Free Radical Biology and Medicine xxx (xxxx) xxx–xxx

Contents lists available at ScienceDirect

Free Radical Biology and Medicine

journal homepage: www.elsevier.com/locate/freeradbiomed

Evolution of photosynthesis and aerobic respiration in the cyanobacteria

Rochelle M. Sooa,∗, James Hempb, Philip Hugenholtza
a
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
b
Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA

ARTICLE INFO ABSTRACT

Keywords: For well over a hundred years, members of the bacterial phylum Cyanobacteria have been considered strictly
Cyanobacteria photosynthetic microorganisms, reflected in their classification as “blue-green algae” in the botanical code.
Oxygenic photosynthesis Recently, genomes recovered from environmental sequencing surveys representing two major uncultured basal
Aerobic respiration lineages (classes) of Cyanobacteria have been found to completely lack photosynthetic and CO2 fixation genes.
The most likely explanation for this finding is that oxygenic photosynthesis was not an ancestral feature of the
Cyanobacteria, and rather originated following divergence of the primary lines of descent. Here we describe
recent findings on the evolution of aerobic respiration in the non-photosynthetic cyanobacterial classes, and how
this has been interpreted by researchers interested in the evolution of oxygenic photosynthesis.

1. Introduction
The origin of oxygenic photosynthesis was a key biological event in
Earth's history, leading to the oxygenation of its surface environment
and giving rise to complex Eukaryotes [1]. Traditionally Cyanobacteria
were thought to be strictly photosynthetic, however this dogma was
challenged when environmental 16S ribosomal RNA gene surveys re-
vealed at least two major basal cyanobacterial lineages, 4C0d-2 and
ML635J-21, in a range of aphotic habitats, including rumen [2], drains
[3], termite guts [4], human guts [5], groundwater [6], a hot-spring
[7], rice paddy soil [8] and a glacier [9].
The recent ability to extract draft genomes of individual microbial
populations from metagenomic datasets (so called metagenome-as-
sembled genomes or MAGs) has provided us with a new and exciting
opportunity to examine the metabolic potential of as-yet uncultured
organisms [10], including basal cyanobacterial lineages. The first non-
photosynthetic Cyanobacteria MAG was reported in 2012 from an
aphotic anaerobic microbial community decomposing poplar wood
chips. This MAG encoded the ability for aerobic respiration, however it
contained no genes associated with photosynthesis. Unfortunately, the
authors did not address its evolutionary importance [11]. In 2013, Di
Rienzi and colleagues reported the first MAG representatives of 4C0d-2,
which they obtained from human faeces and a subsurface aquifer [12].
It was suggested that these MAGs represent a new candidate phylum
sibling to the Cyanobacteria, for which they proposed the name
Melainabacteria, after the Greek nymph of dark waters [12]. Metabolic
inference indicated that the Melainabacteria were markedly different to
the classical Cyanobacteria in that they entirely lack the ability to
perform photosynthesis, aerobic respiration and CO2 fixation [12]. In
2014, additional MAGs belonging to this lineage were obtained from
koala and human faeces, an anaerobic sludge blanket and an enhanced
biological phosphorous removal reactor [13]. Based on this analysis, it
was proposed that the Melainabacteria should be reclassified as a class
within the phylum Cyanobacteria, due to robust monophyly with
photosynthetic Cyanobacteria and shared (inferred) ancestral traits,
such as cell envelope components and circadian rhythm and light-re-
sponse regulators [13]. The latter classification has been recently sup-
ported by the Genome Taxonomy Database (GTDB), a normalised tax-
onomy based on genome phylogeny [14], and four orders are currently
defined in GTDB release 03-RS86 (Fig. 1), although MAGs representing
at least two additional orders have been reported [15]. The 2014 study
also found that MAG representatives of the Melainabacteria lack genes
for photosynthesis and CO2 fixation, but identified genes for aerobic
respiration in representatives of the Obscuribacterales, specifically
Complex III and IV [13].
In 2015, the first cultured representative of the Melainabacteria was
identified serendipitously, Vampirovibrio chlorellavorus [16], an obligate
predator of the microalga Chlorella vulgaris [17]. V. chlorellavorus had
been isolated in co-culture with its host in 1972, but erroneously clas-
sified as a member of the Deltaproteobacteria [18]. Many years later, its

Abbreviations: MAGs, metagenome assembled genomes; ETC, electron transport chain; ACIII, Alternative complex III; RCs, Reaction centres; HGT, horizontal gene
transfer; Ga, billion years ago
∗
Corresponding author.
E-mail address: r.soo@uq.edu.au (R.M. Soo).

https://doi.org/10.1016/j.freeradbiomed.2019.03.029
Received 30 October 2018; Received in revised form 5 March 2019; Accepted 26 March 2019
0891-5849/ © 2019 Elsevier Inc. All rights reserved.

