Marine Rare Earth Elements: Distribution Patterns, Enrichment Mechanisms and Microbial Interactions

Abstract

Rare earth elements and yttrium (REY) are critical metals underpinning high-technology industries. Marine deposits have attracted growing interest due to their abundant REY reserves and high grades. This review synthesizes current knowledge on sources, distribution, and enrichment mechanisms of marine REY, with a particular focus on the role of microorganisms in REY phase transitions, fractionation, and enrichment. We highlight the largely untapped potential of marine-specific microbial strains and critically assess their influence on REY cycling. Key research challenges are proposed, followed by actionable directions to advance understanding of microbial–REY interactions. This review aims to deepen insights into marine REY cycling and support the sustainable development of deep-sea REY resources, emphasizing the need to integrate molecular-scale microbial processes into marine REY biogeochemical models.

1. Introduction

Rare earth elements and yttrium (REY) include scandium (Sc) and yttrium (Y), along with 15 lanthanide elements: lanthanum (La), cerium (Ce), praseodymium (Pr), neodymium (Nd), promethium (Pm, not found naturally on earth), samarium (Sm), europium (Eu), gadolinium (Gd), terbium (Tb), dysprosium (Dy), holmium (Ho), erbium (Er), thulium (Tm), ytterbium (Yb), and lutetium (Lu) [1]. Based on their chemical properties, REY are commonly divided into light REY (LREY) as La, Ce, Pr, Nd, and Pm; Middle REY (MREY) as Sm, Eu, Gd, Tb, and Dy; and Heavy REY (HREY) as Ho, Er, Tm, Yb, Lu, Sc, and Y [2]. Some categorizations do not specifically separate MREY, Sm, and Eu, which are also divided into LREY, while Gd, Tb, and Dy are divided into HREY. Their electronic configurations and physicochemical properties make REY play a critical role in modern industries and military technologies, such as optoelectronics, electric vehicles, superconductors, and nuclear energy [2].

Beyond the traditional terrestrial deposits, REY can enter the marine environment through weathering and erosion of continental materials, windborne dust, and possible hydrothermal activity, ultimately accumulating in deep-sea sediments via complex biogeochemical cycling [3,4,5,6]. With rising demand for REY, the deep sea has recently gained increasing attention as a potential REY resource [4,5]. Understanding the enrichment and circulation processes of marine REY is essential for sustainable development. This review summarizes current knowledge on the occurrence, distribution, and enrichment mechanisms of REY in the marine system, including seawater and deep-sea sediments, with a particular focus on potential microbe–REY interactions. Key findings from recent studies are discussed, alongside unresolved questions requiring further exploration (Figure 1).

2. REY in Seawater

2.1. Sources and Distribution of REY in Seawater

Terrestrial input is the primary source of marine REY, with rivers delivering dissolved and particulate REY from continental weathering into the ocean [5]. Contributions also come from atmospheric deposition, aeolian dust, volcanic emissions, and anthropogenic activities [3,5,6] (Figure 1). However, fluxes from riverine and aeolian sources remain poorly constrained [16]. Spatially, REY concentrations in seawater vary greatly. A recent review reported dissolved REY concentration in open and coastal water columns in detail and revealed seawater REY concentration spanning from the order of 10⁻² to 10², generally decreasing concentrations from LREY to HREY [3]. The highest REY concentrations are typically observed in offshore marine areas, where riverine discharge and anthropogenic activities are control factors [3]. In these areas, REY concentrations decrease with depth before stabilizing, while in the open ocean, concentrations generally increase with depth [3,5]. Notably, Ce exhibits a unique distribution pattern due to its redox sensitivity. In oxic environments, dissolved Ce (III) oxidizes to Ce (IV), forming insoluble CeO₂ and causing concentration characteristic anomalies in seawater [6,17,18,19,20,21]. In recent years, the dissolved REY concentration observed data in the open ocean have been spread across four oceans, with the Pacific Ocean having the largest dataset (Figure 2, Supplementary Table S1). The measurement areas include the Western Pacific, South Pacific, North Pacific, Northwest Pacific, subarctic, and equatorial Pacific, with the deepest sampling depth reaching up to 5663 m (Figure 2, Supplementary Table S1). The highest concentration of dissolved REY was measured in the surface water of the Atlantic Ocean, approximately 423 pmol/kg, which might be due to its sampling location being close to the shore (Figure 2, Supplementary Table S1). However, the REY concentration data in the Indian Ocean is still insufficient (Figure 2, Supplementary Table S1). Ocean circulation and water mass mixing are also major drivers of REY distribution in seawater. In deep-sea environments, vertical flux can be limited by restricted surface water input, constraining vertical mixing. This oceanic supply may exceed terrestrial inputs (e.g., rivers or atmospheric deposition) [3,22]. Additionally, redox conditions (e.g., anoxic or euxinic environments) favor REY retention by inhibiting the oxidative dissolution of carrier phases such as organic matter and sulfides [23]. Recent studies also highlight that biological processes play a role in REY transport to deeper waters, for example, REY uptake by diatoms and subsequent organic matter degradation may facilitate REY enrichment and redistribution in the deep ocean [14].

