A bibliography study of Shewanella oneidensis biofilm

Abstract This study employs a bibliography study method to evaluate 472 papers focused on Shewanella oneidensis biofilms. Biofilms, which are formed when microorganisms adhere to surfaces or interfaces, play a crucial role in various natural, engineered, and medical settings. Within biofilms, microorganisms are enclosed in extracellular polymeric substances (EPS), creating a stable working environment. This characteristic enhances the practicality of biofilm-based systems in natural bioreactors, as they are less susceptible to temperature and pH fluctuations compared to enzyme-based bioprocesses. Shewanella oneidensis, a nonpathogenic bacterium with the ability to transfer electrons, serves as an example of a species isolated from its environment that exhibits extensive biofilm applications. These applications, such as heavy metal removal, offer potential benefits for environmental engineering and human health. This paper presents a comprehensive examination and review of the biology and engineering aspects of Shewanella biofilms, providing valuable insights into their functionality.


Introduction
Biofilms are formed when micr oor ganisms attac h to surfaces or interfaces, giving rise to populations or communities .T hese biofilms are composed of microorganisms that are embedded in extr acellular pol ymeric substances (EPS), whic h pr ovide a fr amework and protection for the microorganisms (Yang et al. 2012 ).EPS constitute more than 90% of the biomass in biofilms, with cells accounting for less than 10% (Flemming and Wingender 2010 ).Micr oor ganisms within biofilms exhibit physiological differ ences compar ed to those in planktonic sta ges, demonstr ating incr eased r esistance to antibiotics and tolerance to harsh envir onments (Ste w art and F ranklin 2008 ).Understanding biofilms is of paramount importance due to their applications in environmental engineering, such as trickling biofilm reactors, as well as their significant role in the field of medical science, where more than 80% of human infections are associated with biofilms (Parker et al. 1989, Battistoni et al. 1992 ). Investigating biofilms can pave the way for the design of more efficient biofilm-based applications and the de v elopment of antibiofilm drugs for public health purposes.
The process of biofilm formation involves sequential stages of attac hment, matur ation, and dispersion.The attachment stage typically lasts for 4-12 h, follo w ed b y a matur ation sta ge lasting ∼12-72 h, after which the biofilms disperse (Dominguez-Zacarias et al. 2006, Takahashi et al. 2010 ).Surface modification r esearc h is focused on either pr e v enting or enhancing biofilm formation (Bazaka et al. 2012, Hou et al. 2013 ), which is crucial in the context of pr e v enting biofilms on medical devices as well as improving biofilm formation in biofilm reactors (Ding et al. 2014 ).Mor eov er, the interactions between biofilms and antibiotics are a significant area of investigation (Anwar et al. 1989 ) due to the high preva-lence of biofilm-related human infections (Wagner and Iglewski 2008, Arif et al. 2010, Bjarnsholt 2013 ).
The biofilm matrix is primarily composed of pr oteins, pol ysacc harides, extr acellular DN A (eDN A), and lipids.These components interact and assemble into three-dimensional structures that serve as the scaffold for the biofilm matrix.The interplay between these components involv es v arious forces, including electr ostatic attr action, ionic attr action, r epulsion, hydr ogen bonding, and van der Waals interactions (Flemming and Wingender 2010 ).Ho w e v er, se v er al k e y questions pertaining to the biofilm matrix r emain unanswer ed, suc h as the specific functions of each component, the primary forces governing their interactions, and the influence of metabolites on matrix stability.Gaining insights into these aspects of the biofilm matrix is of utmost importance for constructing resilient biofilms, preventing biofilm formation, enhancing biofilm-based envir onmental a pplications, and designing efficacious antibiofilm drugs.
This study provides a compr ehensiv e anal ysis of 472 published articles to explore the potential of Shewanella oneidensis , an envir onmentall y isolated bacterium known for its ability to reduce metals.Shewanella oneidensis has been extensively utilized for applications such as uranium immobilization and c hr omium r eduction, thanks to its metal-r educing ca pabilities (Myers and Nealson 1988, Cao et al. 2011, Ding et al. 2014 ).Moreover, its nonpathogenic nature, adaptability to anaerobic and aerobic en vironments , and ca pacity to form r esilient and cohesiv e biofilms make it highly promising for future environmental applications.In comparison to enzyme-based biocatalysis, S. oneidensis biofilm-based biocatalysis offers enhanced stability in natural en vironments , rendering it well-suited for environmental bioreactors and v arious a pplications, including the r emov al of heavy metals .T his r e vie w primaril y focuses on S. oneidensis as a model organism and investigates its biofilm matrix, aiming to provide valuable insights that contribute to the field of environmental engineering.