Please cite this article as: Rochelle M. Soo, James Hemp and Philip Hugenholtz, Free Radical Biology and Medicine,
https://doi.org/10.1016/j.freeradbiomed.2019.03.029
R.M. Soo, et al. Free Radical Biology and Medicine xxx (xxxx) xxx–xxx

Fig. 1. Evolution of oxygenic photosynthesis and aerobic respiration in the Cyanobacteriota. A cladogram of the phylum Cyanobacteriota taken from a larger
tree of the bacterial domain based on phylogenetic inference of 120 concatenated single copy marker proteins scaled according to relative evolutionary divergence
(shown at base of figure; 0 = root of bacterial tree, 1 = extant taxa) [15]. Bootstrap resampling analyses (100 times) with maximum likelihood was performed with
FastTree [47]. Black circles represent interior nodes with ≥90% bootstrap support, grey circles ≥70% bootstrap support and white circles ≥50% bootstrap support.
Current proposed nomenclature based on GTDB [14] is shown to the right of the cladogram. Previously proposed names [12,13,25] for the same groups are shown in
parentheses. Genes for Complexes III & IV, Calvin cycle and phototrophy are distinguished by shape according to the legend at left. Different colours indicate
phylogenetically distinct versions of a given complex. Square brackets denote operon fusions, and a red “X” indicates putative loss of ETCs. PRK, phosphor-
ibulokinase. In this representation, we infer that the Cyanobacteriota were ancestrally nonphototrophic and that the class Cyanobacteriia acquired the ability for
photosynthesis after they diverged from the Vampirovibrionia. However, alternative scenarios have also been proposed (see Fig. 2). The three Cyanobacteriota classes
likely acquired aerobic respiration independently after the rise of oxygen (atmospheric oxygen is represented by a dashed green line). Figure is adapted from Soo
et al., 2017 [15].

16S rRNA gene was sequenced by the American Type Culture Collection
as part of the Living Tree Project [19], alerting researchers to its true
identity. Shotgun sequencing of V. chlorellavorus directly from lyophi-
lised cells confirmed its phylogenetic affiliation (the sole representative
of the order Vampirovibrionales, Fig. 1) and revealed a genome devoid
of photosynthetic and CO2 fixation genes, consistent with all other
known members of the Melainabacteria. However, it had a complete set
of electron transport chain (ETC) genes, including a terminal oxidase
(Complex IV), confirming its known ability to aerobically respire based
on cultivar studies [17,18,20].
The recovery of three additional representatives of the
Caenarcaniphilales in 2016 [21] identified genes encoding Complexes III
and IV, leaving the Gastranaerophilales as the only order lacking evi-
dence for aerobic respiration. Recently Utami and colleagues identified
16S rRNA genes belonging to multiple Gastranaerophilales populations
(Fig. 1) in the gut of a number of termite and cockroach species, where
they are estimated to represent up to 1.9% of the gut community [22].
A partially-complete single-cell genome from one of the Gastranaer-
ophilales populations was obtained which lacked genes required for
photosynthesis, CO2 fixation, and respiratory metabolism. While ha-
bitat and physiology supports the inference of an absence of these
metabolic traits, it should be noted that the estimated genome com-
pleteness was 61% meaning that the presence of these traits cannot be
entirely ruled out based on genomic information alone.
In 2017 [15], MAG representatives of the second basal cyano-
bacterial class identified in 16S rRNA gene surveys (ML635J-21), were
obtained from a coal bed methane well [23], an algae-associated bio-
film from a lab-scale bioreactor and subsurface groundwater [24].
Comparative genome analysis confirmed their affiliation with the Cy-
anobacteria in a lineage distinct from both classical photosynthetic
cyanobacteria and Melainabacteria, and absence of genes for photo-
synthesis and CO2 fixation. As with the Melainabacteria, some members
of the group had genes for aerobic respiration that were inferred to
have been acquired well after the divergence of the primary lines of
descent (Fig. 1 and see below). For this reason the class Sericytochromatia
was proposed, meaning “late cytochromes” [15]. Two orders belonging
to the Sericytochromatia are currently recognised in GTDB release 03-
RS86; S15B-MN24 and UBA7694 (also called GL2-53 [15]) (Fig. 1).
Recently, three additional MAGs belonging to a single species (> 95%
ANI identity between genomes) in the order UBA7694, were reported
from a deep terrestrial aquifer, for which a new candidate phylum name
was proposed, Blackallbacteria [25].
Given the current taxonomic uncertainty of the Cyanobacteria (in-
cluding the non-trivial complication that they are still classified under
the Botanical Code), we are following the GTDB classification which
uses a normalised genome-based phylogenetic framework [14], com-
bined with a recent proposal to formalise the rank of phylum [26].
Consequently, the phylum Cyanobacteria becomes Cyanobacteriota
[27], encompassing the classes Cyanobacteriia comprising all oxygenic
phototrophs (previously called Oxyphotobacteria [13,15]), Vampirovi-
brionia after the first cultured representative and replacing the Candi-
datus name Melainabacteria, and Candidatus Sericytochromatia proposed

