Accepted Manuscript

Building biogenic beachrock: Visualizing microbially-mediatedcarbonate cement precipitation using XFM and a strontium tracer

Jenine McCutcheon, Luke D. Nothdurft, Gregory E. Webb,Jeremiah Shuster, Linda Nothdurft, David Paterson, GordonSoutham

PII: S0009-2541(17)30306-6DOI: doi: 10.1016/j.chemgeo.2017.05.019Reference: CHEMGE 18350

To appear in: Chemical Geology

Received date: 9 February 2017Revised date: 15 May 2017Accepted date: 17 May 2017

Please cite this article as: Jenine McCutcheon, Luke D. Nothdurft, Gregory E. Webb,Jeremiah Shuster, Linda Nothdurft, David Paterson, Gordon Southam , Building biogenicbeachrock: Visualizing microbially-mediated carbonate cement precipitation using XFMand a strontium tracer, Chemical Geology (2016), doi: 10.1016/j.chemgeo.2017.05.019

This is a PDF file of an unedited manuscript that has been accepted for publication. Asa service to our customers we are providing this early version of the manuscript. Themanuscript will undergo copyediting, typesetting, and review of the resulting proof beforeit is published in its final form. Please note that during the production process errors maybe discovered which could affect the content, and all legal disclaimers that apply to thejournal pertain.

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Building biogenic beachrock: Visualizing microbially-mediated carbonate cement

precipitation using XFM and a strontium tracer

Jenine McCutcheon a*

1, Luke D. Nothdurft

b, Gregory E. Webb

a, Jeremiah Shuster

c,d, Linda

Nothdurfta,b

, David Patersone, and Gordon Southam

a

aSchool of Earth & Environmental Sciences, The University of Queensland, St Lucia, QLD

4072, Australia bSchool of

Earth, Environmental and Biological Sciences, Queensland University of

Technology, Brisbane, QLD 4000, Australia cSchool of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia

dCSIRO Land and Water, Glen Osmond, SA 5064, Australia

eAustralian Synchrotron, Clayton, Melbourne, VIC 3168, Australia

*Corresponding author email: j.mccutcheon@leeds.ac.uk

1Present contact information for corresponding author: School of Earth and Environment,

University of Leeds, Leeds, LS2 9JT, United Kingdom; phone: +44 113 343 2846

A manuscript prepared for submission to: Chemical Geology

Keywords: beachrock; carbonate cement; cyanobacteria; sand cays; microbialite; X-ray

fluorescence microscopy; strontium

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Abstract

The fate of reef islands is a topic of ongoing debate in the face of climate change-induced

sea-level rise and increased cyclone intensity. Increased erosion and changes to the supply of

reef-derived sediment may put sand reef cays at risk of dramatic morphological changes.

These changes may have negative implications for the existence of reef cay environments,

which host vital sea turtle and bird rookery habitats. Beachrock, consolidated carbonate beach

sediment in the intertidal zone, forms naturally on many tropical beaches and reduces the

erosion rates of these beaches when compared to unconsolidated sand. In spite of the critical

role beachrock plays in stabilizing some reef cay shores, the method of beachrock formation

is still incompletely understood. In this investigation, beachrock was synthesized using beach

sand and beachrock samples from Heron Island (Great Barrier Reef, Australia) in aquarium

experiments in which natural beachrock formation conditions were simulated. Beachrock was

produced in two aquaria wherein the water chemistry was influenced by microorganisms

derived from the natural beachrock ‘inoculum’, whereas no cementation occurred in an

aquarium that lacked a microbial inoculum and was controlled only by physicochemical

evapoconcentration. The new cements in the synthesized beachrock were analyzed using

synchrotron-based X-ray fluorescence microscopy and were identified using a Sr-tracer

added to the experimental seawater. The resulting precipitates cement sand grains together

and contain abundant microfossils of the microorganisms on whose exopolymer they

nucleated, demonstrating the fundamental role microbes play in beachrock formation. These

results are of interest because beachrock could be utilized as a natural coastline stabilization

strategy on sand reef cays, and in turn, protect the unique habitats reef islands support.

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1. Introduction

Of all coastal environments that will be influenced by sea-level rise and increased

cyclone intensity, sandy beaches on low elevation coral reef cays are among the most

vulnerable due to their susceptibility to erosion. The complex geomorphological changes to

coral reef sand cay size, shape, and structure resulting from sea-level rise have been the focus of

several recent investigations (Cowell and Kench, 2001; Gibbons and Nicholls, 2006; Perry et

al., 2011; Webb and Kench, 2010; Woodroffe, 2008; Zhang et al., 2004). Additionally, damage

to coral reefs caused by an anticipated increase in cyclone intensity will likely outpace the

recovery rate of corals, which in turn negatively affects other species dependent on the reef

(Cheal et al., 2017). These changes, along with island inundation, have the potential to

negatively influence sand cays populated by humans (Ford, 2012) and those that provide

valuable wildlife habitats such as turtle and bird rookeries (Fuentes et al., 2009; Fuentes et al.,

2011; Pike et al., 2015; Poloczanska et al., 2009). Understanding, and potentially counteracting,

these alterations to island morphology may be a necessity for the future of life on reef islands.

An important factor in understanding how sand cays will respond to sea-level rise is the

role ecosystems play in maintaining coastal stability (Perry et al., 2011; Spalding et al., 2014).

Saltwater marshes and mangroves are known to reduce wave energy, wave height, water

velocity and turbulence, and thus reduce erosion and/or increase sedimentation (Christiansen et

al., 2000; Gedan et al., 2010; Möller et al., 1999; Spalding et al., 2014). Reefs generate the

carbonate sediment that make up reef islands, while also providing protection for the islands by

reducing wave energy and thus, erosion rates (Kench and Brander, 2006b; Sheppard et al.,

2005).