2.2. Speciation and Fractionation of REY in Seawater

Once REY enter the marine system, they exist in various forms and are typically categorized by their state and particle size into three groups: (i) “particulate REY”, associated with solid particles (>0.2 or 0.45 μm); (ii) “dissolved REY”, bound to colloids and nanoparticles (<0.2 μm); and (iii) “truly dissolved REY”, present as individual hydrated ions or chemical complexes [3,24]. Within the dissolved fraction, most REY occur as trivalent ions (REY³⁺), except for Ce (which can also exist as Ce⁴⁺) and Eu (which may appear as Eu²⁺ or Eu⁴⁺) due to their distinct redox behaviors [6,17,18,19,20,21,25].

The transformation between particulate and dissolved REYs significantly influences their spatial distribution, vertical transport, and fractionation in the ocean [3,26]. This phase exchange is governed not only by inorganic geochemical processes but also by biogeochemical interactions. Microorganisms, including bacteria, fungi, and certain microalgae, play a crucial role in REY cycling and transformation [3,6,14]. Through biological processes [3,26] such as biosorption, bioaccumulation, and bioprecipitation, they can promote the conversion of dissolved REYs into particulate forms and facilitate their downward transport [5,27]. Processes like redoxolysis, acidolysis, and complexolysis are conducive to particle degradation, conversely [5,27] (Figure 1). This will be further explored in Section 4. Additionally, REY speciation and fractionation in seawater are also influenced by environmental factors, including salinity, temperature, redox conditions, and the availability of ligands, especially phosphates and carbonates [3]. Moreover, pH/redox potential (Eh) changes is another important impact factor; lower pH increases REY solubility, while alkaline conditions promote adsorption/co-precipitation [23,28]. These factors affect both the stability and mobility of REY in marine environments.

Figure 2. Distribution map of dissolved rare earth elements in open ocean. Data are derived from observed data published since 2000 [8,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46], and have been modified manually. Stations were separated by maximum sampling depth and represented by different color in this figure. The circle size represents the maximum value of total dissolved rare earth element concentrations (ΣREY, note Pm, Sc, and Y not included) measured at this station.

Figure 2. Distribution map of dissolved rare earth elements in open ocean. Data are derived from observed data published since 2000 [8,26,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46], and have been modified manually. Stations were separated by maximum sampling depth and represented by different color in this figure. The circle size represents the maximum value of total dissolved rare earth element concentrations (ΣREY, note Pm, Sc, and Y not included) measured at this station.

3. REY in Deep-Sea Sediments

3.1. Deep-Sea Sediments REY Sources and Distribution

After entering the marine system, REY undergo cycling and migration processes, ultimately becoming enriched in deep-sea sediments. High REY concentrations were first reported in deep-sea sediments from the eastern South Pacific and central North Pacific in 2011 [4], with total REY contents reaching 1000–2230 μg/g—comparable to or exceeding those found in South China’s ion-adsorption-type rare earth deposits [4]. Subsequent surveys have detected sedimental REY concentrations in many different sea areas [3,6] and identified additional REY-rich deposits in the Indian Ocean, the Southeastern Pacific, and the Western Pacific [47,48,49,50,51,52,53]. These deposits are typically located in deep-sea basins at depths >4000 m, and are notably enriched in middle to heavy REY, while sediments in marginal seas and shallow waters show relatively low REY concentrations [4]. Based on oceanic geology and sediment REY distribution, four major deep-sea REY metallogenic belts have been identified (

Table 1. Characteristics of deep-sea metallogenic belts.

Deep-Sea REY Metallogenic Belts	Western Pacific	Southeast Pacific	Central-Eastern Pacific	Central Indian Ocean Basin	Wharton Basin
Main sediment types	Deep-sea clay (zeolite clay and oceanic clay)	Deep-sea clay (zeolite clay and oceanic clay)	Deep-sea clay (zeolite clay and oceanic clay)	Deep-sea clay (zeolite clay and oceanic clay)	Deep-sea clay (zeolite clay and oceanic clay)
Main mineral phases	Biogenic apatite, Fe-Mn micronodules	Biogenic apatite, Fe-Mn micronodules	Biogenic apatite, Fe-Mn micronodules	Biogenic apatite, Fe-Mn micronodules	Biogenic apatite, Fe-Mn micronodules
ΣREY range (10−6 μg/g)	700–7974	700–2738	700–1732	700–1987	700–1113
ΣREY average (10−6 μg/g)	1330	1243	910	1120	815
REY enrichment depth	2–12 m (3 layers ΣREY > 2000 × 10−6)	0–10 m	0–64 m (multilayer)	0–5 m	103–122 m

The table is cited from reference [54] and modified manually.