2
R.M. Soo, et al. Free Radical Biology and Medicine xxx (xxxx) xxx–xxx

Table 1
Phylogenetic distribution of complex III and IV genes in GTDB Cyanobacteriota genomesa.
Order Number of genomes petBCa actAB coxABa ccoNO cydAB

bc-complexes ACIII A-family C-family bd oxidase

Cyanobacteriales 329 (0.45) 324 (0.98) 0 (0) 325 (0.99) 3 (0.01) 68 (0.21)
Phormidesmiales 10 (0.01) 10 (1) 0 (0) 10 (1) 0 (0) 0 (0)
Pseudophormidiales 4 (0.005) 4 (1) 0 (0) 4 (1) 0 (0) 0 (0)
Leptolyngbyales 10 (0.01) 2 (1) 0 (0) 10 (1) 0 (0) 0 (0)
Neosynechococcales 2 (0.003) 2 (1) 0 (0) 2 (1) 0 (0) 0 (0)
PCC-7407 1 (0.001) 1 (1) 0 (0) 1 (1) 0 (0) 0 (0)
Thermosynechococcales 7 (0.01) 7 (1) 0 (0) 7 (1) 0 (0) 0 (0)
Synechococcales_B 2 (0.003) 2 (1) 0 (0) 2 (1) 0 (0) 0 (0)
Synechococcales 3 (0.004) 3 (1) 0 (0) 3 (1) 2 (0.67) 1 (0.33)
Limnotrichales 3 (0.004) 3 (1) 0 (0) 3 (1) 0 (0) 0 (0)
Synechococcales_A 246 (0.34) 187 (0.76) 0 (0) 217 (0.88) 3 (0.01) 0 (0)
Gloeomargaritales 1 (0.001) 1 (1) 0 (0) 1 (1) 0 (0) 0 (0)
Pseudanabaenales 12 (0.02) 9 (0.75) 0 (0) 10 (0.83) 1 (0.08) 0 (0)
Eurycoccales 9 (0.01) 9 (1) 0 (0) 9 (1) 0 (0) 6 (0.67)
Gloeobacterales 2 (0.003) 2 (1) 0 (0) 2 (1) 0 (0) 0 (0)
Gastranaerophilales 74 (0.10) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0)
Vampirovibrionales 1 (0.001) 1 (1) 0 (0) 0 (0) 1 (1) 0 (0)
Caenarcaniphilales 4 (0.005) 3 (0.75) 0 (0) 0 (0) 1 (0.25) 0 (0)
Obscuribacterales 2 (0.003) 2 (1) 0 (0) 0 (0) 2 (1) 0 (0)
S15B-MN24 4 (0.005) 2 (0.5) 2 (0.5) 2 (0.5) 2 (0.5) 0 (0)
UBA7694 5 (0.01) 0 (0) 3 (0.6) 5 (1) 3 (0.6) 0 (0)
Total 731 582 (0.80) 5 (0.01) 613 (0.84) 18 (0.02) 75 (0.10)

a
Some genes maybe absent in incomplete Cyanobacteriota MAGs.

by Soo et al. [15], which predates Candidatus Blackallbacteria [25],
noting however, that both names lack a nomenclature type which will
need to be assigned [28] (Fig. 1).
The availability of basal Cyanobacteriota provides an opportunity to
re-evaluate the origin and evolution of oxygen associated metabolisms,
oxygenic photosynthesis and aerobic respiration, in this phylum. We
first address the evolution of aerobic respiration in these lineages and
then discuss the ongoing debate on the evolution of oxygenic photo-
synthesis within the phylum.
2. Evolution of aerobic respiration in Cyanobacteriota
ETC complexes III and IV can be used to provide insights into the
evolution of aerobic respiration in the Cyanobacteriota, as genes en-
coding these complexes are present in all three classes (Fig. 1, Table 1).
2.1. Cyanobacteriia
All members of the Cyanobacteriia share a unique cytochrome b6f
complex in addition to photosystem I, photosystem II and an A-family
oxygen reductase. Approximately 11% of genomes in this class also
contain one or more bd oxidases used in low oxygen habitats (Fig. 1,
Table 1). Phylogenetic analyses suggest that the cytochrome b6f com-
plex, the A-family oxygen reductase and potentially the bd oxidase were
acquired by the ancestor of the Cyanobacteriia after diverging from
Vampirovibrionia and Sericytochromatia. Following acquisition, the b6f
and A-family oxygen reductase genes have been predominantly verti-
cally inherited, whereas the bd oxidases appear to have been ex-
tensively, but exclusively, transferred horizontally within the Cyano-
bacteriia [15]. More recently, a C-family oxygen reductase was acquired
in the genus Synechococcus (Fig. 1 [29]) suggesting that while aerobic
respiration is well established and conserved in the Cyanobacteriia, in-
novations are still occurring.
2.2. Vampirovibrionia
Originally, it was thought that Vampirovibrionia were strictly fer-
mentative as the first set of MAGs described for this class lacked ETC
genes [12]. However, subsequently a number of Vampirovibrionia
lineages were predicted to be capable of aerobic respiration, based on
the presence of near complete gene sets for Complexes III and IV [15].
Of the four described Vampirovibrionia orders, three have re-
presentatives predicted to be capable of aerobic respiration; Vampir-
ovibrionales, Obscuribacterales and Caenarcaniphilales (Fig. 1). It was
originally thought that the Caenarcaniphilales had lost the ability for
aerobic respiration as they adapted to anoxic environments [15] but the
recovery of two additional MAGs [21] have indicated that this ability
has been retained in at least one member of the Caenarcaniphilales,
extracted from a well under high O2 conditions. The Gastranaerophilales
are found primarily in animal gastrointestinal tracts [12,13] and are
inferred to gain energy strictly via fermentation. All aerobic Vampir-
ovibrionia have a unique fused complex III-IV operon consisting of a C-
family oxygen reductase (cbb3-type) and two cytochrome bc-related
proteins, which are inferred to be ancestral to known members of the
class and subsequently lost in the Gastranaerophilales and some mem-
bers of the Caenarcaniphilales. The Obscuribacterales has an additional
fused complex III-IV operon consisting of a cytochrome bc complex and
a bd-like oxidase with a cytochrome c fused to the periplasmic side. An
unfused bd-like oxidase appears to have been independently acquired in
the Vampirovibrionales. As yet, no high oxygen-adapted reductases (A-
family oxygen reductases) have been identified in the Vampirovibrionia
suggesting that the aerobic members of the group are adapted to low-
oxygen conditions [15]. However, it should be stressed that these in-
ferences will need to be reassessed as more MAG representatives are
discovered, and as representatives are cultivated and experimentally
characterised, as activity of these partial and predicted complexes has
yet to be confirmed.
2.3. Sericytochromatia
Presently, the Sericytochromatia are represented by only seven MAGs
but they display a remarkable diversity of respiratory proteins com-
pared to other Cyanobacteriota, with an inferred ability to function in
both high and low-oxygen conditions (Fig. 1 [15]). Members of
UBA8530 have a fused Complex III-IV operon comprised of a cyto-
chrome bc1 and an A-family oxygen reductase that has highly modified
proton channels, suggesting it is unable to pump protons [15]. This
genus also contains a second cytochrome bc1 and a second (unmodified)

