Freshwater Sediments Research Articles

Microbial manganese redox cycling drives co-removal of nitrate and ammonium.

Manganese (Mn), abundant in the Earth's crust, can act as an oxidant or a reductant for diverse nitrogen biotransformation processes. However, the functional microorganisms and their metabolic pathways, as well as interactions, remain largely elusive. Here, a microbial consortium was enriched from a mixture of freshwater sediments and activated sludge by feeding ammonium, nitrate and Mn(II), which established manganese-driven co-removal of nitrate and ammonium with removal rates of 5.83 and 2.30mgN L-1 d-1, respectively. The batch tests and metagenomic analyses revealed a nitrate-dependent anaerobic manganese oxidation (NDMO) process mediated by Anaerolineales and Phycisphaerales and a manganese reduction coupled to anaerobic ammonium oxidation (Mnammox) process mediated by Chthonomonadales. Based on identified key genes involved in the nitrogen and manganese metabolic pathways, nitrate was likely reduced to nitrite and nitrogen gas in the NDMO process while ammonium was oxidized to nitrite in the Mnammox process, which in turn fuelled the Anammox process carried out by Candidatus Brocadia. This revealed the microbial interactions of NDMO, Mnammox, and Anammox processes responsible for manganese-driven co-removal of ammonium and nitrate. These findings provide a potential solution for biological nitrogen removal and expand our understanding of the nitrogen and manganese biogeochemical cycles.

The Pannonian Stage: stratigraphy and geoenergy resources

The youngest regional chronostratigraphic unit of the Central Paratethys, the Pannonian Stage, is benchmarked by the deposits of Lake Pannon, containing a highly endemic, Caspian-type biota, and the sediments of adjacent deltas and fluvial plains. The Pannonian Stage also includes various freshwater lake deposits and vast volcanic formations, especially in the northern and eastern margins of the Pannonian Basin system. The Pannonian correlates with the Tortonian, Messinian, Zanclean and Piacenzian Stages, thus representing 9 Myr between 11.6 and 2.6 Ma. The Pannonian is divided into biochronostratigraphic units by the application of mollusc and dinoflagellate biochronozones in the Lake Pannon deposits and mammal biozones in the freshwater sediments. The Pannonian Stage is a leading geoenergy provider in terms of hydrocarbons and lignite. Prolific oil and gas reservoirs occur in both the deep-water and deltaic sand bodies in the central part of the Pannonian Basin, which is a highly mature exploration area. The practically inexhaustible lignite resource of the Pannonian Stage has been mined or is still being mined in the basin margins in all ten countries of the Pannonian Basin system.

New nucleolin-containing cytoplasmic bodies in an archamoebian protist Pelomyxa belevskii (Amoebozoa, Archamoebae, Pelobiontida).

The representatives of the archamoebian genus Pelomyxa are amoeboid anaerobic protists that inhabit fresh-water anoxic sediments, and most of them are usually multinucleate. The cytoplasm of these unicellular organisms is highly complicated and contains numerous vacuoles of different types, as well as a wide range of prokaryotic endocytobionts, agglomerations of glycogen, lipids, etc. Among the great variety of cytoplasmic structures in P.belevskii, we identified novel organelles termed Cytoplasmic Nucleolin-Rich Bodies (CNRBs) due to their enrichment in nucleolin, a nuclear/nucleolar protein. The P. belevskiiCNRBs differ significantly from known cytoplasmic nucleolin-related organelles encountered in some other eukaryotic cells, but their biological significance remains elusive. The work also provides the first description of the nuclear organization of P. belevskii. The nucleolar apparatus of P. belevskii contains little nucleolin, as determined by quantitative electron microscopic data, suggesting that it is inactive despite its morphological complexity. The presence of CNRBsin Pelomyxa is discussed in the context of the specific habitat conditions and biology of these unicellular eukaryotes.

Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.

Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.

