The Potential Role of S-and Fe-Cycling Bacteria on the Formation of Fe-Bearing Mineral (Pyrite and Vivianite) in Alluvial Sediments from the Upper Chicamocha River Basin, Colombia

: S- and Fe-cycling bacteria can decisively affect the crystallization of Fe-bearing minerals in sediments from ﬂuvial environments. We have studied the relationships between the Fe-bearing mineral assemblage and the bacterial community composition in the sediments rich in organic matter from the upper Chicamocha river basin (Colombia). Rapid ﬂowing sections of the river contain sediments that have a high redox potential, are poor in organic matter and are enriched in kaolinite and quartz. On the other hand, the mineral assemblage of the sediments deposited in the La Playa dam with a high content in organic matter is enriched in Fe-bearing minerals: (a) vivianite and pyrite in the permanently ﬂooded sediments of the dam and (b) pyrite and goethite in the periodically emerged sediments. The bacterial community composition of these sediments reveals anthropic organic matter pollution processes and biodegradation associated with eutrophication. Moreover, periodically emerged sediments in the La Playa dam contain bacterial groups adapted to the alternation of dry and wet periods under oxic or anoxic conditions. Cell-shaped aggregates with a pyritic composition suggest that sulfate-reducing bacteria (SRB) communities were involved in the precipitation of Fe-sulﬁdes. The precipitation of vivianite in the ﬂooded sediments was favored by a greater availability of Fe(II), which promoted the iron-reducing bacteria (IRB) enrichment of the sediments. The presence of sulfur-oxidizing bacteria (SOB) in the ﬂooded sediments and the activity of iron-oxidizing bacteria (IOB) in the periodically emerged sediments favored both pyrite crystallization under a high sulﬁde availability and the oxidation of microbially precipitated monosulﬁdes. Moreover, IOB enhanced goethite formation in the periodically emerged sediments.


Introduction
Alluvial sediments deposited in river systems heavily used by anthropic activities can act as sinks for contaminants affecting the geochemistry of P, S and Fe in river courses and alluvial sediments (see e.g., [1][2][3]). Nutrient and pollutant loads can influence the accumulation of organic matter, sediment-water interactions, redox conditions and microbial activity in alluvial systems, which control mineralogical and biogeochemical processes that affect the fate of these elements [3].
The construction of dams that regulate water outflow has been used as a tool for the remediation of pollution problems of these elements in river courses [4,5]. These reservoirs can modify the composition of the river waters through dilution with rainwater [6].
(Paipa, Colombia) with slow-flowing conditions and periodic flooding produced by the La Playa dam. We aim to evaluate the role of S-and Fe-cycling bacteria in the distribution of these minerals in the sediments and their influence on P, S and Fe immobilization in sediments deposited in the La Playa dam, trying to identify the main microbial communities associated with the biogeochemical processes that influence mineral precipitation. We have combined mineralogical and microbiological methods to explain the presence of Fe-bearing phosphates, sulfides and oxyhydroxides in eutrophicated organic-matter-rich sediments.

Background Context
The area of study (UCRB) belongs to the equatorial Andes (Colombia, Boyacá department) (Figure 1). Fluvial plains that are around 2500 m of altitude above sea level can be found in this area. The length of the UCRB is 62.46 km, its average slope is 0.12% and it flows to the Caribbean Sea [25]. The annual rainfall of the UCRB oscillates from 650-1200 mm and the average year temperature is 13.1 • C.
ides in the organic matter and clay-rich sediments deposited in a river segment of the UCRB (Paipa, Colombia) with slow-flowing conditions and periodic flooding produced by the La Playa dam. We aim to evaluate the role of S-and Fe-cycling bacteria in the distribution of these minerals in the sediments and their influence on P, S and Fe immobilization in sediments deposited in the La Playa dam, trying to identify the main microbial communities associated with the biogeochemical processes that influence mineral precipitation. We have combined mineralogical and microbiological methods to explain the presence of Fe-bearing phosphates, sulfides and oxyhydroxides in eutrophicated organicmatter-rich sediments.