3
R.M. Soo, et al.
A-family oxygen reductase only distantly related to the first, and an
Alternative Complex III (ACIII) and C- family oxygen reductase. All of
these respiratory genes appear to have been acquired after UBA4093
diverged from the family UBA8530 (Fig. 1), although more re-
presentatives of these lineages are needed to refine this inference. In the
other major recognised branch of the class, order UBA7694, all mem-
bers have an ACIII and an A- and C-family oxygen reductase distinct
from those found in UBA8530. The genus GCA-002770975 also has an
additional phylogenetically distinct A-family oxygen reductase. The
presence of numerous complex III and IV genes in the Sericytochromatia
with distantly related homologues in each gene family (Fig. 1) points to
multiple independent acquisitions of aerobic respiration in this class
[15]. Given the extremely limited genomic sampling of this class to
date, it is likely that we have only glimpsed the tip of the respiratory
iceberg in the Sericytochromatia.
2.4. Comparison of cyanobacteriota ETCs
Comparison of the potential for aerobic respiration in the
Cyanobacteriia, Vampirovibrionia and Sericytochromatia indicate that
phylogenetically distinct respiratory genes are used in each class, often
involving novel combinations, particularly instances of fused Complex
III and IV genes (Fig. 1). The most parsimonious interpretation of these
data is that the ancestor of the Cyanobacteriota was not capable of
aerobic respiration and that this capability was independently acquired
in all three classes on multiple occasions following, and likely permitted
by, the rise of atmospheric oxygen [15]. However, other hypotheses
have been presented in the literature following the genomic char-
acterisation of Vampirovibrionia and Sericytochromatia. These are sum-
marised in the next section.
3. The evolution of oxygenic photosynthesis in Cyanobacteriota
There is an ongoing debate concerning the timing and mechanism of
the origin of oxygenic photosynthesis [30]. Some groups propose an
early origin (3.0–3.8 Ga) that potentially preceded the radiation of ex-
tant bacteria [31,32], whereas others argue that the origin directly
preceded the Great Oxygenation event at 2.35 Ga [15,29,30,33,34].
Cyanobacteriota is the only known phylum with members capable of
oxygenic photosynthesis via coupling of type 1 and type 2 reaction
centres. These reaction centres are found individually in anoxygenic
phototrophic members of seven other lineages, RCI in the Chlorobi,
Firmicutes and Acidobacteria, and RCII in the Proteobacteria, Chloro-
flexi, Gemmatimonadetes and most recently in candidate phylum WPS-
2 [35,36].
3.1. Current theories
There are three classes of theories concerning the evolution of
oxygenic photosynthesis in the Cyanobacteriia; the fusion, selective loss
and cyanobacterial export models [1,30]. The fusion model first pro-
posed in 1990 [37] suggests that RCI and RCII were obtained by a non-
photosynthetic cyanobacterial ancestor via horizontal gene transfer
(HGT) from two different anoxyphototrophic bacteria, although there is
no compelling evidence for which lineages developed the original re-
action centres [1]. The selective loss model posits that both RCs were
present in a single unknown photosynthetic ancestor and thereafter all
photosynthetic lineages inheriting those genes either vertically or hor-
izontally, lost either RCI or RCII with the exception of the Cyano-
bacteriia [38-40]. The export hypothesis was first proposed by Mulk-
idjanian and colleagues in 2006 [41]. They compared 15 complete
cyanobacterial genome sequences (all members of the class Cyano-
bacteriia) revealing over 1000 protein families that were core to at least
14 of them. Only a few components of the photosynthetic machinery
were represented in the anoxygenic phototrophs, suggesting that pho-
tosynthesis originated in the cyanobacterial lineage. In this hypothesis,
4
Free Radical Biology and Medicine xxx (xxxx) xxx–xxx