Materials and methods
In June 2023, a compr ehensiv e data collection was conducted using the widely recognized bibliographic database, Web of Science, whic h encompasses v arious subdatabases .T his choice was made to ensure the reliability and extensive utilization of the collected data.The search profile specifically focused on "Shewanella oneidensis biofilm."Web of Science was selected as the primary database due to its reputation as a trusted resource widely emplo y ed within the academic community.
To generate visual representations for the bibliographic analysis, the po w erful data visualization tool, VOSview er, w as utilized.The downloaded data files were imported into VOSviewer, enabling the manipulation and adjustment of parameters based on the specific anal ysis objectiv es and the diverse data sources available.It is important to note that the creation of maps using web data often r equir es data cleaning processes to ensure accuracy and r eliability.Ther efor e, VOSvie wer facilitated efficient handling of such data cleaning procedures, contributing to the production of robust and meaningful visualizations.
Unless otherwise specified, the mapping conducted using VOSview er follo w ed the default settings as per pr e vious studies (Meng et al. 2020, Cavalcante et al. 2021, Huang et al. 2022 ).In the k e yw or d study, a minimum keyw or d occurrence of "20" was selected.For the country study, a minimum of "5" documents from a country were required for inclusion.Similarly, for the organization study, a minimum of "5" documents from an organization wer e consider ed for anal ysis.

Results
Table 1 provides a succinct ov ervie w of the recent strides made in S. oneidensis biofilm r esearc h.Delving into the k e yword analysis presented in Fig. 1 (a), a multitude of k e yw or ds are intricately linked to the process of electron transfer, encompassing terms like "extr acellular electr on tr ansfer," "electricity gener ation," "micr obial fuel cell," and "po w er generation."Further, the k e yw or ds intricately tied to the biofilm matrix, such as "gr owth," "tr ansport," and "fla vins ," offer an insightful glimpse into the multifaceted aspects of this intricate biological phenomenon.
Moving on to the organization analysis, showcased in Fig. 1 (b), it becomes evident that several institutions have assumed pivotal roles in propelling S. oneidensis biofilm research forw ar d.For instance , the En vir onmental Micr obial Biofilm Biotec hnology (EMBB) Gr oup at Nan yang Tec hnological Univ ersity, Singa por e, delved into the influence of outer membrane c-type cytoc hr omes on the particle size and activity of extracellular nanoparticles produced by S. oneidensis (Ng et al. 2013a ).The EMBB group further advanced their research by engineering S. oneidensis to efficiently r emov e the heavy metal pollutant Cr(VI) from water (Ding et al. 2014 ), alongside their significant contribution to the de v elopment of microbial fuel cells based on S. oneidensis to optimize electricity generation efficiency (Yang et al. 2015 ).Moreover, the research endeav ors spearheaded b y Alfred Spormann's team at Stanford Univ ersity explor ed the intricate landsca pe of Shew anella 's environmental systems biology (Fredrickson et al. 2008 ).This exploratory journey also encompassed a thorough investigation into the attachment and detachment processes of S. oneidensis (Thormann et al. 2004(Thormann et al. , 2005(Thormann et al. , 2006 ) ), shedding light on crucial aspects of its beha vior.T he team's studies further v entur ed into the domains of hydrogen metabolism and energy-dependent stability within S. oneidensis (Meshulam-Simon et al. 2007, Saville et al. 2011 ).Notabl y, Liu Fanghua's r esearc h gr oup fr om the Chinese Academy of Sciences made significant strides by unr av eling the potential of S. oneidensis in methane production (Xiao et al. 2020 ) and unr av eling the intricate electr on tr ansfer pr ocess within S. oneidensis (Liu et al. 2020(Liu et al. , 2022 ) ).
Within our compr ehensiv e country anal ysis, r e v ealed in Fig. 1 (c), a constellation of nations has emerged as noteworthy contributors to the domain of S. oneidensis biofilm r esearc h.These nations include a div erse arr ay of participants such as the USA, China, UK, France, Australia, Canada, Spain, the Netherlands, Belgium, Denmark, Japan, South Korea, India, and Singapore.It is particularly intriguing to observe that Western nations, including the USA, UK, Fr ance, Austr alia, Canada, Spain, Netherlands, Belgium, and Denmark, primarily focused their r esearc h on unr av eling the intricate metabolic intricacies of S. oneidensis biofilms .T heir efforts were channeled to w ar d an in-depth comprehension of the underl ying pr ocesses and r eactions within these biofilms, offering a profound understanding of their metabolic capacities and potential applications.On the other hand, Asian nations such as China, Ja pan, South Kor ea, India, and Singa por e demonstr ated a marked emphasis on application-oriented studies concerning S. oneidensis biofilms .T heir r esearc h endeav ors w ere dedicated to exploring the practical applications and potential utilities of this biofilm across various fields .T hrough these explorations, they aspired to harness the potential of S. oneidensis as a sustainable and ecofriendl y solution, with a pplications spanning bior emediation, r ene wable ener gy, and waste water tr eatment.Notabl y, the collabor ativ e efforts acr oss international boundaries and the div ersified spectrum of r esearc h initiativ es hav e substantiall y enric hed our comprehension of S. oneidensis biofilms .T he fusion of expertise and perspectives from both Western and Asian nations has engendered a wealth of insights into the foundational metabolic processes and the pr a gmatic a pplications of this ca ptiv ating biofilm phenomenon.

