit a
saddle near the 80u–90u bin, with abundance peaks located around 50u–
70u and 120u–140u. Relative to the lamination, this saddle is centered on
the 90u–100u bin and abundance peaks are located near 50u–70u and
110u–130u.
The orientation of hourglass-shaped filament bundles within the
rounded pore microfacies is more tightly distributed than the
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FIGURE 8—Binned orientation angles, relative to horizontal and relative to lamination, for the filament fabrics for all microfacies, except the dense laminae microfacies.
FIGURE 9—Binned orientation angles, relative to horizontal and relative to lamination, for A) individual filaments within hourglass-shaped filament bundles in the rounded
pore microfacies; and B) filament bundles within the rounded pore microfacies.
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FIGURE 10—Photomicrograph of filament bundles within the rounded pore
microfacies. Note that the filament bundles are generally oriented vertical—5u off
vertical (left bundle) and 13u off vertical (right bundle)—while the lamination dips 15u
to the right.
orientation of individual filaments (Fig. 9B). Orientations of bundles
are between 60u and 140u relative to horizontal and relative to
lamination. The orientation of most filament bundles relative to
horizontal is vertical to subvertical, with prominent peaks in the 70u–
80u bin and the 90u–100u bin. The orientation of filament bundles
relative to the lamination is more widely distributed and is centered
around 80u–100u. Overall, hourglass-shaped filament bundles are
oriented subvertically to vertically, but the orientation of individual
filaments is much more variable (Fig. 10).
DISCUSSION
Factors Determining Filament Orientation
The orientation scores reveal, at first approximation, that those
microfacies with an open filament network and a high primary porosity
show a higher degree of orientation than those with closely spaced
filaments. The orientation of filament fabrics relative to horizontal and
relative to lamination for each microfacies reveals that most of the
microfacies do not show a preferred vertical or subvertical orientation,
which would be expected for a conventionally defined phototactic
response (Figs. 11A–B). Rather, an orientation of 90u +/2 10u to
lamination (i.e., approximately surface normal, Fig. 11C) either
matches closely or exceeds the counts recorded for filament fabrics
relative to horizontal. All the microfacies and filament orientation data
show that there is not an overwhelming phototactic signal within the
stromatolite, in contrast to previous stromatolite studies that claim
filaments orient vertically toward light during the day (Monty, 1967;
Gebelein, 1969; Golubic, 1973; Walter et al., 1972, 1976; Golubic and
Focke, 1978). In fact, the total distributions of filament fabric relative
to horizontal and relative to lamination are not easily distinguishable
from each other. There may even be a slight preference for surface
normal over vertical filament fabrics, which has been shown by Petroff
et al. (2010) to be a response to nutrient diffusion (Fig. 11D). If
filament fabric was influenced by phototaxis, a preference for vertical
filaments would especially be expected in the most light-limited areas of
the stromatolites, primarily the sides. However, on the sides of the
stromatolite (region 2 of Fig. 3), filaments are preferentially oriented bimodally, perpendicular and parallel to the lamination (Fig. 12). This
suggests that a different process, other than a photic response, may
control a subvertical fabric in stromatolites, or alternatively, that the
phototactic response has been overstated with respect to vertical
orientation towards incident light.
PALAIOS
FIGURE 11—Possible relationships between filament orientation and lamination in
stromatolites. A) and B) illustrate the expected vertical orientation for filaments with
a phototactic response to a direct light source (modified from Golubic, 1973). B) and
C) illustrate filaments growing normal to the lamination. Filaments in OPP
stromatolites are neither strongly vertically oriented or perpendicular to the
lamination direction, suggesting that they are not strongly recording a phototactic
response. D) illustrates the more complex filament orientation, with a slight
preference for surface normal orientation that characterizes the filament fabric of
OPP stromatolites.
The orientation of individual filaments within hourglass-shaped
bundles versus filament bundle orientation provides insights into the
processes controlling stromatolite fabric. The distribution of individual
filament orientations within hourglass-shaped bundles in the rounded
pore microfacies is nearly indistinguishable between those relative to
horizontal and relative to lamination. This may indicate that there is no
prominent process that preferentially orients the filaments relative to
either horizontal or to the underlying lamination. It may also suggest
that the difference between the lamina angle and horizontal is minimal,
resulting in only subtle differences between the two datasets. The saddle
centered around 80u–100u and peaks around 50u–70u and 110u–140u in
both datasets likely reflect the tapering angles of filaments within the
observed filament bundles. Filaments that comprise these hourglassshaped bundles are widely spaced at the base and top of the bundles,
but converge on the central portion of the bundle. A peak on either side
of 90u simply reflects the fact that filaments are converging on the
central axis of the bundle from both sides.
