Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia

Microbial mixotrophic denitrification using iron(II) as an assisted electron donor

Mixotrophic denitrification processes have a great potential in nitrogen removal in biological wastewater treatment processes. However, so far, few studies have focused on the mixotrophic denitrification system using Fe(II) as an exclusively assisted electron donors and the underlying mechanisms in such a process remain unclear. Furthermore, the mechanisms by which microorganisms cover carbon, nitrogen, phosphorus and iron in an iron-assisted mixotrophic system remain unrevealed. In this work, we explore the feasibility of using Fe(II) as an assisted electron donor for enhancing simultaneous nitrogen and phosphorus removal via long-term reactor operation and batch tests. The results show that Fe(II) could provide electrons for efficient nitrate reduction and that biological reactions played a predominant role in these systems. In these systems Thermomonas, a strain of nitrate-reduction Fe(II)-oxidation bacterium, was enriched and accounted for a maximum abundance of 60.2%. These findings indicate a great potential of the Fe(II)-assisted mixotrophic denitrification system for practical use as an efficient simultaneous nitrogen and phosphorus removal process.

Continuous cultivation of the lithoautotrophic nitrate-reducing Fe(II)-oxidizing culture KS in a chemostat bioreactor

Laboratory-based studies on microbial Fe(II) oxidation are commonly performed for 5-10 days in small volumes with high substrate concentrations, resulting in geochemical gradients and volumetric effects caused by sampling. We used a chemostat to enable uninterrupted supply of medium and investigated autotrophic nitrate-reducing Fe(II)-oxidizing culture KS for 24 days. We analysed Fe- and N-speciation, cell-mineral associations, and the identity of minerals. Results were compared to batch systems (50 and 700 mL-static/shaken). The Fe(II) oxidation rate was highest in the chemostat with 7.57 mM Fe(II) d^-1 , while the extent of oxidation was similar to the other experimental setups (average oxidation of 92% of all Fe(II)). Short-range ordered Fe(III) phases, presumably ferrihydrite, precipitated and later goethite was detected in the chemostat. The 1 mM solid phase Fe(II) remained in the chemostat, up to 15 μM of reactive nitrite was measured, and 42% of visualized cells were partially or completely mineral-encrusted, likely caused by abiotic oxidation of Fe(II) by nitrite. Despite (partial) encrustation, cells were still viable. Our results show that even with similar oxidation rates as in batch cultures, cultivating Fe(II)-oxidizing microorganisms under continuous conditions reveals the importance of reactive nitrogen intermediates on Fe(II) oxidation, mineral formation and cell-mineral interactions.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota"

Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes)

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.

Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes

Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0.67 g/L to 346 g/L). MPN results showed that the abundance of NRFeOx microorganisms significantly (P < 0.05) decreased with increasing lake salinity, from 7.55 × 10³ to 8.09 cells/g dry sediment. The community composition of the NRFeOx enrichment cultures obtained from the MPNs differed distinctly among the five lakes and clustered with lake salinity. Two stable enrichment cultures, named FeN-EHL and FeN-CKL, were obtained from microcosm incubations of sediment from freshwater Lake Erhai and hypersaline Lake Chaka. The culture FeN-EHL was dominated by genus Gallionella (68.4%), while the culture FeN-CKL was dominated by genus Marinobacter (71.2%), with the former growing autotrophically and the latter requiring an additional organic substrate (acetate) and Fe(II) oxidation, caused to a large extent by chemodenitrification [reaction of nitrite with Fe(II)]. Short-range ordered Fe(III) (oxyhydr)oxides were the product of Fe(II) oxidation, and the cells were partially attached to or encrusted by the formed iron minerals in both cultures. In summary, different types of interactions between Fe(II) and nitrate-reducing bacteria may exist in freshwater and hypersaline lakes, i.e., autotrophic NRFeOx and chemodenitrification in freshwater and hypersaline environments, respectively. IMPORTANCE NRFeOx microorganisms are globally distributed in various types of environments and play a vital role in iron transformation and nitrate and heavy metal removal. However, most known NRFeOx microorganisms were isolated from freshwater and marine environments, while their identity and activity under hypersaline conditions remain unknown. Here, we demonstrated that salinity may affect the abundance, identity, and nutrition modes of NRFeOx microorganisms. Autotrophy was only detectable in a freshwater lake but not in the saline lake investigated. We enriched a mixotrophic culture capable of nitrate-reducing Fe(II) oxidation from hypersaline lake sediments. However, Fe(II) oxidation was probably caused by abiotic nitrite reduction (chemodenitrification) rather than by a biologically mediated process. Consequently, our study suggests that in hypersaline environments, Fe(II) oxidation is largely caused by chemodentrification initiated by nitrite formation by chemoheterotrophic bacteria, and additional experiments are needed to demonstrate whether or to what extent Fe(II) is enzymatically oxidized.