Analysis of Bacterial Community Composition in Sediments of the Mainstream and Tributaries in the Wanzhou Section of the Three Gorges Reservoir Area, China

River ecosystems are intricately connected to the biogeochemical processes mediated by sediment bacterial communities. The Three Gorges Reservoir, a critical freshwater resource, has seen limited research on bacterial community composition, particularly in comparative studies between its mainstream and tributaries. High-throughput sequencing was utilized to examine bacterial diversity and community structure in the sediments of the Wanzhou section. The analysis uncovered significant spatiotemporal heterogeneity and revealed similar community structures between the mainstream and tributaries, with Proteobacteria, Actinobacteria, and Bacteroidetes as the predominant phyla. Although no significant phylum-level differences were observed among the top five dominant species, their relative abundances showed notable variations. These differences are attributed to the reservoir’s cyclical water storage and release, which alter nutrient concentrations and induce seasonal variations in bacterial communities. The intrinsic growth characteristics of microorganisms and their adaptive responses to environmental changes are identified as key factors influencing bacterial community differentiation. These insights enhance the understanding of bacterial dynamics in freshwater sediments and contribute to ecological assessments and environmental management in the Three Gorges Reservoir area.

Complete genome sequence of a methanotrophic bacterium, Methylomicrobium lacus strain 22M6SE5-12 isolated from a freshwater sediment environment.

We assembled the complete genome of Methylomicrobium lacus strain 22M6SE5-12 isolated from a freshwater sediment in South Korea. The genome consists of a 4.36-Mbp chromosome and two plasmids and has 3,961 coding sequences, 12 rRNA genes, and 55 tRNA genes. We identified a gene set encoding the particulate methane monooxygenase subunits.

The Eemian Stage interglacial marine transgression in the south-western Baltic region

Abstract. Through detailed investigations, three sequences of marine and associated deposits in the south-west Baltic area are shown to represent the Eemian interglacial transgression. Pollen analyses and foraminiferal and ostracod analyses are combined to provide the evolution of relative sea-level change. An independent chronology is established by correlation of the pollen record with that from the Bispingen laminated lake deposits in north Germany. Additional published sites from the area are included in a wider reconstruction of events. Ostracod analyses indicate that freshwater lakes initially existed in the basin prior to the marine inundation. This was followed by an early marine transgression. In the south-west Baltic the first marine ingression took place at the base of regional pollen zone E3, with fully marine conditions established in E4 continuing into the lower part of E5. The regression of the sea during zone E6 was followed by freshwater deposition in E7. The linking of the sequences in the south-west Baltic demonstrates that the Eemian transgression occurred both through northern Germany and through the Danish belts–Kattegat seaway, indicating that connections to the North Sea and North Atlantic were present in the area during the maximum interglacial sea-level highstand.

Riverine Cu-distribution in sediments of the Jaba-Kawerong river system 30 years after cease of mining at Panguna/Bougainville

The investigation of surface and river sediments over 30 years after the cease of large scale Cu and Au mining operation at Panguna (Bougainville) shows the impact of mining and tailings disposal on the associated riverine environment. While Zn, Pb and Cd have elevated concentrations in the former mining area and are low (< 100, < 28, < 1 mg/kg, respectively) in sediment of the Jaba-Kawerong river system, Cu represents the dominant environmental metal emission. Sediments of active streams and overbank deposits range between 1000 and 3000 mg/kg Cu. Most samples exceed freshwater sediment or soil quality guideline values, indicating the probability of toxic effects on sediment dwelling or aquatic organisms and ecological or health risks associated to agricultural use of the former mining area and floodplains. Copper in surface and river sediments is associated to bornite, chalcopyrite and chloritized biotite of the primary Panguna ore mineral assemblage. This attests to ongoing remobilization of sediment and/or reflects mobilization of additional Cu bearing material from the waste rock dump of the Panguna mine. Copper in surface and river sediments is also contained in secondary Cu-phases such as covellite as well as hydrated basic Cu-sulfates, which formed under locally variable redox conditions. Fe-oxihydroxides, occurring in variable abundance as reflected by Fe concentrations between 18,200 and 379,000 mg/kg (Mn 145–3086 mg/kg), can be identified as further Cu-carriers, taking up the metal from the aqueous phase in the sedimentary pore space. Mine derived input of Cu bearing minerals is confined to the sedimentary body of the Jaba-Kawerong river system. The diversity of Cu bearing phases with different environmental and processing properties sets constraints on re-processing sediments as secondary Cu-ores or re-using of sediments as building material.

