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Photographs of Zetaproteobacteria habitats. (A-D) Marine hydrothermal vent mats, where Zetaproteobacteria have been found in highest abundance. (A) Curdtype and (B) veil-type Fe mats, from Loihi Seamount. (C) Mn-crusted Fe mat from the Ula Nui site, Loihi. Fe mat visible under broken surface (bottom right). (D) Fe mats on the Golden Horn Chimney, at the Urashima vent site, Mariana Trough. (E) Transition from reduced to Fe(III) (oxyhydr)oxide-stained marine sediments (dashed line) in 26 m below seafloor core from the hydrothermal circulation cell of Iheya North vent field, Okinawa Trough. See Takai et al. (2012) for details. (F) Terrestrial saline CO2-rich spring at Crystal Geyser, UT, USA. (G) Fe(III) (oxyhydr)oxide-coated worm burrows from the beach at Cape Shores, DE, USA. (H) Mild steel corrosion biofilm formed by isolate M. sp. GSB-2. Original photography reproduced with permission: (H) by Joyce M. McBeth, (F) by Chris T. Brown.
Source publication
The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal s...
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... the environment, such oriented filaments are common. At Loihi Seamount, curd-type mats (cohesive Fe mats with a bumpy surface reminiscent of cheese curds) often form directly above a vent orifice (Fig. 4A) (Chan et al. 2016). Micrographs of intact curd ...
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... response to changes in the environment (Chan et al. 2016). The mechanism by which these cells actively control their directionality through stalk production is currently unknown. Beyond stalks, Loihi Seamount also hosts sheath-rich veiltype mats, which form millimeters-thick Fe mat draped over rock or older Fe mat in diffuse venting environments (Fig. 4B). These mats are created by organisms that form hollow Fe(III) (oxyhydr)oxide sheaths ( Fig. 2D-F), similar to those produced by the terrestrial Betaproteobacteria Leptothrix. In the marine environment, however, these sheaths are formed by Zetaproteobacteria ), informally called zetathrix. From studies based on the terrestrial ...
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... seawater oxygen concentrations are ∼50 μM at the summit of Loihi Seamount, due to its location within the oxygen minimum zone (Glazer and Rouxel 2009 Sotolongo and Izaguirre 1987;Emerson et al. 2015). Thus, the conditions at Loihi Seamount have favored the growth of Fe microbial mats ranging from centimeters to meters thick and up to 15 km 2 (Fig. 4A-C) (Edwards et al. 2011;Chan et al. 2016). The extensive Fe mats at Loihi Seamount may reflect years-to decades-long stable Fe mat production by the Zetaproteobacteria, based on productivity estimates (Chan et al. 2016;Emerson et al. ...
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... Loihi, Zetaproteobacteria are hosted by many other hydrothermal systems. Extensive Fe mats form around vents at seamounts and island arc systems (Fig. 4D) Emerson and Moyer Makita et al. 2016;Bortoluzzi et al. 2017;Hager et al. 2017). However, Fe mats have also been found at spreading ridge systems, within diffuse flow at the periphery of high-temperature chimneys and vents (Dekov et al. 2010;Breier et al. 2012;Scott et al. 2015; Vander Roost, Thorseth and Dahle 2017). Most hydrothermal ...
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... the marine subsurface. There, oxygenated seawater can mix with anoxic Fe(II)-rich fluids, providing a favorable environment for Fe(II) oxidation. Zetaproteobacteria have been observed by both 16S rRNA gene surveys and metagenomic reconstruction up to 332 meters below the sea floor, within both hydrothermal recharge and cold oxic circulation cells (Fig. 4E) (Yanagawa et al. 2013;Meyer et al. 2016;Tully et al. 2018). In many near surface sediments, shallow mixing introduces O 2 into an Fe(II)-rich environment, leading to abundant Zetaproteobacteria populations ( Davis et al. 2009;Kato et al. 2009b;Handley et al. 2010;Gonnella et al. 2016). As hydrothermal systems age and cool, basalts and ...