Background Context
The area of study (UCRB) belongs to the equatorial Andes (Colombia, Boyacá department) (Figure 1). Fluvial plains that are around 2500 m of altitude above sea level can be found in this area. The length of the UCRB is 62.46 km, its average slope is 0.12% and it flows to the Caribbean Sea [25]. The annual rainfall of the UCRB oscillates from 650-1200 mm and the average year temperature is 13.1 °C.
The most relevant anthropic change in the UCRB is the La Playa dam, which divides the UCRB into three segments: a central segment with slow-flowing conditions and two fast-flowing sections situated downstream and upstream of the dam (Figure 1). The reservoir of the La Playa dam receives wastewaters (urban sewage) from the towns of the region and waters of the agricultural activities, which generate a high nutrient load and intense eutrophication [26]. Fast flowing sections of the Chicamocha river show sediments enriched in quartz and kaolinite with low contents in organic matter (TOC < 0.52%), a high redox potential (around 70 mV) and low electrical conductivity (around 200 µ S/cm) [27]. The sediments from the La Playa dam are characterized by alternating bands of microlaminated organicmatter-rich layers and clay-rich layers [27], showing a high organic matter content (TOC of up to 11.1 %), low redox potential (around −230 mV) and high electrical conductivity (2625 µ S/cm) [27]. Fe-bearing minerals were exclusively found in sediments from the La The most relevant anthropic change in the UCRB is the La Playa dam, which divides the UCRB into three segments: a central segment with slow-flowing conditions and two fastflowing sections situated downstream and upstream of the dam (Figure 1). The reservoir of the La Playa dam receives wastewaters (urban sewage) from the towns of the region and waters of the agricultural activities, which generate a high nutrient load and intense eutrophication [26].
Fast flowing sections of the Chicamocha river show sediments enriched in quartz and kaolinite with low contents in organic matter (TOC < 0.52%), a high redox potential (around 70 mV) and low electrical conductivity (around 200 µS/cm) [27]. The sediments from the La Playa dam are characterized by alternating bands of microlaminated organicmatter-rich layers and clay-rich layers [27], showing a high organic matter content (TOC of up to 11.1%), low redox potential (around −230 mV) and high electrical conductivity (2625 µS/cm) [27]. Fe-bearing minerals were exclusively found in sediments from the La Playa dam and were absent from the rest of the alluvial sediments from the Chicamocha river basin [9,27].
The quantitative chemical composition and mineral composition of the untreated samples of the studied sediments in the La Playa dam, as well as their in situ physicochemical properties, are shown in Table 1. Table 1. Sediment characterization of La Playa sediments. Major element sediment compositions of the untreated samples determined by XRF (X-ray fluorescence spectroscopy), loss of ignition (LOI), content in total organic carbon (TOC) and mineral abundances determined by XRD (in weight percentage, except for S in mg/kg). In situ physicochemical properties. R.P.: redox potential (mV); E.C.: electrical conductivity (µS/cm); Qz: quartz; Py: pyrite; Viv: vivianite; Gth: goethite.

Materials
A network with 25 points of sediment sampling through the three segments of the UCRB was designed ( Figure 1). Sediment cores were obtained with a stainless Shelby tube. Hanna Instruments meters for sediments and soils (HI98168 and HI98168) were used to determine in situ sediment pH, redox potential and electrical conductivity, respectively. The samples of sediment were dried at 40 • C in an oven as a previous step for other mineralogical treatments.