Zwitterionic, cationic, and anionic PFAS in freshwater sediments from AFFF-impacted and non-impacted sites of Eastern Canada

Zwitterionic, cationic, and anionic per- and polyfluoroalkyl substances (PFAS) were investigated in freshwater sediments of Canada, including sites impacted by aqueous film-forming foams (AFFFs). The first step of the project involved optimizing the extraction method with equilibrated sediment-water-AFFF samples. The analytical method had acceptable linearity, accuracy, and precision in the sediment matrix, and was further validated with NIST SRM 1936. In the second step of the project, the method was applied to determine over 70 target PFAS in field-collected sediments (n = 102). At federal contaminated sites of Ontario, Newfoundland, and Québec (ditches and creeks at international airports with fire training or fire equipment testing areas), summed PFAS averaged 30 ng/g (maximum of 160 ng/g) with molecular patterns dominated by perfluorooctane sulfonate (maximum PFOS: 84 ng/g). Based on maximum observed concentrations >10 ng/g, other key PFAS at these AFFF-impacted sites included negative ion mode perfluorohexane sulfonate, perfluorohexane sulfonamide, fluorotelomer sulfonates (6:2 FTS and 8:2 FTS) and 5:3 fluorotelomer acid, and positive ion mode N-dimethylammoniopropyl perfluorohexane sulfonamide and 5:1:2 fluorotelomer betaine. In contrast, environmental sediment samples collected at a larger spatial scale (province-wide survey) were characterized by low ΣPFAS (generally <1 ng/g), with PFOS/PFOA below chronic toxicity thresholds for aquatic life.

Distribution characteristics and influencing factors of benthic diatoms on several typical beaches along the southern coast of China

Benthic diatoms are the primary beach vegetation on sandy coasts, acting as the main primary producers in such environments. Changes in their community structure and biomass can have substantial impact on both the entire micro-food web and the nearshore shallow marine ecosystem. This study focused on four typical beaches along the southern coast of China (Fuzhou Changle Beach, Xiamen Huizhan Beach, Xiamen Guanyinshan Beach, and Beihai Silver Beach). Analysis of benthic diatoms and environmental factors revealed that the distribution of benthic diatom communities on the studied beaches is influenced by elevation, salinity changes due to freshwater inputs, sediment composition, and hydrodynamic factors. The most important factor is elevation, which reflects the location of the beach in the tidal zone. On Beihai Silver Beach and the Xiamen beaches, the mid-tidal and low tidal zones are more conducive to growth and reproduction of benthic diatoms, and some diatom species show preference for different tidal zones. On dissipative beaches, benthic diatom abundance peaks in the mid-tidal zone, whereas on low tidal terrace beaches, diatom abundance is generally low in the high tidal zone and relatively high in the low tidal zone. Additionally, low tidal terrace beaches exhibit a “steep increase zone” of diatom abundance at the junction of the steep and gentle slopes, indicating that benthic diatom abundance responds more to this type of beach landform than to that of dissipative beaches.

Combined response of polar magnetotaxis to oxygen and pH: Insights from hanging drop assays and microcosm experiments

