TREATISE

ONLINE
Number 160

Part B, Volume 2, Chapter 7:

Microfossils of Prokaryotes (Bacteria and Archaea):
Research History, Taphonomy, and Paleobiology

Shuhai Xiao and Qing Tang

2021

Lawrence, Kansas, USA

ISSN 2153-4012
paleo.ku.edu/treatiseonline
 Microfossils of Prokaryotes 1

PART B, VOLUME 2, CHAPTER 7

MICROFOSSILS OF PROKARYOTES (BACTERIA
AND ARCHAEA): RESEARCH HISTORY, TAPHONOMY,
AND PALEOBIOLOGY
Shuhai Xiao1 and Qing Tang2
[1Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA, [email protected]; 2Department of Earth Sciences,
University of Hong Kong, Pokfulam Road, Hong Kong, China, [email protected]]

INTRODUCTION and some cyanobacteria (B enzerara &

others, 2014)—do not perform biologically
Bacteria and archaea make up the para-
controlled mineralization. Thus, the pres-
phyletic group of prokaryotes, and together
ervation of prokaryotes as fossils requires
with eukaryotes they form the three major
specific taphonomic conditions. Further-
domains of life. One can easily envi-
more, the microscopic size and simple
sion a world without eukaryotes, but it is
morphology of prokaryotic fossils means that
difficult to imagine a biosphere without
they are difficult to study because of poten-
prokaryotes. Today prokaryotes colonize
tial problems related to contamination from
virtually every corner of the surface Earth
younger microbes, conflation with abiotic
system, from human guts to oceanic gyres
structures, and convergence with eukaryotic
to hydrothermal vents. Earth is home to
microbes. Despite these challenges, there have
millions of prokaryote species (S chloss
been many reports of fossil prokaryotes since
& others, 2016), which amount to a stag-
the late ninteenth century. This chapter is an
gering number of individuals (W hitman ,
overview of fossil prokaryotes, with a focus on
C oleman , & W iebe , 1998; F lemming &
bacteria, particularly cyanobacteria, preserved
W uertz , 2019; L ocey & L ennon , 2019)
in Precambrian rocks.
and account for ~14–50% of carbon in the
biosphere (Whitman, Coleman, & Wiebe, HISTORY OF THE STUDY OF
1998; Bar-On, Phillips, & Milo, 2018). In
fact, the biochemical capability to fix carbon
BACTERIAL FOSSILS
and to produce oxygen can be evolutionarily More detailed accounts of the history of
traced to prokaryotes (cyanobacteria to be fossil prokaryote research can be found in
exact), and nitrogen fixation in nature is Fenton (1946), Banks and others (1967),
exclusively carried out by prokaryotes. Thus, Schopf (1992a), and Taylor, Taylor, and
it is safe to say that there would not be a Krings (2009). Prokaryotic fossils had been
biosphere without prokaryotes. reported in the literature by the late nine-
There are no credible reasons to doubt teenth century, although some were not
that prokaryotes were as abundant and originally identified as such, others may be
important in the geological past as they are eukaryotic, and still others were later proven
today. Yet, the fossil record of prokaryotes is abiotic. For example, the tubular microfossil
extremely poor. This poor record is largely Girvanella Nicholson & Etheridge, 1878
related to the fact that most prokaryotes— was first described as a foraminifer from
with the prominent exception of magneto- Ordovician strata but later understood as
tactic bacteria (Bazylinski & Frankel, 2003) a cyanobacterium (W ood , 1957; R iding ,

© 2021, The University of Kansas, Paleontological Institute, ISSN (online) 2153-4012