Mineralogical Methods
Random and oriented aggregates were used to obtain XRD data. An isodynamic magnetic separator was used to obtain a fraction of the total sample enriched in Fe-bearing minerals. A Panalytical X'Pert Pro diffractometer (CuKα radiation, 45 kV, 40 mA) (CICT of the Universidad de Jaén, Jaén, Spain) equipped with a X'Celerator solid-state linear detector was used to acquire the diffraction patterns (step increment 0.008 • 2θ, counting time 10 s/step).
Field emission scanning electron microscope (FESEM, Merlin Carl Zeiss, Oberkochen, Germany) was used for textural and chemical characterization of sediments. Back-scattered electron (BSE) images were obtained from polished sections. We used secondary electron (SE) images for the study of sediment fragments. Elemental mineral composition was obtained with energy dispersive X-ray spectrometry (EDX).
High resolution transmission electron microscopy (HRTEM) study was carried out in selected samples in a HAADF FEI TITAN G2 microscope operated at 300 kV (CIC, University of Granada, Granada, Spain). Samples were deposited on coated Au and Cu grids. Nanoparticle qualitative analyses were acquired by energy-dispersive X-ray spectroscopy (EDX) in the mode scanning transmission electron microscope.

Microbiological Methods
A DNeasy PowerSoil Kit (Quiagen, Barcelona, Spain) was used for DNA extraction from the samples following the instructions of the manufacturer. A QuantiFluor ® ONE dsDNA system (Promega, Madison, USA) was employed to determine the quality and the amount of the obtained DNA. The DNA was stored at -20 • C until analysis. Regarding DNA sequencing and analysis, 16S rDNA gene amplicons were obtained following the 16S rDNA gene Metagenomic Sequencing Library Preparation Illumina protocol (Cod. 15044223 Rev. A). The gene-specific sequences used in this protocol targeted the 16S rDNA gene V3 and V4 region. Illumina adapter overhang nucleotide sequences were added to the gene-specific sequences. The primers were selected from Klindworth et al. [28]. The following 16S rDNA gene amplicon PCR primer sequences were used: forward primer, 5'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCC-TACGGGNGGCWGCAG3'; reverse primer, 5'GTCTCGTGGGCTCGGAGATGTGTATAA-GAGACAGGACTACHVGGGTATCTAATCC3'. Microbial genomic DNA (5 ng/µL in 10 mM Tris pH 8.5) was used to initiate the protocol. After 16S rDNA gene amplification, the multiplexing step was performed using a Nextera XT Index Kit (FC-131-1096) (Illumina, Cambridge, UK). One µL of the PCR product was run on a Bioanalyzer DNA 1000 chip to verify the size (expected size~550 bp). Following size verification, the libraries were sequenced using a 2 × 300 pb paired-end run (MiSeq Reagent kit v3 (MS-102-3001)) on a MiSeq Sequencer according to the manufacturer's instructions (Illumina, Cambridge, UK). Quality assessment was performed with the use of the prinseq-lite program [29]. The sequence data were analyzed using the qiime2 pipeline [30]. Denoising, paired-end joining and chimera depletion were performed, starting with paired-end data using the DADA2 pipeline [31]. Taxonomic affiliations were assigned using the Naive Bayesian classifier integrated in the qiime2 plugins and the SILVA_release_132 database [32]. Statistical analysis was carried out with SPSS software version 24 (IBM Corp., Foster City, CA, USA). The sequencing output files will be available at the Sequence Read Archive (SRA) service of the European Bioinformatics Institute (EBI) database under Accession Number PRJEB47878.

Fe-Bearing Minerals of the Sediments
Fe-bearing minerals are absent in the fast-flowing sections of the UCRB (Samples PR, Figure 1). On the contrary, the mineral assemblage of the La Playa dam is rich in clay minerals and characterized by the abundance of kaolinite, illite-dioctahedral vermiculite mixed layers (I-DV), framboids pyrite, vivianite and goethite ( Figure 2) [9]. Disrupted organic matter microbands alternate with clay-rich microlaminae ( Figure 3A) in permanently flooded sediments and periodically emerged materials of the dam. size (expected size ~550 bp). Following size verification, the libr ing a 2 × 300 pb paired-end run (MiSeq Reagent kit v3 (MS-1 quencer according to the manufacturer's instructions (Illumina, assessment was performed with the use of the prinseq-lite pro data were analyzed using the qiime2 pipeline [30]. Denoising, pa mera depletion were performed, starting with paired-end data u [31]. Taxonomic affiliations were assigned using the Naive Bay in the qiime2 plugins and the SILVA_release_132 database [32 carried out with SPSS software version 24 (IBM Corp., Foster quencing output files will be available at the Sequence Read Ar European Bioinformatics Institute (EBI) database under Accessi