Unlocking the potential of ca tal ysis in diverse environments
Biofilms are formed by the a ggr egation of micr oor ganisms at surfaces or interfaces, where they are embedded within selfpr oduced EPS, cr eating a population or comm unity.These biofilms ar e pr esent ubiquitousl y, spanning fr om natur al envir onments to human diseases (Hall-Stoodley et al. 2004 ).In natural settings, ther e ar e typicall y two distinct sta ges of cellular existence: the planktonic stage and the biofilm stage (Daw et al. 2012 ).This is primarily due to the protective nature of EPS, which serves as a "House of the biofilm cells," safeguarding the biofilm cells within the matrix (Flemming et al. 2007 ).
T his no v el c har acter contributes to the field of biotechnology, particularly in the development of biofilm-based catalysis.Unlike conv entional biocatal ysis, whic h primaril y r elies on enzymebased catal ysis (Csor egi et al. 2001, Sjode et al. 2008 ).this c har acter offers a catalytic approach that is less sensitive to environmental fluctuations .Enzyme-based catalysis , while efficient, can be easily affected by small temper atur e c hanges, r esulting in fluctuations in the r eaction.Ther efor e, ther e is a strong demand for a biotechnology that exhibits less sensitivity in catalysis.Biofilm-based catalysis shows promising potential in environmental applications due to the increased tolerance and stability of biofilm cells within their envir onment.Pr esentl y, biofilm-based trickling filter reactors have been established to enhance the catal ytic r eactions (P arker et al. 1989(P arker et al. , Battistoni et al. 1992 ).These reactors employ biofilms to impr ov e the efficiency and stability of the catalytic process , pro viding a more robust and reliable appr oac h for environmental applications.

Dynamics of biofilm formation: attachment, ma tur a tion, and dispersal processes
Biofilms undergo a distinct life cycle characterized by five primary stages: (1) initial attachment, (2) irreversible attachment, (3) early maturation, (4) late maturation, and (5) dispersion.The attachment sta ge typicall y spans a period of 4-48 h, and it plays a crucial role in biofilm formation (Gottenbos et al. 2000, Thormann et al. 2004, Das et al. 2010, Tian et al. 2014 ).During this stage, eDNA and pol ysacc harides perform vital functions in the initial attachment pr ocess, ultimatel y influencing the ov er all biofilm formation (Jermy 2010, Orgad et al. 2011 ).Surface modification techniques, including adjustments to surface hydrophobicity and other factors, can also impact the initial attachment of biofilms (Stanley 1983, Takahashi et al. 2010, Bazaka et al. 2012 ).
The maturation stage, which typically lasts around 48-144 h, is c har acterized by the de v elopment of matur e biofilms exhibiting thr ee-dimensional (3D) structur es, suc h as m ushr oom-like formations, with a thickness ranging from 10 to 100 μm.Subsequently, as a response to oxygen and nutrient limitations, cells within the mature biofilms initiate the dispersion process (Dominguez-Zacarias et al. 2006, Rice et al. 2009, Ding et al. 2014 ).Dispersal cells are released into the surrounding environment, seeking surfaces for r eattac hment and initiating the initial attachment phase once again.The primary modes of motility for these cells include s wimming, s warming, and twitching (Di Bonaventura et al. 2008, Pompilio et al. 2008, Kearns 2010 ).

