Early in Earth's history, when the planet's atmosphere lacked oxygen, life was strictly anaerobic. The first microbial metabolisms used electron acceptors such as carbon dioxide, iron(III), sulfate or elemental sulfur. The evolution of cyanobacteria and subsequent increasing oxygen concentration in the atmosphere during the Great Oxidation Event (GOE)-sometime between 2.4-2.1 billion years ago-imposed a strong selective pressure on microbes to adapt to the presence of oxygen. Some lineages evolved to respire oxygen, which offers a high energy yield but at the cost of generating harmful byproducts known as reactive oxygen species (ROS). Others remained strictly anaerobic, avoiding oxygen entirely and adapting exclusively to anaerobic habitats. Some even developed the ability to switch between the 2 modes of respiration, based on their immediate environment. In all cases, microbes had to rely on anaerobic enzymatic systems that predated the GOE and were evolutionarily honed to deal with oxygen over time.
When scientists began systematically studying microbial life, they used behavior in the presence or absence of oxygen as one way to classify the organisms. The microbes that thrived in oxygen and perished without it were deemed "obligately aerobic." Those that died when exposed to oxygen and could only grow in its absence were "obligately anaerobic." And the group of microbes capable of growing both in the presence and absence of oxygen were called facultative microbes.
This classification provided a convenient framework for understanding microbial physiology and ecology. It became widely accepted that facultative microbes would naturally prioritize aerobic respiration when oxygen was available, since this process yields the most energy, and switch to anaerobic respiration only when oxygen was depleted. This "oxygen first, anaerobic later" paradigm became deeply entrenched in microbiology.
The Classic View: Why Oxygen Comes First
The traditional hierarchy of electron acceptors in microbial respiration is rooted in thermodynamics. Electron acceptors are generally used in sequence based on their redox potential: oxygen, after all, with its high redox potential (+820 mV), yields the most energy, followed by nitrate, manganese oxides, iron(III), sulfate and CO2 in decreasing energy yields. Nitrous oxide (+1350 mV), though thermodynamically an even stronger electron acceptor than oxygen, usually acts as a transient intermediate in the denitrification pathway and is reduced to N2 when present.
This logic is further supported by biochemistry. Many key enzymes involved in anaerobic pathways are oxygen-sensitive, and ROS generated under oxic conditions can damage biomolecules. This creates a strong selective pressure for microbes to favor aerobic respiration when oxygen is available-not only because it yields more energy, but also because maintaining anaerobic machinery under oxic conditions is metabolically risky and inefficient. As a result, gene regulation in facultative microbes typically prioritizes aerobic pathways and actively represses anaerobic systems in the presence of oxygen.
Cracks in the Paradigm
Recent work suggests that certain microbes buck the trend of the "either/or" model of respiration. Four notable examples-Hydrogenobacter, Synechocystis, Shewanella oneidensis and Microbacterium deferre-demonstrate simultaneous aerobic and anaerobic respiration under conditions where oxygen is present but fluctuating.
Case 1: Hydrogenobacter, a Chemolithotroph in Hot Springs
A recent study reported a striking example of simultaneous aerobic and anaerobic respiration in Hydrogenobacter RSW1, a chemolithoautotroph isolated from Yellowstone hot springs. When provided with hydrogen (H2), elemental sulfur (S) and oxygen, Hydrogenobacter grew faster and to higher densities when it used both oxygen and sulfur as electron acceptors simultaneously, rather than relying on 1 pathway alone.
Gas chromatography confirmed concurrent oxygen consumption and sulfur reduction by Hydrogenobacter, and transcriptomic data revealed active expression of both oxygen-reducing and sulfur-reducing enzymes. Notably, this was not a transient phenomenon driven by fluctuating oxygen levels; the cells maintained this hybrid respiration as a stable strategy.
The mechanism involves a sophisticated electron transport chain with multiple [NiFe]-hydrogenases and a sulfur reductase complex (SreABC), allowing flexible channelling of electrons derived from H2 oxidation to either oxygen or sulfur reduction pathways.
Case 2: Synechocystis, a Metabolically Flexible Cyanobacterium
Another striking example comes from Synechocystis sp. PCC 6803, a cyanobacterium traditionally viewed as an obligate aerobe. Recent work demonstrated that Synechocystis can reduce Fe(III) oxides via extracellular electron transfer (EET) even under fully oxic conditions, both in the light and in the dark when glucose is supplied as a carbon source. This ability to perform EET in parallel with oxygen respiration underscores the versatility of microbial electron flow and highlights that such hybrid strategies are not confined to facultative anaerobes or heterotrophic bacteria; they can also occur in phototrophic organisms. While the current findings are from laboratory studies, it is likely that this hybrid respiration strategy also operates in natural freshwater habitats, where light availability, oxygen levels and redox conditions fluctuate daily. This flexibility may help Synechocystis maintain redox balance and iron acquisition even when photosynthetic activity is limited.
Case 3: Shewanella oneidensis-An Electroactive Hybrid
Shewanella oneidensis, a facultative anaerobe famed for its extracellular electron transfer (EET) abilities, provides another example. A recent study used microfluidic devices with oxygen sensors to monitor Fe(III) reduction by Shewanella under fully oxic conditions. Surprisingly, Fe(III) reduction occurred robustly even when oxygen remained at saturation, without evidence of localized anoxic microsites. This indicated that Shewanella cells were simultaneously performing aerobic respiration while transferring electrons to Fe(III), likely through secreted reduced flavins and outer membrane cytochromes.