Fe-Bearing Minerals of the Sediments
Fe-bearing minerals are absent in the fast-flowing sections o Figure 1). On the contrary, the mineral assemblage of the La minerals and characterized by the abundance of kaolinite, illite mixed layers (I-DV), framboids pyrite, vivianite and goethite (F ganic matter microbands alternate with clay-rich microlamina nently flooded sediments and periodically emerged materials o    Figure 3D,E) in permanently flooded sediments and smaller microframboids (< 5µ m) containing regular nanocrystals with a honeycomb disposition in periodically emerged sediments ( Figure 3F).
XRD patterns indicated that the presence of vivianite is restricted to the permanently flooded sediments (6.70 and 2.52 Å peaks, Figure 2A). Vivianite appears as small prismatic to flat nanocrystals frequently associated with the occurrence of plant fragments ( Figure  4A,B). HRTEM images and EDX elemental mapping revealed the presence of crystals with a vivianite composition ( Figure 4C-F) and lattice fringes around 6.7 Å , which can be produced by the (020) spacing of vivianite. XRD patterns indicated that the presence of vivianite is restricted to the permanently flooded sediments (6.70 and 2.52 Å peaks, Figure 2A). Vivianite appears as small prismatic to flat nanocrystals frequently associated with the occurrence of plant fragments ( Figure 4A,B). HRTEM images and EDX elemental mapping revealed the presence of crystals with a vivianite composition ( Figure 4C-F) and lattice fringes around 6.7 Å, which can be produced by the (020) spacing of vivianite.
Goethite was only identified in the XRD patterns of the periodically emerged sediments by a small peak at 4.18 Å and a peak at 2.46 Å over-imposed to clays ( Figure 2B). The SEM images revealed that goethite occurs as crusts with dendritic and botryoidal morphologies in the silicate-rich bands of the sediments ( Figure 5). Goethite was only identified in the XRD patterns of the periodically emerged s ments by a small peak at 4.18 Å and a peak at 2.46 Å over-imposed to clays (Figure The SEM images revealed that goethite occurs as crusts with dendritic and botryo morphologies in the silicate-rich bands of the sediments ( Figure 5).  Goethite was only identified in the XRD patterns of the periodically emerged sediments by a small peak at 4.18 Å and a peak at 2.46 Å over-imposed to clays ( Figure 2B). The SEM images revealed that goethite occurs as crusts with dendritic and botryoidal morphologies in the silicate-rich bands of the sediments ( Figure 5).

Bacterial Populations
Proteobacteria were very abundant in all of the studied samples (25-29%). Rhodanobacter, Geobacter, Aquabacterium, Dechloromonas, Pseudomonas, Dyella, Desulfomicrobium and Desulfobulbus are the most abundant genera of this phylum in the permanently flooded sediments (3.6-0.7%), whereas the periodically emerged sediments are characterized by the presence of order Elsterales, families Micropepsaceae, Acetobacteraceae, Gallionellaceae (including genus Sideroxydans) and genera Syntrophobacter, Acidibacter, Desulfobacca and Thauera (3.5-0.8%) ( Figure 6). Due to the high bacterial diversity of the studied sediments, and given that Figure 6 only shows groups with a relative abundance of at least 1%, the percentage of diversity represented in Figure 6 oscillates between 53-65%.
Minerals 2021, 11, x FOR PEER REVIEW