Although individual filaments in the rounded pore microfacies do not
have an overall preferential orientation, hourglass-shaped bundles of
filaments are preferentially oriented vertically (90u +/2 10u). This suggests
that a subvertical to vertical fabric in these stromatolites is not produced
by a phototactic response by individual filaments, but rather reflects the
orientation of bundles of filaments adjacent to rounded pores.
The Origin of Rounded Pores and Fenestral Fabrics
The origin of fenestral fabrics in ancient sedimentary rocks has been
highly debated, especially in regard to those associated with ancient
stromatolites. Fenestral fabrics consist of primary voids and pores that
are larger than could be sustained by surrounding sediment (Tebbutt
et al., 1965) and are fabric selective (Choquette and Pray, 1970), as
opposed to fractures and vugs that do not necessarily follow rock
fabric. While it is clear that fenestrae represent the preservation of
primary pore space, due to either early lithification of the surrounding
sediments, or to early filling of voids with cement before compaction,
the mechanisms behind the void generation are varied and may be
PALAIOS
STROMATOLITE FILAMENT ORIENTATION
215
FIGURE 13—Scanning electron micrograph of a spherical pore in the rounded pore
microfacies. Silicified filaments contouring the edges of the pore are interpreted as
representing stabilization of a gas bubble produced on the surface of the stromatolite.
FIGURE 12—Orientation of filaments on the base and side of the stromatolite in an
area with very steeply dipping laminae (region 2 of Fig. 3). There is no preference for
vertical filaments even on these steeply dipping laminae in a light-limited area of the
stromatolite. A) Photomicrograph showing light-dark lamination couplets with
filaments oriented nonvertically, and closely resembling the schematic of Figure 11D.
B) Binned orientation angles for the filament fabrics within region 2. Filaments are
preferentially oriented perpendicular and parallel to lamination.
unique to each type of fenestrae (Ham, 1952; Tebbutt et al., 1965; Wolf,
1965; Shinn, 1968; Choquette and Pray, 1970; Logan, 1974; Shinn,
1983). Laminoid fenestral fabrics (sensu Tebbutt et al., 1965)—in which
voids are irregular, horizontally elongate, and parallel to bedding—are
generally regarded as forming either through shrinkage during
intertidal or supratidal desiccation or through expansion due to gas
produced through the breakdown and decay of a laminar microbial mat
(Choquette and Pray, 1970). Highly rounded pores appear most closely
allied with irregular fenestrae (Logan, 1974; Grover and Read, 1978),
similar to keystone vugs (Dunham, 1970), that are generally equidimensional and do not orient with bedding. These fenestrae are
commonly interpreted as the preserved remnant of bubbles generated
through the evolution of gas—which may be microbially derived from
photosynthesis (Tebbutt et al., 1965; Von der Borch et al., 1977) or the
breakdown of organic matter (Cloud, 1960; Tebbutt et al., 1965)—or
due to emergent conditions and desiccation (Illing, 1959; Shinn, 1968;
Dunham, 1970; Bain and Kindler, 1994). Often, these more rounded
and regular pore spaces have been termed birdseyes (Shinn, 1968);
however, birdseyes have become more synonymous with fenestrae (e.g.,
Choquette and Pray, 1970).
A unique type of fenestral fabric was documented by Bosak et al.
(2009) in which round fenestrae are concentrated at the peaks of conical
stromatolites with ages ranging from the Archean through the
Mesoproterozoic. These fenestrae form a linear series of stacked
rounded pores that highlight the central axis of the conical stromatolite
represented by the peaks of upward projecting chevrons, and are rare in
portions of the laminae away from the central axis. These fenestrae are
interpreted by Bosak et al. (2009) as preserved fossil oxygen-rich
bubbles that formed during photosynthesis concentrated at the tips of
growing conical-shaped aggregates of microbial filaments. This seems a
valid interpretation as modern filamentous cyanobacteria are known to
be capable of surrounding and enmeshing oxygen-rich bubbles
generated during photosynthesis, and this process leads to the
formation and preservation of rounded pores within a meshwork of
filaments (Bosak et al., 2010).
Fenestrae (i.e., rounded pores) from the stromatolites of Obsidian Pool
Prime in Yellowstone National Park are most easily interpreted as fabrics
created around photosynthetically derived gas bubbles. This interpretation is based on the observation that the filaments contour around these
spherical features (Fig. 13). The pore-contoured filaments indicate a
primary origin and a window of formation during which the filaments
were still motile or at least still flexible, which is consistent with the
findings of Bosak et al. (2010) that filaments are capable of producing,
capturing, and stabilizing bubbles. Gas bubbles forming on, and within,
laminae of OPP stromatolites significantly influenced the orientation of
filaments and filament bundles during the formation of laminae within
the stromatolite. While filament bundles in the rounded pore facies show
216
MATA ET AL.