A coastal ecosystem that has received little attention for its potential to aid in

maintaining sand cay stability is beachrock. Beachrock forms on many subtropical beaches

through the lithification of sediment by cement composed of one or both, aragonite and calcite

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(Gischler, 2008; Hanor, 1978; Neumeier, 1999; Scoffin and Stoddart, 1983; Vousdoukas et al.,

2007; Webb et al., 1999). Beachrock formation has previously been attributed to strictly abiotic

physicochemical processes (Alexandersson, 1969; Alexandersson, 1972; Davies and Kinsey,

1973; Dickinson, 1999; El-Sayed, 1988; Ginsburg, 1953; Gischler and Lomando, 1997; Meyers,

1987; Moore, 1973; Russell and McIntire, 1965). Biological processes also have been suggested

(Davies and Kinsey, 1973; Krumbein, 1979; Maxwell, 1962) with recent studies highlighting

the potential importance of microorganisms in beachrock cementation processes (Danjo and

Kawasaki, 2013; Khan et al., 2016; Krumbein, 1979; Neumeier, 1999; Novitsky, 1981; Webb

and Jell, 1997; Webb et al., 1999). Our recent work (McCutcheon et al., 2016) examining

beachrock from Heron Island (Capricorn Group, Great Barrier Reef, Australia) demonstrated

that microbes are actively contributing to carbonate dissolution and precipitation in beachrock.

Beachrock hosts a unique shoreline ecosystem of lithophytic microorganisms that aid in

generating these lithified deposits by enabling carbonate cement precipitation (Díez et al., 2007;

McCutcheon et al., 2016; Webb and Jell, 1997; Webb et al., 1999). Beachrock forms only in the

intertidal zone, and is known to form relatively quickly on timescales as short as a few years

(Chivas et al., 1986; Easton, 1974; Frankel, 1968; Vousdoukas et al., 2007). These spatial and

temporal constraints on beachrock cementation have allowed relict beachrock to be utilized as

Quaternary sea-level and shore-line indicators (Mauz et al., 2015; Ramsay and Cooper, 2002;

Tatumi et al., 2003; Vousdoukas et al., 2007). Although beachrock has long been known to

reduce erosion of unconsolidated beach sediments by protecting them from wave action (Calvet

et al., 2003; Chowdhury et al., 1997; Dickinson, 1999; Kindler and Bain, 1993), there has been

little investigation into the potential use of beachrock as a means of stabilizing beaches that are

susceptible to erosion. In addition, as the health of many coral reefs decline (Pandolfi et al.,

2011) the extent of the protection they provide to their associated islands decreases, making it

critical to seek alternative strategies for protecting reef islands (Sheppard et al., 2005).

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Although there is a growing body of research suggesting that microorganisms play an

important role in beachrock formation, there has been little experimental work linking microbial

activity to beachrock cement precipitation. In this investigation, natural beachrock formation

conditions were simulated in the laboratory to test the role of microbial activity in beachrock

cementation. Synchrotron-based X-ray fluorescence microscopy (XFM) was used to

characterize the newly formed carbonate cements. These results provide a better understanding

of the role of microorganisms in beachrock generation, and could be used to guide future studies

examining in situ beachrock formation with the aim of stabilizing reef islands as sea-level rises.

2. Materials and Methods

2.1 Field site description and sample collection. Heron Island (750 m × 240 m) is a sand cay

on Heron Reef, a lagoonal platform reef (4.5 km × 10 km) in the Capricorn Group in the

southern Great Barrier Reef (Fig. 1a) (Jell and Webb, 2012; Webb et al., 1999). The northern

and southern shores of Heron Island host beachrock outcrops as much as 20 m in width,

which dip seaward at slopes of 4-16°. The beachrock is lithified primarily by isopachous,

acicular aragonite as well as micritic cements (Gischler, 2008; Webb et al., 1999). The

presence of cemented microbialites in the Heron Island beachrock has been one of the

primary pieces of evidence suggesting a microbial influence in the lithification of these

deposits (McCutcheon et al., 2016; Webb and Jell, 1997; Webb et al., 1999). The microbial

beachrock ecosystem is composed of a consortium of microbial endoliths living on, within,

and between the carbonate grains that make up these deposits (McCutcheon et al., 2016).

Several generations of beachrock occur on Heron Island, with blocks of older beachrock

cemented in place by younger beachrock. Examination of the different beachrock generations

suggests that cementation is an ongoing process; boring of carbonate grains by euendolithic

cyanobacteria releases ions into solution which are precipitated as new cement (McCutcheon

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et al., 2016). Over time, this process results in a transition from high porosity and low cement

content, to low porosity and high cement content. The ‘self-healing’ property of beachrock to

re-cement blocks into place after they have been ripped up by storm activity is examined in

this study. Samples of carbonate beach sand, the apparent youngest generation of beachrock

and associated microbial endoliths were collected from the southern beachrock outcrop of

Heron Island. The carbonate beach sand was collected from the supratidal portion of the

beach and consisted of carbonate sediment 0.5-3 mm in diameter. The apparent youngest

generation of beachrock was selected as a starting material for this study because it contains

less cement than its older counterpart, a characteristic of beachrock that results in the younger

generations being more porous and hosting more microbial biomass relative to older

beachrock (McCutcheon et al., 2016). Furthermore, younger beachrock was chosen for

experimental use as it contains less cement than the older beachrock, making it easier to

discern the precipitation of new cements during the experiment.

2.2 Experimental aquaria design. The samples described above were used in three

experimental aquaria to reconstruct the biogeochemical conditions of the Heron Island beach.

The aquaria were housed in a Conviron Adaptis A1000 growth chamber operating at 25°C,

and 12 h of light (06:00 - 18:00; light intensity: 700 mol) and 12 h of dark (18:00 - 06:00).