anoxygenic photosynthetic lineages acquired their reaction centres via
HGT from anoxygenic ancestors of the extant cyanobacteria referred to
as “procyanobacteria”. Magnabosco et al. (2018) [42] used molecular
clock analyses to explore the different scenarios using what they con-
sider to be the three most ancient phototrophic groups, the Cyano-
bacteriota, Chloroflexi and Chlorobi. They concluded that the stem
Cyanobacteriota are unlikely to be the recipient of an RCI from
Chlorobi but could still have been either the donor or recipient of RCII
proteins from the Chloroflexi prior to the rise of O2. Another molecular
clock analysis concluded that phototrophy was acquired in Chloroflexi
significantly after the Great Oxygenation Event and therefore the
Chloroflexi could not have donated photosynthetic genes to the an-
cestor of the Cyanobacteriia [43], which is consistent with unique
structural indels found in PSII and RCII [31].
3.2. Recent debate in light of discovery of basal non-photosynthetic
cyanobacterial lineages
The recent discovery of basal non-photosynthetic Cyanobacteriota
adds to the long-standing debate on how oxygenic photosynthesis
evolved in this phylum by providing potential new time constraints.
The complete absence of photosynthetic and CO2 fixation genes in the
currently available Vampirovibrionia and Sericytochromatia genomes
point to at least three possible scenarios (Fig. 2). The first posits that
RCs were acquired by the immediate ancestor of the class Cyano-
bacteriia after diverging from the other two classes (Fig. 2a) [15,30,34].
This implies that the Vampirovibrionia and Sericytochromatia were never
photosynthetic. Shih et al. [34] estimated that the Cyanobacteriia and
Vampirovibrionia diverged approximately 2.5 to 2.6 billion years ago
(Ga), before the rise of oxygen estimated at ∼2.3 Ga, and that the
crown group Cyanobacteriia postdate the rise of oxygen, diverging
∼2.0 Ga. Matheus-Carnevali et al. [44] noted that two uncultured
candidate phyla robustly affiliated with the Cyanobacteriota, the
Fig. 2. Three possible scenarios for the evolution of oxygenic photo-
synthesis in Cyanobacteriota. A. Acquisition of RCs by the Cyanobacteriia
after primary divergence of classes [15,34]. B. Acquisition of RCs by the an-
cestor of the Cyanobacteriia and Vampirovibrionia, with subsequent loss of RCs in
the Vampirovibrionia [45]. C. Acquisition of RCs prior to divergence of all three
classes, with subsequent loss of RCs in the Vampirovibrionia and Ser-
icytochromatia. Green arrows represent acquisition events and red arrows re-
present loss [45,46].
R.M. Soo, et al.
Margulisbacteria (previously known as RBX-1 or ZB3) and Sa-
ganbacteria (WOR-1), also completely lack photosynthetic and CO2
fixation genes, which they suggested further supports ancestral absence
of these traits in the Cyanobacteriota.
By contrast, Martin et al. [45] suggest that the Cyanobacteriota
ancestor was chlorophototrophic and that the classes Vampirovibrionia
and Sericytochromatia lost their photosynthetic capability (scenario
Fig. 2c) akin to the subsequent inferred loss of aerobic respiration in
some Vampirovibrionia lineages, notably the order Gastranaerophilales.
Thiel et al. [46] also suggested that it is equally possible that the
Vampirovibrionia and Sericytochromatia lost their photosynthetic capa-
city and enzymes for CO2 fixation following divergence from the Cya-
nobacteriia, although this scenario requires independent losses of these
genes in the two basal classes (Fig. 2c). A third and intermediate pos-
sibility is that the ancestor of the Cyanobacteriia and Vampirovibrionia
acquired RCs after diverging from the Sericytochromatia followed by a
subsequent gene loss in only the Vampirovibrionia (scenario Fig. 2b).
The complete absence of RC and CO2 fixation genes in the available
representatives of the basal cyanobacterial classes means that we
cannot presently rule out any of these scenarios, or even more complex
variations, highlighting the uncertainty of these ancient events. If no