) [54]: (1) Western Pacific deep-sea REY deposit, (2) the Central-Eastern Pacific deep-sea REY deposit, (3) Southeastern Pacific deep-sea REY deposit, and (4) Central Indian Ocean Basin–Wharton Basin deep-sea REY deposit. Among them, the Western Pacific deposit shows the highest REY concentrations, with ΣREY values reaching 6000–8000 × 10⁻⁶ μg/g, indicating its significant resource potential for REY exploration [49,51,55].

Current evidence suggests that the direct sources of REY in deep-sea sediments are seawater and pore water. Diffusion from pore water may serve as an important benthic input for sediment REY [7,8], yet available pore water REY concentration data remain scarce, with fewer than 500 reported measurements to date [6]. Additionally, volcanic and hydrothermal processes have also been proposed as potential contributors to REY enrichment in deep-sea sediments [4]. Studies in the southeastern Pacific show that REY-rich mud formation and REY mobilization appear closely associated with hydrothermal activity along the East Pacific Rise [56,57,58]. Microorganisms at oceanic ridge hydrothermal vents can also facilitate REY-rich mineral formation through sulfide redox mediation, and rapid fluid quenching at vent sites also precipitates REY-bearing particles [59]. However, in the Central and Northern Pacific, Western Pacific, and Indian Ocean, REY enrichment in sediments seems to lack direct hydrothermal influence [50,52,55,58]. The overall influence of volcanic and hydrothermal processes remains debated.

3.2. REY Enrichment Process in Deep-Sea Sediments

A primary pathway for REY removal from seawater is vertical transport via surface adsorption and particle settling, leading to their sequestration in sediments [3]. Low sedimentation rates (<1 cm/kyr) enhance REY enrichment through prolonged seawater–particle interaction [60]. Authigenic mineral phases, such as biogenic apatite at the sediment-water interface, can further capture REY from overlying seawater through lattice incorporation or surface adsorption [6,61,62] (Figure 1). Additionally, microbial activity in sediments may facilitate REY enrichment through biosorption and metabolic processes [11,12,63]; this topic is explored further in Section 4 on microbe–REY interactions. REY accumulation in deep-sea sediments is influenced by multiple factors, including early diagenesis—the process of secondary precipitate authigenic phases formed on or around diagenesis [7,53,64]. Other factors, such as sedimentation rate [4], bottom currents [49,53,65,66], and hydrothermal activity, can also influence REY enrichment in sediment [4,56], biological productivity [65,67,68], and redox conditions [67]. The carbonate compensation depth (CCD), silica compensation depth (SCD), and mineralogical composition also significantly influence REY occurrence and distribution [4,65,67,69,70]. Once incorporated into sediments, REY may either become mineralized and permanently sequestered or be remobilized and re-enter geochemical cycling depending on microbial activity, sedimentation rate, and hydrodynamics [3]. However, current evidence suggests that REY remobilization back into the marine cycle is minimal.

In deep-sea sediments, REY are primarily hosted in biogenic apatite, clay minerals, and Fe-Mn micronodules, with strong associations to elements such as phosphorus (P), calcium (Ca), and aluminum (Al) [48,66,71]. Among these, biogenic apatite is considered the most significant host due to its high REY-loading capacity [67], with concentrations typically one–two orders of magnitude higher than other carrier phases, reaching up to 10⁴ ppm [9,67,72]. The formation of REY-rich phosphates in deep-sea sediments is influenced by low sedimentation rates, high background REY levels, and deep-water non-carbonate depositional environments [9]. REY enrichment within apatite lattices primarily occurs via ion exchange, where REY is substituted for Ca²⁺ within crystal structures [69]. Aluminosilicate clay minerals (<2 μm) serve as potential REY carriers [73,74]. Clay interlayer exchangeable cation sites, along with electrostatic adsorption and complexation, enhance their REY-binding capacity. Clay-charged surfaces also bind REY via ion exchange, especially in coastal zones influenced by terrestrial input [75,76]. Clays may also release REY to pore water or biogenic apatite through early diagenetic processes, contributing to REY redistribution within sediments [77,78,79]. The role of Fe-Mn micronodules in REY enrichment and sequestration remains debated. Early studies suggested that Fe-Mn oxides strongly absorb REY and aid in their removal from seawater via redox cycling [51,72,80,81]. Slow-growing Fe-Mn nodules and crusts can incorporate REY directly from seawater through hydrogenetic precipitation, aided by microbial mats that stabilize particle surfaces [75]. However, recent studies attribute the marine sediments’ Fe-REY correlation to the sorption capacity of iron-rich clay minerals (e.g., aquamarine), rather than Fe-Mn oxides [5,79]. Notably, REY can also be redistributed among sedimentary mineral phases through pore water. During sediment deposition, micronodules and clays may act as temporary REY hosts, later releasing REY into pore water under early diagenetic conditions, where it is ultimately sequestered by biogenic apatite as the final host mineral [74,77,78,79] (Figure 1).