PALAIOS
a preference for a vertical orientation, the filaments that comprise them
do not (Fig. 13). This may be due to the upward buoyancy of gas bubbles
that preferentially rotate filament bundles into a vertical orientation as
they exert an upward force. The general absence of the rounded pore
microfacies from laminae dipping steeper than 60u may be due to the
absence of significant gas production on steeply dipping limbs, the
production of micro-bubbles that could be more subject to gaseous
dissolution into the aqueous phase, or may be due to an inability to trap
bubbles generated on surfaces steeper than this angle.
Rounded pores and associated hourglass structures also provide
information about environmental conditions that allowed for textural
preservation. OPP stromatolite laminae lithified very rapidly, on the
scale of days (Berelson et al., 2011). Extremely rapid lithification is
likely required to preserve the morphology of a bubble as a rounded
pore, and to prevent collapse of vertically oriented filaments and
bundles. High levels of dissolved silica in Obsidian Prime Pool
facilitated very rapid silica precipitation and the stabilization of
microbial filaments (Berelson et al., 2011). Bosak et al. (2010) also
suggest that syngenetic precipitation of crystals in the biomass
surrounding bubbles is required for preservation. As in OPP
stromatolites, the rounded pores generated during the trapping of gas
bubbles remain open (Bosak et al., 2010) and are later filled in with
cements, like in the Beck Spring stromatolites presented below. Thus,
the presence of rounded pores and associated hourglass structures in
ancient stromatolites requires not only motile filamentous microbial
communities producing and trapping gas bubbles, but also rapid
lithification in order to preserve the fabric. The rapid lithification
required for preservation of hourglass structures and rounded pores
may prevent this fabric from being widespread in ancient stromatolites.
Hourglass Structures and Rounded Pores as a Biosignature
The fabric and porosity generated by hourglass structures associated
with rounded pores is most closely allied with fenestral fabric porosity,
as it is fabric selective and follows lamination rather than cutting it.
However, the rounded pore microfacies is distinctly different from
typical fenestral fabrics and is herein termed hourglass-associated
fenestral fabric. While most fenestral fabrics are defined by the shape
and arrangement of pore spaces, the fabric of the Yellowstone
stromatolites is defined uniquely by the hourglass-shaped structures
formed from filament bundles that occur in association with pore
spaces. Rounded pores within the stromatolite are highly regular,
follow lamination, and only rarely exhibit irregular or horizontally
elongate morphologies due to the lateral amalgamation of pore spaces.
Hourglass structures are typically 10–60 mm at the central taper and
contour rounded pores that are approximately 40–200 mm in diameter
in their longest dimension.
The hourglass-associated fenestral fabric generated by these hourglass structures and associated rounded pores can be differentiated
from other fenestral fabrics based on a few unique features. Hourglassassociated fenestral fabrics are distinct from laminoid fenestral fabrics
due to the paucity of laterally amalgamated fenestrae that generate
horizontally elongate and irregularly shaped voids (Figs. 14A–B).
‹
FIGURE 14—A comparison of the rounded fenestral fabric containing hourglass
structures with similar porosity fabrics. A) Rounded fenestral fabric with hourglass
structures generated within the stromatolite due to the orientation of microbial
filament bundles (left) and the resulting fabric that may be found in a rock if the
morphology of the fabric were preserved without the preservation of individual
filaments (right). B) Laminoid fenestral fabric consisting of horizontally elongate
irregularly shaped pore spaces that orient with and follow the host fabric. C) Irregular
fenestral fabric comprised of equidimensional pore spaces that are round to irregular
and do not orient with, but do follow, the host fabric. D) Keystone vugs are pore
spaces typically formed in sandstone, are not fabric selective, and can cut across
primary depositional features.
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STROMATOLITE FILAMENT ORIENTATION
217
FIGURE 15—Hourglass structures (arrows) and rounded pores in stromatolites from the Neoproterozoic Beck Spring Dolomite; photomicrographs, plane-polarized light. A)
Well-defined subvertical hourglass structure spans the distance between successive stromatolite laminae. Arrow points down the long axis of the hourglass structure. B)
Hourglass structures with only a fragmentary portion connected with overlying laminae preserved (marked by arrows). C) Less well-preserved hourglass structures defined by
dark pigments in fine-grained carbonate were likely more degraded prior to lithification (marked by arrows). D) Higher magnification of hourglass structure in (C).