Metagenomic insights into the environmental adaptation and metabolism of Candidatus Haloplasmatales, one archaeal order thriving in saline lakes

The KTK 4A-related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%-33.0%) within a Chinese soda-saline lake using culture-independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single-copy proteins and genome-level identity analyses among the metagenome-assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable 'salt-in' strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC-mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC-MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales. Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca. Haloplasmatales.

Zinc removal from highly acidic and sulfate-rich wastewater in horizontal sub-surface constructed wetland

This study demonstrated the successful use of a laboratory-scale baffled horizontal constructed wetland substituted with mixed organic media for zinc removal from high acidity (∼610 mg L^-1 as CaCO₃), sulfate-rich (∼1,300 mg L^-1) wastewater. The wetland was planted with Typha latifolia. The mean zinc concentration in the influent was gradually increased from 0.56 ± 0.02 mg L^-1 to 5.3 ± 0.42 mg L^-1. The mean zinc concentration in the outflow was 0.22 ± 0.19 mg L^-1, which accounted for 95% zinc removal throughout the study. However, total zinc uptake by the plants was 533 mg kg^-1, accounting for only 1.2% of total zinc removal; therefore, major zinc retention occurred within wetland media (83%). The overall activity and specific sulfidogenic activity decreased at the end of the study to 1.43 mg chemical oxygen demand removed per mg of TVS per day and 0.60 mg sulfate reduced per mg of TVS per day, respectively. Additionally, 16S rRNA sequencing revealed major dominant phyla present: Firmicutes (36%), Proteobacteria (16%), Actinobacteria (8.8%), Planctomycetes (7.8%), Chloroflexi (3.5%), Acidobacteria (1.9%) and Fibrobacteres (1.5%).

The oil spill and the use of chemical surfactant reduce microbial corrosion on API 5L steel buried in saline soil

In order to evaluate the biocorrosion of API 5L metal buried in saline soils, three different conditions in microcosms were evaluated. The control microcosm contained only saline soil, the second had the addition of petroleum, and the third contained the addition of both petroleum and surfactant. The corrosion rate of the metals was measured by loss of mass after 30 days, and the microbial communities were delineated using 16S rRNA gene sequencing techniques. The species were dominated by halophiles in all samples analyzed. Among the bacteria, the predominant group was Proteobacteria, with emphasis on the Alphaproteobacteria and Gammaproteobacteria. Betaproteobacteria and Deltaproteobacteria members were also identified in a smaller number in all conditions. Firmicutes were especially abundant in the control system, although it was persistently present in other conditions evaluated. Bacteroidetes and Actinobacteria were also present in a considerable number of OTUs in the three microcosms. Halobacteria were predominant among archaea and were present in all conditions. The analysis pointed to a conclusion that in the control microcosm, the corrosion rate was higher, while the microcosm containing only oil had the lowest corrosion rate. These results suggest that, under these conditions, the entry of other carbon sources favors the presence of petroleum degraders, rather than samples involved in the corrosion of metals.

Onshore soil microbes and endophytes respond differently to geochemical and mineralogical changes in the Aral Sea

There is limited knowledge about how microbiome develops along the geochemical and mineralogical change in onshore soils derived from continuous desiccation of lakes. In this study, geochemistry and mineralogy were studied in the Aral Sea onshore soils exposed in different periods (from the 1970s to 2018), followed by microbial analyses on the studied soils and the aboveground organs of dominant plants. The soils exhibited an increasing gradient of total soluble salts (TSS: 0.4-0.5 g/L to 71.3 g/L) and evaporite minerals (e.g., gypsum, halite) from the farshore to the nearshore. In the studied soils, microbial diversity decreased with increasing TSS, and microbial community dissimilarities among samples was positively correlated with the contents of gypsum and calcite minerals. Among the measured environmental variables, minerals contributed most to the observed microbial variation. In contrast, the endophytic microbial communities in the aboveground organs of dominant plants were not related to any of the measured variables, indicating that they differed from their soil counterparts with respect to their responses to geochemical and mineralogical variations in soils. In summary, these results help us understand the response of onshore soil microbiome to the decline of lake water caused by continuous desiccation.