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... et al. 2016;Otte et al. 2018). Also in these sediments, bioturbation from plant roots and animal burrows provides conduits of O 2 to this Fe(II)-rich groundwater. Biotic and abiotic Fe(II) oxidation in these environments leads to the formation of Fe(III) (oxyhydr)oxides, which coat sands, salt grass and mangrove roots and burrows (Fig. 4G) (Taketani et al. 2010;McBeth et al. 2011;McAllister et al. 2015;Beam et al. 2018). Beam et al. (2018) found the abundance of Zetaproteobacteria within Fe(III) oxide-coated worm burrows to be an order of magnitude higher than surrounding bulk sediment, suggesting that Zetaproteobacteria growth and biotic Fe(II) oxidation can be favored ...
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... in CO 2 -rich terrestrial springs. Surveys of the 16S rRNA genes from carbonic springs at Tierra Amarilla Spring, New Mexico (∼9 ppt salinity) revealed a microbial population up to one third Zetaproteobacteria (Colman et al. 2014). Similarly, 16S rRNA gene and metagenomic work at the CO 2 -rich Crystal Geyser, Utah, (∼11-14 ppt salinity; Fig. 4F) found the Zetaproteobacteria to be both abundant and consistently present over a year of observation ( Emerson et al. 2016;Probst et al. 2017Probst et al. , 2018. These springs represent the first habitat with abundant populations of both Zetaproteobacteria and Betaproteobacteria FeOB (Gallionellaceae), whose abundance is likely driven ...
Citations
... We are hesitant to ascribe function from 16S identity alone, except in cases where there is substantial evidence that a certain metabolic capacity is shared amongst all or most members of that clade (e.g., the Desulfobulbaceae and Shewanellaceae mentioned above). All isolated members of the Zetaproteobacteria, for example, are experimentally-validated FeOB, and all Zetaproteobacterial genomes encode the putative iron oxidase Cyc2 (Koeksoy et al., 2021;McAllister, Moore, et al., 2019;McAllister, Polson, et al., 2020). However, no Zetaproteobacterial 16S sequences were identified in our samples based on analysis with ZetaHunter . ...
Deep‐sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe²⁺) can be produced by organoclastic iron reduction, methanotrophic‐coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate‐reducing bacteria at these sites. The prevalence of Fe²⁺in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron‐oxidising microbes. However, it is unclear to what extent Fe²⁺ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron‐oxidising bacteria, operating under the reasoning that if iron‐oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe²⁺ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially‐driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate‐depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate‐containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep‐derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria‐domainated ecosystem to one dominated by Rhodobacteraceae (Alphaproteobacteria). Our data suggest that, in most cases, sulfur cycling may restrict the biological “ferrous wheel” in contemporary environments through a combination of the sulfur‐adapted sediment‐dwelling ecosystems and the abiotic reactions they influence.
... In general, microbes are small in size and simple in form, and usually lack hard components that can be preserved as fossils (Chi Fru et al., 2013). A notable characteristic of Fe-oxidizing bacteria (FeOB) is that they can produce twisted, branching stalks or sheaths containing organic components and control the precipitation of Fe-oxyhydroxides in modern and ancient records (Krepski et al., 2013;McAllister et al., 2018;Dong et al., 2022). These iron oxides are influenced by organic ligands and silicification in hydrothermal environments, resulting in slower diagenesis than iron oxides of chemical origin (McAllister et al., 2011). ...
... Alternatively, taxa belonging to Acidimicrobiia, Nitrospiria, Thermodesulfovibrionia and Planctomycetia were present in samples from Mosh Pit and Lucky's Mound but rare in samples from Bio9 (Fig. 4a). The presence of Zetaproteobacteria is supported by scanning electron microscopy images of twisted stalks associated with this class (Fig. 4b) 27 . ...
Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of ¹⁴C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin–Benson–Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.
... They ar e the ne west described class of Proteobacteria with one described genus, Mariprofundus (Emerson et al. 2007. Since their original identification at hydr othermal v ents, Zeta pr oteobacteria hav e been shown to reside in specific ecological niches dispersed worldwide (McAllister et al. 2019 ). ...
... There are currently 59 OTUs of Zeta pr oteobacteria (zOTUs), four of whic h ar e consider ed cosmopolitan and another 12-15 of which have high endemic abundances . T he remaining zO TUs ha ve rarely been observed (McAllister et al. 2019 ). A few isolates have been grown in pure culture including Mariprofundus ferrooxydans (strains PV-1 and JV-1) from Kama'ehuakanaloa Seamount and isolates from the estuarine water column of Chesapeake Bay, among others (Chiu et al. 2017 ). ...