Exploring the role of matrix components in S. oneidensis biofilms: proteins, polysaccharides, eDNA, and lipids
In the biofilm matrix, proteins, polysaccharides, eDNA, and lipids are the main components.In terms of biomass, proteins and pol ysacc harides collectiv el y account for mor e than 90%, with the pr otein-to-pol ysacc haride r atio typicall y r anging fr om 1:1 to 5:1 depending on the species (Yang et al. 2012 ).These matrix components interact with each other to form the scaffold of the biofilm matrix.The for ces betw een these components include electr ostatic attr action, ionic attr action, r epulsion, hydr ogen bonding, and van der Waals interactions (Flemming and Wingender 2010 ).
Regarding proteomics studies of S. oneidensis , it has been found that the genome contains a total of 4758 pr edicted pr oteinencoding open reading frames (CDSs), with ∼54.4% of the proteins assigned a biological function (Heidelberg et al. 2002 ).Among these pr oteins, a lar ge 285 kDa pr otein called Ba p/RTX hybrid cell surface protein (SO4317) has been identified as a k e y mediator of biofilm formation in S. oneidensis MR-1.This protein, known as the biofilm-promoting factor A (BpfA), plays a crucial role, as demonstrated by the observation that knockout of the BpfA gene leads to a reduced ability of S. oneidensis to form biofilms (Theunissen et al. 2010 ).Pr e vious r esearc h has also utilized the fusion of r edoxsensitiv e fluor escence pr otein to BpfA, enabling the visualization of the protein in S. oneidensis biofilms under a microscope (Sivakumar et al. 2014 ).
A recent study reported that the ratio of polysaccharides to proteins in S. oneidensis is around 1-2, indicating a higher production of pol ysacc harides compar ed to other species (Ding et al. 2014 ).In pr e vious studies, it has been reported that Pel, Psl, and alginate are the main types of pol ysacc harides in Pseudomonas aeruginosa , with Pel and Psl playing a critical role in the initial attachment stage (Orgad et al. 2011 ).Ho w ever, the composition and structure of pol ysacc harides in S. oneidensis during the initial attachment stage have not been fully characterized.It is hypothesized that further studies on pol ysacc harides ar e necessary, as they ma y pla y an important role in the initial attachment and maturation of biofilms in S. oneidensis .
Meanwhile, eDNA has been reported to play an essential role in initial cell attachment and biofilm maturation in Staphylococcus aureus .Removal of eDNA from the biofilm matrix significantly weakens biofilm formation (Jermy 2010 ).The specific function of eDNA in S. oneidensis at this stage remains unclear, but it is speculated that eDNA may also contribute to the initial attachment and maturation of biofilms in S. oneidensis , similar to other species.Regarding lipid studies, it is proposed that lipids may alter surface c har ges (Hatzios et al. 2011, Zhao et al. 2011 ), and surface c har ges can influence biofilm formation (Ding et al. 2014 ).Ther efor e, lipids may also impact biofilm formation in S. oneidensis .

Surface modification: a key strategy to control biofilm formation in S. oneidensis
Multiple factors can influence the formation, disruption, or dispersal of biofilms .T hese factors include surface properties , oxygen and nutrient a vailability, en vironmental stress , and metabolites (Tsai et al. 2004, Bazaka et al. 2012 ).Surface modification is a common a ppr oac h to enhance or disrupt biofilm formation by altering the surfaces to promote or hinder initial attachment and maturation of cells (Bazaka et al. 2012, Kim et al. 2012, Hou et al. 2013 ).Pr e vious studies have demonstrated that surface modification can effectiv el y pr e v ent the initial attac hment of micr oor ganisms and subsequent biofilm formation (Bazaka et al. 2012 ).Additionall y, r esearc h on hollow fiber membranes has shown that surface modification can impact the biofilm formation capability (Hou et al. 2013 ).
Following medical surgeries, the surfaces of implanted or inserted medical devices are susceptible to biofilm formation, which can lead to health complications (Jass et al. 2003 , Shunm uga perumal 2010 ).Ther efor e, ther e is a pressing need for the development of surface materials with antibiofilm properties.By designing impr ov ed antibiofilm surface materials, it becomes possible to create medical devices that effectively prevent such infections associated with biofilm formation.

