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Environmental biotechnologies can make water pollutants part of the path to mitigating climate change


To slow and ultimately reverse global climate change, society needs to replace fossil sources of energy and chemicals with renewable forms. Environmental biotechnologies, which utilize microbial communities that can provide human society with sustainability services, can play key roles towards this goal in two ways that are the focus of this perspective. First, technologies that employ anaerobic microbial communities can produce renewable, carbon-neutral energy by transforming the energy contained in the organic matter in wastewaters to methane gas, hydrogen gas, or organic chemicals used in the chemical industry. High-strength organic wastewaters are common from many facets of our systems of food supply: e.g., animal farms, food processing, uneaten food, and biosolids from sewage treatment. While anaerobic digestion of sewage biosolids is a long-standing method for making renewable methane, new, more-advanced environmental biotechnologies are making energy-generating anaerobic treatment more reliable and cost-effective for treating the wide range of organics-bearing wastewaters and for producing output with greater economic benefit than methane. Second, photovoltaic, wind, battery, and catalytic technologies require large inputs of critical ninerals and materials: e.g., Rare Earth Elements, Platinum Groups Metals, gold, silver, lithium, copper, and nickel. Environmental biotechnologies can create new, renewable sources of the critical materials by recovering them from wastewaters from mining, ore-processing, refining, and recycling operations. When provided with hydrogen gas as an electron donor, anaerobic bacteria in biofilms carry out reduction reactions that lead to the formation of nanoparticles that are retained in the biofilm and can then be harvested to serve as feedstock for the photovoltaic, wind, battery, and catalytic technologies. This perspective describes both ways in which environmental biotechnologies will help society achieves it sustainability goals.

Pressing challenges and an opportunity

While humans in the 21st Century face many pressing challenges, the one that is the most pervasive and, perhaps, most difficult to overcome is slowing and eventually reversing the buildup of greenhouse gases in the Earth’s atmosphere [1]. Not meeting the challenge will mean that humans will endure the increasingly catastrophic effects of global climate change. The most important step will be replacing fossil sources of fuel and organic chemicals in ways that ensure energy and economic security.

Replacing fossil sources will demand large investments in photovoltaic, wind, battery, and catalytic technologies that are carbon-neutral or -negative. Those technologies will require large inputs of Critical Minerals and Materials (CMM) that already are in short supply [2]: Rare Earth Elements (REE), Platinum Groups Metals (PGM), gold, silver, lithium, copper, and nickel. Thus, the corollary challenge is to develop new and renewable sources for CMM.

An important new source of renewable fuels, chemicals, and CMM can be wastewaters that contain pollutants that can become tomorrow’s renewable resources. Here, I propose that environmental biotechnology presents an opportunity for recovering renewable fuels, chemicals, and CMM from wastewaters. I define environmental biotechnology as forming partnerships with microbial communities so that they provide human society with sustainability services [3]. Environmental biotechnology is a “win-win” strategy: Human society becomes more sustainable, while the microbial communities gain a “great microorganism life.”

Converting organic pollutants to renewable methane gas

Organic pollutants embed renewable energy in their carbon. The measure of the energy potential is the Chemical Oxygen Demand (COD), which represents electron equivalents that can be transferred from the original organic materials into a chemical form readily used in human society. Two prime examples of readily usable products are methane gas (CH4) and hydrogen gas (H2), and this section addresses CH4.

Waste streams with significant concentrations of organics are plentiful. Most of these waste streams stem from our agriculture and food system: e.g., animal manures, food- and beverage-processing wastewaters, wasted food, human sewage, and the biosolids generated from treating these wastewaters. Today, only a tiny fraction of the energy potential in the wastewaters is being realized, because the anaerobic processes that convert COD to CH4 or H2 are perceived as too expensive, large, and unreliable. However, recent science and technology advances are turning that perception upside-down by making modern anaerobic treatment less expensive, smaller, and more reliable than conventional approaches.