photosynthetic genes or gene remnants are discovered in the non-
photosynthetic classes it may be difficult to deconvolute this aspect of
the history of photosynthesis in the Cyanobacteriota. It is, however,
unequivocal that aerobic respiration evolved independently in each of
the three classes presumably in response to rising atmospheric oxygen
(Fig. 1).
4. Conclusion
The rapid genomic elucidation of uncultured microbial lineages
through high throughput metagenomics is providing fresh perspectives
on long debated topics such as the origin of oxygenic photosynthesis
and aerobic respiration. While the current dataset does not definitively
resolve the timing and evolutionary history of these traits in the
Cyanobacteriota, it does provide additional constraints which can help
to refine hypotheses. Additional cyanobacterial MAGs will certainly
refine our emerging picture of aerobic respiration in the
Cyanobacteriota and other parts of the bacterial domain.
Acknowledgements
We thank Maria Chuvochina for etymological advice. This work was
supported by an Australian Laureate Fellowship (FL150100038) from
the Australian Research Council.
References
[1] M.F. Hohmann-Marriott, R.E. Blankenship, Evolution of photosynthesis, Annu. Rev.
Plant Biol. 62 (2011) 515–548.
[2] K. Tajima, A. Shozo, K. Ogata, T. Nagamine, H. Matsui, M. Nakmura, R.I. Aminov,
Y. Benno, Rumen bacterial community transition during adaptation to high-grain
diet, Anaerobe 6 (5) (2000) 273–284.
[3] B.Y. Smith, S.J. Turner, K.A. Rodgers, Opal-A and associated microbes from
Wairakei, New Zealand: the first 300 days, Mineral. Mag. 67 (3) (2003) 563–579.
[4] F. Warnecke, P. Luginbühl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege,
M. Cayouette, A.C. McHardy, G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe,
M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto,
A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen,
X. Zhang, M. Hernádes, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green,
C. Chang, E.M. Rubin, E.J. Mathur, D.E. Robertson, P. Hugenholtz, J.R. Leadbetter,
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding
higher termite, Nature 450 (7169) (2007) 560–565.
[5] R.E. Ley, F. Bäckhed, P. Turnbaugh, C.A. Lozupone, R.D. Knight, J.I. Gordon,
Obesity alters gut microbial ecology, PNAS 102 (31) (2005) 11070–11075.
[6] J.M. Yagi, E.F. Neuhauser, J.A. Ripp, D.M. Mauro, E.L. Madsen, Subsurface eco-
system resilience: long-term attenuation of subsurface contaminants supports a
dynamic microbial community, ISME J. 4 (1) (2010) 131–143.
[7] C. Takashima, A. Kano, T. Naganuma, K. Tazaki, Laminated iron texture by iron-
oxidizing bacteria in a calcite travertine, Geomicrobiol. J. 25 (3–4) (2008)
193–202.
5
Free Radical Biology and Medicine xxx (xxxx) xxx–xxx
[8] S. Ishii, M. Yamamoto, M. Kikuchi, K. Oshima, M. Hattori, S. Otsuka, K. Senoo,
Microbial populations responsive to denitrification-inducing conditions in rice
paddy soil, as revealed by comparative 16S rRNA gene analysis, Appl. Environ.
Microbiol. 75 (22) (2009) 7070–7078.
[9] S. Pradhan, T.N. Srinivas, P.K. Pindi, K.H. Kishore, Z. Begum, P.K. Singh,
A.K. Singh, M.S. Pratibha, A.K. Ysala, G.S. Reddy, S. Shivaji, Bacterial biodiversity
from roopkund glacier, himalayan mountain ranges, India, Extremophiles 14 (4)
(2010) 377–395.
[10] D.H. Parks, C. Rinke, M. Chuvochina, P.-A. Chaumeil, B.J. Woodcroft, P.N. Evans,
P. Hugenholtz, G.W. Tyson, Recovery of nearly 8,000 metagenome-assembled
genomes substantially revises the tree of life, Nat. Biotechnol. 2 (11) (2017)
1533–1542.
[11] D. van der Lelie, S. Taghavi, S.M. McCorkle, L.-L. Li, S.A. Malfatii, D. Monteleone,
B.S. Donohoe, S.-Y. Ding, W.S. Adney, M.E. Himmel, S.G. Tringe, The metagenome
of an anaerobic microbial community decomposing poplar wood chips, PLoS ONE 7
(5) (2012) e36740.
[12] S.C. Di Rienzi, I. Sharon, K.C. Wrighton, O. Koren, L.A. Hug, B.C. Thomas,
J.K. Goodrich, J.T. Bell, T.D. Spector, J.F. Banfield, R.E. Ley, The human gut and
groundwater harbor non-photosynthetic bacteria belonging to a new candidate