Nutrient and oxygen: vital factors influencing the biofilm matrix in S. oneidensis
In addition to surface properties, the environment is another crucial factor that influences biofilm formation and dispersal.Nutrient availability plays a significant role in shaping the biofilm matrix (Sawyer and Hermanowicz 1998 , Hunt et al. 2004, Dominguez-Zacarias et al. 2006 ).Cells and biofilms r equir e nutrients for growth, and as the nutrient supply becomes depleted, biofilms initiate detachment, with cells dispersing into the environment in search of new surfaces for attachment (Hunt et al. 2004, Dominguez-Zacarias et al. 2006 ).
Similarl y, oxygen av ailability affects the gr owth and de v elopment of aerobic cells and biofilms.Research has shown that oxygen can promote biofilm formation in Shew anella putref aciens CN32 thr ough the involv ement of diguan ylate cyclase and an adhesin (Wu et al. 2013 ).In matured S. oneidensis biofilms, when the flow of medium is stopped for se v er al minutes, the biofilms initiate dispersal due to o xygen de pletion (Thormann et al. 2005 ).T hus , nutrient and oxygen av ailability ar e important factors that influence the biofilm matrix.
Heavy metals are another influential factor that impacts the biofilm matrix.Taking c hr omium as an example, a pr e vious study reported that hexavalent chromium induces biofilm detachment.In this study, S. oneidensis MR-1 biofilm w as gro wn using modified M1 media.Once the biofilms had de v eloped, hexav alent c hr omium was intr oduced into the media, r esulting in biofilm detac hment.The study r e v ealed that while S. oneidensis MR-1 biofilm is capable of reducing Cr(VI) to Cr(III), the presence of Cr(VI) induces biofilm detachment.

Quorum sensing in S. oneidensis : unveiling the language of biofilm communication
In scenarios involving nutrient and oxygen limitation, an intriguing r esearc h topic arises: how do cells comm unicate with eac h other?Within mature biofilms, certain cells may experience insufficient nutrient or oxygen suppl y, typicall y in the inner regions due to limited nutrient dispersion, while other cells, pr edominantl y in the outer regions, continue to r eceiv e ample n utrient and o xygen.In suc h cases, starv ed cells m ust comm unicate their inability to survive and their intention to disperse .T herefore , there is a necessity for cell-to-cell comm unication.Researc hers hav e discovered that cells employ a quorum sensing system for communication (Flickinger et al. 2011 ).Quorum sensing facilitates biofilm formation, enabling bacteria to persist for longer periods, and is regulated by c-di-GMP, a second messenger that plays a crucial role in quorum sensing and subsequent biofilm formation (Sharma et al. 2014 ).Often, high concentrations of c-di-GMP lead to increased biofilm formation capability while reducing cellular motility (Ueda andWood 2009 , Sharma et al. 2014 ).Quorum sensing is significant as it serves as the communication language among cells.Understanding this language allows scientists to manipulate biofilms, promoting the growth of more robust biofilms or inducing dispersal, depending on the specific context.

Polyamines in biofilm dynamics: balancing formation and dispersal in S. oneidensis
Self-pr oduced metabolites serv e as another influential factor that can impact biofilm formation.Various types of self-produced metabolites have been identified to affect the stability of biofilms.P olyamines , such as putrescine , cada verine , spermidine , and spermine, ar e or ganic compounds with two or more primary amino groups.Although the synthesis pathways of polyamines in cells ar e well-r egulated, their exact functions within cells are still not completely understood (Rato et al. 2011 ).
Numer ous studies hav e r eported that pol yamines ar e essential for the growth of cells and biofilms (Patel et al. 2006, Wortham et al. 2010, Sakamoto et al. 2012, Karatan and Michael 2013 ).For instance, norspermidine has been suggested to enhance biofilm formation in Vibrio c holer ae, while spermidine r educes biofilm formation (Karatan et al. 2005, McGinnis et al. 2009 ).In Bacillus subtilis , D-amino acids and norspermidine induce biofilm dispersal (Xu andLiu 2011 , Kolodkin-Gal et al. 2012 ), although some studies hav e r aised questions r egarding these findings (Hobley et al. 2014 ).Ov er all, the pr ecise r ole of pol yamines in cell metabolism and biofilm formation remains incompletely understood.Ho w ever, it is evident that polyamines can influence cell growth and the composition of the biofilm matrix.It is hypothesized that under normal conditions, polyamines may enhance biofilm formation.Nevertheless, at high concentr ations, pol yamines may affect biofilm stability by altering the interactions between matrix components, potentially leading to biofilm dispersal.Ther efor e, self-pr oduced metabolites r epr esent another significant factor that can influence biofilm formation.