4. Microorganism–REY Interactions

Microorganisms are widely distributed across various mineralization environments, including the ocean, and microorganism–mineral interactions play a critical role in elemental cycling and ore formation [13]. Minerals provide essential substrates and energy sources for microbial communities; conversely, microorganisms actively mediate elemental deposition and mineralization through biosorption, bioaccumulation, and gene-regulated metabolic processes [3,11,63] (Figure 1 and Figure 3). Furthermore, microbial activities such as bioleaching can enhance the solubilization of particulate-bound elements into bioavailable dissolved forms [12] (Figure 1 and Figure 3). This section summarizes recent advances in REY biosorption, bioaccumulation, utilization, and bioleaching, with a focus on emerging insights into marine microbial–REY interactions and current research challenges.

4.1. REY Biosorption and Bioprecipitation

Negatively charged functional groups on microorganism cell surfaces or extracellular polymers, such as amino, carboxyl, hydroxyl, phosphate, and thiol groups in glycoproteins and polysaccharides, facilitate REY adsorption and precipitation via electrostatic interactions and ion exchange (Figure 3). These processes directly promote deep-sea REY mineralization [86,87]. Notably, biosorption is typically independent of metabolic activity and can occur on dead cells [11,13]; the composition and structure of microbial communities significantly influence REY enrichment and fractionation [11,63,88]. For instance, studies on regolith-hosted REY deposits in southeastern China revealed that bacteria play a pivotal role in HREY and LREY fractionation [63]. Specifically, actinomycetes and Gram-positive bacteria exhibit higher REY adsorption capacities than Gram-negative bacteria, fungi, and yeast, largely due to their teichoic acids-rich cell walls, which confer strong negative surface charges [63].

Current research on microbial REY biosorption mechanisms primarily focuses on species isolated from terrestrial REY deposits or on model organisms such as Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, and Saccharomyces cerevisiae [11,27,86,87,89,90,91,92,93]. A total of 26 fungal and bacterial species with demonstrated REY absorption ability are listed in Table 2. These studies provide direct evidence that microorganisms can mineralize REY (e.g., Ce, Yb, Sm) after adsorption, forming REY-containing mineral particles or amorphous phosphate precipitates on cell surfaces [86,90,91]. However, most research only focuses on a limited subset of REY, lacking comprehensive data across the entire REY series. Recently, genetically engineered microbial strains with enhanced REY enrichment capabilities have shown promising results in the extraction of terrestrial REY resources [94,95], highlighting the potential of microbial biotechnologies for deep-sea REY resources development.

However, compared with terrestrial microorganisms, the discovery of marine strains with REY biosorption capacity remains severely limited. To date, fewer than six marine REY-enriching bacterial species have been identified (Table 2). Recent studies have isolated marine bacterial strains (Paenisporosarcina sp., Sulfitobacter sp., Jeotgalibacillus sp.) capable of adsorbing Ce from marine sediments [10]. During Ce biomineralization, nucleation sites first form on the cell surface, followed by the development of amorphous Ce-containing mineral particles. The efficiency of enrichment is significantly affected by the REY-to-biomass ratio and the cell wall structure properties [10]. Additionally, Gram-negative bacteria Leisingera methylohalidivorans and Phaeobacter inhibens, isolated from seawater, also exhibit HREY enrichment capabilities [96,97].

In addition to promoting REY enrichment through biosorption, microorganisms can also facilitate REY enrichment via more complex, gene-regulated, or metabolically induced pathways, collectively referred to as bioprecipitation [63,98]. Some microorganisms enhance REY enrichment by altering pH or local ion concentrations [99,100]. For example, Serratia sp. has been reported to produce inorganic phosphates to extracellular polymers through cellular metabolism, which then bind with REY, leading to REY enrichment and precipitation [99].

Table 2. Fungi and bacteria identified to have REY biosorption or bioleaching capabilities.