Each aquarium was 25 × 17 × 19 cm (l × w × h) in size and contained 8 cm of sediment in the

bottom (Fig. 2). Two of the aquaria acted as experimental systems while the third was used as

a control. The beachrock samples were fragmented so that the ~1 cm-thick surface layer

containing macroscopically visible endoliths was separated from the underlying ‘inner’

beachrock. The ‘fragmented beachrock’ (henceforth referred to as FBR) aquarium contained

7 cm of fragmented inner beachrock covered with 1 cm of the fragmented surface layer

beachrock (Fig. 2). The ‘sand’ aquarium (henceforth referred to as Sand) contained 7 cm of

90% (by weight) beach sand seeded with 10% inner beachrock fragments. This layer was

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topped with 1 cm of 90% beach sand seeded with 10% surface beachrock fragments (Fig. 2).

The control aquarium (Control) contained 8 cm of beach sand from Heron Island with no

beachrock ‘inoculum’. The base of each aquarium was wrapped with aluminium foil up to the

surface of the sediment to prevent light from stimulating cyanobacteria growth through the

sides of the glass.

One end of each aquarium was partitioned off with a plastic mesh screen creating a

sediment-free reservoir for the addition and removal of seawater. The seawater was able to

passively flow through the screen to infiltrate the sediment as a means of mimicking tidal

activity. In each aquarium, the alternating addition (06:00 – 06:30 and 18:00 – 18:30), and

removal of seawater (00:00 - 00:30 and 12:00 - 12:30) occurred at 6 hour intervals using

Masterflex L/S® Precision Variable-Speed Console Drive (07528 series) peristaltic pumps

and Norprene® tubing (internal diameter of 2.4 mm). A volume of 1 L of seawater remained

in each aquarium at all times saturating the bottom 2 cm of the sediment and acted as ‘low

tide’. A volume of 3 L was added to each aquarium as an incoming ‘high tide’, resulting in a

water depth of 13 cm (5 cm above the surface of the sediment). It is important to note that

‘fresh’ seawater (Tropic Marin™ Sea Salt, salinity of 35.0) was prepared for each incoming

tide and the ‘old’ seawater discarded after each outgoing tide. Nitrogen and phosphorous

were added to the seawater in concentrations equal to 10% of those in standard BG-11

cyanobacteria growth medium (109 mg/L NO3- added as NaNO3; 2.2 mg/L PO4

3- added as

K2HPO4) (Vonshak, 1986). These concentrations are comparable to those measured in

groundwater on Heron Island (Chen, 2000). Strontium (40 mg/L Sr2+

added as SrCl2·6H2O)

was used as a tracer to distinguish new carbonate cement from that already present in the

natural material (Banner, 1995; Capo et al., 1998). The concentration of Sr was chosen such

that new cement could be identified by a higher than normal Sr content, but would not be so

high as to interfere with mineral precipitation or cause the aquaria to be supersaturated with

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respect to strontium carbonate minerals. This latter point was confirmed by checking mineral

saturation indices using PHREEQC Interactive Version 3.1.1 (Parkhurst and Appelo, 1999).

The experimental aquaria were run for eight weeks.

2.3 Water chemistry analysis. Water samples were collected every 7 days. On each sampling

day, waters were collected at 07:00, 09:00, 11:00, 19:00, 21:00, and 23:00; providing a means

of documenting aqueous geochemistry conditions in the aquaria at the beginning, middle, and

end of high tide under both light and dark conditions. The pH, conductivity (mS/cm, then

converted to salinity) and dissolved oxygen (DO) (mg/L) of the bulk water were measured in

each aquarium at each sampling time point. Dissolved inorganic carbon was determined by

analyzing water samples using a Shimadzu TOC-L CSH Total Organic Carbon Analyzer by

measuring total inorganic carbon (TIC). Water samples were collected, filtered (0.45 µm

pore-size), and analyzed for cations (Ca2+

, K+, Mg

2+, S

6+, Sr

2+) using inductively coupled

plasma-atomic emission spectroscopy (ICP-AES) using a Perkin Elmer Optima 3300 DV

(measurement uncertainty: 12%). Phosphorous (P as PO43-

) and nitrogen (N as NOx)

concentrations were measured using a Lachat QuikChem8500 Flow Injection Analyzer

(FIA).

2.4 Cement characterization. The surface of the sediment in each aquarium was visually

checked weekly for signs of lithification, with samples of what appeared to be newly lithified

beachrock being collected each week after the first two weeks. Polished thin sections of the

original beach sand, fragmented inner beachrock, fragmented surface beachrock, and weekly

samples of synthetic beachrock collected from the Sand and FBR aquaria were analyzed on

the X-ray fluorescence microscopy (XFM) beamline at the Australian Synchrotron (Paterson

et al., 2011). The petrographic thin sections were affixed to a Perspex sample holder using

Mylar tape and mounted on the sample translation stages of the X-ray microprobe. A

monochromatic X-ray beam (18.5 keV) was focused to ~2.0 µm using Kirkpatrick-Baez

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mirrors (Paterson et al., 2011). The Maia detection system used on the XFM beamline

enables fast, high definition elemental mapping of complex natural materials (Paterson et al.,

2011; Ryan et al., 2010; Ryan et al., 2014). Regions of interest on each thin section were

raster-scanned on-the-fly through the focused beam to accumulate X-ray fluorescence spectra

at each scan pixel. The pixel size was 1×1 µm, 2×2 µm or 10×10 µm and the dwell time per

pixel was between 0.33 and 1.0 msec. GeoPIXE software was used to produce elemental

concentration maps from the raw data (CSIRO, 2011). Elemental concentrations were

quantified by calibrating to thin foil standards of Pt, Fe, and Mn of known areal density. A

large number of elements were simultaneously mapped and analyzed (P, S, Cl, Ar, K, Ca, Cr,

Mn, Fe, Co, Ni, Cu, Zn, Br, Sr) and the information from maps of Ca and Sr were the main

focus of this investigation.