From motility to metal reduction: unraveling the biofilm phenomenon in S. oneidensis
Shewanella oneidensis MR-1 is an environmental bacterium that was first isolated in 1988 (Myers and Nealson 1988 ).It is a nonpathogenic bacterium known for its ability to reduce metals.Shewanella oneidensis cells exhibit various modes of motility, including s wimming, s warming, and twitc hing, and the matur ation pr ocess of its biofilms typically takes ∼96 h, with a continuous supply of nutrients.Mature S. oneidensis biofilms form three-dimensional structures with a thickness ranging from 20 to 50 μm.The biofilm matrix of S. oneidensis primarily consists of pr oteins, pol ysacc harides, and eDNA.Notably, the pol ysacc haride content in S. oneidensis biofilm matrix is compar ativ el y high compar ed to that of P. aeruginosa , with a pr otein-to-pol ysacc haride r atio of ∼1:1.Additionall y, the cohesiv eness and r obustness of S. oneidensis biofilms can be enhanced through genetic manipulation (Ding et al. 2014 ).
Shewanella oneidensis is capable of surviving and forming biofilms under both aerobic and anaerobic conditions.In aerobic conditions, the cells utilize oxygen as an electron acceptor.Under anaerobic conditions, S. oneidensis can r espir e using v arious electron acceptors, including metal ions, metal oxides, and solid electr odes.It demonstr ates the ability to r educe differ ent types of metals, such as manganese (Myers and Nealson 1988 ), c hr omium (Ding et al. 2014 ), iron (Ahmed et al. 2012 ) and palladium (Ng et al. 2013a ).This metal-reducing capability of the S. oneidensis biofilm matrix holds significant potential for environmental applications.
The ingestion of heavy metals poses a significant risk to human health (Tchounwou et al. 2012 ).Hexavalent chromium, for instance, is a particularly concerning heavy metal.In many developing countries, the direct disposal of hexavalent chromium into w aterw ays without proper pretreatment is a common practice in industrial pr oduction.Consequentl y, individuals who consume water contaminated with high concentrations of hexavalent c hr omium may experience stomac h ulcers and an incr eased risk of stomach cancer.Consequently, the development of technologies to r emov e heavy metals from water sources is crucial.
Various methods have been emplo y ed for the removal of heavy metals, including those based on physical adsorption (Yavuz et al. 2006, Di Natale et al. 2007 ) or c hemical r eactions (Lv et al. 2014, Mystrioti et al. 2014 ).Ho w e v er, these methods hav e certain limitations.Physical adsorption methods may not pr e v ent the desor ption of c hr omium ov er long timescales (Bai andAbraham 2003 , Gupta andRastogi 2008 ), and chemical methods relying on oxidation-reduction processes can be expensive due to the r equir ed c hemical materials.In this context, r esearc h on nov el bior emediation a ppr oac hes shows pr omise.
Shewanella oneidensis MR-1, a metal-reducing bacterium, offers an emerging bioremediation technique through its biofilm matrix.This technique demonstrates high efficiency while having minimal negative environmental impacts.Previous studies have utilized genetic manipulation to construct more robust and cohesiv e biofilms, ther eby impr oving the efficiency of c hr omium r eduction.By harnessing the metal-r educing ca pabilities of S. oneidensis biofilms, this r esearc h holds potential for effectiv e and envir onmentall y friendl y heavy metal r emediation.
Uranium (U) is a naturally radioactive element that undergoes a series of alpha or beta particle emissions, ultimately transforming into the stable element lead.While uranium has applications in electricity generation, nuclear po w er, and military w eaponry, industrial activities have also led to environmental contamination (Davesne and Blanchardon 2014 ).Uranium contamination in sites managed by the U.S. Department of Energy (DOE) poses significant challenges and incurs substantial remediation costs due to its presence in soils and groundwater (Ahmed et al. 2012 ).One such site is Hanford 300A, characterized by heavy uranium contamination in soils , sediments , and ground water (Si vaswam y et al. 2011 ).
Researc hers hav e explor ed the potential of S. oneidensis sp.HRCR-1 in immobilizing uranium within biofilm matrices.In a study conducted at a hollow fiber membrane biofilm reactor, scientists isolated loosely associated EPS and bound EPS from S. oneidensis sp.HRCR-1 biofilms and assessed their reactivity with U(VI).The findings r e v ealed that the isolated cell-free EPS fractions, upon reduction, were able to reduce U(VI) as well.Polysacc harides pr esent in the EPS likel y contributed to U(VI) sor ption, pr edominantl y in the loosely associated EPS, while redo x-acti ve components, particularly within the bound EPS, potentially facilitated U(VI) reduction (Cao et al. 2011 ).These results highlight the potential of the biofilm matrix of S. oneidensis sp.HRCR-1 in immobilizing uranium, offering insights for remediation strategies in uranium-contaminated en vironments .
In the realm of industrial production, nanomaterials have emerged as k e y components.Efficient production methods for nanomaterials have become an intriguing area of research.Previous studies have explored the utilization of S. oneidensis MR-1 biofilms to produce palladium and silver nanoparticles through r eduction pr ocesses (Ng et al. 2013a , b ). or instance, the reduction of tetr ac hlor opalladate (Pd(II)) by the dissimilatory metalr educing ca pabilities of S. oneidensis MR-1 led to the production of catalytic palladium (Pd) nanoparticles, offering a novel approach in nanomaterial production (Ng et al. 2013b ).
Another study investigated the use of S. oneidensis MR-1 for the production of extracellular silver nanoparticles .T he research highlighted the significant roles played by outer membrane c-type cytoc hr omes MtrC and OmcA in the synthesis of these nanoparticles .T he absence of c-type cytoc hr omes on the cell surface of S. oneidensis resulted in a reduction in the particle size of the extr acellular biogenic silv er nanoparticles .T his finding suggests the possibility of controlling the size and activity of such nanoparticles through the regulated expression of genes encoding surface proteins (Ng et al. 2013a ).
These studies showcase the potential of S. oneidensis MR-1 biofilms as a platform for efficient production of nanomaterials, demonstrating the ability to generate catalytic palladium nanoparticles and control the size of extracellular silver nanoparticles .T hese findings open up exciting possibilities for the de v elopment of sustainable and controlled nanomaterial production processes.