Mechanism	Categories	Strains	Tested REY	References
Biosorption	F	Aspergillus flavus	Ce	[101]
	F	Aspergillus niger	Ce	[101]
	F	Botryosphaeria rhodina	La, Sm	[102]
	F	Candida colliculosa	Nd	[103]
	F	Candida utilis	La, Sm, Sc, Y	[104]
	F	Catenulostroma chromoblastomyces	Ce, Nd, Gd, Dy	[96]
	F	Debaryomyces hansenii	Nd	[103]
	F	Fusarium sp.	Nd, Gd, Dy, Lu	[96]
	F	Kluyveromyces marxianus	Nd	[103]
	F	Pichia naganishii	La, Nd, Dy, Yb	[96]
	F	Pichia sp.	La, Nd, Dy, Yb	[96]
	F	Saccharomyces cerevisiae	La, Sm, Gd, Dy, Yb, Lu, Ce	[90,91,92,96,103,105]
	N	Agrobacterium sp.	La, Ce	[106]
	N	Caulobacter crescentus	Tb	[107]
	N	Escherichia coli	HREY	[87,89]
	N	Leisingera methylohalidivorans	HREY	[96]
	N	Magnetospirillum magneticum	La	[108]
	N	Methylobacterium extorquens *	Ln	[100,109]
	N	Paenisporosarcina sp.	Ce	[10]
	N	Phaeobacter inhibens	HREY	[96,97]
	N	Pseudomonas aeruginosa	La, Eu, Yb	[110]
	N	Pseudomonas fluorescens	Ce, Sm	[86]
	N	Sulfitobacter sp.	Ce	[10]
	P	Bacillus licheniformis	Ce	[111]
	P	Bacillus thuringiensis	Eu	[112]
	P	Jeotgalibacillus sp.	Ce	[10]
Bioleaching	F	Aspergillus flavus	Ce; REY from industry wastes	[101]
	F	Aspergillus niger	REY ore	[113,114,115,116,117]
	F	Aspergillus terreus	La, Ce, Nd, Pr	[118]
	F	Aspergillus sp.	Nd, Pm, Sm, Eu, Gd	[119]
	F	Candida bombicola	REY from coal fly ash	[120]
	F	Cryptococcus curvatus	REY from coal fly ash	[120]
	F	Paecilomyces sp.	La, Ce, Nd, Pr	[118,121]
	F	Penicillium chrysogenum	La, Ce, Y	[122]
	F	Penicillium tricolor	La, Ce, Nd, Sc, Y	[123]
	F	Penicillium sp.	REY from monazite	[124]
	F	Phanerochaete chrysosporium	La, Ce, Nd, Sc, Y	[120]
	F	Yarrowia lipolytica	La, Nd, Ce	[115]
	N	Acetobacter aceti	REY from monazite	[125]
	N	Acetobacter sp.	La, Ce, Nd, Sc, Y	[126]
	N	Acetobacter tropicalis	Sc	[127]
	N	Acidianus manzaensis	Ce, Gd, Sc, Y,	[128]
	N	Acidithiobacillus ferrooxidans	Nd, Pm, Sm, Eu, Gd, REY from phosphogypsum	[119,129,130,131,132]
	N	Acidithiobacillus thiooxidans	La, Ce, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Y	[133,134]
	N	Acidophilium multivorum	Ce, Dy, Er, Eu, Gd, Ho, La, Nd, Pr, Sm, Tb, Tm, Lu	[135]
	N	Aspergillus ficuum	REY from monazite	[136]
	N	Burkholderia thailandensis	REY from monazite	[137]
	N	Enterobacter aerogenes	REY from monazite	[124]
	N	Gluconobacter oxydans	REY ore	[138,139,140]
	N	Leptospirillum ferriphilum	La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Lu	[135]
	N	Pantoea agglomerans	REY from monazite	[124]
	N	Pseudomonas aeruginosa	REY from monazite; coal fly ash	[120,136]
	N	Pseudomonas putida	REY from monazite	[124]
	P	Alicyclobacillus tolerans	La, Ce, Nd	[141]
	P	Arthrobacter nicotianae	REY ore	[89]
	P	Bacillus licheniformis	Ce; REY from industry wastes	[111]
	P	Bacillus sp.	La, Ce, Dy, Lu	[142]
	P	Streptomyces sp.	La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Y	[143]

F: Fungi; N: Gram-negative bacteria; P: Gram-positive bacteria; Red color: microorganism isolated from ocean or live in the ocean; * Methylobacterium extorquens facilitate REY enrichment via both biosorption and metabolic processes.

Table 2. Fungi and bacteria identified to have REY biosorption or bioleaching capabilities.