Magnetotactic bacteria (MTB) combine passive alignment with the Earth magnetic field with a chemotactic response (magneto-chemotaxis) to reach their optimal living depth in chemically stratified environments. Current magneto-aerotaxis models fail to explain the occurrence of MTB far below the oxic-anoxic interface and the coexistence of MTB cells with opposite magnetotactic polarity at depths that are unrelated with the redox gradient. Here we propose a modified model of polar magnetotaxis which explains these observations, as well as the distinct concentration profiles and magnetotactic advantages of two types of MTB inhabiting a freshwater sediment: a group of unidentified cocci (MC), and a giant rod-shaped bacterium (MB) apparently identical to M. bavaricum (MB). This model assumed that magnetotactic polarity is set by a threshold mechanism in counter gradients of oxygen and a second group of repellents, with, in case of MB, includes H+ ions. MTB possessing this type of polar magnetotaxis can shuttle between two limit depths across the redox gradient (redox taxis), as previously postulated for M. bavaricum and other members of the Nitrospirota group. The magnetotaxis of MB and MC is predominantly dipolar whenever the presence of a magnetic field ensures a magnetotactic advantage. In addition, MB can overcome unfavorable magnetic field configurations through a temporal sensing mechanism. The availability of threshold and temporal sensing mechanisms of different substances can generate a rich variety of responses by different types of MTB, enabling them to exploit multiple ecological niches.

Higher temperatures exacerbate effects of antibiotics on methanogenesis in freshwater sediment

Methane (CH4) emissions from natural systems are rising in a concerning manner with an incomplete understanding of its drivers. Recently, chemical stressors such as antibiotics have been suggested as a thus far overlooked factor increasing methanogenesis in freshwaters. Since usage and toxicological impact of antibiotics could increase in a warming climate, we assessed the temperature-dependence of antibiotic effects on methanogenesis. In this light, we conducted anaerobic incubations with freshwater sediment at 10, 15, and 20 °C in presence of a mixture of five antibiotics at field-relevant concentrations. Weekly measurements of CH4 showed a strong temperature dependence of antibiotic effects by changing effect sizes, directions and dynamics. While antibiotics reduced CH4 production at 10 °C, methanogenesis was elevated at 15 °C with the most pronounced increase occurring at 20 °C. Furthermore, antibiotics changed the prokaryotic assemblage at all temperatures and effect patterns of CH4 producing Methanomicrobia strongly followed the patterns observed for methanogenesis. While analyses of compound-specific stable isotopes and the metatranscriptome suggest the acetoclastic pathway as most relevant, linking prokaryotic structure to function remains one of the most significant research challenges. Nevertheless, the evidence provided by this study suggests a positive relationship between temperature and the stimulating effects of antibiotics on CH4 production.

Sulfate availability affect sulfate reduction pathways and methane consumption in freshwater wetland sediments

Methane (CH4) emissions from wetlands significantly contribute to global greenhouse gas fluxes, yet the mechanisms regulating CH4 production and oxidation in freshwater wetlands remain underexplored, particularly in the role of sulfate in the anaerobic oxidation of CH4. This study investigated the production, consumption, and release of CH4 in the sediments of the Qilihai wetland, focusing on the roles of hydrogenotrophic methanogenesis and sulfate dynamics across different seasons. CH4 concentrations ranged from 2.42 to 2290.52 μmol L⁻1, and δ13C–CH4 values became progressively more negative with depth, ranging from −87.37‰ to −57.18‰. Results indicate that hydrogenotrophic methanogenesis is the dominant pathway for CH4 production, particularly in sulfate-depleted environments, with CH4 concentrations in the sulfate-methane transition zone (SMTZ) strongly correlated with sulfate availability. Sulfate consumption through Sulfate Anaerobic Oxidation of Methane (SAOM) and Organoclastic Sulfate Reduction (OSR) demonstrated significant seasonal variation, with OSR accounting for up to 73% of sulfate consumption in the SMTZ. The SMTZ exhibited variations ranging from 2 to 40 cm in October, narrowing to 2–4 cm in July. These findings emphasize the complex interactions between sulfate availability, methanogenic pathways, and CH4 emissions in freshwater wetlands, highlighting the need for further research on sulfate dynamics and their implications for greenhouse gas emissions in the context of global climate change.

Diversity of Clostridioides difficile PCR ribotypes isolated from freshwater sediments depends on the isolation method.