Bacterial Populations
Proteobacteria were very abundant in all of the studied samples (25-29%). Rhod ter, Geobacter, Aquabacterium, Dechloromonas, Pseudomonas, Dyella, Desulfomicrobi Desulfobulbus are the most abundant genera of this phylum in the permanently sediments (3.6-0.7%), whereas the periodically emerged sediments are character the presence of order Elsterales, families Micropepsaceae, Acetobacteraceae, Gallionella cluding genus Sideroxydans) and genera Syntrophobacter, Acidibacter, Desulfobac Thauera (3.5-0.8%) ( Figure 6). Due to the high bacterial diversity of the studied sed and given that Figure 6 only shows groups with a relative abundance of at least percentage of diversity represented in Figure 6 oscillates between 53-65%. Figure 6. Bacterial diversity in the organic matter-rich sediments from La Playa dam. LP LP7B are samples that are permanently flooded. LP8A and LP8B are samples that are per emerged. "A samples" belong to the surficial part of the core sediment, whereas "B sample taken from the deepest part of the core sediment in LP7 and LP8 sampling points. 16S rR quences with a relative abundance of at least 1% are shown. Sequences were assigned to gen or the corresponding higher taxonomic group.
The abundance of other phyla depends on the type of sediments analyzed. Im differences can be observed between the permanently flooded and the perio emerged sediments of the dam.
High representations of Bacteroidetes (28%) and Firmicutes (12%) were observe Figure 6. Bacterial diversity in the organic matter-rich sediments from La Playa dam. LP7A and LP7B are samples that are permanently flooded. LP8A and LP8B are samples that are periodically emerged. "A samples" belong to the surficial part of the core sediment, whereas "B samples" were taken from the deepest part of the core sediment in LP7 and LP8 sampling points. 16S rRNA sequences with a relative abundance of at least 1% are shown. Sequences were assigned to genus level or the corresponding higher taxonomic group. The abundance of other phyla depends on the type of sediments analyzed. Important differences can be observed between the permanently flooded and the periodically emerged sediments of the dam.
High representations of Bacteroidetes (28%) and Firmicutes (12%) were observed in the permanently flooded sediments of the dam. Rikenellaceae family members are the best-represented communities of Bacteroidetes (around 5%). Other Bacteroidetes genera documented in these sediments were WCHB1-32, BVS13 and Macellibacteroides and Paludibacter. The phylum Firmicutes is represented by the Christensenellaceae family and Syntrophomonadaceae members in the flooded sediments. Significant amounts of Epsilonbacteraeota phyla (around 5%) are also identified in these sediments, with genera Sulfuricurvum and Arcobacter as the main representative communities.