Mechanism	Categories	Strains	Tested REY	References
Biosorption	F	Aspergillus flavus	Ce	[101]
	F	Aspergillus niger	Ce	[101]
	F	Botryosphaeria rhodina	La, Sm	[102]
	F	Candida colliculosa	Nd	[103]
	F	Candida utilis	La, Sm, Sc, Y	[104]
	F	Catenulostroma chromoblastomyces	Ce, Nd, Gd, Dy	[96]
	F	Debaryomyces hansenii	Nd	[103]
	F	Fusarium sp.	Nd, Gd, Dy, Lu	[96]
	F	Kluyveromyces marxianus	Nd	[103]
	F	Pichia naganishii	La, Nd, Dy, Yb	[96]
	F	Pichia sp.	La, Nd, Dy, Yb	[96]
	F	Saccharomyces cerevisiae	La, Sm, Gd, Dy, Yb, Lu, Ce	[90,91,92,96,103,105]
	N	Agrobacterium sp.	La, Ce	[106]
	N	Caulobacter crescentus	Tb	[107]
	N	Escherichia coli	HREY	[87,89]
	N	Leisingera methylohalidivorans	HREY	[96]
	N	Magnetospirillum magneticum	La	[108]
	N	Methylobacterium extorquens *	Ln	[100,109]
	N	Paenisporosarcina sp.	Ce	[10]
	N	Phaeobacter inhibens	HREY	[96,97]
	N	Pseudomonas aeruginosa	La, Eu, Yb	[110]
	N	Pseudomonas fluorescens	Ce, Sm	[86]
	N	Sulfitobacter sp.	Ce	[10]
	P	Bacillus licheniformis	Ce	[111]
	P	Bacillus thuringiensis	Eu	[112]
	P	Jeotgalibacillus sp.	Ce	[10]
Bioleaching	F	Aspergillus flavus	Ce; REY from industry wastes	[101]
	F	Aspergillus niger	REY ore	[113,114,115,116,117]
	F	Aspergillus terreus	La, Ce, Nd, Pr	[118]
	F	Aspergillus sp.	Nd, Pm, Sm, Eu, Gd	[119]
	F	Candida bombicola	REY from coal fly ash	[120]
	F	Cryptococcus curvatus	REY from coal fly ash	[120]
	F	Paecilomyces sp.	La, Ce, Nd, Pr	[118,121]
	F	Penicillium chrysogenum	La, Ce, Y	[122]
	F	Penicillium tricolor	La, Ce, Nd, Sc, Y	[123]
	F	Penicillium sp.	REY from monazite	[124]
	F	Phanerochaete chrysosporium	La, Ce, Nd, Sc, Y	[120]
	F	Yarrowia lipolytica	La, Nd, Ce	[115]
	N	Acetobacter aceti	REY from monazite	[125]
	N	Acetobacter sp.	La, Ce, Nd, Sc, Y	[126]
	N	Acetobacter tropicalis	Sc	[127]
	N	Acidianus manzaensis	Ce, Gd, Sc, Y,	[128]
	N	Acidithiobacillus ferrooxidans	Nd, Pm, Sm, Eu, Gd, REY from phosphogypsum	[119,129,130,131,132]
	N	Acidithiobacillus thiooxidans	La, Ce, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Y	[133,134]
	N	Acidophilium multivorum	Ce, Dy, Er, Eu, Gd, Ho, La, Nd, Pr, Sm, Tb, Tm, Lu	[135]
	N	Aspergillus ficuum	REY from monazite	[136]
	N	Burkholderia thailandensis	REY from monazite	[137]
	N	Enterobacter aerogenes	REY from monazite	[124]
	N	Gluconobacter oxydans	REY ore	[138,139,140]
	N	Leptospirillum ferriphilum	La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Lu	[135]
	N	Pantoea agglomerans	REY from monazite	[124]
	N	Pseudomonas aeruginosa	REY from monazite; coal fly ash	[120,136]
	N	Pseudomonas putida	REY from monazite	[124]
	P	Alicyclobacillus tolerans	La, Ce, Nd	[141]
	P	Arthrobacter nicotianae	REY ore	[89]
	P	Bacillus licheniformis	Ce; REY from industry wastes	[111]
	P	Bacillus sp.	La, Ce, Dy, Lu	[142]
	P	Streptomyces sp.	La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Y	[143]

F: Fungi; N: Gram-negative bacteria; P: Gram-positive bacteria; Red color: microorganism isolated from ocean or live in the ocean; * Methylobacterium extorquens facilitate REY enrichment via both biosorption and metabolic processes.

4.2. REY Bioaccumulation and Utilization

REY enrichment mechanisms are not limited to adsorption; they can also be actively taken up by living cells, where they accumulate and form granules, collectively referred to as bioaccumulation [5,13,144]. After REY-absorbed plankton die, their sinking organic matter releases REY into sediments through remineralization [28]. Unlike passive biosorption, this bioaccumulation involves energy metabolism and possibly gene-regulated biochemical processes. For instance, in Methylobacterium extorquens, genes have been identified that regulate methylolanthanin, a metal-binding molecule that complexes with lanthanides [100,109], facilitating REY transport into cells and storage in granule-like structures called lanthasomes [99,100,109]. Studies have shown that REY can accumulate in a wide range of marine organisms, including phytoplankton, zooplankton, benthic organisms, and other invertebrates [3,27,88,145]. However, bioaccumulation tends to decrease with trophic levels, a phenomenon known as “trophic dilution” [145]. Primary producers such as plankton and algae often show higher REY concentrations, likely due to their direct interaction with REY ions in seawater. Strady et al. [146] were the first to measure REY content across different-sized plankton, finding strong correlations with trivalent REY forms. Fischer et al. [147] discovered that cyanobacteria can accumulate dissolved Eu, Sm, and Nd intracellularly, with amorphous Eu particles observed inside cells for the first time.