The conversion of organic matter to CH4 gas, i.e., methanogenesis, has been used for many decades to treat sludges at wastewater treatment facilities [4,5]. The conventional approach treats a slurry of organic solids in a large, well-mixed anaerobic digester [3,6,7]. Anaerobic microbial communities hydrolyze the organic solids to soluble organics that are then fermented in multiple steps to form CH4, which bubbles out of the liquid and can be used to replace fossil natural gas [3,7,8]. Due to the needs to hydrolyze the input solids and to retain slow-growing methanogens, conventional anaerobic digesters have large volumes: e.g., hydraulic retention times of at least 15 days and often much longer [3,7]. Although methanogenesis is well-established, its characteristics lead to the well-known drawbacks: large and expensive reactors that are subject to upsets that compromise performance [3,7,9,10].

Fortunately, several advanced processes for producing CH4 are overcoming the cost, size, and performance limitations. The advanced processes employ one or more of three innovations: pre-treatment to make the organic solid more rapidly hydrolyzed, filtration membranes to remove all solids from the effluent, and biofilm carriers to accumulate more biomass per reactor volume.

The first innovation is pre-treatment of the wastewater to make the organic solids more rapidly biodegradable. Thermal, mechanical, electro-mechanical, acid, and enzymatic methods disrupt the physical and chemical structures of the organic solids, which accelerates their hydrolysis and increases the fraction of the organic matter that is converted to CH4 [11,12]. As illustrated in Fig 1, these solids-treatment methods mimic the mechanisms humans use to make their food more digestible: cutting and chewing, cooking, and enzymes and low pH in the stomach. A key concern for any pre-treatment technology is whether its energy and financial costs are exceeded by its benefits from more solid destruction and CH4 production.

Fig 1. Analogies of biosolids pre-treatment to how humans prepare and digest food.

The most common pre-treatment today is a heat treatment, such as the Cambi process, which uses heat (150–165°C), steam pressurization in a closed reactor, and rapid decompression to disrupt the solids and accelerate hydrolysis [12]. Cambi clearly can increase the rates of solids hydrolysis and conversion to CH4, but the heating and pressurization incur energy costs, which may challenge the process’s overall sustainability. In addition, heat treatment can release toxins that inhibit methanogenesis and that may increase the level of hazardous organic molecules in the output biosolids [13,14].

Other pre-treatment methods have proven to offer substantial net benefits. For example, a full-scale trial of the Pulsed Electric Field (PEF) technology (an electro-mechanical approach) provided a 60% increase in CH4 production from thickened primary plus activated sludge, which led to an increase in energy output that was 2.7- to 5.2-fold the energy input and a payback period of 3 years [11]. Laboratory testing also demonstrated an 80% increase in CH4 generation from pig manure and a 100% increase with waste activated sludge [15].

The second innovation is employing filtration membranes to removal all solids from the effluent, creating an Anaerobic Membrane BioReactor (AnMBR) [1618]. The AnMBR is derived from the aerobic MBR (AeMBR), which is now well-established for aerobic treatment of low-strength wastewaters, such as domestic sewage, particularly for small installations [1921]. AeMBRs and AnMBRs share certain features. In particular, perfect solids removal by the membranes can make the solids retention time (SRT) much greater than the HRT, which enhances hydrolysis of organic solids, retains slow-growing microorganisms (e.g., methanogens in an AnMBR), and increases the concentration of the mixed-liquor suspended solids (MLSS), which makes the reactor smaller and less expensive. The major difference between the AnMBR and the AeMBR is supplying oxygen gas (O2). The AeMBR must be vigorously aerated to provide O2 for aerobic respiration and to minimize fouling of the membranes; vigorous aeration is energy consuming, which is a well-known drawback of AeMBRs. In contrast, the AnMBR excludes O2 and produces CH4 gas, making it a net energy producer.

While still a relatively new technology, the AnMBRs is in full-scale practice. By using anaerobic metabolism, the AnMBR accentuates the benefits of solids retention and a long SRT. On the one hand, anaerobic microorganisms have much lower biomass yields than do aerobic microorganisms [3], which means that very long SRTs can be obtained while still having a realistic MLSS concentration. On the other hand, realistic MLSS concentrations in AeMBRs are limited by O2 delivery [3], which is not relevant for an AnMBR. Thus, AnMBRs can operate with large SRT/HRT ratios that lead to relatively short HRTs and small reactor volumes. Perfect solids removal and retention of slow-growing methanogens also lead to reliably good effluent quality and CH4 generation in AnMBRs, compared to anaerobic reactors without membranes.