Mineral Distribution
The mineral distribution is related to the two main types of materials that can be distinguished in the La Playa dam. Pyrite is present in all of the sediments deposited in the reservoir. Quevedo et al. [9,27] indicated that the enrichment in the clay minerals and organic matter (TOC up to 13.84%) of the sediments from the La Playa reservoir, with regard to the quartz-rich sediments from the rest of the sediments of the UCRB, favored the precipitation of sulfide minerals.
However, the spatial distribution of Fe-bearing phosphate and hydroxide in the sediments of the La Playa dam seems to be associated with the flooding conditions of the sediments. Permanently flooded sediments that are richer in organic matter and have a lower redox potential (around −230mV) [27] from the northern part of the reservoir are characterized by the presence of vivianite and, by contrast, periodically emerged sediments from the southern part of the reservoir with lower organic matter contents (4.29%) and higher Eh values (−10mV) contain goethite. These data suggest that redox conditions and the organic matter content are two important factors controlling the formation of the Fe-bearing minerals of the sediments.
Pyrite and vivianite were found together in the flooded sediments of the La Playa reservoir, which is relatively uncommon in natural sediments (see e.g., [33]). The presence of pyrite is very common in anoxic sediments formed in sulfate-rich water environments. Pyrite exhibited two types of morphologies in the studied sediments. On the one hand, the presence of small dispersed crystals forming encrusted cell-shaped aggregates ( Figure 4B,C) suggests the importance of microorganisms in the nucleation of sulfide minerals. On the other hand, the formation of microframboids, including hopper pyrite crystals, suggests transformation processes under high supersaturation values of Fe and sulfide, which promote the fast accumulation of growth units at the crystal edges, causing the typical faces of hopper grains [34].
Pyrite formation can compete with the precipitation of vivianite for the available reduced Fe of the environment, avoiding vivianite crystallization when the concentration of sulfide is very high [35]. Iron can act on the immobilization of phosphorous under anoxic conditions through the biotic and abiotic precipitation of Fe(II) vivianite in highly eutrophized environments [36][37][38]. Indeed, vivianite is considered as a main phosphorus sink in natural and engineered environments [39][40][41]. Rothe et al. [36] suggested that vivianite authigenesis is mainly controlled by the ratio between sulfide and Fe(II) availability. Thus, the formation of vivianite is frequently restricted to environments where an excess of Fe in dissolution is available after the crystallization of sulfides. However, microorganisms can play an important role in the availability of these substances and, therefore, in the concomitant crystallization of phosphates and sulfides [37]. In the next section, we explore some relationships between the mineral distribution and the presence of microorganisms in the sediments.
The Fe-bearing minerals in the periodically emerged sediments from the La Playa dam were goethite and pyrite. When the dam is drained, as a result, a modification of the moisture conditions is produced, which can lead to the fluctuation of the redox conditions in the sediments. Therefore, the variation of the water level is an important factor in regulating the sediment redox conditions and can affect the iron redox cycle, which is considered as a crucial factor for controlling the biogeochemistry of organicmatter-rich sediments. Watanabe et al. [14] showed that repeated cycles of wetting and drying produced a significant oscillation of the iron redox status of soils. The presence of goethite in the periodically emerged sediments suggests that processes of Fe oxidation occurred. Druschel et al. [42] indicated that iron oxidation kinetics are mainly affected by oxygen availability, although pH, temperature, the surface area of the Fe (III) bearing minerals and the presence of iron-oxidizing microorganisms can influence the rate of the process. Cornell and Schwertmann [12] indicated that iron oxides/oxyhydroxides are prevalent in oxic sediments; even those deposited in eutrophic environments [13]. The formation of Fe (III) can affect the stability of the rest of the Fe-bearing minerals in the sediments. Duverger et al. [38] suggested that the presence of ferric iron can promote the conversion of mackinawite, favoring the pyrite enrichment of the sediments.