In some aquatic organisms, REY accumulation shows site-specific localization and selectivity, potentially affecting REY fractionation and migration to the deep sea [14,148]. REY can penetrate siliceous shells, enter the cytoplasm, and even reach intracellular organelles [27] (Figure 3). In Desmodesmus quadricauda, La and Gd preferentially accumulate in the cytoplasm, while Nd and Ce concentrate in chloroplasts [149]. Similar localizations have been observed in the chloroplasts of Chlorella vulgaris and Euglena gracilis [150,151]. It has been suggested that REY incorporation into diatom siliceous shells may play a significant role in REY transport to the deep sea [14,15,82], although the extent of this impact remains debated [83,152]. While REY bioaccumulation within cells is well documented, the mechanisms underlying REY uptake, membrane transport, intracellular storage, and regulation are still poorly understood. Palasz and Czekaj [153] hypothesize that REY may enter cells via calcium ion channels, providing a promising avenue for future research into REY transport in microbial cells.

The widespread bioaccumulation of REY in marine organisms highlights their potential bioavailability. Although REY are extensively accumulated, particularly by primary producers in marine systems, their biological roles remain poorly understood and are still generally considered as non-essential elements [5]. However, growing evidence suggests that certain biological functions of REY may have been overlooked. REY have been identified as an essential cofactor in key microbial enzymes and involved in multicarbon metabolisms, such as methanol oxidation [6,84,154,155]. The first lanthanide-dependent ethanol dehydrogenase (EDH) and XoxF-type methanol dehydrogenase (MDH) were discovered in Methylobacterium extorquens AM1, whose growth is entirely REY-dependent [156]. Subsequently, REY-dependent MDH and EDH enzymes have also been found in other Gram-negative bacteria, such as Methylacidiphilum fumariolicum [157,158], Bradyrhizobium sp. [159], Methylotenera mobilis [160], Methylomonas sp. [160], Methylobacterium radiotolerans [161], and Pseudomonas putida [162] (

Table 3. Enzymes in microorganisms identified as REY-dependent.

Category	Strain	Enzyme/Protein	Interacted REY	References
N	Methylacidiphilum fumariolicum SolV	MDH XoxF	La3+, Ce3+, Pr3+, Nd3+, Eu3+, Lu3+	[157,158]
N	Methylorubrum extorquens AM1	EDH ExaF, MDH XoxF1, Lanmodulin	La3+, Nd3+, Ln3+	[109,156,164,165,166]
N	Bradyrhizobium sp.	MDH XoxF	Ce3+	[159]
N	Methylotenera mobilis JLW8	MDH XoxF4-1/XoxF4-2	Ce3+	[160]
N	Methylomonas sp. LW13	MDH XoxF5	Ce3+	[160]
N	Methylobacterium radiotolerans	MDH XoxF	La3+	[161]
N	Pseudomonas putida	EDH PedH	La3+, Ce3+, Pr3+, Sm3+, Nd3+	[162]
——	Marine microorganism metagenome	MDH, EDH, putative SDH and GDH	LREY	[154]

N: Gram-negative bacteria; —— mixed metagenome data, no specific category; MDH: methanol dehydrogenase; EDH: ethanol dehydrogenase; SDH: sorbose dehydrogenase; GDH: glucose dehydrogenase.

). Additionally, a lanthanide-binding molecule, “Lanmodulin”, has also been found in Methylobacterium extorquens AM1; it is located between bacterial outer membranes and coexists with REY-dependent dehydrogenases, though its precise function remains unclear [109]. Recent analyses of global marine metagenomic and metatranscriptomic datasets have extended the known biological roles of REY to a wider range of enzymes and microbes, suggesting marine microorganisms may possess dozens of unique lanthanide-dependent genes [154]. Currently, research into REY bioutilization is still in its early stages. Some studies propose that the biological activities of REY may derive from their chemical similarity to calcium [85], with LREY more readily assimilated as free REY ions than HREY [5,146]. Among the LREY, La³⁺ and its hydroxide form (LaOH²⁺) are considered the most bioavailable, due to their high charge-to-volume ratio and strong protein-binding affinity [163].