Xiao, Shuhai, & Qing Tang. 2021. Part B, Volume 2, Chapter 7: Microfossils of Prokaryotes (Bacteria and Archaea):
Research History, Taphonomy, and Paleobiology. Treatise Online 160:1–37, 9 fig., 1 table.
 Microfossils of Prokaryotes 3
hoorn & T yler , 1965; C loud , 1965). Since the 1960–1970s, paleontologists
The Gunflint fossils include stromatolite- have also been investigating Precambrian
associated coccoidal and filamentous fossils organic-walled microfossils preserved in
(Fig. 1.1) (B arghoorn & T yler , 1965), fine-grained siliciclastic rocks or shales using
as well as coccoidal planktonic microbes hydrofluoric acid maceration techniques
(Knoll, Barghoorn, & Awramik, 1978). (Xing & Liu, 1973; Timofeev, Hermann, &
These fossils were compared with extant Mikhailova, 1976; Vidal, 1976), and some
cyanobacteria, iron-oxidizing bacteria, and of these are filamentous microfossils that
fungi (Barghoorn & Tyler, 1965; Cloud, are interpreted as cyanobacteria (Hermann,
1965). Serving as a search image in the 1974). This line of research opened a new
field and in the laboratory, Gunflint-type taphonomic window onto the Precambrian
stromatolitic cherts and microfossils soon microbial world (Vidal, 1981; Hofmann &
opened the floodgates to numerous discov- Jackson, 1994; Grey, 2005; Tang & others,
eries of Precambrian microfossils. Within 2013). Together, microfossils preserved in
a decade, Precambrian microfossils had cherts and shales provide a broader view of
been reported from many Precambrian the paleoecology and taphonomy of Precam-
cherts in North America and Australia, brian microbes.
including the Neoproterozoic Bitter Springs
Formation in Australia (Fig. 1.7) (B arg - MODES OF PRESERVATION
hoorn & S chopf , 1965; S chopf , 1968; Because most prokaryotic microfossils
S chopf & B l acic , 1971), the Neopro- are preserved in cherts and shales, silicifi-
terozoic Skillogalee Dolomite in South cation and carbonaceous compression are
Australia (S chopf & B arghoorn , 1969; the main modes of preservation. However,
Knoll, Barghoorn, & Golubic, 1975), the prokaryotic microfossils can also be repli-
Neoproterozoic Beck Springs Formation in cated by phosphate, pyrite, gypsum, and
eastern California (Cloud & others, 1969), other minerals; and they have been reported
the Paleoproterozoic Belcher Supergroup in from ambers. These taphonomic modes are
Canada (Hofmann, 1974; Hofmann, 1976), briefly described below.
Archean strata in South Africa (Schopf &
SILICIFICATION
Barghoorn, 1967; Knoll & Barghoorn,
1977), and many other units. These were As a major permineralization pathway,
followed by reports of silicified microfossils, silicification is responsible for the preserva-
many of which are interpreted as cyano- tion of the majority of prokaryotic micro-
bacteria, from Precambrian cherts around fossils (Fig. 1), including those preserved
the world (see summary in Schopf, 1983; in cherts of the Gunflint Formation (Fig.
Schopf & Klein, 1992; Sergeev, Sharma, & 1.1–1.3) and Bitter Springs Group in
Shukla, 2012). Among these, Paleoarchean Australia (Fig. 1.7). Generally understood
microfossils from Western Australia are as a taphonomic process through which
the most contentious (A wramik , S chopf , organisms are replaced by diagenetic silica,
& Walter, 1983; Buick, 1984; Schopf & silicification of microbes is neither molecule-
P acker , 1987; S chopf , 1993; B rasier & by-molecule replacement of cellular struc-
others, 2002; Schopf & others, 2002). The tures by silica nor wholesale replacement
combined geochemical, paleontological, of the entire organism by silica, as some-
and sedimentological data indicate the exis- times occurs in silicification of animal skel-
tence of a microbial ecosystem on Earth at etons (Butts, 2014). Rather, at the micro-
~3500 Ma or earlier (Rosing, 1999; Schopf, scopic level, silicification is fundamentally
2006b), perhaps with diverse microbial a casting and molding process, with silica
metabolic pathways (S chopf & others, precipitating on organic substrates, such
2018). as cell walls and laminae of cyanobacterial
4 Treatise Online, number 160

20 μm 10 μm 5 μm
1 2 3

4 20 μm 5 50 μm 6 30 μm

7 20 μm 8 2 mm 9 500 μm

10 200 μm 11 200 μm 12 50 μm

Fig. 1. Thin section photomicrographs of silicified prokaryotic microfossils from the ~1880 Ma Gunflint Forma-
tion in Canada (1–3), ~1400–1500 Ma Billyakh Group in Siberia (4–5), Tonian Draken Formation in Svalbard
(6 ), Tonian Bitter Springs Group in Australia (7 ), and Tonian Jiudingshan Formation in North China (8–12).
1, Coccoidal specimens of Huroniospora Barghoorn in Barghoorn & Tyler, 1965 and filamentous specimens
of Gunflintia Barghoorn in Barghoorn & Tyler, 1965. Although Gunflintia was described as a multicellular
filament (Barghoorn & Tyler, 1965), most specimens do not preserve trichome structure and may be identified
as Siphonophycus; 2, Kakabekia Barghoorn in Barghoorn & Tyler, 1965; 3, possibly Eoastrion Barghoorn in
Barghoorn & Tyler,1965; 4, Archaeoellipsoides Horodyski & Donaldson, 1980; 5, Eoentophysalis Hofmann, 1976;
6, Polybessurus Green & others, 1987; 7, Myxococcoides Schopf, 1968; 8, stromatolites consisting of filamentous
Siphonophycus Schopf, 1968; 9–11, close-up views of Siphonophycus filaments, 9 being a magnification of 8 (dotted
line box); 12, Caryosphaeroides Schopf, 1968 in the center, with coccoidal cells arranged in tetrads and enclosed in
a common envelope. Note intracellular inclusions that were interpreted as degraded nuclei (Schopf, 1968; but see
Knoll & Barghoorn, 1975). Also note Siphonophycus filaments co-occurring with Caryosphaeroides. Fig. 1.1–1.3
and 1.7–1.12, new; Fig. 1.4–1.6 courtesy of Andrew H. Knoll, previously published as fig. 10, 2 and 17, 4 in Sergeev,
Knoll, & Grotzinger, 1995, and fig. 12, 5 in Knoll, Swett, & Mark, 1991, respectively.
 Microfossils of Prokaryotes 5
sheaths, through chemical bonds between bacterial morphology in three dimensions
organic functional groups and silicic acids (Oehler & Schopf, 1971; Westall, Boni,
(L eo & B arghoorn , 1976) and perhaps & G uerzoni , 1995; T oporski & others,
assisted by the presence of metallic ions 2002; N ewman & others, 2017). These
(F erris , F yfe , & B everidge , 1988), thus encrustation and permeation processes
producing molds or casts of microbial cells may have been facilitated or accelerated by
and sheaths. Thus, the organic substrates elevated silica concentrations in Precambrian
are encased within the replicating silica seawaters and pore waters (Maliva, Knoll,
and are subsequently degraded to various & S imonson , 2005) and photosynthetic
degrees. The taphonomic survival of the activity of cyanobacteria themselves (Moore
organic substrates, albeit in degraded forms & others, 2020). Thus, it is not surprising
and in trace amounts, aids the recognition that microbial silicification was common
and identification of these fossils in thin in Precambrian marine environments, but
section microscopy and is regarded by some as biosilification (e.g., in sponges, radiolar-
geologists as an indispensable criterion for ians, and diatoms) became more important
affirmation of biogenicity (Buick, 1990). and dissolved silica concentrations declined
A number of taphonomic experiments in Phanerozoic oceans (Conley & others,
have been carried out to understand the silic- 2017), this taphonomic mode declined in
ification process. Degradation experiments and throughout the Phanerozoic, not only
have demonstrated that cyanobacterial cells for bacterial silicification but for silicification
degrade over periods of days to months in general (S chubert , K idder , & E rwin ,
but cyanobacterial sheaths are much more 1997). Nor is it surprising that microbial
resistant and can remain recognizable over silicification is common in hydrothermal
longer time (Golubic & Barghoorn, 1977; settings (e.g., modern hot spring and Devo-
B artley , 1996). These experiments have nian Rhynie chert) where dissolved silica
been borne out by field observations showing concentrations are high.
the degraded but still recognizable cyano- Yet silicification is not ubiquitous in all
bacterial cells and sheaths in pigment-poor Precambrian marine environments. Knoll
layers of modern microbial mats (Gomes & (1985a) identified three sedimentary and
others, 2020), and they indicate that fossil geochemical factors that control microbial
mineralization must have occurred rapidly silicification: 1) sediment permeability, 2)
during early diagenesis in order to preserve silica availability in pore waters, and 3)
cellular structures. Indeed, field observations local concentration of organic matter. It is
of microbial silicification in modern hot possible that these factors can interact with
spring sinters, which are widely regarded as each other to promote silicification. For
modern taphonomic analogs of microbial example, the degradation of organic matter
silicification in Precambrian oceans, indicate (and the partial degradation of organic
that cyanobacterial and other microbes can substrates) can activate organic functional
be silicified shortly after death or even in groups, thus facilitating the nucleation
vivo (Renaut, Jones, & Tiercelin, 1998), of silica. It can also drive down local pH
and that cyanobacterial sheaths are prefer- values, thus promoting the precipitation of
entially preserved through silica encrusta- silica as the solubility of silica decreases with
tion and permeation (R enaut , J ones , & pH. These sedimentary and geochemical
T iercelin , 1998; K onhauser & others, factors mean that silicification of microbes is
2003). Mineralization experiments have also environmentally restricted. Indeed, although
demonstrated that silica and clay minerals there are notable exceptions (e.g., the
can coat on cyanobacterial sheaths, and silica Ediacaran Doushantuo Formation Zhang
can permeate cyanobacterial sheaths and & others, 1998; M u s c e n t e , H aw k i n s ,
cell walls, thus rapidly replicating cyano- & X iao , 2015), most silicified microbial
6 Treatise Online, number 160