... Additionally, the concentrations of iron and sulfide impact community composition resulting in low Campylobacteria abundance at Kama'ehuakanaloa Seamount when sulfide is also low in high-temper atur e incubations. Zeta pr oteobacterial isolates hav e narr ow gr owth temper atur es fr om 20 to 35ºC wher eas Campylobacterial isolates hav e a wider growth temperature from 20 to 70ºC (Campbell et al. 2006, Nakagawa and Takai 2008, McAllister et al. 2019. When including the metadata collected alongside the MGCs, vent location, year, temper atur e, hydr oten sulfide and dissolv ed ir on wer e significant by permanova analysis. ...
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kamaʻehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kamaʻehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
... Interestingly the only genera found in our study within the Zetaproteobacteria class was Mariprofundus. This class of bacterium is a model organism for microbial iron oxidation in marine environments (McAllister et al., 2019). The detection of genera Mariprofundus in CC and NC perhaps originated from the mining activities at Mandovi estuary which has deposited several tonnes of iron ore. ...
In Goa, salt production from the local salt pans is an age-old practice. These salt pans harbor a rich diversity of halophilic microbes with immense biotechnological applications, as they tolerate extremely harsh conditions. Detecting the existence of these microbes by a metabarcoding approach could be a primary step to harness their potential. Three salt pans viz. Agarwado, Curca, and Nerul adjoining prominent estuaries of Goa were selected based on their unique geographical locations. The sediments of these salt pans were examined for their bacterial community and function by 16S rRNA amplicon-sequencing. These salt pans were hypersaline (400–450 PSU) and alkaline (pH 7.6–8.25), with 0.036–0.081 mg/L nitrite, 0.0031–0.016 mg/L nitrate, 6.66–15.81 mg/L sulfate, and 20.8–25.6 mg/L sulfide. The relative abundance revealed that the Pseudomonadota was dominant in salt pans of Nerul (13.9%), Curca (19.6%), and Agarwado (32.4%). The predominant genera in Nerul, Curca, and Agarwado salt pan sediments were Rhodopirellula (1.12%), Sulfurivermis (1.28%), and Psychrobacter (25.5%) respectively. The highest alpha diversity (Shannon-diversity Index) was observed in the Nerul salt pan (4.8) followed by Curca (4.3) and Agarwado (2.03). Beta diversity indicated the highest dissimilarity between Agarwado and the other two salt pans (0.73) viz. Nerul and Curca and the lowest dissimilarity was observed between Nerul and Curca salt pans (0.48). Additionally, in the Agarwado salt pan, 125 unique genera were detected, while in Nerul 119, and in Curca 28 distinct genera were noted. The presence of these exclusive microorganisms in a specific salt pan and its absence in the others indicate that the adjacent estuaries play a critical role in determining salt pan bacterial diversity. Further, the functional prediction of bacterial communities indicated the predominance of stress adaptation genes involved in osmotic balance, membrane modification, and DNA repair mechanisms. This is the first study to report the bacterial community structure and its functional genes in these three salt pans using Next-Generation Sequencing. The data generated could be used as a reference by other researchers across the world for bioprospecting these organisms for novel compounds having biotechnological and biomedical potential.
... Recent work has expanded our knowledge of microorganisms with an endogenous ability to perform extracellular electron uptake from cathodes (cathodic EET). These include acetogens and methanogens (Villano et al., 2010), sulfur and sulfate-reducing bacteria (Rowe et al., 2015;Agostino and Rosenbaum, 2018), denitrifiers (Tejedor-Sanz et al., 2016), photosynthetic and non-photosynthetic Fe 2+ -oxidizing bacteria (McAllister et al., 2019;Gupta et al., 2020). All these microorganisms reduce external electron acceptors to conserve energy and perform respiration. ...