phylum sibling to Cyanobacteria, eLife 2 (2013) e01102.
[13] R.M. Soo, C.T. Skennerton, Y. Sekiguchi, M. Imelfort, S.J. Paech, P.G. Dennis,
J.A. Steen, D.H. Parks, G.W. Tyson, P. Hugenholtz, An expanded genomic re-
presentation of the phylum cyanobacteria, Genome Biol. Evol. 6 (5) (2014)
1031–1045.
[14] D.H. Parks, M. Chuvochina, D.W. Waite, C. Rinke, A. Skarshewski, P.-A. Chaumeil,
P. Hugenholtz, A standardized bacterial taxonomy based on genome phylogeny
substantially revises the tree of life, Nat. Biotechnol. 36 (2018) 996–1004.
[15] R.M. Soo, J. Hemp, D.H. Parks, W.W. Fischer, P. Hugenholtz, On the origins of
oxygenic photosynthesis and aerobic respiration in Cyanobacteria, Science 355
(6332) (2017) 1436–1440.
[16] R.M. Soo, B.J. Woodcroft, D.H. Parks, G.W. Tyson, P. Hugenholtz, Back from the
dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus,
PeerJ 3 (2015) e968.
[17] D. Coder, M. Starr, Antagonistic association of the chlorellavorus bacterium
(“Bdellovibrio chlorellavorus”) with Chlorella vulgaris, Curr. Microbiol. 1 (1) (1978)
59–64.
[18] B.V. Gromov, K.A. Mamkaeva, Electron microscopic study of parasitism by
Bdellovibrio chlorellavorus bacteria on cells of the green alga Chlorella vulgaris,
Tsitologiia 14 (2) (1972) 256–260.
[19] P. Yarza, C. Spröer, J. Swiderski, N. Mrotzek, S. Spring, B.J. Tindall, S. Gronow,
R. Pukall, H.-P. Klenk, E. Lang, S. Verbarg, A. Crouch, T. Lilburn, B. Beck,
C. Unosson, S. Cardew, E.R.B. Moore, M. Gomila, Y. Nakagawa, D. Janssens, P. De
Vos, J. Peiren, T. Suttels, D. Clermont, C. Bizet, M. Sakamoto, T. Iida, T. Kudo,
Y. Kosako, Y. Oshida, M. Ohkuma, D.R. Arahal, E. Spieck, A.P. Roeser, M. Figge,
D. Park, P. Buchanan, A. Cifuentes, R. Munoz, J.P. Euzéby, K.-H. Schleifer,
W. Ludwig, R. Amann, F.O. Glöckner, R. Rosselló-Móra, Sequencing orphan species
initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all
species with validly published names, Syst. Appl. Microbiol. 36 (1) (2013) 69–73.
[20] D. Coder, L.J. Goff, The host range of the Chlorellavorous bacterium
("VAMPIROVIBRIO CHLORELLAVORUS"), J. Phycol. 22 (4) (1986) 543–546.
[21] K. Anantharaman, C.T. Brown, L.A. Hug, I. Sharon, C.J. Castelle, A.J. Probst,
B.C. Thomas, A. Singh, M.J. Wilkins, U. Karaoz, E.L. Brodie, K.H. Williams,
S.S. Hubbard, J.F. Banfield, Thousands of microbial genomes shed light on inter-
connected biogeochemical processes in an aquifer system, Nat. Commun. 7 (2016)
13219.
[22] Y.D. Utami, H. Kuwahara, T. Murakami, T. Morikawa, K. Sugaya, K. Kihara,
M. Yuki, N. Lo, P. Deevong, S. Hasin, W. Boonriam, T. Inoue, A. Yamada,
M. Ohkuma, Y. Hongoh, Phylogenetic Diversity and Single-Cell Genome Analysis of
“Melainabacteria”, a Non-Photosynthetic Cyanobacterial Group, in the Termite Gut,
Microb. Environ. 33 (1) (2018) 50–57.
[23] D. An, S.M. Caffrey, J. Soh, A. Agrawal, D. Brown, K. Budwill, X. Dong,
P.F. Dunfield, J. Foght, L.M. Gieg, S.J. Hallam, N.W. Hanson, Z. He, T.R. Jack,
J. Klassen, K.M. Konwar, E. Kuatsjah, C. Li, S. Larter, V. Leopatra, C.L. NesbØ,
T. Oldenburg, A.P. Pagé, E. Ramos-Padron, F.F. Rochman, A. Saidi-Mehrabad,
C.W. Sensen, P. Sipahimalani, Y.C. Song, S. Wilson, G. Wolbring, M.L. Wong,
G. Voordouw, Metagenomics of hydrocarbon resource environments indicates
aerobic taxa and genes to be unexpectedly common, Environ. Sci. Technol. 47 (18)
(2013) 10708–10717.
[24] L.A. Hug, B.C. Thomas, C.T. Brown, K.R. Frischkorn, K.H. Williams, S.G. Tringe,
J.F. Banfield, Aquifer environment selects for microbial species cohorts in sediment
and groundwater, ISME J. 9 (8) (2015) 1846–1856.
[25] A.J. Probst, B. Ladd, J.K. Jarett, D.E. Geller-McGrath, C.M.K. Sieber, J.B. Emerson,
K. Anantharaman, B.C. Thomas, R.R. Malmstrom, M. Stieglmeier, A. Klingl,
T. Woyke, M.C. Ryan, J.F. Banfield, Differential depth distribution of microbial
function and putative symbionts through sediment-hosted aquifers in the deep
terrestrial subsurface, Nat. Microbiol. 3 (2018) 328–336.
[26] A. Oren, M.S. da Costa, G.M. Garrity, F.A. Rainey, R. Rosselló-Móra, B. Schink,