assemblages are preserved in either peritidal and rod-shaped structures interpreted as

or hydrothermal environments (K noll , bacteria (Lamboy & others, 1994; Cosmidis
1985a; K noll , 1985b; T rewin , F ayers , & others, 2013; Pesquero & others, 2014),
& K elman , 2003). As such, silicification although some of these spherical structures
provides a limited and probably biased may be alternatively interpreted as phos-
view of the environmental and ecological phatic granules that may have been present
ranges of prokaryotic microbes (K noll , in the digestive guts of some invertebrate
1985b; Butterfield & Chandler, 1992). animals (B utterfield , 2002; H awkins &
Fortunately, this limitation is mitigated to others, 2018).
some degree by other taphonomic modes, Relative to silicification, taphonomic
such as phosphatization and pyritization that experiments of phosphatization have been less
are also known to preserve microbial fossils. successful and mostly focused on invertebrate
degradation and mineralization (Briggs &
PHOSPHATIZATION McMahon, 2016). Degradation experiments
Although a different fossil mineralization indicate that animal cells and tissues can be
process, phosphatization is mechanisti- pseudomorphed by heterotrophic microbes
cally similar to silicification, and fossilif- and microbial biofilms (Raff & others, 2008;
erous phosphorites tend to be siliceous (Yao Raff & others, 2013; Butler & others, 2015),
& others, 2005; D ong & others, 2009; thus helping to stabilize anatomical details
Sergeev, Schopf, & Kudryavtsev, 2020). to be phosphatized during subsequent fossil
Like silicification, phosphate encrustation mineralization. However, the giant sulfur
and impregnation of organic substrates are bacterium Thiomargarita Schulz & others,
key processes that are responsible for the 1999 subjected to similar experiments did
three-dimensional preservation of micro- not seem to be pseudomorphed by microbial
bial cell morphology (X iao , Z hang , & biofilms during degradation (Cunningham
Knoll, 1998; Xiao & Schiffbauer, 2009). & others, 2012). Mineralization experiments
Unlike silicification, however, the phos- thus far are limited and have only been able
phatization is largely restricted to subtidal to partially phosphatize invertebrate animals
environments (Z hang & others, 1998; (Wilby & Briggs, 1997; Martin, Briggs, &
M uscente , H awkins , & X iao , 2015) and Parkes, 2003; Hippler & others, 2011). To
occurs mostly in the Ediacaran and the our knowledge, no mineralization experi-
Phanerozoic (Schiffbauer & others, 2014a; ments have been carried out on prokaryotic
Muscente & others, 2017). Phosphatized organisms, and this represents a key gap in
cyanobacteria, for example, are best known the study of prokaryote phosphatization and
from Ediacaran-Cambrian strata, including an area for future research.
the Ediacaran Doushantuo Formation in Exceptional preservation of microbial
the South China Craton (Fig. 2) (Z hang fossils through silicification and phosphati-
& others, 1998; Y uan , X iao , & T aylor , zation depends on a delicate balance between
2005), the early Cambrian (Terreneuvian) rapid mineralization and over-mineraliza-
Yurtus Formation in the Tarim Basin of tion. Over-mineralization results in thick
northwestern China (Yao & others, 2005; mineral coats that bias and disguise micro-
Dong & others, 2009) and equivalent strata bial morphologies, making it difficult to
in the South China Craton (Wang & others, recognize mineralized microfossils in micros-
1984; D ong & others, 2009; G uo , L i , copy, particularly when organic substrates,
& Shu, 2010), and the middle Cambrian such as cell walls and sheaths are completely
(Guzhuangian) Alum Shale Formation in obliterated. This has been observed in
Sweden (C astellani & others, 2018). In modern hot spring sinters (Jones, Renaut,
addition, many Phanerozoic coprolites and & R osen , 2001; P eng & J ones , 2012)
cololites contain micrometer-sized spherical as well as phosphatized microbes in the
 Microfossils of Prokaryotes 7