A subset of microorganisms that perform respiration can endogenously utilize insoluble electron donors, such as Fe(II) or a cathode, in a process called extracellular electron transfer (EET). However, it is unknown whether similar endogenous EET can be performed by primarily fermentative species like lactic acid bacteria. We report for the first time electron uptake from a cathode by Lactiplantibacillus plantarum , a primarily fermentative bacteria found in the gut of mammals and in fermented foods. L. plantarum consumed electrons from a cathode and coupled this oxidation to the reduction of both an endogenous organic (pyruvate) and an exogenous inorganic electron acceptor (nitrate). This electron uptake from a cathode reroutes glucose fermentation toward lactate degradation and provides cells with a higher viability upon sugar exhaustion. Moreover, the associated genes and cofactors indicate that this activity is mechanistically different from that one employed by lactic acid bacteria to reduce an anode and to perform respiration. Our results expand our knowledge of the diversity of electroactive species and of the metabolic and bioenergetic strategies used by lactic acid bacteria.
... In addition to increases in iron transport genes, Zetaproteobacteria were identified in February and May samples which also contained iron oxidation genes ( Figure 4A). Zetaproteobacteria are marine iron oxidizing bacterium that play a role in iron cycling (Makita et al., 2017;McAllister et al., 2019). Iron concentrations in estuaries have previously been influenced by salinity, temperature, pH, and many other physico-chemical properties but can also be influenced by biotic interactions such as iron oxidizing bacteria (Daneshvar, 2015). ...
In Arctic regions, glaciers are major sources of iron to rivers and streams; however, estuaries are considered iron sinks due to the coagulation and flocculation processes that occur at higher salinities. It is unknown how iron dynamics in a glacial influenced river and estuary environment affect microbial mechanisms for iron acquisition. Microbial taxonomic and functional sequencing was performed on samples taken throughout the year from the Kenai River and the estuary, Alaska. Despite distinct iron, sodium, and other nutrient concentrations, the river and estuary did not have statistically different microbial communities nor was time of sampling significant. However, ferrous iron transport (Feo) system genes were more abundant in river environments, while siderophore genes were more abundant and diverse in estuary environments. Siderophore transport and iron storage genes were found in all samples, but gene abundance and distribution were potentially influenced by physical drivers such as discharge rates and nutrient distributions. Differences in iron metabolism between river and estuary ecosystems indicate environmental conditions drive microbial mechanisms to sequester iron. This could have implications for iron transport as the Arctic continues to warm.
... Anoxygenic phototrophs, owing to their low light requirements (Manske et al., 2005), luxuriously use the upwelling phosphate nutrient and oxidize most Fe(II) in the lower photic zone. In the oxic-anoxic transition zone, where trace amounts of dissolved oxygen and Fe(II) remain, microaerophilic IOB effectively compete with abiotic reactions and photoferrotrophy to precipitate any residual upwelling Fe(II), similar to observations from laboratory culture-based experiments (Druschel, Emerson, Sutka, Suchecki, & Luther III, 2008;McAllister et al., 2019). As a result, abiotic Fe oxidation pathways are effectively marginalized from the water column. ...
Banded Iron Formations (BIFs) are both the world’s largest ore deposits and important geological archives that record the early evolution of the Earth-Life system. BIFs were likely deposited as the result of ferrous iron [Fe(II)] oxidation, precipitation, and sedimentation from iron-rich (ferruginous) seawater, mostly during the Archean Eon. Proposed mechanisms for iron oxidation include abiotic reactions with photosynthetic oxygen, reaction with oxygen catalyzed by iron-oxidizing bacteria (IOB), and anoxic oxidation by anoxygenic iron-oxidizing phototrophic bacteria (photoferrotrophs). These iron oxidation processes may have operated concurrently, but their relative contributions to BIF deposition have not been considered. Here, we developed a 1-D ferruginous ocean model incorporating abiotic iron cycling and the physiology of oxygenic phototrophs, microaerophilic IOB, photoferrotrophs, and iron-reducing bacteria. Our model shows that, under Archean ocean conditions, most iron oxidation and precipitation would have been driven by photoferrotrophy, with a small fraction by microaerophilic IOB and a negligible contribution from abiotic reactions. The combined activities of these pathways led to BIF deposition at rates in line with geological records and, importantly, allowed the development of an Fe(II)-free surface ocean conducive to the formation of oxygen oases and the proliferation of oxygenic phototrophs.
Teaser
Archean ocean simulation shows that photoferrotrophs dominated the precipitation of BIFs and promoted the formation of marine oxygen oases.
... 10.5281/zenodo.8297777) for expected CO 2 fixation pathways in representative lineages (40,63,81,82); however, key genes for the serine variant of the reductive glycine pathway were observed in a Campylobacterota MAG (83). Form I RubisCO genes were identified in the Ghiorsea MAG Faaavne_M6_B18, and in a Gammaproteobacteria and Alphaproteobacteria MAG, using LithoGenie within MagicLamp (84). ...