Clostridioides difficile is an intestinal pathogen of humans and animals. In community-associated infections, the environment is suggested to play a significant role in overall transmission routes. Although the prevalence of C. difficile in freshwater and soil has been widely studied, little is known about its presence in sediments. In this study, we tested 15 sediment samples collected from various freshwater sources. C. difficile was isolated from all sampled sites, yielding a total of 171 strains grouped into 26 ribotypes, with 001/072 and 014/020 being the most prevalent. Genome sequencing of 37 isolates from 17 PCR ribotypes confirmed the presence of highly related strains in the geographically distant and unlinked water samples. Eight divergent PCR ribotypes from clades C-II and C-III were found in six samples. In each sample, the unbound fraction (supernatant after sediment wash) and bound fraction (sonicated sediment sample) were subjected to enrichment. Sonication was only slightly better than washing in terms of sample positivity (14 positive samples with sonication and 11 with washing). However, sonication substantially increased the diversity of the PCR ribotypes obtained (23 in sonicated samples vs nine in washed samples). In conclusion, sediments are a rich source for investigating the diversity of environmental C. difficile, including isolates from divergent lineages. Selection of the isolation method can significantly impact the diversity of captured PCR ribotypes.IMPORTANCEClostridioides difficile, a pathogenic bacterium that can cause intestinal infections in humans and animals, thrives in the gut but also disperses widely through spores found in the environment. Clinical and environmental strains often overlap with common PCR ribotypes, which are consistently isolated worldwide. Environmental studies have mostly focused on water and soil, but sediments have been very poorly studied. In this study, we investigated the presence of C. difficile in various freshwater sediments and evaluated the effectiveness of two different isolation approaches on positivity rates and strain diversity. C. difficile was found to be highly prevalent in sediments, with an isolation rate of 100%. Sonication proved to be more effective than simple washing for capturing a greater diversity of PCR ribotypes. Overall, this study underscores the widespread presence of C. difficile in freshwater sediments and emphasizes the importance of continued surveillance and monitoring to understand its ecology and transmission dynamics.

Response of denitrifying anaerobic methane oxidation processes in freshwater and marine sediments to polyvinyl chloride microplastics

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays a crucial role in mitigating methane (CH4) in natural environments. The increasing presence of microplastics (MPs) in these environments due to human activities is a growing concern. However, the impact of MPs on n-DAMO microorganisms and their role in greenhouse gas regulation, particularly CH4 reduction, remains unclear. This study investigates the effects of polyvinyl chloride (PVC) MPs on n-DAMO activity and the associated microbial communities in freshwater and marine sediments at varying concentrations of (R0/M0-no addition, R1/M1–0.5 %, R2/M2–2%). The results showed that the presence of MPs significantly increased the n-DAMO rate (2.89–3.58 nmol 13CO2 g−1 d−1) compared to the control groups (R0: 1.29 nmol 13CO2 g−1 d−1, M0: 0.11 nmol 13CO2 g−1 d−1), with marine sediments showing a more pronounced response. Additionally, the proportional contribution of nitrate-DAMO processes increased following MP exposure. The presence of PVC MPs also altered the microbial diversity of n-DAMO. Upon the addition of MPs, the microbial community composition of n-DAMO in marine sediments changed more significantly. This study provides the first evidence of a positive impact of PVC MPs on n-DAMO processes, suggesting that the presence of PVC MPs in sediments could potentially contribute to the reduction of CH4 emissions.

Environmental and human health risk of potentially toxic metals in freshwater and brackish water Nile tilapia (Oreochromis niloticus) aquaculture.