1 500 μm 2 20 μm

3 20 μm 4 20 μm

Fig. 2. Phosphatized Siphonophycus filaments from the Ediacaran Doushantuo Formation in South China. 1–3,
thin section photomicrographs (new; photos taken by and courtesy of Lei Chen); 4, scanning electron microscopic
(SEM) image (new; image by Shuhai Xiao).

Ediacaran Doushantuo Formation in South the size range of tens to hundreds of nano-
China (Xiao & Schiffbauer, 2009). meters is self-suppressed or self-inhibited by
The inhibition of post-mineralization the limited formation and growth of dissolu-
recrystallization is also an integral part of tion pits, the size of which is constrained by
exceptional preservation through phos- the nanocrystal size (Tang, Nancollas, &
phatization (X iao & H ochella , 2017). Orme, 2001). This may be a fruitful area for
The successful fossilization of microscopic future exploration of phosphatization (Xiao
prokaryotic organisms, in particular, is & Hochella, 2017).
critically dependent on the maintenance
of fossilization minerals at micrometers or CALCIFICATION
even nanometers in size; this is analogous to Microbial calcification can occur as
the achievement of the highest resolution in biologically controlled in vivo intracellular
digital imaging by the smallest pixels. Excep- mineralization, biologically induced
tionally phosphatized microfossils from the in vivo extracellular mineralization, or
Ediacaran Doushantuo Formation (Fig. extrinsically induced in vivo or post-mortem
2), for example, are replicated by apatite extracellular mineralization. All three
minerals of tens to hundreds of nanometers forms of mineralization can be found in
in size (Xiao & Schiffbauer, 2009). It is not cyanobacteria. Some cyanobacteria carry
completely understood why these apatite out biologically controlled mineralization
nanocrystals were prevented from dissolu- and precipitate intracellular carbonates
tion and then recrystallization to become (C ouradeau & others, 2012; B enzerara
larger crystals. However, it is possible that & others, 2014), but thus far these cyano-
the dissolution of phosphate nanocrystals in bacterial biominerals are not known to be
8 Treatise Online, number 160

1 500 μm 2 100 μm 3 500 μm

4 50 μm 5 20 μm 6 5 μm

Fig. 3. Prokaryotic microfossils preserved in carbonate rocks. 1–2, Girvanella Nicholson & Etheridge, 1878 from
the Lower Ordovician Fenhsiang Formation at the Liujiachang section, Songzi, Hubei Province, South China; 3,
Epiphyton Bornemann, 1886 from Cambrian Stage 3, Zhangxia Formation in Laiwu, Shandong Province, North
China. Both Girvanella and Epiphyton have been interpreted as calcified cyanobacteria (Riding, 1991); 4–6, Coc-
coid microfossils, interpreted as methanogens on the basis of extremely high δ13Ccarb values up to 20‰ of the
host dolomite concretions from the Middle Permian lacustrine deposits of the Lucaogou Formation in Xinjiang,
northwestern China (Sun & others, 2020). Note two size classes in 5, representing two different taxa. 1–4 are thin
section photomicrographs and 5–6 are SEM images. Images 1–3, new; photos taken by and courtesy of Jianbo
Liu; 4–6, courtesy of Funing Sun and Wenxuan Hu, previously published as fig. 2D, 2G, and 2F, respectively, in
Sun & others, 2020.

preserved and identified in the fossil record. Microbial calcification is not uniformly
More commonly, metabolic activities of distributed across geological time, sedimen-
cyanobacteria, particularly photosynthesis tary environments, and taxonomic groups.
and carbon dioxide concentration mech- As calcification is critically dependent on
anisms, promote an increase in local pH carbonate supersaturation levels, it is not
values and induce in vivo precipitation of surprising that microbial calcification tends
calcium carbonate that impregnate the sheath to be focused on tropical shallow marine
(Riding, 2006). This form of biologically realms, for example evaporitic, peritidal,
induced mineralization results in extracellular and reefal or mud mound environments. In
sheath calcification and may be responsible addition, because various microbial metabo-
for the preservation of the majority of lisms have different impacts on the precipita-
calcified cyanobacterial fossils, such as tion and dissolution of carbonate minerals
Girvanella Nicholson & Etheridge, 1878 (Canfield & Raiswell, 1991), it is antici-
(Fig. 3.1–3.2), Epiphyton Bornemann, 1886 pated that different groups of microbes have
(Fig. 3.3), and Renalcis V ologdin , 1932. different propensities to induce calcification.
Finally, microbes can be entombed in-vivo As mentioned earlier, photosynthesis and
or postmortem in carbonate deposits (Fig. carbon dioxide concentration mechanisms of
3.4–3.6) (Kremer & others, 2012; Sun & cyanobacteria facilitate fossilization through
others, 2020)—including tufas, travertines, calcification (Riding, 2006). But calcified
and speleothems whose precipitation is cyanobacterial fossils have a non-uniform
primarily driven by abiotic processes such distribution in warm shallow marine envi-
as CO2 degassing, although it is not always ronments across geological history. Although
possible to determine whether biological they range from the Meso-Neoprotero-
processes also play a secondary role in zoic (K noll , F airchild , & S wett , 1993;
facilitating calcification (Jones & Peng, 2012; Turner, Narbonne, & James, 1993; Kah
Li & others, 2013; Jones & Peng, 2014). & R iding , 2007) to the Cenozoic (A rp ,
10 Treatise Online, number 160