Bioc hemical pathw a ys of hea vy metal reduction in S. oneidensis MR-1: insights into electron transfer mechanisms
In 1988, S. oneidensis was initially isolated from the environment, and it was discov er ed to have the ability to reduce manganese (Myers and Nealson 1988 ).Subsequent r esearc h has r e v ealed that this species can also reduce various other metals, including iron (Caccavo et al. 1997 ), uranium (Cao et al. 2011 ), palladium (Ng et al. 2013b ), and c hr omium (Ding et al. 2014 ).In aer obic envir onments, S. oneidensis prefers oxygen as the electron acceptor, while in anaerobic en vironments , it utilizes metals as electron acceptors for metabolism.Se v er al carbonate hydr ates, suc h as lactate (Ng et al. 2013a ) and pyruvate (Pinchuk et al. 2011 ), can serve as electron donors and carbon sour ces.Ho w ever, the gro wth of S. oneiden-sis is not observed when glucose is added, suggesting that glucose may not function as an electron donor or carbon source for this species.
The reduction of heavy metals by S. oneidensis r equir es electr on tr ansfer.The mec hanisms of electr on tr ansfer hav e been explained thr ough differ ent hypotheses , including in volvement of cytoc hr omes MtrC and OmcA (Belchik et al. 2011, Richardson et al. 2012 ), electron shuttles (Wu et al. 2013 ), and nano wires (Gorb y et al. 2006, El-Naggar et al. 2010, Pirbadian et al. 2014 ).In S. oneidensis MR-1, electron transfer occurs through cytochromes.MtrC and OmcA are outer membrane c-type cytochromes in S. oneidensis MR-1.Pr e vious studies hav e r eported that S. oneidensis cells utilize cytoc hr omes MtrC and OmcA for r espir ation on hematite (Mitchell et al. 2012 ) and the reduction of extracellular hexavalent c hr omium (Belc hik et al. 2011 ).In microbial fuel cells, cytoc hr omes MtrC and OmcA have also been found to play a crucial role in transferring electrons from S. oneidensis to oxide electrodes (Jani et al. 2010 ).The electron transfer system involving cytoc hr omes is illustrated in Fig. 2 .MtrA and MtrB are membrane proteins, while c-type cytochromes MtrC and OmcA attach to the outer membrane, forming an electron transfer pathway at the cell membrane.Another study focusing on S. putrefaciens MR-1 discussed the presence of the CymA protein in the cytoplasmic membrane and soluble fraction.This protein shares partial amino acid sequence homology with multiheme c-type cytoc hr omes found in other bacteria, which are involved in the transfer of electrons from the cytoplasmic membrane to acceptors in the periplasm.The electrons in S. oneidensis cells can pass through the pathway (formed by CymA, MtrA, MtrB, MtrC, and OmcA) to the exterior, initiating r eduction r eactions .T he hea vy metals then accept the electrons and undergo reduction.
An alternative explanation for electron transfer in S. oneidensis MR-1 involves the role of electron shuttles.It has been found that S. oneidensis MR-1 can secrete flavins as electron shuttles, which play a crucial role in extracellular electron transfer.The study reports that the secretion of flavins and subsequent microbial extracellular electr on tr ansfer can be significantl y influenced by electron acceptors (Wu et al. 2013 ).The presence of electron shuttles for extracellular electron transfer has also been observed in other Shew anella species (Turic k et al. 2002, Wu et al. 2014, Zhu et al. 2014 ).
In recent years, a new theory called "nanowir es" has emer ged to explain electron transfer in Shewanella species (Gorby et al. 2006, El-Naggar et al. 2010, Pirbadian et al. 2014 ).Researchers have reported that nanowires are extensions of the extracellular electr on tr ansport components in the outer membr ane and periplasmic space (Pirbadian et al. 2014 ).Another study demonstrated that nanowires in S. oneidensis MR-1 exhibit electrical conductivity ov er micr ometer-length scales, with electr on tr ansport r ates up to 10 9 /s at 100 mV and a measured resistivity on the order of 1 cm (El-Naggar, Wanger et al. 2010 ).