Tilapia aquaculture is rapidly expanding worldwide, particularly in Bangladesh. However, metal pollution in aquaculture presents significant environmental and human health risks. This study aimed to evaluate the concentrations of 13 potentially toxic metals (As, Be, Cd, Co, Cr, Cu, Hg, Ni, Pb, V, Mn, Se, and Zn) in Nile tilapia (Oreochromis niloticus), surface water, and sediment from freshwater and brackish water aquaculture ponds. The study also assessed the associated environmental and human health risks. Samples of tilapia, water, and sediment were collected between October and November 2021 and analyzed using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The estimated daily intake (EDI) of As, Cr, Pb, Se, and Zn in tilapia muscle of both freshwater and brackish water, as well as Cd and Ni in brackish water, exceeded recommended EDI values. The Target Hazard Quotient (THQ) was less than 1 for most metals, except for As in brackish water tilapia and Cr in both freshwater and brackish water tilapia, indicating potential health risks. The Target Cancer Risk (TR) values for As in both freshwater and brackish water tilapia, and for Cr and Ni in freshwater tilapia, exceeded acceptable ranges. While the concentrations of metals in surface water of both freshwater and brackish water tilapia farms varied, all mean concentrations were below WHO recommended limits. The contamination factor (Cf) values were less than 1 for all metals in both types of aquaculture ponds, except for Zn in freshwater sediment and Se in brackish water sediment. Additionally, the calculated risk indices including the Pollution Load Index (PLI), Geoaccumulation Index (Igeo), Ecological Risk Factor (Er), and Potential Ecological Risk Factor (PER) for sediment were below the risk thresholds values (PLI < 1, Igeo < 0, Er < 40, and PER < 150). The significant positive correlations were found between tilapia muscle and the sediment of the respective ponds for arsenic (As) (ρ= 0.8, p<0.002) and Cr (ρ= 0.7, p<0.02). Although the levels of studied metals in water and sediment from freshwater and brackish water aquaculture ponds were generally within recommended guidelines, this study underscores the need for continuous monitoring and preventative measures, particularly to address elevated levels of As and Cr in tilapia muscle, which may pose potential risks to human health.

Distribution and in situ bioaccumulation test of radioecologically relevant metals in boreal freshwater sediments

Sediments act as important sinks for metals and their radionuclides in aquatic environments and play a crucial role in their transfer and uptake to aquatic organisms. Traditional radioecological models use radionuclide concentrations in water to predict concentrations in aquatic organisms. In this study, we investigated the distribution of radioecologically important metals (Ba, Co, Ni, Sr, U) among sediment, porewater and hypolimnion over seasons. We also studied the uptake of these metals to benthic organisms and importance of sediment as an uptake source by conducting a 28-day in situ bioaccumulation experiment with oligochaete worms (Lumbriculus variegatus). The studied metals were chosen based on common occurrence of their radioactive isotopes in nuclear fuel cycle. Measurements of total elemental concentration were used as proxies to study the behavior of specific radionuclides. Sediment and water samples were collected from two small lakes connected to a former uranium mine in Eastern Finland, and from a nearby reference lake connected to a different drainage area. Environmental characteristics and concentrations measured from sediment, porewater and overlying water indicated only minor changes between seasons. Measured metals were highly associated with sediment particles, rather than porewater or hypolimnion. Both the distribution of metals and in situ experiment indicated the importance of sediment as the main source of bioaccumulation. Significant differences in Ba, Ni and U concentrations between treatments containing contaminated sediment and reference sediment were noted, regardless of water concentrations. Additionally, as U contaminated lakes lacked seasonal overturn during our monitoring period, metal distribution and environmental conditions remained unchanged in deeper parts of those lakes. Lastly, the results of this in situ bioaccumulation experiment are in line with the findings of our previous laboratory study using sediments from these same lakes.

Decadal changes in microplastic accumulation in freshwater sediments: Evaluating influencing factors

Microplastics are small plastic particles with sizes ranging between 1 μm and 5 mm. Microplastics can originate from macro plastics and degrade to a smaller size or be produced directly by manufacturers. Few studies have examined microplastic contamination in freshwater sediment cores to estimate changes in microplastic contamination over time. We present the results of a study that examined sediment cores from four watersheds, Kiskiminetas River, Blacklick Creek, Raystown Lake, and Darby Creek, in Pennsylvania, USA to reveal the history of microplastic accumulation and factors that contribute to microplastic distribution. The abundance and morphology of microplastics varied over time and between these four locations. The highest microplastic abundance was found in Raystown Lake, ranging from 704 to 5397 particles kg−1 with fiber as the dominant microplastic type, while Darby Creek (0–3000 particles kg−1), Kiskiminetas River (0–448 particles kg−1), and Blacklick Creek (0–156 particles kg−1) had lower microplastic concentration. Moreover, Darby Creek had the most diverse microplastic morphology and a trend of decreasing concentration with depth. Although the Darby Creek watershed has the most developed area and highest population density, it did not have the highest microplastic concentration. Averaged over the four cores, microplastic abundance increased as global plastics production increased from the 1950s–2010s. Our findings provide insights into the fate and transport of microplastic contamination in freshwater environments, which is vital to establishing sustainable mitigation strategies.