100 μm
100 μm

10 μm
1 2 3
Fig. 4. Thin section photomicrographs of pyritized Siphonophycus filaments from the Ediacaran Krol Group in
northern India. 3 is magnified view of 2 (yellow dotted-line box). Note that organic sheath is largely degraded in
1 and well preserved in 2–3. All images are new and were taken by Shuhai Xiao.

produce biologically induced biominerals fine-grained siliciclastic rocks may manifest

with distinct morphologies. For example, as compressed organic-walled structures with
the iron bacteria Gallionella E hrenberg , little mineral permeation or impregnation
1838 and Mariprofundus Emerson & others, (Xiao & others, 2002; Callow & Brasier,
2007 can produce extracellular ferric-oxyhy- 2009), and these fossils can be extracted
droxide stalks that are twisted, branched, or from the rock matrix using hydrofluoric acid
organized into ribbon-like bands (Frankel digestion methods without compromising
& Bazylinski, 2003; Chan & others, 2011; their structural integrity (Fig. 6) (Tang &
Krepski & others, 2013). Morphologically others, 2013; T ang & others, 2015). In
similar stalks have also been identified in addition to carbonaceous compressions,
the fossil record and interpreted as evidence structurally recognizable organic residues of
for iron bacteria (Hofmann & others, 2008; prokaryotic microbes can also be preserved
Krepski & others, 2013; Crosby, Bailey, & in ambers (Poinar, Waggoner, & Bauer,
Sharma, 2014). 1993; Waggoner, 1994; Dörfelt, Schmidt,
& Wunderlich, 2000; Schmidt & Schäfer,
CARBONACEOUS PRESERVATION 2005). Finally, carbonaceous coccoids, fila-
Although traces of carbonaceous mate- ments, and sheets have been reported on
rial are commonly found in mineralized the basis of scanning electron microscopic
prokaryotic fossils, they are typically impreg- observation of fractured rock surface (some-
nated or penetrated by replicating minerals times after acid etching), and these have been
such as microquartz and apatite, so that interpreted as fossil microbes or as extracel-
extraction of coherent organic-walled micro- lular polymeric substances (Westall & Folk,
fossils using hydrofluoric (HF) digestion 2003; Dai, Song, & Shen, 2004; Rozanov
method is difficult. In contrast, carbona- & Astafieva, 2009; Lan & others, 2020),
ceous preservation of prokaryotic fossils in although it is a significant challenge to
 Microfossils of Prokaryotes 11

100 nm

20 nm
1 μm

1 2 3
Fig. 5. Bright-field TEM (transmission electron microscopy) images (1–2) and high-resolution TEM image (3)
of chains of straight bullet-shaped magnetite nanocrystals produced by extant magnetotactic deltaproteobacteria
(strain WYHR-1) collected from Weiyang Lake, north of Xi’an city, Shaanxi Province, North China (Li & others,
2020). Images are new and courtesy of Jinhua Li.

50 μm
1 50 μm 2

3 50 μm 4 50 μm

5 20 μm 6 10 μm

Fig. 6. Prokaryotic microfossils preserved as carbonaceous compressions in fine-grained sediments. 1, Ostiana