Hourglass-associated fenestrae can also be differentiated from irregular
fenestrae in that they show a high degree of regularity in their
distribution, unlike irregular fenestrae that do not orient with bedding
(Fig. 14C). Highly rounded keystone vugs that resemble hourglassassociated fenestrae usually occur in clean sandstones, typically of a
sandy foreshore or backshore environment, and are not fabric selective
(Dunham, 1970; Bain and Kindler, 1994). More commonly, keystone
vugs cut inclined stratification (Bain and Kindler, 1994), which differs
from the highly regular and fabric selective nature of the hourglassassociated fenestral fabric (Fig. 14D).
If the hourglass-associated fenestral fabric can be unambiguously
identified in the rock record, then it can serve as a biosignature.
Stromatolites in exceptionally preserved shallow marine carbonates of the
Neoproterozoic Beck Spring Dolomite (e.g., Harwood and Sumner, 2011)
display rounded pores associated with hourglass-shaped structures
(Fig. 15). These rounded fenestrae are interpreted to result from the
lithification of filaments bundled around gas bubbles based on the similar
fabric of hourglass-shaped bundles and rounded pores in OPP
stromatolites. Hourglass structures in Beck Spring stromatolites, defined
by the presence of dark pigments in carbonate, are 20–90 mm at the central
taper, with rounded pore spaces approximately 150–300 mm in diameter in
their longest dimension (Fig. 15). As in the OPP stromatolites, hourglass
structures in Beck Spring stromatolites are subvertical to vertical, and
connect stacked laminae. Thus, they are structurally similar in size and
geometry to OPP stromatolite hourglass structures.
The utility of the hourglass-associated fenestral fabric is that it is not
restricted solely to deposits in which distinct microfossils are found. Beck
Spring Dolomite stromatolite microfabrics demonstrate that it is possible
to recognize this fabric in the rock record in the absence of discrete
filaments. Beck Spring stromatolites do not preserve individual filaments
in isolation or in filament bundles, yet the rounded pore and hourglass
structure fabric is easily recognized. Its recognition is contingent
primarily on the presence of hourglass structures that appear to have a
limited size distribution, being typically less than 90 mm at the central
constriction and within the vertical scale of the lamination. The
preservation of rounded pores without significant horizontal amalgamation is another hallmark of this fenestral fabric, which is atypical for
other fenestral fabrics in which amalgamation of adjacent pores is
common. The presence of the hourglass-associated fenestral fabric
reflects the upward growth of microbial filaments around gas bubbles or
the generation of gas bubbles within a network of filaments, resulting in
filament deflection. At present, there are no porosity fabrics in the rock
record or in the modern record that perfectly resemble or reproduce all
the features generated from the contouring of microbial filaments around
gas bubbles to form hourglass structures, and therefore it is unique.
Interpreting Phototaxis and Photosynthesis from Ancient Stromatolites
Microbial microfossils are not preserved in the majority of ancient
stromatolites (e.g., Grotzinger and Knoll, 1999). Thus, interpreting
218
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MATA ET AL.
microbial behaviors—including phototaxis—and microbial metabolisms
in the rock record is difficult. In the absence of preserved microfossils,
other morphologic and microstructural features have been used as
evidence of phototaxis. One such feature is the thickening of laminae
over crests within stromatolites (e.g., Gebelein, 1969; Walter et al., 1976;
Buick et al., 1981; Walter, 1983). This is typically interpreted as
migration of microbial filaments toward a light source, moving up
inclines and concentrating near crests, which mark the highest points on
the stromatolite at a given point in time (e.g., Gebelein, 1969; Walter
et al., 1976; Buick et al., 1981; Walter, 1983). The other feature commonly
used to interpret phototaxis is the alternation of thick light laminae and
thin dark laminae, which is interpreted as the vertical orientation of
filaments during the day as they reach toward the light and the horizontal
orientation of filaments at night when the light stimulus is removed,
respectively (Monty, 1967; Gebelein, 1969; Golubic, 1973; Walter et al.,
1972, 1976; Golubic and Focke, 1978). While actual filamentous
microfossils do show some support for vertical-horizontal filament
fabrics in the rock record (e.g., Seong-Joo and Golubic, 1998, 1999), the
majority of ancient stromatolites show the alternations of light and dark
laminae, but lack the microfossils. In the absence of microfossils, largerscale fabrics are all that remain for deciphering the potential behaviors,
phototactic or otherwise, of microbes within ancient stromatolites.