The main challenge of the AnMBR (like all MBRs) is fouling of the membranes by the accumulation of solids and biofilm on the membrane, which leads to excessive pressure drops across the membranes. Fouling by a cake layer may be accentuated in AnMBRs as the MLSS concentration is increased, which means that means to minimize or reverse cake formation are essential. The simplest means to mitigate cake fouling is to sparge biogas into the membrane modules to dislodge excess solids accumulation [1618].

The third innovation is adding mobile biofilm carriers, which enhance the retention of slow-growing microorganisms; adding biofilm carriers creates an Anaerobic Moving Bed Biofilm Reactor (AnMBBR). Aerobic MBBRs (AeMBBRs) are well-established (e.g, [22,23]), and the AnMBBR has gained interest more recently (e.g., [2428]). The carriers, which usually are made of light-weight plastic, are held in the reactor by screens; the right side of Fig 2 shows two examples of mobile biofilm carriers. The carriers retain most biomass, especially the slow-growing methanogens in an AnMBBR, which keeps the concentration of suspended biomass low. Thus, a main advantage of the AnMBBR is that biofilm accumulation on the carriers increases the allowable biomass density in the reactor, but without having a high MLSS concentration.

Fig 2. Examples of AnBfMBRs.

(Left) The two-stage SAF MBR using granular activated carbon as the biofilm carrier in both stages [29]. (Right) An AnBfMBR with mobile plastic carriers and ceramic membranes.

The ultimate strategy is to combine membranes and mobile carriers to form an Anaerobic Biofilm Membrane BioReactor (AnBfMBR); Fi 2 illustrates two types of AnBfMBfRs. A particularly good example of an AnBfMBR is the Staged Anaerobic Fluidized Membrane BioReactor (SAF-MBR), which was developed in South Korea by Professors Perry McCarty and Jaeho Bae [2933]. As shown on the left side of Fig 2, the SAF MBR includes granular activated carbon (GAC, ~ 1.1-mm diameter) as a fluidized biofilm carrier in both stages, with membranes in the second stage. Large-scale testing with domestic wastewater documented that the SAF-MBR’s effluent could meet secondary-treatment standards and minimize energy inputs for treatment. A major advantage of the SAF-MBR is that the fluidized GAC particles naturally scour solids from the membrane surface, which helps maintain a low pressure drop for permeate flow. A drawback is that the GAC abrades the polymeric membranes, leading to the need to replace the membranes [34].

The right side of Fig 2 shows another AnBfMBR configuration, one in which plastic carriers accumulate biofilm, while the membranes are made of ceramic material that resists abrasion from the mobile carriers [35]. Most of the methanogens reside on the carriers, while most of the fermenting bacteria and their hydrolytic enzymes are in suspension. Techno-economic analysis indicates that this form of the AnBfMBR optimizes COD conversion to CH4 and minimizes reactor size and levelized treatment costs for high-COD wastewaters.

Converting organic pollutants to renewable hydrogen gas

Hydrogen gas (H2) is an even more valuable energy feedstock than CH4, because it has multiple uses as a reductant in industry, powers fuel cells and rockets, and drives reduction of many oxidized contaminants [3638]. Because of this wide usefulness, H2 has economic value that is 2.5- to 10-fold greater than CH4 on a per-electron basis.

Almost all H2 used today comes from reforming fossil natural gas, but environmental biotechnologies can produce renewable H2 from organic waste streams in two ways. First, renewable H2 can be produced indirectly by reforming the CH4 generated in any of the methanogenic processes (e.g., [39,40]). Second, H2 can be produced directly using a Microbial Electrolysis Cell (MEC). As illustrated in Fig 3, simple organic molecules produced by fermentation of waste-stream organics are oxidized by bacteria that live as a biofilm on the anode of an electrochemical cell [3,4144]. These anode-respiring bacteria transfer the electrons to the anode through their unique extracellular electron transport. The electrons then move through an electrical circuit to the cathode of the electrochemical cells, where they reduce H+ (from the anode or H2O) to form H2 gas that bubbles out of solution. MECs still are in the research-and-development stage, but they offer great potential for directly converting waste organics to renewable H2 gas.

Fig 3. Simplified schematic of a microbial electrolysis cell (MEC).

Simple organic molecules (shown as CH2O) are oxidized to CO2, electrons (e-), and protons (H+) by a biofilm of anode-respiring bacteria (ARB) on the anode. The electrons move to the cathode though an electrical circuit, protons or other cations move to the cathode through an ion-exchange membrane, and protons and electrons combine to generate H2 gas at the cathode.

