Microbial electroactive biofilms dominated by Geoalkalibacter spp. from a highly saline-alkaline environment

Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.

High rates of nitrogen removal in aerated VFCWs treating sewage through C-N-S cycle

The efficiency of deep aerated vertical flow constructed wetlands (DA-VFCWs) being operated in Hyderabad, India, was evaluated herein using physicochemical analysis and 16S rRNA amplicon sequencing. The results showed 2-4-fold higher removal rate coefficients for Biochemical oxygen demand (1.32---3.53 m/d) and nitrogen (0.88--1.36 m/d) in DA-VFCWs than those of passive VFCWs. Elevated sulfate concentration in the DA-VFCWs effluent (84-113 mg/L) indicated possibility of sulfur-driven autotrophic denitrification (SDAD) as a major pathway operating in these wetlands besides the classical nitrogen removal pathways. The presence of nitrifiers (3.09-10.02 %), heterotrophic and aerobic denitrifiers (0.79-0.83 %), anammox bacteria (1.31-2.22 %) and SDAD bacteria (0.08-0.73 %) in the biofilm samples collected from the DA-VFCWs exemplify an interplay of Carbon-Nitrogen-Sulfur cycles in these systems. If proven, the presence of an operational SDAD pathway in DA-VFCWs can help reduce surface area requirement in VFCWs substantially besides alleviating biological clogging of the wetland substrate.

Towards a new understanding of bioelectrochemical systems from the perspective of microecosystems: A critical review

Bioelectrochemical system (BES) holds promise for sustainable energy generation and wastewater treatment. The microbial communities, as the core of BES, play a crucial role in its performance, thus needing to be systematically studied. However, researches considering microbial communities in BES from an ecological perspective are limited. This review provided a comprehensive summary of the BES with special emphasis on microecological principles, commencing with the dynamic formation and succession of the microbial communities. It also clarified the intricate interspecies relationships and quorum-sensing mechanisms regulated by dominant species. Furthermore, this review addressed the crucial themes in BES-related researches on ecological processes, including growth patterns, ecological structures, and defense strategies against external disturbances. By offering this novel perspective, it would contribute to enhancing the understanding of BES-centered technologies and facilitating future research in this field.

Halo-alkaliphilic microbes as an effective tool for heavy metal pollution abatement and resource recovery: challenges and future prospects

The current study presents an overview of heavy metals bioremediation from halo-alkaline conditions by using extremophilic microorganisms. Heavy metal remediation from the extreme environment with high pH and elevated salt concentration is a challenge as mesophilic microorganisms are unable to thrive under these polyextremophilic conditions. Thus, for effective bioremediation of extreme systems, specialized microbes (extremophiles) are projected as potential bioremediating agents, that not only thrive under such extreme conditions but are also capable of remediating heavy metals from these environments. The physiological versatility of extremophiles especially halophiles and alkaliphiles and their enzymes (extremozymes) could conveniently be harnessed to remediate and detoxify heavy metals from the high alkaline saline environment. Bibliometric analysis has shown that research in this direction has found pace in recent years and thus this review is a timely attempt to highlight the importance of halo-alkaliphiles for effective contaminant removal in extreme conditions. Also, this review systematically presents insights on adaptive measures utilized by extremophiles to cope with harsh environments and outlines the role of extremophilic microbes in industrial wastewater treatment and recovery of metals from waste with relevant examples. Further, the major challenges and way forward for the effective applicability of halo-alkaliphilic microbes in heavy metals bioremediation from extremophilic conditions are also highlighted.

Mechanistic insights into the response of electroactive biofilms to Cd2+ shock: bacterial viability and electron transfer behavior at the cellular and community levels

Electroactive biofilms (EABs) play a crucial role in environmental bioremediation due to their excellent extracellular electron transfer (EET) capabilities. However, Cd2+ can have toxic effects on the electrochemical performance of EABs, and the comprehensive inhibition mechanism of EABs in response to Cd2+ shock remains elusive. This study indicated that Cd2+ shock significantly reduced biomass and increased oxidative stress in EABs at the cellular level. The bacterial viability of EABs in phase III under 0.5 mM Cd2+ shock (EABCd2+-III0.5) decreased by 16.31% compared to EABCK-III. Moreover, intracellular NADH, c-Cyts, and the abundance of electroactive species were essential indicators to evaluate EET behavior of EABs. In EABCd2+-III0.5, these indicators decreased by 26.32%, 33.40%, and 20.65%, respectively. Structural equation modeling analysis established quantitative correlations between core components and electrochemical activity at cellular and community levels. The correlation analysis revealed that the growth and electron transfer functions of EABs were predictive indicators for their electrochemical performance, with standardized path coefficients of 0.407 and 0.358, respectively. These findings enhance our understanding of EABs' response to Cd2+ shock and provide insights for improving their performance in heavy metal wastewater.