4.3. REY Bioleaching and Degradation

Microorganisms play a crucial role not only in the enrichment and mineralization of REY but also in the decomposition and leaching of rare earth minerals. These processes include redoxolysis, acidolysis, and complexolysis [27,93] (Figure 3). Studies have identified microbes such as Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans as contributors to rare earth mineral decomposition via redox reactions [93,130,167,168,169]. These microbes oxidize Fe²⁺ to Fe³⁺, transferring electrons from the minerals to themselves and facilitating dissolution. Acidolysis involves the direct destruction of mineral lattices by protons, typically driven by the metabolic activity of sulfur and phosphate-oxidizing bacteria that produce sulfuric and phosphoric acids, which dissolve minerals and release REY [119,134,170]. Additionally, microbial metabolites such as organic acids and siderophores are key to complexation-mediated dissolution. These metabolites act as ligands that bind REY to form soluble complexes. For example, organic acids secreted by Aspergillus niger in synthetic media have been shown to efficiently dissolve REY, such as Ce, from monazite minerals, with citric acid being the most effective [93,171,172].

With the growing demand for REY, bioleaching has gained significant attention as a sustainable method for dissolving and extracting REY from terrestrial resources [93], particularly secondary sources such as phosphogypsum, red mud, and low-grade ores (Table 3). Compared with traditional chemical extraction methods, bioleaching offers advantages such as low energy consumption and environmental friendliness, making it especially suitable for processing complex mineral resources. However, current bioleaching studies remain largely focused on terrestrial REY deposits, with limited investigation into marine sediments as a potential resource. Despite its promise, the practical application still faces challenges, including efficiency improvement and cost reduction. Future research should prioritize optimizing microorganism–mineral interface interactions to enhance REY leaching performance, discovering novel microbial strains, and exploring gene regulatory mechanisms. The vast, largely unexplored diversity of marine microorganisms offers a promising frontier for developing innovative strategies in REY resource utilization.

5. Conclusions: Existing Challenges and Future Perspectives

REY are crucial to high-tech industries, driving increasing global demand [1,2]. Since the discovery of REY-rich deep-sea sediments in the Pacific Ocean, these deposits have been considered promising alternatives to terrestrial resources [4]. Significant progress has been made so far in understanding marine REY geochemical cycling, including the identification of sources, concentration and distribution patterns, fractionation behavior, and enrichment mechanisms. REY enter the ocean via continental weathering and erosion, windborne dust, and possible hydrothermal activity. Through complex biogeochemical processes—such as particle adsorption scavenging, microbe–REY interactions, and sedimentary remineralization—REY become enriched in deep-sea sediments [1,13,61] (Figure 1). To date, four deep-sea REY mineralization zones have been identified, with the largest reserves (ΣREY 6000–8000 × 10⁻⁶ μg/g) in the Western Pacific [54]. However, key gaps in marine REY research remain. First, the contribution of hydrothermal and volcanic activity to sedimentary REY enrichment varies regionally—being significant in the Eastern Pacific [56,57,58] but minor in the Central Pacific and Indian Ocean [50,52,55,58]—warranting further investigation. Second, the role of Fe-Mn micronodules in REY enrichment remains debated [5,51,72,75,79,80,81]. More evidence is needed to determine whether the observed REY-Fe correlation is driven by micronodules or by iron-rich clays, such as aquamarine [5,79]. Finally, the scarcity of REY data in pore water hampers accurate estimation of benthic REY fluxes [6].

Microbial interactions play a crucial role in mediating REY phase transitions between particulate and dissolved states, as well as REY enrichment, thus affecting REY distribution, sedimentation, bioavailability, and fractionation (Figure 3) [5,27]. Terrestrial microorganisms have been shown to promote REY enrichment through synergistic mechanisms involving surface adsorption and gene-regulated metabolisms [5,98]. However, under the extreme conditions of deep-sea sediments, such as high pressure, anaerobiosis, coexisting metals, and exceptional REY conditions, the mechanisms by which microorganisms contribute to REY enrichment still remain poorly understood. Current research mainly focuses on the inorganic adsorption mechanism, while microbial composition, functional genes, and metabolic characteristics of relevant strains in deep-sea REY-rich environments are still unclear. Microbial multi-omics approaches (e.g., metagenomic sequencing) offer essential tools to address this gap. Additionally, the challenges of culturing marine bacteria have hindered progress in studying REY-microbe interactions. As the field is still in its early stages, targeted simulation experiments are essential for advancing knowledge. Although REY are known to bioaccumulate in microbial cells, the mechanisms underlying REY uptake, membrane transport, intracellular storage, and regulation remain poorly characterized. Given the vast diversity of marine microorganisms, exploiting their metabolic potential for REY extraction and utilization represents a promising research avenue. Another major challenge is quantifying the microbial contribution to the marine REY cycle. The extent of microbial influence on REY transport and enrichment in marine environments remains difficult to assess and requires further investigation. Bridging these knowledge gaps is essential for advancing marine REY biogeochemistry and accessing its potential applications in resource development.