The polished thin sections of synthesized beachrock and whole mount samples of the

associated microbial mats collected from the aquaria were characterized using scanning

electron microscopy and energy dispersive X-ray spectroscopy (SEM-EDS) using a JEOL

JSM-7100F Field Emission SEM (FE-SEM). The whole mount samples of microbial mat and

associated grains were fixed using 2.5% glutaraldehyde and dehydrated through an ethanol

dehydration series (25%, 50%, 75%, 100%, 100%, 100%) using a Pelco Biowave microwave

(each step: 250 W, 40 s, no vacuum) prior to being critical point dried (Tousimis Samdri-

PVT-3B critical point dryer). The dried samples were mounted on stainless steel slug stubs

using adhesive carbon tabs. All thin sections and whole mount samples were coated with 5

nm of iridium using a Quarum Q150T S sputter coater. The thin sections were examined

using back-scattered electron (BSE-SEM) mode at 15 kV and a working distance of 12 mm.

Whole mount samples were examined using secondary electron (SE-SEM) mode at 1, 2, or 5

kV at a working distance of 9 mm. Polished thin-sections of beachrock were observed using a

Leica DM6000M microscope equipped with a Leica DFC310 FX camera. The starting

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materials used to construct the aquaria were characterized using light microscopy and XFM

as described above (Fig. 3).

3. Results

3.1 Water chemistry. The average pH, and DO of the initial seawater were 8.30 and 9.1 mg/L,

respectively (Fig. 4a-b). The pH of the FBR and Sand aquaria increased during the day to

average values of 8.77 and 8.79 at 11:00, respectively; and decreased during the night to

average values of 8.15 and 8.18 at 23:00, respectively (Fig. 4a). The pH of the Control

aquarium remained steady at ~8.30 during both light and dark conditions (Fig. 4a). The DO of

the FBR and Sand aquaria increased to average values of 16.8 and 15.5 mg/L at 11:00 and

decreased to average values of 4.1 and 4.9 at 23:00, respectively (Fig. 4b). The 11:00 averages

are underestimates of the oxygen content of the FBR and Sand aquaria, as they reached the

saturation limit of the DO meter of 20 mg/L by week 5 and 4 of the experiment, respectively.

The DO of the seawater decreased upon addition to the Control aquarium, followed by a slight

increase during the day to a 11:00 time point average of 8.6 mg/L, and a small decrease at night

to a 23:00 time point average of 7.4 mg/L (Fig. 4b). The salinity of the initial seawater was

35.0, and the average salinity in the FBR, Sand, and Control aquaria over the course of the

experiment were 38.4, 38.3, and 37.9, respectively.

The concentration of DIC in the Control aquarium increased from 30.4 mg/L in the

initial seawater during the day to 33.4 mg/L at 11:00, and at night to 33.6 mg/L h at 23:00 (Fig.

4c). DIC in the FBR and Sand aquaria followed the same trend, increasing by 9:00 to 32.5 mg/L

and 33.2 mg/L, and then respectively declining to 26.9 mg/L and 28.0 mg/L by 11:00. At night,

the DIC increased to 38.2 mg/L in both aquaria by 23:00 (Fig. 4c).

The concentrations of Ca2+

and Mg2+

increased during both light and dark conditions in

all three aquaria (Fig. 4d,e). The concentration of Sr2+

measured in the initial seawater was 39.1

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ppm (vs. target of 40 ppm) and exhibited minor fluctuations between 38.4 and 40.9 ppm in all

three aquaria during light and dark conditions (Fig. 4f). Nutrient (N and P) concentrations

decreased during both light and dark conditions in the FBR and Sand aquaria (Fig. 4g,h). From

an initial seawater concentration of 24.7 ppm, nitrogen (as N in NOx) decreased in the FBR and

Sand aquaria to 11:00 average values of 22.9 and 21.5 ppm, and 23:00 average values of 23.9

and 22.2 ppm, respectively (Fig. 4g). Phosphorous (as P in PO43-

) decreased from 0.79 ppm in

the initial seawater to 0.56 and 0.49 ppm by 11:00 and to 0.72 and 0.61 ppm by 23:00 in the

FBR and Sand aquaria, respectively (Fig. 4h).

3.2 Cement formation and characterization. Over the eight week experiment, microbial

growth in the FBR and Sand aquaria resulted in the formation of microbial mats on the

surface of the sediment, reminiscent of those found on the beachrock on Heron Island.

Secondary electron SEM of whole-mount samples of the microbial mats revealed extensive

growth of filamentous cyanobacteria in association with cocci and bacilli bacteria (Fig. 5).

Small, millimeter- to centimeter-sized pieces of beachrock were synthesized in the top

5 cm of sediment in the FBR and Sand aquaria. Beachrock synthesis was first observed three

weeks into the experiment. The relative size of the new beachrock grains increased over time

to a maximum grain diameter of 2 cm. No cemented grains were found in the Control

aquarium at any point during the experiment.

X-ray florescence microscopy of thin sections of the synthesized beachrock from the

FBR and Sand aquaria revealed that the new cement precipitates could be easily identified

due to being enrichment in Sr (Fig. 6-9,11) compared to the original carbonate sediment and

cements (Fig. 3). The original aragonite sand grains and cements contained 0.13 atomic % Sr

while the new cements precipitated during the experiment contained an average of 0.85

atomic % Sr based on EDS analysis. Figure 6 shows cement precipitation in a large region of

a sample collected from the surface of the FBR aquarium after eight weeks, in which the

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plane of the thin section is parallel to the surface of the sediment in the aquarium, while

Figures 7-9a-d highlight smaller structures within this region. The new precipitates can be

seen cementing sand grains together and coating grain surfaces (Fig. 7a,d,e). Viewing the

new cements using SEM revealed abundant microfossils exhibiting a diverse range of cell

morphologies (Fig. 7b) that are commonly preserved as fossilized microcolonies (Fig. 7f-h).