Retracted: The bidirectional extracellular electron transfer process aids iron cycling by Geoalkalibacter halelectricus in a highly saline-alkaline condition

Bidirectional extracellular electron transfer (EET) is crucial to upholding microbial metabolism with insoluble electron acceptors or donors in anoxic environments. Investigating bidirectional EET-capable microorganisms is desired to understand the cell-cell and microbe-mineral interactions and their role in mineral cycling besides leveraging their energy generation and conversion, biosensing, and bio-battery applications. Here, we report on iron cycling by haloalkaliphilic Geoalkalibacter halelectricus via bidirectional EET under haloalkaline conditions. It efficiently reduces Fe3+ oxide (Fe2O3) to Fe0 at a 0.75 ± 0.08 mM/mgprotein/d rate linked to acetate oxidation via outward EET and oxidizes Fe0 to Fe3+ at a 0.24 ± 0.03 mM/mgprotein/d rate via inward EET to reduce fumarate. Bioelectrochemical cultivation confirmed its outward and inward EET capabilities. It produced 895 ± 23 µA/cm2 current by linking acetate oxidation to anode reduction via outward EET and reduced fumarate by drawing electrons from the cathode (‒2.5 ± 0.3 µA/cm2) via inward EET. The cyclic voltammograms of G. halelectricus biofilms revealed redox moieties with different formal potentials, suggesting the involvement of different membrane components in bidirectional EET. The cyclic voltammetry and GC-MS analysis of the cell-free spent medium revealed the lack of soluble redox mediators, suggesting direct electron transfer by G. halelecctricus in achieving bidirectional EET. By reporting on the first haloalkaliphilic bacterium capable of oxidizing and reducing insoluble Fe0 and Fe3+ oxide, respectively, this study advances the limited understanding of the metabolic capabilities of extremophiles to respire on insoluble electron acceptors or donors via bidirectional EET and invokes the possible role of G. halelectricus in iron cycling in barely studied haloalkaline environments. IMPORTANCE Bidirectional extracellular electron transfer (EET) appears to be a key microbial metabolic process in anoxic environments that are depleted in soluble electron donor and acceptor molecules. Though it is an ecologically important and applied microbial phenomenon, it has been reported with a few microorganisms, mostly from nonextreme environments. Moreover, direct electron transfer-based bidirectional EET is studied for very few microorganisms with electrodes in engineered systems and barely with the natural insoluble electron acceptor and donor molecules in anoxic conditions. This study advances the understanding of extremophilic microbial taxa capable of bidirectional EET and its role in barely investigated Fe cycling in highly saline-alkaline environments. It also offers research opportunities for understanding the membrane components involved in the bidirectional EET of G. halelectricus. The high rate of Fe3+ oxide reduction activity by G. halelectricus suggests its possible use as a biocatalyst in the anaerobic iron bioleaching process under neutral-alkaline pH conditions.

Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment

The extracellular electron transfer (EET)-capable electroactive microorganisms (EAMs) play crucial roles in mineral cycling and interspecies electron transfer in different environments and are used as biocatalysts in microbial electrochemical technologies. Studying EAMs from extreme environments is desired to advance the electromicrobiology discipline, understanding their unique metabolic traits with implications to extreme microbiology, and develop specific bioelectrochemical applications. Here, we present a novel haloalkaliphilic bacterium named Geoalkalibacter halelectricus SAP-1, isolated from a microbial electroactive biofilm enriched from the haloalkaline lake sediments. It is a rod-shaped Gram-negative heterotrophic anaerobe that uses various carbon and energy sources and respires on soluble and insoluble terminal electron acceptors. Besides 16S-rRNA and whole-genome-based phylogeny, the GGDC values of 21.7 %, ANI of 78.5, and 2.77 % genomic DNA GC content difference with the closest validly named species Geoalkalibacter ferrihydriticus (DSM 17813^T ) confirmed its novelty. When grown with the solid-state electrode as the only electron acceptor, it produced 460±23 μA/cm² bioelectrocatalytic current, thereby confirming its electroactivity. Further electrochemical analysis revealed the presence of membrane redox components with high formal potentials, putatively involved in the direct mode of EET. These are distinct from EET components reported for any known electroactive microorganisms, including well-studied Geobacter spp., Shewanella spp. and Desulfuromonas acetexigens. Further the capabilities of G. halelectricus SAP-1 to respire soluble as well insoluble electron acceptors including fumarate, SO₄ ^2- , Fe³⁺ , and Mn⁴⁺ suggests its role in cycling these elements in haloalkaline environments. This article is protected by copyright. All rights reserved.

Protocol for bioelectrochemical enrichment, cultivation, and characterization of extreme electroactive microorganisms

Electroactive microorganisms (EAMs) are a group of microbes that can access solid extracellular electron donors or acceptors via extracellular electron transfer processes. EAMs are useful in developing various microbial electrochemical technologies. This protocol describes the use of bioelectrochemical systems (BESs) to enrich EAMs at the cathode from an extreme haloalkaline habitat. It also provides information for a detailed characterization of enriched cathodic biofilms via various cross-disciplinary techniques, including electrochemical, analytical, microscopic, and gene sequencing techniques.