microcystis Hermann in Timofeev, Hermann, & Mikhailova, 1976, a possible cyanobacterium (Butterfield,
Knoll, & Swett, 1994); 2–3, Siphonophycus typicum (Hermann, 1974; transferred to the genus Siphonophycus by
Butterfield in Butterfield, Knoll, & Swett, 1994); 4–5, Polytrichoides lineatus Hermann, 1974; 6, ellipsoidal
cells of Eosynechococcus moorei Hofmann, 1976. All specimens were extracted from shale samples using hydrofluoric
acid digestion method. 1–4 are from the Tonian Liulaobei Formation in the North China Craton (Tang & others,
2013, fig. 5G, 13C, 13D, and 14A, respectively), and 5–6 are from the Tonian Gouhou Formation in the North
China Craton (Tang & others, 2015, fig. 19E and 5B, respectively). Fig. 1–5 are transmitted light photomicro-
graphs; 6 is an SEM image.
 Microfossils of Prokaryotes 13
to dated metamorphic events (B engtson syngenicity and biogenicity. He argued that
& others, 2017), or (when carbonaceous bona-fide microfossils should be observed
material is available) Raman spectroscopic in petrographic thin sections, preserved
analysis of carbonaceous material to deter- in sedimentary rocks or low-grade meta-
mine maximum metamorphic temperatures sediments, no smaller than the smallest
(S chopf & others, 2005; S chiffbauer & extant modern microbes (i.e., >0.01 μm3),
others, 2007; Javaux, Marshall, & Bekker, comprised of kerogen, part of a larger
2010). population of similar morphologies, hollow
structures, and show cellular elaborations.
BIOGENICITY Subsequently, a number of authors proposed
Biogenicity refers to the biological origin additional criteria to assess the morphology,
of the purported microfossils. It should be ontogeny, metabolism, behavior, tapho-
emphasized that, to prove biogenicity, the nomy, chemistry, and geological context of
morphologies of the microfossils must be purported microfossils (Schopf & others,
shown to be biological in origin. This is 2010; Brasier & Wacey, 2012; Rouillard
a distinction between morphological and & others, 2018; Javaux, 2019; Rouillard &
chemical biosignatures. For example, a pyrite others, 2021). For example, bona fide micro-
concretion may preserve chemical biosigna- fossils should have a stable species-specific
tures because its sulfur isotopic composi- morphology with a unimodal size distribu-
tion indicates the involvement of microbial tion and would exhibit evidence of develop-
sulfate reduction, but this by itself does not ment (e.g., cell division and development
offer evidence for a biological origin of the of branching filaments), distinct cell wall
pyrite concretion. ultrastructures, taphonomic degradation
C loud (1965, p. 27) argued that the (e.g., degradation of cytoplasm, deflation of
null hypothesis in Precambrian micropale- cell vesicles, and deformation of cell walls
ontology should be that purported micro- and sheaths), ecological interactions (e.g.,
fossils be initially regarded as abiotic in aggregations and attachment to substrates),
origin. He wrote, “... in considering what and metabolic activities (e.g., organic C and
we may accept as unequivocal Precambrian N isotope signatures, trace metal enrich-
fossils, the crucial point is not whether mate- ment) (Lepot, 2020).
rials observed might conceivably be of vital Recent exploration of ancient microfos-
origin, but whether they could have been sils have pushed the envelope beyond the
produced by non-vital processes; and, if not, preservation of organic-walled structures in
whether they are sure endemic to authentic sedimentary rocks as stipulated by B uick
Precambrian rocks.” Only after an abiotic (1990). Coccoidal, rod-shaped, and fila-
origin can be ruled out and syngenicity is mentous structures preserved in igneous
confirmed can Precambrian microfossils be rocks, sometimes with no traces of organic
accepted. This restrictive approach is neces- walls, may represent evidence for ancient
sary because of the possibility of biomorphs life, including both prokaryotes and eukary-
that are abiotic in origin but morphologi- otes (Fig. 7.1) (Bengtson & others, 2017;
cally mimic microfossils (G arcía -R uiz & Ivarsson & others, 2020). More controver-
others, 2003; Javaux, 2019) and also because sial are micrometer-sized titanite filaments
the profound ramifications of false positives or microtextures in altered volcanic glass of
in the study of Precambrian (particularly Paleoarchean pillow basalts that have been
Archean) microfossils. interpreted as bioerosional structures or trace
In early debates on putative microfos- fossils produced by chasmoendolithic and
sils from the Paleoarchean Warrawoona euendolithic microbes (Fig. 7.2) (F urnes
Group in Western Australia, Buick (1990) & others, 2004; Staudigel & others, 2006)
proposed a seven-point test to assess their and micrometer-sized hematitic tubular
 Microfossils of Prokaryotes 15
only more complex features such as spinose fission (e.g., Prochlorococcus C hisholm &
cell wall ornaments, differentiated hold- others, 1992, Synechococcus Nägeli, 1849,
fast, apical meristem, and parenchymatous Gloeocapsa, Entophysalis K ützing , 1843,
thallus are regarded diagnostic characters Chroococcus). Subsection II includes unicel-
for eukaryotes (K noll & others, 2006). lular/colonial cyanobacteria that reproduce
Cell wall ultrastructures can also be useful. by internal multiple fissions and forma-
For example, the trilaminar structure with tion baeocytes (e.g., Pleurocapsa Thuret in
two electron-dense layers around a thicker Hauck, 1885, Hyella Bornet & Flahault,
electron-tenuous layer is said to be char- 1888). Subsection III (e.g., Lyngbya Agardh
acteristic of eukaryotic cell walls (J avaux , ex Gomont, 1892b, Microcoleus Desmazières
Knoll, & Walter, 2004; Moczydłowska, ex G omont , 1892a, Oscillatoria V aucher
Schopf, & Willman, 2010), although cell ex G omont , 1892b, Spirulina T urpin ex
wall ultrastructures of modern eukaryotes Gomont, 1892b, Trichodesmium Ehrenberg
and prokaryotes have not been thoroughly ex G omont , 1892b) and Subsection IV
surveyed. Geochemical evidence can also be (e.g., Anabaena, Nostoc Vaucher ex Bornet
used to infer the prokaryotic versus eukary- & F lahault , 1886b, Calothrix A gardh
otic affinities of microfossils. For example, ex B ornet & F lahault , 1886a) are both
combined micro-FTIR (Fourier-transform characterized by uniseriate and unbranched
infrared spectroscopy) and Raman spectro- trichomes produced by binary fission in one