Many of the cement coatings on grain surfaces form dendritic microbialites; they contain

mineralized cells as well as new microbial borings (Fig. 8). Structurally, these newly formed

microbialites are very similar to those pre-existing in the fragmented beachrock added to the

aquaria but can be differentiated from those due to the difference in Sr content (Fig. 9).

Some of the precipitates exhibit a ‘wheat-sheaf’ morphology, interpreted as aragonite

(Fig. 10a,b), while others are present as nanoscale granules (c,d). When viewed in a whole-

mount sample, these precipitates are found in association with extracellular polymeric

substances (EPS) (Fig. 10a,c). EDS of the cement (Fig. 10 e-g) showed a range of Mg-

content, from 0.01 to 12 atomic %, suggesting that co-precipitation of aragonite and calcite

may be occurring within microenvironments in the beachrock system (Berner, 1975; Ries et

al., 2008). The biofilm observed growing on the top surface of the sediment and in the

interstices between sediment grains contains both trapped-and-bound material and newly

precipitated carbonate (Fig. 11).

4. Discussion

4.1 Diurnal microbial activity as a trigger for beachrock cementation through carbonate

dissolution and precipitation. The data presented in Figure 4 is intended to demonstrate the

overall trends in the water chemistry as a function of the diurnal changes in microbial activity

in the FBR and Sand aquaria. During the day, cyanobacterial and algal oxygenic

photosynthesis resulted in the measured increase in dissolved oxygen, coincidentally

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increasing the pH through hydroxyl anion production. At night, heterotrophy would have

been the dominant form of microbial metabolism, resulting in oxygen consumption and a

decline in pH after dark. Note, the changes in water chemistry only reflect the bulk water

overlying the sediment and do not represent the pore water in the biofilm or underlying sand.

As a result, the changes that were measured are a diluted product of what is taking place in

the sediment and it is expected that changes in water chemistry between the grains are far

greater in magnitude. There is also potential that the bulk water chemistry does not reflect

other forms of microbial metabolism known to contribute to carbonate mineral precipitation,

such as that of sulfate reducing bacteria (SRB) (Braissant et al., 2007; Gallagher et al., 2012)

and ureolytic bacteria (Ferris et al., 2004; Mitchell and Ferris, 2006). Although natural

beachrock forms in the intertidal zone, and is thus well oxygenated overall, these organisms

could be found in protected anaerobic microenvironments below the surface of the

beachrock.

The increase in the concentrations of Ca2+

and Mg2+

in the Control aquarium are

likely a result of evaporation (Fig. 4d,e). Interpreting the changes in cation concentrations in

the FBR and Sand aquaria is more difficult because they represent the combined effects of:

evaporation, microbial processes, mineral dissolution, and mineral precipitation. The

summation of these processes makes it difficult to discern which processes took place in the

aquaria at any given time. However, the overall changes in Ca2+

and Mg2+

concentrations are

expected to be largely representative of the net balance between mineral dissolution and

precipitation. For instance, the concentration of Ca2+

measured at 07:00 in all three aquaria

was greater than that measured in the ‘fresh’ seawater added at 06:00. The increase in Ca2+

concentration measured in the Control aquaria was likely a result of evaporation, however,

the greater magnitude increases measured in the FBR and Sand aquaria were likely the

product of two microbial processes taking place contemporaneously: 1) mineral dissolution

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resulting from cyanobacteria boring into the grains; and 2) heterotrophic consumption of

EPS. First, endolithic cyanobacteria in the FBR and Sand aquaria were dissolving carbonate

in detrital grains, producing cations in solution. Some cyanobacteria are known to induce

spontaneous carbonate dissolution at the cell-borehole interface by causing a reduction in the

ion activity product of carbonate (Garcia-Pichel et al., 2010). Once in solution, the Ca2+

ions

are internalized by the apical cell of the cyanobacterium filament, transported down the

length of the filament through intercellular Ca2+

-ATPase pumps, and finally expelled away

from the borehole into the surrounding solution (Garcia-Pichel et al., 2010). Antiparallel

transport of two protons along the filament towards the boring front is necessary to balance

each Ca2+

ion moving away from the excavation site via this intercellular pathway (Garcia-

Pichel et al., 2010). These protons can then contribute to carbonate dissolution, after which

the resultant HCO3- can be utilized by the cyanobacterium for photosynthesis (Garcia-Pichel

et al., 2010). Previous studies on the occurrence of phototrophic boring in coastal

environments suggest that it can dissolve up to 0.6 kg of CaCO3/m2/year (Chazottes et al.,

1995). In natural beachrock formation in the intertidal zone, possible explanations for

cyanobacterial boring include: nutrient or space acquisition; and protection from grazing, UV

radiation, wave activity, and desiccation during low tide (Cockell and Herrera, 2008;

McCutcheon et al., 2016). Some of the borings were likely present in the grains prior to

sample collection; however, those found in the newly precipitated cements indicate that

active microbial boring was taking place during the experiment (Fig. 8b). In the aquaria, the

microbes lacked stressors such as wave activity, macroscopic grazers, nutrient limitation, and

solar UV radiation, suggesting that space acquisition or protection from desiccation during

low tide may be the incentive for microbial boring in beachrock. Some of the pre-existing and

new borings have been filled with new cement made visible by its high Sr-content (Fig. 6,7),

which is consistent with reports of carbonate re-precipitation as a result of localized

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microenvironments of carbonate supersaturation where Ca2+

ions are being excreted by

boring phototrophs (Bathurst, 1966; Garcia-Pichel et al., 2010; Margolis and Rex, 1971). The

presence of cement-filled borings across grain boundaries has been known to provide strength

to carbonate structures, such as stromatolites (Macintyre et al., 2000).