Expanded gene and taxon sampling of diplomonads shows multiple switches to parasitic and free-living lifestyle

BackgroundDiplomonads are anaerobic flagellates classified within Metamonada. They contain both host-associated commensals and parasites that reside in the intestinal tracts of animals, including humans (e.g., Giardia intestinalis), as well as free-living representatives that inhabit freshwater and marine anoxic sediments (e.g., Hexamita inflata). The evolutionary trajectories within this group are particularly unusual as the free-living taxa appear to be nested within a clade of host-associated species, suggesting a reversal from host-dependence to a secondarily free-living lifestyle. This is thought to be an exceedingly rare event as parasites often lose genes for metabolic pathways that are essential to a free-living life strategy, as they become increasingly reliant on their host for nutrients and metabolites. To revert to a free-living lifestyle would require the reconstruction of numerous metabolic pathways. All previous studies of diplomonad evolution suffered from either low taxon sampling, low gene sampling, or both, especially among free-living diplomonads, which has weakened the phylogenetic resolution and hindered evolutionary insights into this fascinating transition.ResultsWe sequenced transcriptomes from 1 host-associated and 13 free-living diplomonad isolates; expanding the genome scale data sampling for diplomonads by roughly threefold. Phylogenomic analyses clearly show that free-living diplomonads form several branches nested within endobiotic species. Moreover, the phylogenetic distribution of genes related to an endobiotic lifestyle suggest their acquisition at the root of diplomonads, while traces of these genes have been identified in free-living diplomonads as well. Based on these results, we propose an evolutionary scenario of ancestral and derived lifestyle transitions across diplomonads.ConclusionsFree-living taxa form several clades nested within endobiotic taxa in our phylogenomic analyses, implying multiple transitions between free-living and endobiotic lifestyles. The evolutionary history of numerous virulence factors corroborates the inference of an endobiotic ancestry of diplomonads, suggesting that there have been several reversals to a free-living lifestyle. Regaining host independence may have been facilitated by a subset of laterally transferred genes. We conclude that the extant diversity of diplomonads has evolved from a non-specialized endobiont, with some taxa becoming highly specialized parasites, others becoming free-living, and some becoming capable of both free-living and endobiotic lifestyles.

Sedimentary Greigite Formation

Revised thermodynamic data for greigite (Fe3S4) indicate that it is a stable sedimentary Fe-S phase. Greigite was previously regarded as metastable. Equilibrium computations using revised data explain apparently contradictory observations regarding greigite occurrences in sediments and sedimentary rocks. Greigite has a large stability area in pe-pH space relative to pyrite. It dominates in low pe regimes especially near the lower water stability boundary, which is consistent with its widespread occurrence in methanic sediments. It also has a small but significant stability zone near the sulfate-sulfide stability boundary. Its significance increases in regimes with relatively high dissolved Fe:S ratios, which explains its occurrence in freshwater sediments and iron-enriched marine sediments. It is also a paleoenvironmental marker for transitional environments, especially between freshwater and marine systems. It is stable relative to pyrrhotite and smythite, although their formation together with greigite in low pe environments may be facilitated by catalytic processes. The greigite-smythite (pyrrhotite)-siderite association is a potential marker for ancient methanogenesis. Greigite is relatively sensitive to oxidation and its long-term geological preservation depends mostly on protection from oxidation by low sediment permeability or enclosure in other minerals or organic remains. Most sedimentary and biological greigite forms via equilibrium reactions involving mackinawite-like precursors, with no direct coupling of greigite with pyrite; these minerals form independently during sedimentary diagenesis. Magnetosomal greigite production by magnetotactic bacteria is a consequence of relative greigite stability, its decoupling from pyrite, and its protection from oxidation by cell membranes.