Based on the concept that phototaxis influences stromatolite fabrics,
subvertical to vertical structures in ancient stromatolites might be
interpreted as microbial filaments orienting with incoming light.
Alternatively, we suggest that this pattern may represent the trapping
of gas bubbles generated during photosynthesis. The resulting vertical
fabric is a product of the orientation of filament bundles as the gas
exerts an upward force due to buoyancy. Even without the presence of
individual filaments, as in Beck Spring stromatolites, the distinct and
well-defined fabric of the hourglass-associated fenestral fabric allows
recognition of ancient microbial influences and clarifies the potential
origin of some ancient vertical-dominant fabrics in the rock record. In
the case of the OPP stromatolite, vertically oriented microfabrics
actually reflect filament bundles contouring around gas bubbles rather
than a physical photic response of microbial communities.
Herein, we have proposed that the hourglass-associated fenestral
fabric represents the interaction of microbial mats with gas bubbles. In
the modern examples from Yellowstone, the gas bubbles clearly
originate from oxygenic photosynthesis, as we have noted throughout
the text. On the one hand, it is possible that any process that produces
gas (microbial degradation as well as oxygenic photosynthesis) could
foster the formation of the hourglass-associated fenestral fabric.
However, the very nature of the fabric suggests the gas was formed in
situ within the laminae; that is, it did not form via degradation of
underlying mats, as no gas escape structures are noted in the fabric.
Furthermore, the degradation of biomass from the lamination itself
would not provide enough gas to create the bubbles. Therefore, we
cautiously suggest that an hourglass-associated fenestral fabric may
specifically be the hallmark of oxygenic photosynthesis, and as such,
would provide a method to track the presence of oxygenic photosynthesis in the rock record, where conical stromatolites may or may not be
present (e.g., Bosak et al., 2009).
CONCLUSIONS
The alternation of laminae with vertically and horizontally oriented
filaments within stromatolites is commonly interpreted as a phototactic
response in which the microbes grew upward vertically during the
day and reclined at night. Quantitative analysis of filament fabric
orientation within a siliceous stromatolite from Obsidian Pool Prime,
Yellowstone National Park, Wyoming, reveals that fabrics in which
filaments are oriented perpendicular to the lamination match or exceed
fabrics with vertically oriented filaments. This suggests that either
phototaxis is not important in influencing filament fabric, or that the
case for phototaxis driving vertically oriented filaments has been
overstated in the past. Alternatively, hourglass-shaped bundles of
filaments—termed hourglass structures—within the rounded pore
microfacies are preferentially vertically oriented, although the constituent filaments that form the bundles show a wide distribution of
orientations with no preference. Rounded pores associated with
hourglass-shaped bundles are interpreted as preserving the morphology
of gas bubbles that were stabilized by filamentous microbial communities. Thus, the vertical orientation of filament bundles is likely due to
the filament bundles trapping oxygen-rich gas bubbles generated during
photosynthesis. These bubbles would exert an upward-directed force
due to buoyancy and may therefore have deflected or supported the
filament bundles into a vertical orientation. Thus, vertical fabrics in the
stromatolite likely reflect filament bundles associated with gas
production rather than phototaxis.
Rounded pores and associated hourglass structures of the rounded
pore microfacies define a new style of fenestral fabric, termed the
hourglass-associated fenestral fabric, which is easily distinguishable
from similar fenestral fabrics and vugs. It consists of highly regular and
well-defined rounded pores spaces separated by thin hourglass
structures. Pore spaces are typically less than 300 mm in diameter
within both modern and ancient examples, while the hourglass
structures range from 10 to 90 mm at their central constriction. In
ancient stromatolites, the pore spaces are fabric selective and within the
scale of the lamination because they reflect processes that occurred
contemporaneously with stromatolite growth and lithification. Stromatolites from the Neoproterozoic Beck Spring Dolomite reveal that
rounded pores and hourglass structures can be recognized in the ancient
rock record and therefore may serve as an important biosignature,
especially in ancient stromatolites in which microbial filaments are not
preserved and biogenicity is ambiguous.
ACKNOWLEDGMENTS
We would like to thank and acknowledge the Yellowstone Center for
Resources for all their help and assistance through the development of
this project, and would like to thank the 2010 International Geobiology
Course for the stimulating discussions and guidance that made it all
possible. We would also like to thank T. Bosak, J.P. Zonneveld, and
two anonymous reviewers for their constructive and helpful reviews
that greatly strengthened this manuscript. Funding was provided by the
Agouron Institute, the Gordon and Betty Moore Foundation, NASA
Exobiology, and the National Science Foundation.
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ACCEPTED JANUARY 17, 2012