The second possible cause for the increase in Ca2+

concentration is heterotrophic

consumption of EPS. This substance is rich in carboxyl groups that give it a net negative

charge, enabling it to bind cations such as Ca2+

that, in turn, attract low molecular weight

organic compounds (Braissant et al., 2009; Flemming and Wingender, 2010; Körstgens et al.,

2001). Decho et al. (2005) demonstrated that the EPS production rate in cyanobacterial mats

coincides closely with photosynthesis, with the greatest EPS production occurring during

midday. In the present study, as cyanobacterial photosynthesis began to produce oxygen in

the morning, heterotrophic metabolism in the aquarium would have increased and

destabilized the EPS structure by oxidizing the organic compounds to bicarbonate (Braissant

et al., 2009; Decho et al., 2005). The bicarbonate would have then been able to react with the

‘reservoir’ of cations available in the EPS microenvironment. Decho et al. (2005) also

demonstrated that heterotrophic consumption of EPS has a diurnal cycle that peaks with

maximum photosynthesis during the day, as well as just after dark. Consumption of the EPS

releases the adsorbed cations back into solution, causing the concentration of Ca2+

in solution

to increase and making carbonate precipitation favorable. Carbonate mineral precipitation by

this process has resulted in mat lithification in many past and modern environments (Aloisi,

2008; Altermann et al., 2006; Braissant et al., 2007; Dupraz et al., 2009; Dupraz and

Visscher, 2005). Note, the intricate relationships between the dissolved cations and mineral

dissolution and precipitation, biofilm adsorption, and evaporation make it difficult to interpret

the cation concentration data beyond the described overarching trends.

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The beginning of the cementation process, which resulted in the formation of the

mineralized microbialites observed in the aquaria (Fig. 7-10), is captured in the nucleation of

new Sr-enriched carbonate grains within the biofilms (Fig. 11). The production of biofilm on

near surface grains in the FBR and Sand aquaria was extensive enough to provide nucleation

sites for carbonate precipitation such that the resultant cements were able to connect grains in

the span of only eight weeks, demonstrating the rapid nature of this process. This

characteristic is also highlighted by the presence of borings in the new cements (Fig. 8b) and

new cements filling borings, illustrating that beachrock is exceptionally dynamic. It is likely

that the initial stabilization and cementation of sand by microbes allows the longer-term,

more pervasive isopachous cement, common in the older beachrock, to form in the

underlying sand. As consolidation progresses, it appears that the interstitial spaces in the

beachrock become increasingly filled with cement, causing a reduction in the volume of pore

space available for habitation by endolithic cyanobacteria (McCutcheon et al., 2016). The

reduced porosity has a two-fold effect on microbial growth: while decreasing the space

available for biofilm growth it also reduces the amount of water than can be retained in the

beachrock interstices during low tide, thus increasing the likelihood of biofilm desiccation.

Although the older beachrock still hosts an endolithic microbial community, a decline in

microbial biomass over time would likely cause a corresponding decrease in the microbial

contribution to cementation. A subsequent increase in porosity of the beachrock, such as

would occur through damage to the outcrop by storm activity, could instigate a resurgence of

microbial activity and cementation.

4.2 Sea-level rise, beachrock, and island stability. The response of reef islands to sea-level

rise is one of ongoing discussion. Several studies have suggested that these islands will be

vulnerable to sea-level rise through increased erosion, inundation, and salinization of the

water table (Church et al., 2006; Gibbons and Nicholls, 2006; Khan et al., 2002; McLean and

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Tsyban, 2001; Mimura, 1999; Nicholls et al., 2007; Roy and Connell, 1991; Woodroffe,

2008; Yamano et al., 2007). The prevailing hypothesis, that reef islands will be subjected to

extensive erosion in the event of sea-level rise, is largely due to application of the Bruun Rule

to these shorelines (Bruun, 1962; Schwartz, 1967). Such predictions, however, have been

criticized because island shores cannot be treated in the same manner as linear continental

coastlines (Cooper and Pilkey, 2004; Cowell and Kench, 2001; Webb and Kench, 2010).

Reef islands, and particularly sand cays, are dynamic structures that change in morphology as

a result of changes in: wave regimes, longshore currents, ocean dynamics, sea-level, and

weather, particularly storm events (Cheal et al., 2017; Church et al., 2006; Kench and

Brander, 2006a; Mimura et al., 2007). High energy events such as cyclones and tsunamis can

result in either net island erosion (Harmelin-Vivien, 1994; Stoddart, 1963) or accretion

(Kench et al., 2006; Maragos et al., 1973). Cyclone intensity is predicted to increase in the

coming years and result in degradation of coral reefs, a trend already being observed in the

central-south part of the GBR (Cheal et al., 2017). The frequency at which a particular reef

island experiences storms affects the size of the sediment of which the island is comprised.

Sand-sized grains dominate islands that experience low storm frequencies, while islands that

experience frequent storms tend to be composed of rubble (Chivas et al., 1986; Gourlay,

1988; Stoddart, 1963). Some models suggest that reef islands are less delicate than previously

thought and will remain stable in the event of the projected sea-level rise of ~0.5 m by 2100

(Kench et al., 2005). That is not to say, however, that island morphology and location will not

change with increasing sea-level. Predicting these changes requires a better understanding of

the many factors that influence reef island morphodynamics, which necessitates better

monitoring of current changes to reef island morphology (Kench and Harvey, 2003; Webb

and Kench, 2010).