The implication is profound: rather than shutting down EET machinery in the presence of oxygen, Shewanella continues to operate it in parallel-presumably balancing energy production and redox homeostasis.
Case 4: Microbacterium deferre-A Gram-Positive Pioneer
Perhaps the most intriguing case comes from Microbacterium deferre A1-JKT, a novel Gram-positive bacterium isolated from redox-dynamic freshwater sediments. These environments contain filamentous cable bacteria that create distinct oxygen, sulfide and pH gradients. In the oxic-anoxic interface of such environments, oxygen levels constantly fluctuate. In electrochemical and biochemical assays, M. deferre displayed simultaneous oxygen and Fe(III) reduction via secretion of reduced flavins mediating extracellular electron transfer.
Very surprisingly, under oxygen-saturated conditions, planktonic M. deferre cells continued reducing Fe(III)-again defying the long-held belief that microbial Fe(III) reduction is strictly anaerobic. Mechanistically, M. deferre employs a non-canonical flavin-based EET (FLEET) system involving proteins FccA and FmnA, but lacks other known FLEET components. Riboflavin was secreted as a redox shuttle even under oxic conditions, demonstrating that M. deferre A1-JK actively produces flavins even under oxic conditions to optimize its energy generation in fluctuating environments.
Why Didn't We See Simultaneous Aerobic and Anaerobic Respiration Sooner?
If simultaneous aerobic and anaerobic respiration is possible, why did microbiologists long believe otherwise? Several factors likely contributed to this oversight. Many known anaerobic enzymes are oxygen-labile, and laboratory strains are often cultivated under strictly defined "oxic" or "anoxic" conditions. Hybrid respiration was simply not tested or expected. In addition, the prevailing paradigm of gene regulation reinforced the assumption that oxygen presence strictly represses anaerobic gene expression. However, newer studies reveal more nuanced regulatory responses, including post-translational control that allows for greater metabolic flexibility.
Experimental design also played a role: many studies relied on static cultures or bulk oxygen measurements, which would have missed subtle microscale gradients or the operation of simultaneous pathways. The recent introduction of microfluidics and advanced electrochemical sensors now provide the resolution needed to detect these dynamics. Finally, in cases like sulfur or iron reduction, abiotic re-oxidation of reduced products under oxic conditions may have masked biological activity in earlier studies, or convinced the researchers that it was impossible to measure in the first place.
Why Would Microbes Simultaneously Perform Aerobic and Anaerobic Respiration?
The ability to perform simultaneous aerobic and anaerobic respiration likely offers several adaptive advantages, particularly in fluctuating environments. Maintaining some electron flow toward extracellular acceptors, such as flavins or metals, could help balance intracellular redox states and minimize the formation of ROS during aerobic respiration. Hybrid respiration also provides flexibility and resilience in environments where oxygen availability fluctuates on spatial and temporal scales, such as during the GOE and in modern sediments.
Moreover, by partitioning electrons across multiple pathways, microbes can optimize ATP yield and avoid bottlenecks in the respiratory chain. In dynamic redox niches, such as sediment oxic-anoxic interfaces, hybrid respirers can simultaneously exploit both oxygen and anaerobic electron acceptors-offering a distinct competitive edge.
Implications and Future Directions
The emerging picture of hybrid respiration has broad implications for microbial ecology, evolution and biotechnology.
Simultaneous metal reduction and oxygen respiration may reshape our understanding of iron, sulfur and carbon cycling in soils, sediments and aquatic systems. Facultative aerobes capable of hybrid respiration could dominate fluctuating redox zones, potentially explaining patterns like the persistence of metabolically versatile taxa at oxic-anoxic interfaces and the enrichment of electroactive microbes in sediments where oxygen and alternative electron acceptors coexist.
Evolutionarily, the ability to perform mixed respiration may have helped ancestral microbes survive during Earth's progressive oxygenation. The examples of Hydrogenobacter and Microbacterium suggest that this trait is ancient and may have provided a bridge from anaerobic to aerobic metabolisms during the GOE.
From a biotechnological perspective, harnessing hybrid respirers could enhance the performance of bioelectrochemical systems, improve bioremediation strategies in redox-dynamic environments and inspire synthetic biology approaches that aim to balance intracellular redox conditions.
Microbial respiration is far more versatile than once thought. The simple model of "oxygen first, anaerobic later" is giving way to a more dynamic view: in certain contexts, aerobic and anaerobic respiration can occur in parallel. The examples of Hydrogenobacter, Shewanella and Microbacterium illustrate how microbes creatively rewire their electron flows to thrive in complex environments. As tools like microfluidics, transcriptomics and advanced electrochemistry continue to mature, we are likely to uncover even more surprising facets of microbial respiration. For microbiologists, this is an exciting time to revisit old assumptions-and to explore the remarkable flexibility of the microbial world.
The journey of life on Earth, from non-living chemical compounds to early unicellular life, to the vast diversity of organisms we see today is nothing short of extraordinary. The American Academy of Microbiology report, funded by a grant from the Gordon and Betty Moore Foundation, examines the origins and trajectory of early microbial life and sheds light on what this research could mean for the future.