I. Sutcliffe, M.E. Trujilllo, W.B. Whitman, Proposal to include the rank of phylum in
the International Code of Nomenclature of Prokaryotes, Int. J. Syst. Evol. Microbiol.
65 (11) (2015) 4284–4287.
[27] W.B. Whitman, A. Oren, M. Chuvochina, M.S. da Costa, G.M. Garrity, F.A. Rainey,
R. Rossello-Mora, B. Schink, I. Sutcliffe, M.E. Trujillo, S. Ventura, Proposal of the
suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in
the International Code of Nomenclature of Prokaryotes’, Int. J. Syst. Evol.
Microbiol. 68 (2018) 967–969.
[28] M. Chuvochina, C. Rinke, D.H. Parks, M. S Rappé, G.W. Tyson, P. Yilmaz,
R.M. Soo, et al.
W.B. Whitman, P. Hugenholtz, The importance of designating type material for
uncultured taxa, Sys. Appl. Microbiol. 42 (1) (2019) 15–21.
[29] G. Schmetterer, The Respiratory Terminal Oxidases (RTOs) of Cyanobacteria
Cytochrome Complexes: Evolution, Structures, Energy Transduction, and
Signalling, (2016), pp. 331–355.
[30] W.W. Fischer, J. Hemp, J.E. Johnson, Evolution of oxygenic photosynthesis, Annu.
Rev. Earth Planet Sci. 44 (2016) 647–683.
[31] S.A. Crowe, L.N. Døssing, N.J. Beukes, M. Bau, S.J. Kruger, R. Frei, D.E. Canfield,
Atmospheric oxygenation three billion years ago, Nature 501 (2013) 535–538.
[32] T. Cardona, P. Sanchez-Baracaldo, W.W. Rutherford, A. Larkum, Molecular evi-
dence for the early evolution of photosynthetic water oxidation, BioRxiv (2017)
109447.
[33] L.M. Ward, J.L. Kirschvink, W.W. Fischer, Timescales of oxygenation following the
evolution of oxygenic photosynthesis, Orig. Life Evol. Biosp. 46 (1) (2016) 51–65.
[34] P.M. Shih, J. Hemp, L.M. Ward, N.J. Matzke, W.W. Fischer, Crown group
Oxyphotobacteria postdate the rise of oxygen, Geobiology 15 (1) (2017) 19–29.
[35] T. Cardona, A fresh look at the evolution and diversification of photochemical re-
action centers, Photosyn. Res. 126 (1) (2015) 111–134.
[36] H. Holland-Moritz, J. Stuart, L.R. Lewis, S. Miller, M.C. Mack, S.F. McDaniel,
N. Fierer, Novel bacterial lineages associated with boreal moss species, Environ.
Microbiol. 20 (7) (2018) 2625–2638.
[37] P. Mathis, Compared structure of plant and bacterial photosynthetic reaction cen-
ters. Evolutionary implications, Biochim. Biophys. Acta 1018 (2-3) (1990) 163–167.
[38] J.M. Olson, The Evolution of Photosynthesis, Science 168 (3930) (1970) 438–446.
Free Radical Biology and Medicine xxx (xxxx) xxx–xxx
[39] J.M. Olson, B.K. Pierson, Origin and evolution of photosynthetic reaction centres,
Orig. Life 17 (3-4) (1987) 419–430.
[40] T. Cardona, Photosystem II is a chimera of reaction centers, J. Mol. Evol. 84 (2-3)
(2017) 149–151.
[41] A.Y. Mulkidjanian, E.V. Koonin, K.S. Makarova, S.L. Mekhedov, A. Sorokin,
Y.I. Wolf, A. Dufresne, F. Partensky, H. Burd, D. Kaznadzey, R. Haselkorn,
M.Y. Galperin, The cyanobacterial genome core and the origin of photosynthesis,
PNAS 103 (35) (2006) 13126–13131.
[42] C. Magnabosco, K.R. Moore, J.M. Wolfe, G.P. Fournier, Dating phototrophic mi-
crobial lineages with reticulate gene histories, Geobio 16 (2) (2018) 179–189.
[43] P.M. Shih, W.M. Ward, W.W. Fischer, Evolution of the 3-hydroxypropionate bicycle
and recent transfer of anoxygenic photosynthesis into the Chloroflexi, PNAS 114
(40) (2017) 10749–10754.
[44] P.B. Matheus-Carnevali, F. Schulz, C.J. Castelle, R. Kantor, P. Shih, I. Sharon,
J. Santini, M. Olm, Y. Amano, B.C. Thomas, K. Anantharaman, D. Burstain,
E.D. Becraft, R. Stepanauskas, T. Woyke, J.F. Banfield, Hydrogen-based metabolism
as an ancestral trait in lineages sibling to the Cyanobacteria, Nat. Comm. 10 (2019)
463.
[45] W.F. Martin, D.A. Bryant, J.T. Beatty, A physiological perspective on the origin and
evolution of photosynthesis, FEMS Microbiol. Rev. 42 (2) (2018) 205–231.
[46] V. Thiel, M. Tank, D.A. Bryant, Diversity of chlorophototrophic bacteria revealed in
the omics era, Annu. Rev. Plant Biol. 69 (2018) 21–49.
[47] M.N. Price, P.S. Dehal, A.P. Arkin, FastTree 2 – approximately maximum-likelihood
trees for large alignments, PLoS ONE 5 (3) (2010) e9490.