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A major factor in reef island sedimentological processes is the type and health of the

reef from which the islands’ sediments are derived (Woodroffe et al., 2007). The reef acts as a

sediment factory by producing carbonate grains from the skeletal remains of invertebrates living

in and on the reef, as well as through erosion of the reef framework by physical and biological

processes (Perry et al., 2011). Once sediment is generated by the reef, the grains are susceptible

to physical abrasion, microbial boring, and chemical dissolution; the summation of these

processes alter size, shape, and density of the sediment that reaches the island (Perry, 2000).

The sediment is deposited on the beach, where it becomes the starting material for potential

beachrock formation. The species richness and relative abundances of the organisms (corals,

coralline algae, foraminifera, molluscs) from which reef sediment is generated will alter the

type, quantity, hydrodynamic properties, and rate of deposition of the sediment available for

island building (Perry et al., 2011; Yamano et al., 2000). Predicting how ecological problems

such as overfishing, pollution, coral disease and bleaching, changes in storm intensity, sea-

level- rise, and ocean acidification will alter reef health is not a small task (Hoegh-Guldberg et

al., 2007; Jackson et al., 2001; Kuroyanagi et al., 2009; Pandolfi et al., 2003; Perry et al., 2011;

Ries et al., 2009), however, understanding how reefs will respond to these changes is necessary

for predicting their ability to supply sediment for reef island building as sea-level rises.

The dynamic nature of reef islands means that it will not be possible to avoid all changes

to island shape, size, and position on the reef flat. In cases where island erosion is likely to

increase in undesirable locations, such as those inhabited by humans or that provide unique

habitats for organisms, implementing strategies to minimize erosion may be necessary. Beaches

dominated by sand-sized grains are more susceptible to erosion than those composed of rubble

(Perry et al., 2011), and the prevalence of beaches composed of rubble grade sediment may

increase in the event of mass coral bleaching (Baker et al., 2008). The combination of these

factors means that sand beaches may be particularly vulnerable, and erosion or inundation of

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these shorelines may negatively impact sea turtles that rely on supratidal sandy beaches for

nesting (Fuentes et al., 2009; Fuentes et al., 2011; Pike et al., 2015; Van Houtan and Bass,

2007). Beachrock formation may provide a natural means of reducing erosion of sand beaches

on reef islands. The intrinsic process by which beachrock forms, demonstrated in this study,

restricts it to the intertidal zone where it will absorb a large portion of the wave energy that

reaches the shore and protect the supratidal part of the beach from storm activity and erosion.

Since lithification is limited to the intertidal zone, the supratidal sand remains unconsolidated

and suitable for nesting. Beachrock is found naturally on islands that host turtle rookeries,

which is a critical point in the potential to employ beachrock as a means of stabilizing beaches

because it maintains the shore as a ‘beach’, unlike other coastline habitats such as saltwater

marshes or mangroves (Christiansen et al., 2000; Gedan et al., 2010; Spalding et al., 2014). The

dynamic nature of beachrock means that it may continue to form in the intertidal zone even in

the event the island migrates on the reef flat, continuing to protect the unconsolidated sand

further up the shore.

The beachrock on Heron Island shows evidence of multiple generations of

cementation through the presence of older beachrock blocks, presumably ripped up during

storms, being cemented in place by younger beachrock. We have previously proposed an

explanation for how beachrock blocks are re-cemented by microbially generated precipitates

(McCutcheon et al., 2016). This ‘self-healing’ characteristic of beachrock is useful for

stabilizing shorelines because these outcrops can regenerate on decadal or shorter time scales.

The FBR aquarium was, in part, designed as a means of investigating this self-healing

property of beachrock and successfully recreated a small-scale version of a beachrock

outcrop damaged by a storm. This system also provides a natural analogue to the recent

advances in self-healing bioconcrete (Jonkers et al., 2010; Wiktor and Jonkers, 2011).

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It is currently unknown how widespread formation of beachrock could alter large-scale

beach morphodynamics through changes in sediment erosion and deposition (Cooper, 1991;

Larson and Kraus, 2000; Sumer et al., 2005; Vousdoukas et al., 2007). The presence of

beachrock on cay shores should be considered when predicting the morphological behavior of

reef cays, making it necessary to understand the processes driving beachrock formation. Further

investigations are required to understand how beachrock will factor into the already complex

conversation surrounding reef island responses to sea-level rise and reef health, especially if

there is potential to purposefully enhance these dynamic shoreline structures as a strategy for

maintaining reef cay stability.

5. Conclusions

The beachrock synthesis experiment conducted in this study demonstrated the

fundamental role microorganisms play in beachrock cementation processes, and suggested that

physicochemical controls such as evaporation and tidal wetting and drying are not sufficient to

instigate cement precipitation. The use of strontium enriched seawater enabled identification of

the new cements using XFM. Cementation appears to be driven by cation generation through

cyanobacteria dissolution of carbonate grains and subsequent precipitation of new cements in

association with EPS. High-resolution SEM of these precipitates, composed primarily of

aragonite, revealed abundant microfossils. The diversity of observed microfossils indicates that

entire microbial biofilms were becoming mineralized during the beachrock formation process.

These results provide a valuable contribution to the current understanding of the

biogeochemical controls on beachrock formation. These findings may be applied to designing in

situ beachrock cementation experiments, which, in turn, may aid in developing strategies to

utilize beachrock as a natural means of stabilizing vulnerable reef islands against sea-level rise.