Converting organic pollutants to renewable organic chemicals

Organic acids and alcohols can be produced in fermentations that exclude methanogens, usually by maintaining a low pH. While fermentation of defined feedstock (e.g., sugars) is mature [45], fermentation of organics in waste streams is much more difficult [46], because the input material is heterogeneous and comes with microbial “contaminants.” Fermentation today often produces ethanol, but interest is growing in fermentations to carboxylic acids [47], which are important industrial feedstock.

An important trend in carboxylate fermentation is microbial chain elongation (MCE), in which short-chain organic acids are increased in chain length (and economic value) by reversing b-oxidation [4852]. Here are three examples of chain elongation:

C1 to C3


C2 to C4


C4 to C6


Carboxylic acids with longer chain lengths are easier to separate and also have higher economic value per carbon [51,53,54]. One trend to notice in the three examples is that chain elongation is a reduction process, which means that delivering an electron donor, such as H2 (shown here) or an alcohol, can upgrade the chain length and value of the organic products [52,55,56].

Recovering CMM by bioreduction

Many industries generate wastewater streams that contain CMM in chemical forms that are water pollutants: e.g., mining, ore processing, refining, and metals recycling [57,58]. Most of the CMM in the wastewater streams are oxyanions, which means that they are bonded to oxygen (O) and present as water-soluble anions. Performing bioreductions, certain bacteria are able to convert the CMMs to chemical forms that are insoluble, recoverable, and valuable [5961].

An important example of this kind of bioreduction is the PGMs (Pt, Pd, Rh, Ru, Ir, and Os), along with gold (Au) and silver (Ag). Certain bacteria, utilizing these oxyanions as respiratory electron acceptors, form elemental nanoparticles that are retained in the extracellular polymer substances (EPS) that surround the bacteria [6163]. This mechanism is illustrated in the top part of Fig 4 when the electron donor is H2 gas. The valuable nanoparticles are recovered by periodically harvesting some of the biofilm and become renewable feedstock to metals refiners.

Fig 4.

Illustrations of how the H2-based Membrane Biofilm Reactor (MBfR) enables reductions of valuable nano-particles, which are identified by boldface on the right side of the reactions: (top) Reduction and deposition of elemental PGM nanoparticles, with Pd and Rh as examples. This mechanism works for all the PGM, as well as for gold and silver. (bottom) Reduction of sulfate to produce sulfide that creates REE-sulfide nanoparticles, with Nd and Dy as examples. The graphics were created by Dr. Chen Zhou.

The second important example pertains to REE (e.g., Y, La, Dy, and Nd), lithium (Li), copper (Cu), and nickel (Ni), which precipitate with carbonate (CO32-), hydroxide (OH-), or sulfide (S2-) produced by sulfate-reducing bacteria (SRB) [64,65]. As illustrated for sulfide in the lower part of Fig 4, with H2 as the electron donor, the metal-sulfides become nanoparticles that are retained in the EPS. They also are recovered with periodic biofilm harvesting.

A successful environmental biotechnology for bioreduction has two features. First, it delivers an electron donor that the bacteria can use while respiring the CMM or sulfate. An ideal choice is H2 gas, which can be produced in a renewable form by the methods described above and works as an electron donor for sulfate and all the PGM plus gold and silver. Second, the technology must provide excellent biomass retention, because the capable bacteria are autotrophs (fix CO2 as their carbon source and grow slowly [3,61,62]. The H2-based Membrane Biofilm Reactor (MBfR) is ideal in this setting, since it delivers H2 directly to a biofilm living on the gas-transfer membranes that deliver the H2 [44,6163,6668]. Due to those advantages, the H2-based MBfR setting is illustrated in Fig 4, and Precient Technologies ( is commercializing the MBfR for this application.


Emerging today are innovative environmental biotechnologies that can generate renewable energy, organic chemicals, and CMM nanoparticles from wastewater streams. Examples described here are the AnMBR, AnMBBR, and AnBfMBR to generate CH4; the MEC to generate H2; MEC to produce medium-chain carboxylic acids; and the MBfR to recover valuable metals. All will be essential as human society moves away from fossil sources with the goal of mitigating global climate change.


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