The Role of the Bacterial Communities
Sediments that are rich in organic matter from the La Playa dam (Chicamocha River Basin, Colombia) are characterized by a bacterial community with a diverse composition. Processes of organic matter degradation and mineral transformation in the C, Fe, P and S cycles are associated with the bacterial activity of the dam sediments.
The permanently flooded sediments of the dam are characterized by the high amount of Bacteroidetes and Firmicutes phyla. Most of the bacterial communities from these groups identified in this type of sediment have been documented in the biodegradation of organic matter deposits from anthropogenic activities in sediments from dams that favors endogenous water pollution and eutrophication, which is a potential threat for the pond environment [43][44][45]. The high representation of the Rikenellaceae family (Bacteroidetes) in these sediments can be associated with being responsible for the decomposition of harmful algal bloom in ponds [43]. The rest of Bacteroidetes genera identified in these sediments, such as WCHB1-32, BVS13 and Macellibacteroides [16], have been thought to be important in the formation of methanogenic precursors from organic matter degradation. Hou et al. [46] suggested that members of the phylum Firmicutes, such as the Christensenellaceae family, are frequently reported in human feces and other animal feces, and show a fairly high capability for degrading carbohydrates and carboxylic acids. Within the phylum Firmicutes, the presence of relevant amounts of Syntrophomonadaceae members in the flooded sediments from the La Playa dam can contribute to produce H 2 used by sulfate-reducing bacteria (SRB) acting as syntrophic partners [47].
On the other hand, in samples that are periodically emerged and dried in the La Playa dam, several members of the phylum Acidobacteria, such as Candidatus Koribacter and Candidatus Solibacter, are very well represented in this type of sediment from the La Playa dam. These groups have been reported in high amounts in organic-matter-rich soils from dry seasons that are affected by fertirrigation practices [48] and have a high salinity [49]. Other bacterial groups described in soils and sediments rich in organic matter with a high salinity, such as members of the Verrucomicrobia (see e.g., [49]) and Actinobacteria [50,51], were also enriched in the periodically emerged sediments from the La Playa dam. Berg et al. [35] indicated that Actinobacteria have a mostly aerobic style of life. This is also consistent with the enrichment in the Planctomycetes phylum of these sediments (7,7%). Dedysh et al. [52] indicated that these bacteria are able to colonize oxic peat layers from boreal and subarctic wetlands. Regardless, the periodically emerged sediments are also characterized by the presence of significant amounts of Anaerolineaceae from the Chloroflexi phyllum (up to 7.7%), which are anaerobic organisms with the capability of fermentation [53]. The abundance of these communities can be related to anoxic conditions and high organic matter contents. Cifuentes et al. [54] suggested that Anaerolineaceae and Bacteroidetes_vadinHA17 are important communities involved in the final degradation stages of organic matter in sulfidic zones. The presence of the Ignavibacteriales order in the periodically emerged sediments can be related to CO 2 fixation processes [55].
Lin et al. [53] indicated that Anaerolineaceae can act as biogeochemical linkers that relate the reactions of C and S in mangrove sediments, favoring the mobility of these elements in the system, which can affect the cycle of Fe and other metals of the sediments and the activity of iron-and sulfur-cycling bacteria, sulfur-and sulfate-reducing bacteria (SRB), sulfide-oxidizing bacteria (SOB), iron-reducing bacteria (IRB) and iron-oxidizing bacteria (IOB). SRB, SOB, IRB and IOB communities have been reported in the La Playa dam sediments, but their distributions are not homogeneous.
SRB are present in all of the organic matter rich sediments from La Playa. Flooded sediments contain Pseudomonas (up to 2.9%), Desulfomicrobium and Desulfobulbus (up to 1%) genera. Hazra et al. [56] documented that Pseudomonas plays an important role in the synthesis of spherical ZnS nanoparticles. Moreover, this bacterial group is characterized by its elevated levels of metal resistance [57] and its ability to colonize in sewage [58] and remove organic carbon in the wetland ponds [59]. Liu et al. [60] indicated that Pseudomonas are responsible for the hydrocarbon degradation of sediments coupled to the reaction of Fe reduction in sediments. Rigorously anaerobic SRB Desulfomicrobium and Desulfobulbus have been reported as microorganisms that are involved in sulfate reduction, promoting P release at contaminated sediments [60].
On the contrary, predominant SRB communities in periodically emerged sediments are Syntrophobacter (up to 1.9%), Thermodesulfovibrionia (up to 1.7%) and Desulfobacca (0.8%). Li et al. [61] reported that Syntrophobacter are SRB that are frequently present in sulfate-rich wetlands. Gessink et al. [62] indicated that Thermodesulfovibrionia play a crucial role in the cycles of nitrogen and sulfur in groundwaters. Desulfobacca is commonly found in sludge environments and paddy soils [63].
IRB are very well represented in the flooded sediments where the Proteobacteria genera Geobacter (3%), Dechloromonas (3%) and Pseudomonas (2%), as well as the Bacteroidetes genus Paludibacter (3%), are present. Wang et al. [63] documented that the presence of Geobacter and Paludibacter was associated with organic-matter-rich sediments with humic acids, playing an essential function in the release of Fe(II) to the interstitials waters of sediments under anaerobic conditions. Dechloromonas has been found to be related to the reduction of Fe(III) to Fe(II) in sludges that contain P and Fe, promoting the reaction of Fe(II) with PO 4 3to form vivianite [41]. Moreover, Zhang et al. [64] indicated that the genus Dechloromonas is frequently associated with phosphate accumulations and that high phosphate contents favor its growth. Berg et al. [35] showed the presence of Pseudomonas as one of the IRB in the Lake Pavin water column. Liu et al. [60] indicated that Pseudomonas can play an active role in the connection of the carbon cycle with the Fe reductions reactions in hydrocarbon-rich sediments. Sanchez-Andrea et al. [65] described Paludibacter as a fermentative microorganism in high sulfate and metal concentration environments that is able to transfer electrons from anaerobic oxidations to promote the reduction of iron.
In contrast, Acidibacter (up to 2%) is the only IRB genus reported in the periodically emerged sediments of the La Playa dam. This genus has been classified as acidophilic, with the capability of reducing dissolved Fe(III) in low pH and high Fe environments [66].
IOB are absent in the flooded sediments, but members of the Gallionellaceae family (2%) and the Sideroxydans genus (up to 1.9%) are very well represented in the periodically emerged sediments of the La Playa dam. Watanabe et al. [14] revealed the importance of bacteria that belong to the Gallionellaceae family and the Sideroxydans genus on the oxidation of Fe(II) in soils that alternate wetting and drying periods, reporting that the amount of IOB was higher in the surface oxic layer of these types of soils. Berg et al. [35] identified the presence of the obligately aerobic to microaerobic iron oxidizer Gallionella sequences in anoxic waters, because they can be adapted to low oxygen levels.
In flooded sediments of the La Playa dam, two genera of anaerobic SOBs, Sulfuricurvum (around 3%) and Arcobacter (up to 2%), were detected. However, these groups of bacteria were absent in the periodically emerged sediments. Berg et al. [35] observed that Sulfuricurvum was the dominant SOB under elevated free sulfide concentrations. Zhang et al. [67] suggested that the presence of Arcobacter can be used as an indicator of sewer and human fecal pollution.
Duverger et al. [38] revealed that the SOB presence could increase the pyrite crystallization rate, suggesting that the SRB-induced formation of pyrite can be enhanced by the SOB simultaneous activity.