Conclusion
Biofilms r epr esent a fascinating and widespread mode of microbial life, with their distinctive EPS providing a protective and adaptiv e envir onment for micr oor ganisms.EPS contribute to the physiological differences between biofilm cells and their planktonic counter parts, enabling surviv al in hostile conditions and facilitating dispersion for colonization of new habitats.In this r e vie w, we hav e explor ed the fundamental aspects of biofilm matrix, including its life cycle, matrix components, and factors influencing formation and stability.Taking S. oneidensis as a model organism, we hav e specificall y examined its biofilm matrix.Shew anella oneidensis , as an envir onmentall y isolated and nonpathogenic bacterium, exhibits remarkable capabilities for heavy metal reduction and immobilization.The unique c har acteristics of S. oneidensis and its biofilm matrix offer promising prospects for various bioapplications, particularly in the areas of heavy metal remediation and immobilization.

F igure 1 .
VOSview er's analysis of (A) k e yw or ds , (B) organizations , and (C) country/region.Fig. 1 (a): k e yw or d clusters-VOSview er identifies thematic clusters by analyzing k e yword co-occurrence.Colors denote distinct thematic groups of frequently associated k e yw or ds.Fig. 1 (b) and (c): collaboration networks-colors in these networks indicate varied collaborative clusters among connected institutions or countries.

Figur e 2 .
Figur e 2. T he function of c-type cytoc hr omes MtrC and OmcA in S. oneidensis electron transfer.The theory is derived from previous studies (Belchik et al. 2011 , Richardson et al. 2012 ), and the figure has been drawn by the authors of this paper.

Table 1 .
Significant de v elopment of S. oneidensis biofilm.