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Acknowledgements

Part of this research was undertaken on the X-ray Fluorescence Microscopy beamline at the

Australian Synchrotron, Victoria, Australia. This work was supported by the Multi-modal

Australian ScienceS Imaging and Visualisation Environment (MASSIVE)

(www.massive.org.au). For their technical assistance, we thank Marietjie Mostert and Tracey

Crossingham of the Environmental Analytical and Geochemistry Unit at The University of

Queensland (ICP-OES), Dr. Beatrice Keller-Lehmann and Nathan Clayton of the Advanced

Water Management Centre at The University of Queensland (FIA and DIC), Dr. Ron Rasch

and the staff of the UQ Centre for Microscopy and Microanalysis (SEM-EDS). Beachrock

and sand samples were collected with permission from the Great Barrier Reef Marine Parks

Authority (permit no.: G14/37249.1). J. McCutcheon was supported by a National Sciences

and Engineering Research Council of Canada PhD Postgraduate Scholarship. Funding to G.

Southam was provided in part by Carbon Management Canada (C390).

Figure Captions

Figure 1. (a) Location of Heron Island on Heron Reef in the Capricorn Group of the Great

Barrier Reef off the east coast of Queensland, Australia (Google Earth, 2014). (b) Beachrock

in the intertidal zone along the southern shore of Heron Island. (c) The natural beachrock was

used as a starting material in the beachrock synthesis experiments. (d) Visible growth of

endolithic cyanobacteria near the surface of the beachrock.

Figure 2. The aquarium design used in the beachrock formation experiments. Adding and

removing seawater to and from each of the three aquaria using peristaltic pumps simulated

tidal activity. The three aquaria differed in their sediment content: 1) the fragmented

beachrock (FBR) aquarium contained 100% broken beachrock; 2) the Sand aquarium

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contained 10 wt% fragmented beachrock and 90 wt% beach sand; and 3) the Control

aquarium contained 100% beach sand.

Figure 3. Characterization of the fragmented beachrock and beach sand used in the beachrock

formation experiments. These materials are characterized using: 1) photography of whole

samples, 2) plane-polarized light (PPL), 3) cross-polarized light (XPL), 4) XFM of Ca

content, and 5) XFM of Sr content of polished thin sections. XFM scan conditions: pixel size:

10×10 µm, dwell time: 0.56 msec.

Figure 4. Water chemistry plots showing the change over time of mean (a) pH, and

concentrations of (b) dissolved oxygen, (c) DIC, (d) Ca2+

, (e) Mg2+

, (f) Sr2+

, (g) NOx-N, and

(h) PO43-

-P. Each data point is a time point average for the eight week experiment to reflect

overall trends in the water chemistry.

Figure 5. Secondary electron micrographs showing the biofilms that formed on the surfaces

of the (a-b) FBR and (c-f) Sand aquaria after the eight week experiment. The biofilms are

composed of filamentous cyanobacteria producing abundant EPS, and associated

heterotrophs.

Figure 6. XFM showing the (a) Sr and (b) Sr-Ca content in a sample collected from the

surface of the FBR aquarium after eight weeks of the experiment. In (a) the color scale

indicates Sr concentration, with bright yellow regions having the highest Sr content. In (b)

bright yellow regions indicate higher Sr content, while bright blue indicates higher Ca

content. Note, Sr-rich regions (bright yellow in (a) and (b)) indicate new cement

precipitation. The plane of the sample is parallel to the surface of the sediment in the

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aquarium. Boxes in (b) indicate regions depicted in Fig. 7-9. XFM scan conditions: pixel

size: 2×2 µm, dwell time: 0.33 msec.

Figure 7. (a) XFM showing the Sr-Ca content of a portion of the week 8 Sand aquarium

sample shown in Fig. 6. Note, bright yellow regions indicate higher strontium content, while

bright blue indicates higher calcium content. (b-c) These new cements (yellow in (a)) show a

diverse assortment of microfossil morphologies. (d-e) The newly precipitated carbonate can

be seen cementing sand grains together. (f-h) In many cases the new cements contain

fossilized microcolonies. XFM scan conditions: pixel size: 2×2 µm, dwell time: 0.33 msec.

Figure 8. (a) XFM and BSE-SEM showing the Sr-Ca content and structure of a small region

of the sample depicted in Fig. 6. Note, bright yellow regions indicate higher strontium

content, while bright blue indicates higher calcium content. (b) In-filled microfossils of

filamentous cyanobacteria seen in longitudinal section along with new borings visible among

the microfossils. Most of the new carbonate contains microfossils (c-f) enclosed in EPS and

infilled with micritic cement (f). XFM scan conditions: pixel size: 2×2 µm, dwell time: 0.33

msec.

Figure 9. (a) XFM highlighting the Sr-Ca content and (b) BSE-SEM micrograph of a Sr-

enriched microbialite that formed in the FBR aquarium. Compared to (c) XFM and (d) BSE-

SEM of a natural Heron Island beachrock microbialite, cementing detrital grains together.

Note, in (a) and (c), bright yellow regions indicate higher strontium content, while bright blue

indicates higher calcium content. XFM scan conditions: (a) pixel size: 2×2 µm, dwell time:

0.33 msec; (c) pixel size: 2×2 µm, dwell time: 1.0 msec.

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Figure 10. BSE-SEM micrographs with EDS demonstrating the structural and chemical

heterogeneity of carbonate precipitates: a wheat-sheaf morphology as (a) a whole mount and

(b) a thin section, interpreted as aragonite, and as nanometer-scale granules of carbonate

precipitated on EPS in (c) a whole mount and (d) thin section. EDS spectra (e-g) demonstrate

varying Mg-content.

Figure 11. A cross-section of an embedded biofilm collected from the surface of the Sand

aquarium after eight weeks viewed using (a) optical microscopy and (b) XFM. The bright

yellow grains in (b) show the occurrence of new mineral nucleation, while the blue grains

indicate trapping-and-binding. Bright yellow regions indicate higher strontium content, while

bright blue indicates higher calcium content. XFM scan conditions: pixel size: 1×1 µm, dwell

time: 1.0 msec.

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Graphical Abstract

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