scopic data—that is, FTIR CH3/CH2 absor- plane, but the latter have differentiated cells
bance ratio and Raman I-1350/I-1600 ratio (e.g., specialized N2-fixing heterocysts and
of carbonaceous material—may be useful in resting akinetes). Subsection V is character-
distinguishing prokaryotic from eukaryotic ized by multiseriate or branching trichomes
microfossils (Igisu & others, 2009; Qu & produced by binary fission in more than one
others, 2015; Qu & others, 2018; Bonnev- plane, with some members having differen-
ille & others, 2020), although diagenetic tiated heterocysts (e.g., Stigonema Agardh
and thermal alteration of these parameters ex Bornet & Flahault 1886c, Fischerella).
has not been completely understood (Igisu Recent Phylogenetic analyses indicate that
& others, 2018). As another example, meth- Subsections IV and V are monophyletic
anogenic archaea can generate large carbon groups, whereas the other three are para-
isotope fractionations that can be preserved phyletic (Sánchez-Baracaldo, 2015; Schir-
in the geological record (Stueken & others, rmeister, Gugger, & Donoghue, 2015).
2017; L epot , 2020). The assignment of Cyanobacteria play a major role in modern
prokaryotic microfossils to the various ecosystems and in the global carbon and
phylogenetic and physiological groups is oxygen cycles. The cyanobacteria Prochlo-
another major challenge; but ecological, rococcus and Synechococcus are the most
morphological, and chemical comparison abundant photosynthetic organisms in
with modern prokaryotic groups can provide modern oceans, accounting for about 10%
some insights. This is discussed below for of the total ocean picoplankton cells in
selected groups of prokaryotic microfossils. the euphotic zone and responsible for as
much as 25% of ocean net primary produc-
SELECTED GROUPS tivity (Flombaum & others, 2013). A single
OF PROKARYOTIC cyanobacterial genus, Trichodesmium, is
MICROFOSSILS responsible for nearly 50% of global marine
N2 fixation (Sohm, Webb, & Capone, 2011;
CYANOBACTERIA Bergman & others, 2013). Benthic cyano-
Modern cyanobacteria consist of five bacteria are also important sedimentary
morphological groups (Castenholz, 2001). agents. They build microbial mats and stro-
Subsection I includes unicellular/colonial matolites (Stal, 2012), stabilize sediments
cyanobacteria that reproduce by binary (Noffke, 2010), and perform bioerosion and
 Microfossils of Prokaryotes 17
ular clocks give divergent results, with Basin of Mauritania in northwestern Africa
the estimated divergence time of crown- (Gueneli & others, 2018).
group cyanobacteria ranging widely from The Archean micropaleontological record
more than 3600 Ma to less than 2000 Ma, is sparse and intensely debated. Various
with very large error bars (Schirrmeister, microfossils have been reported from the
G ugger , & D onoghue , 2015; S hih & ~3400–3500 Ma Warrawoona Group and
others, 2017; see summary in D emoulin Strelley Pool Formation in Western Australia
& others, 2019; Garcia-Pichel & others, (S chopf , 2006a; S chopf , 2006b; S ugi -
2019). Stable carbon isotope signatures tania & others, 2013), and some have been
of Archean organic carbon are consistent compared with and interpreted as cyano-
with but are not uniquely diagnostic of bacteria (Awramik , S chopf , & W alter ,
cyanobacterial metabolism (D emoulin & 1983; S chopf & P acker , 1987; S chopf ,
others, 2019), although Lyons, Reinhard, 1993), although their biogenicity is a
and Planavsky (2014) argue that the total continual debate (Buick, 1984; Brasier &
organic carbon content in Archean shales others, 2002; Wacey, Eiloart, & Saunders,
presents strong evidence for oxygenic photo- 2019). More convincing Archean and early
synthesis (and perhaps cyanobacteria) before Paleoproterozoic filamentous microfossils
the Great Oxidation Event at 2320–2450 have been known from ~3235 Ma volca-
Ma (B ekker & others, 2004; H olland , nogenic massive sulfide deposit in in Sulfur
2006; Luo & others, 2016). The report of Spring Group (Rasmussen, 2000) and the
2-methylhopanoids—which were regarded 2450–2210 Ma Kazput Formation of the
as a biomarker of cyanobacteria—from the Turee Creek Group in Western Australia
~2700 Ma Jeerinah Formation in Western (Schopf & others, 2015; Fadel & others,
Australia (Brocks & others, 1999) was later 2017; B arlow & K ranendonk , 2018),
shown to be compromised by contamina- but none of these have been interpreted
tions (Rasmussen & others, 2008; French & as cyanobacterial filaments. Filamentous
others, 2015), leaving the 1.64 Barney Creek microfossils described as Siphonophycus
Formation in Western Australia as the oldest transvaalensis Beukes, Klein, & Schopf in
known unit to contain appreciable amount Klein, Beukes, & Schopf, 1987 from the
of 2-methylhopanoids (Summons & others, ~2500 Ma Gamohaan Formation and the
1999; Brocks & others, 2005). More recent ~2600 Ma Campbellrand Group of the
studies, however, have brought uncertainty Transvaal Supergroup in South Africa are
to the interpretation of 2-methylhopanoids among the oldest microfossils that have been
as a cyanobacterial biomarker; it seems that interpreted as cyanobacteria (Klein, Beukes,
2-methylhopanoids can also be produced & S chopf , 1987; A ltermann & S chopf ,
by diverse alphaproteobacteria, including 1995), but the simple morphology of Sipho-
the anoxygenic purple nonsulfur photo- nophycus (see Fig. 1.9–1.12, 2, 4, 6.2–6.3)
troph Rhodopseudomonas palustris (Rashby & means that this interpretation is open to
others, 2007) and the nitrifying bacterium scrutiny. Indeed, among the genera listed in
Nitrobacter vulgaris (Elling & others, 2020). Table 1, only Eoentophysalis (Fig. 1.5), Eohy-
Thus, it is possible that the biochemical ella, and Polybessurus (Fig. 1.6) are regarded
capability to synthesize 2-methylhopanoids as uncontested cyanobacteria (Demoulin &
may have a broader phylogenetic distribu- others, 2019), although several others are
tion and a deeper evolutionary history than likely or probable cyanobacteria when addi-
cyanobacteria. More convincing biomarker tional paleonenvironmental and taphonomic
evidence for cyanobacteria comes from conditions are considered together with
fossil porphyrins, coupled with compound- morphological features (Knoll, 2015). As
specific nitrogen isotope data, from the such, Eoentophysalis belcherensis Hofmann,
~1100 Ma El Mreïti Group in the Taoudeni 1976 from the 2015–2018 Ma Belcher
 Microfossils of Prokaryotes 21