... The only known cultivated exception is G. bivora, capable of using H 2 simultaneously with Fe(II), or as sole electron donor (53). It has been suggested that members of Ghiorsea (ZetaOTU9) not only occupy environments rich in Fe(II) but also combined with predicted presence of H 2 , such as at hydrothermal vents (53), in corrosion of steel (8,85), and mineral weathering (40,85,86). The presence of hydrogen in these Ghiorsea environments has mainly been based on hypotheses until the current study. ...
... Hence, this diversity indicates an absence of a monopolizing niche player in H 2 -poor diffuse flow, in contrast to Ghiorsea in the black smoker Fe mat where H 2 is available. This pattern of distribution supports the hypothesis that H 2 acts as a niche-determining factor for Ghiorsea at Fe(II)-rich hydrothermal vents (40). The ability of Ghiorsea to utilize H 2 affords it a competitive advantage as H 2 is a thermodynami cally more favorable energy source than Fe(II), supporting faster cell growth (53). ...
Iron-oxidizing Zetaproteobacteria are well known to colonize deep-sea hydrothermal vent fields around the world where iron-rich fluids are discharged into oxic seawater. How inter-field and intra-field differences in geochemistry influence the diversity of Zetaproteobacteria, however, remains largely unknown. Here, we characterize Zetaproteobacteria phylogenomic diversity, metabolic potential, and morphologies of the iron oxides they form, with a focus on the recently discovered Fåvne vent field. Located along the Mohns ridge in the Arctic, this vent field is a unique study site with vent fluids containing both iron and hydrogen with thick iron microbial mats (Fe mats) covering porously venting high-temperature (227-267°C) black smoker chimneys. Through genome-resolved metagenomics, we demonstrate that Zetaproteobacteria, Ghiorsea spp., likely produce tubular iron oxide sheaths dominating the Fe mats at Fåvne, as observed via microscopy. With these structures, Ghiorsea may provide a surface area for members of other abundant taxa such as Campylobacterota, Gammaproteobacteria, and Alphaproteobacteria. Furthermore, Ghiorsea likely oxidizes both iron and hydrogen present in the fluids, with several Ghiorsea populations co-existing in the same niche. Homologs of Zetaproteobacteria Ni,Fe hydrogenases and iron oxidation gene cyc2 were found in genomes of other community members, suggesting exchange of these genes could have happened in similar environments. Our study provides new insights into Zetaproteobacteria in hydrothermal vents, their diversity, energy metabolism and niche formation.
IMPORTANCE
Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron-and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
... Regardless of structure type, Mariprofundus (Zetaproteobacteria) and Sulfurimonas (Campylobacteria) together compose nearly half of sequences in communities, which was also observed in steel biofilms near (�2 m) steel-and woodenhulled shipwrecks in a prior work (Mugge et al. 2019a). Mariprofundus is widespread in the marine environment and capable of autotrophic iron oxidation on steel surfaces, in sediments, and in the water column (Chiu et al. 2017;McAllister et al. 2019). Within steel biofilms, iron-oxidizing bacteria such as Mariprofundus have been implicated as early colonizers, and can use iron released from the steel surface as an electron donor for growth (McBeth and Emerson 2016;Emerson 2018). ...
The rapidly expanding built environment in the northern Gulf of Mexico includes thousands of
human built structures (e.g. platforms, shipwrecks) on the seabed. Primary-colonizing microbial
biofilms transform structures into artificial reefs capable of supporting biodiversity, yet little is
known about formation and recruitment of biofilms. Short-term seafloor experiments containing
steel surfaces were placed near six structures, including historic shipwrecks and modern decommissioned
energy platforms. Biofilms were analyzed for changes in phylogenetic composition,
richness, and diversity relative to proximity to the structures. The biofilm core microbiome was
primarily composed of iron-oxidizing Mariprofundus, sulfur-oxidizing Sulfurimonas, and biofilmforming
Rhodobacteraceae. Alpha diversity and richness significantly declined as a function of
distance from structures. This study explores how built structures influence marine biofilms and
contributes knowledge on how anthropogenic activity impacts microbiomes on the seabed.