For complete details on the use and execution of this protocol, please refer to Chaudhary et al. (2021).

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Detailed protocol for the electrochemical enrichment of extreme microorganisms

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Useful for cultivating different microbes at cathode of bioelectrochemical systems

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Protocols for characterizing electrotrophic biofilm and metabolic products provided

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These include electrochemical, analytical, microscopic, and gene sequencing techniques

Extremophilic electroactive microorganisms: Promising biocatalysts for bioprocessing applications

Electroactive microorganisms (EAMs) use extracellular electron transfer (EET) processes to access insoluble electron donors or acceptors in cellular respiration. These are used in developing microbial electrochemical technologies (METs) for biosensing and bioelectronics applications and the valorization of liquid and gaseous wastes. EAMs from extreme environments can be useful to overcome the existing limitations of METs operated with non-extreme microorganisms. Studying extreme EAMs is also necessary to improve understanding of respiratory processes involving EET. This article first discusses the advantages of using extreme EAMs in METs and summarizes the diversity of EAMs from different extreme environments. It is followed by a detailed discussion on their use as biocatalysts in various bioprocessing applications via bioelectrochemical systems. Finally, the challenges associated with operating METs under extreme conditions and promising research opportunities on fundamental and applied aspects of extreme EAMs are presented.

Extracellular electron transfer influences the transport and retention of ferrihydrite nanoparticles in quartz sand coated with Shewanella oneidensis biofilm

Microbial biofilm has been found to impact the mobility of nanoparticles in saturated porous media by altering physicochemical properties of collector surface. However, little is known about the influence of biofilm's biological activity on nanoparticle transport and retention. Here, the transport of ferrihydrite nanoparticles (FhNPs) was studied in quartz sands coated with biofilm of Shewanella oneidensis MR-1 that is capable of reducing Fe(III) through extracellular electron transfer (EET). It was found that MR-1 biofilm coating enhanced FhNPs' deposition under different pH/ionic strength conditions and humic acid concentrations. More importantly, when the influent electron donor (glucose) concentration was increased to promote biofilm's EET activity, the breakthrough of FhNPs in biofilm-coated sands was inhibited. A lack of continuous and stable supply of electron donor, on the contrary, led to remobilization and release of the originally retained FhNPs. Column experiments with biofilm of EET-deficient MR-1 mutants (ΔomcA/ΔmtrC and ΔcymA) further indicated that the impairment of EET activity decreased the retention of FhNPs. It is proposed that the effective surface binding and adhesion of FhNPs that is required by direct EET cannot be neglected when evaluating the transport of FhNPs in sands coated with electroactive biofilm.

High throughput techniques for the rapid identification of electroactive microorganisms

Electroactive microorganisms (EAM), capable of executing extracellular electron transfer (EET) in/out of a cell, are employed in microbial electrochemical technologies (MET) and bioelectronics for harnessing electricity from wastewater, bioremediation and as biosensors. Thus, investigation on EAM is becoming a topic of interest for multidisciplinary areas, such as environmental science, energy and health sectors. Though, EAM are widespread in three domains of life, nevertheless, only a few hundred EAM have been identified so far and hence, the rapid identification of EAM is imperative. In this review, the techniques that are developed for the direct identification of EAM, such as azo dye and WO₃ based techniques, dielectrophoresis, potentiostatic/galvanometric techniques, and other indirect methods, such as spectroscopy and molecular biology techniques, are highlighted with a special focus on time required for the detection of these EAM. The bottlenecks for identifying EAM and the knowledge gaps based on the present investigations are also discussed. Thus, this review is intended to encourage researchers for devolving high-throughput techniques for identifying EAM with more accuracy, while consuming less time.

Electrochemical enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode of bioelectrochemical systems

Electrotrophic microorganisms have not been well studied in extreme environments. Here, we report on the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment. The biofilm enriched via electrochemical approach under 9.5 pH and 20 g NaCl/L salinity conditions achieved −43.5±7.2μA/cm2 current density and 49.5±13.2%nitrate reduction efficiency via partial and complete denitrification. Voltammetric characterization of the biocathodes revealed a redox center with −0.294±0.003V (vs. Ag/AgCl) formal potential putatively involved in the electron uptake process. The lack of soluble redox mediators and hydrogen-driven nitrate reduction suggests direct-contact cathodic electron uptake by the nitrate-reducing microorganisms in the enriched biofilm. 16S-rRNA amplicon sequencing of the cathodic biofilm revealed the presence of unreported Pseudomonas, Natronococcus, and Pseudoalteromonas spp. at 31.45%,11.82%, and 9.69% relative sequence abundances, respectively. The enriched nitrate-reducing microorganisms also reduced nitrate efficiently using soluble electron donors found in the lake sediments, thereby suggesting their role in N-cycling in such environments.

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Enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode

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Cathodic reduction current corresponded to the nitrate reduction process

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Pseudomonas, Natronococcus, and Pseudoalteromonas spp. enriched in the cathodic biofilm

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Enriched culture reduced nitrate efficiently with soluble electron donor sources