1 2

3 4 5 cm

Fig. 9. Field photographs of representative Archean and Paleoproterozoic stromatolites. 1, possible coniform stro-
matolites (top view) from the ~3470 Ma Dresser Formation, North Pole, Western Australia (Buick, Dunlop, &
Groves, 1981); 2, Conical stromatolite (vertical cross-sectional view) from the ~3430 Ma Strelley Pool Formation in
Western Australia (Hofmann & others, 1999; Allwood & others, 2006); 3, microbial stromatolites (cross-sectional
view) from the ~2700 Ma Tumbiana Formation of the Fortescue Group in Western Australia (Awramik & Buch-
heim, 2009); 4, branching stromatolites (cross-sectional view) from the ~2450–2210 Ma Kazput Formation of the
Turee Creek Group in Western Australia (Martindale & others, 2015). All photos are new and by Shuhai Xiao.
 Microfossils of Prokaryotes 23
and crystallographic features that allow their the South China Craton as a giant sulfide-
identification in the fossil record (see Fig. 5) oxidizing bacterium analogous to the extant
(Bazylinski & Frankel, 2003; Li & others, genus Thiomargarita, but this interpretation
2020). Magnetofossils have been reported has been refuted (X iao , Z hou , & Y uan ,
from Mesozoic and Cenozoic sediments 2007; Cunningham & others, 2012).
(C hang & K irschvink , 1989; K opp &
METHANOGENS AND
Kirschvink, 2008; Roberts & others, 2011)
METHANOTROPHS
and even Precambrian stromatolites (Chang
& others, 1989). Microbial activities of methanogens in
the geological record are chiefly inferred
SULFUR-METABOLIZING MICROBES from δ 13 C data, because they produce a
Sulfur cycling in the water column and CH 4 pool extremely depleted in 13C and
sediments can be inferred from geochemical correspondingly a CO 2 pool enriched in
data. For example, sulfate reduction, sulfide
13
C (Lepot, 2020). This isotopic signal can
oxidation, and sulfur disproportionation be recorded as extremely high δ13Ccarb values
can be inferred from sulfur isotope data of carbonate sourced from the CO2 pool as
(C anfield & R aiswell , 1999; S hen & long as CH4 is effectively removed from the
Buick, 2004; Johnston & others, 2005), system (Sun & others, 2020) or as extremely
and anoxygenic photosynthesizers such negative δ13Ccarb values of carbonate related
as green and purple sulfur bacteria can to anaerobic oxidation of methane (Jiang,
be inferred from biomarker data (B rocks Kennedy, & Christie-Blick, 2003; Wang
& others, 2005). The body fossil record & others, 2008), or as extremely negative
of sulfur-metabolizing microbes is scarce, δ13Corg values of organic carbon produced
primarily because they generally do not by methanotrophs or methylotrophs in
have diagnostic morphological features. general (Stueken & others, 2017; Xiao &
Nonetheless, sulfur-metabolizing microbial others, 2017). Thus, extremely negative
fossils have been reported in the literature. δ 13C org values (as low as -57‰) from the
For example, S chopf and others (2015) ~2700 Ma Fortescue Group in Western
reported filamentous microbial communi- Australia indicate that both methanogens
ties from the Paleoproterozoic Turee Creek and methanotrophs must have evolved by
Group and Duck Creek Formation in the Neoarchean. Body fossils of metha-
Australia, and interpreted them as sulfureta notrophs or methylotrophs, however, are
in which sulfate/sulfur-reducing and sulfide- extremely rare, although S un and others
oxidizing microbes worked together to cycle (2020) recently reported micrometer-sized
sulfur species. This interpretation is based coccoidal methanogens from dolomite
on inferred community ecology and the concretions in Permian lacustrine deposits
cobweb-like microbial fabrics that are often of northwestern China. These coccoids are
found in sulfureta. It is possible that these morphologically indistinct and their inter-
microbes also recycled iron species (Fadel pretation as fossil methanogens was largely
& others, 2017). Additionally, Bailey and based on the extremely positive δ 13 C carb
others (2013) reported septate filamentous values of the host dolomite concretions.
microfossils with sparse intracellular sulfur
globules from the Ediacaran Doushantuo SUMMARY AND FUTURE
Formation and interpreted them as sulfide- PROSPECTS
oxidizing bacteria analogous to the extant Prokaryotes (bacteria and archaea) are
Beggiatoa. Finally, Bailey and others (2007) ubiquitous, abundant, and physiologically
interpreted the animal embryo-like micro- diverse. They play essential roles in modern
fossil Megasphaera Chen & Liu, 1986 from Earth systems and were likely as important
the Ediacaran Doushantuo Formation in in the geological past as they are today. Yet,
26 Treatise Online, number 160
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