1.
The high content in bacterial communities from the Bacteroidetes and Firmicutes phyla of the permanently flooded sediments of the La Playa dam reveal anthropic organic matter pollution processes (e.g., the presence of groups commonly found in feces, such as the Christensenellaceae family) and biodegradation associated with eutrophication (Rikenellaceae family, WCHB1-32, BVS13 and Macellibacteroides); 2.
The composition of the bacterial communities of the periodically emerged and dried sediments in the La Playa dam is characterized by the presence of groups frequently reported in high salinity soils (Verrucomicrobia and Actinobacteria) affected by the alternation of dry and wet periods (Candidatus Koribacter and Candidatus Solibacter) with oxic conditions (Planctomycetes), as well as by the presence of anaerobic microorganisms related to anoxic conditions (Anaerolineaceae); 3.
Both flooded and periodically emerged sediments show relevant SRB communities involved in the precipitation of Fe-sulfides ( Figure 7). SEM images showing cell-shaped aggregates with a pyritic composition support the importance of the bacterial communities in the nucleation and transformation of sulfide minerals. The activity of these bacterial groups in the flooded sediments can be reinforced by syntrophic partners to produce H 2 used by SRB (Syntrophomonadaceae) and increase the sulfide availability; Minerals 2021, 11, x FOR PEER REVIEW 12 of 16 In flooded sediments of the La Playa dam, two genera of anaerobic SOBs, Sulfuricurvum (around 3%) and Arcobacter (up to 2%), were detected. However, these groups of bacteria were absent in the periodically emerged sediments. Berg et al. [35] observed that Sulfuricurvum was the dominant SOB under elevated free sulfide concentrations. Zhang et al. [67] suggested that the presence of Arcobacter can be used as an indicator of sewer and human fecal pollution.
Duverger et al. [38] revealed that the SOB presence could increase the pyrite crystallization rate, suggesting that the SRB-induced formation of pyrite can be enhanced by the SOB simultaneous activity.

5.
Bacterial activity should favor supersaturation in Fe(II) (promoted by IRB and SRB) and sulfide (stimulated by SRB and their syntrophic partners that produce H 2 ), which can be associated with the crystallization of hopper pyrite crystals in the permanently flooded sediments; 6.
Moreover, the SOB presence in the flooded sediments and the presence of Fe(III) due to aerobic conditions and the activity of IOB in the periodically emerged sediments can favor both pyrite crystallization under a high sulfide availability and the oxidation of microbially precipitated monosulfides. Moreover, IOB could enhance the precipitation of goethite in the periodically emerged sediments, even under low oxygen levels. Author