Iron Elution from Iron and Steel Slag Using Bacterial Complex Identified from the Seawater

Iron and steel slag (ISS) is a byproduct of iron refining processes. The lack of iron in seawater can cause barren grounds where algae cannot grow. To improve the barren grounds of the sea, a supply of iron to the seawater is necessary. This study focused on bacteria interacting with ISS and promoting iron elution in seawater. Sulfitobacter sp. (TO1A) and Pseudomonas sp. (TO1B) were isolated from Tokyo Bay and Sagami Bay. The co-culture of both bacteria promoted more iron elution than individual cultures. After the incubation of both bacteria with ISS, quartz and vaterite appeared on the surface of the ISS. To maintain continuous iron elution from the ISS in the seawater, we also isolated Pseudoalteromonas sp. (TO7) that formed a yellow biofilm on the ISS. Iron was eluted by TO1A and TO1B, and biofilm was synthesized by TO7 continuously in the seawater. The present research is expected to contribute to the improvement of ISS usage as a material for the construction of seaweed forests.

A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake

The environment of a high altitude brackish water lake presents an unprecedented reservoir for the microbial community with adaptability towards surviving stressful conditions. Pangong lake is a high altitude brackish water lake of the Himalayas situated in the eastern part of Ladakh (Indian Tibet), at the height of 4250 m above the sea level. Shotgun metagenomics sequencing of Pangong Lake sediments was performed to examine the taxonomic diversity and functional adaptations of the resident psychrophilic and psychrotolerant microbial communities of the lake (September; a temperature of ±10 °C). Proteobacteria was the most prominent phylum, and Methylophaga, Halomonas, and Marinobacter were mainly abundant at the genus level. Enzyme pathways responsible for methane metabolism, nitrogen metabolism, sulfur reduction, benzoate, and xylene degradation appeared to be complete in the metagenomic dataset. Stress response genes responsible for adaption to pH, cold, salt tolerance, osmotic stress, and oxidative stress were also found in abundance in the metagenome. We compared the Pangong lake metagenome sample to sediments and water samples from three different aquatic habitats, namely saline lake, freshwater lakes and marine ecosystem using MG-RAST server against RefSeq and Subsystem databases. The Pangong lake microbial community contains six unique genera. Regression analysis using metagenome samples suggested that Pangong lake was most closely related to the Trophic South Pacific Ocean (R² = 0.971) and Socompa lake ecosystem (R² = 0.991) at phylum and functional level II, respectively. Our study signifies that the functional metabolic potentiality of Pangong lake is strongly influenced by the taxonomic structure and environmental conditions. We are reporting the metagenome of the sediment sample of the Pangong lake, which unveils the microbial diversity and their functional potential.

Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes

Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO₂ reduction with H₂, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.

Surviving onshore soil microbial communities differ among the Qing-Tibetan lakes with different salinity

Little is known about the onshore microbial contribution to the microbial communities in nearby lakes and its response to salinity. In this study, transplanting experiments were established by caging onshore soils with dialysis bags followed by in situ 50-day incubation in nearby lakes with different salinity on the Qinghai-Tibetan Plateau. At the end of the experiment, geochemical and microbial analyses were performed on the original soils, caged soils and lake waters and sediments at the incubation sites. The results showed that the salinity increased significantly (P < 0.05) in the caged soils and such salinity increases showed significant (P < 0.05) positive correlation with the salinity of the studied lakes. The microbial community composition and predicted functions in the caged soils were significantly (P < 0.05) changed in comparison with their corresponding original soils, and such variation could be mainly explained by the succession of members of the Proteobacteria, Bacteroidetes and Actinobacteria from the original soils to their corresponding caged soils. The onshore microbial contribution appeared to be limited (up to 11.2% for sediment and negligible for water, respectively) to nearby lake microbial communities. Nevertheless, the survival of onshore soil microbial communities was mainly limited by the salinity of the receiving lakes.

Microbial Diversity in Deep-Subsurface Hot Brines of Northwest Poland: from Community Structure to Isolate Characteristics

Deep-subsurface hot brines in northwest Poland, extracted through boreholes reaching 1.6 and 2.6 km below the ground surface, were microbiologically investigated using culture-independent and culture-dependent methods. The high-throughput sequencing of 16S rRNA gene amplicons showed a very low diversity of bacterial communities, which were dominated by phyla Proteobacteria and Firmicutes Bacterial genera potentially involved in sulfur oxidation and nitrate reduction (Halothiobacillus and Methylobacterium) prevailed in both waters over the sulfate reducers ("Candidatus Desulforudis" and Desulfotomaculum). Only one archaeal taxon, affiliated with the order Thermoplasmatales, was detected in analyzed samples. Bacterial isolates obtained from these deep hot brines were closely related to Bacillus paralicheniformis based on the 16S rRNA sequence similarity. However, genomic and physiological analyses made for one of the isolates, Bacillus paralicheniformis strain TS6, revealed the existence of more diverse metabolic pathways than those of its moderate-temperature counterpart. These specific traits may be associated with the ecological adaptations to the extreme habitat, which suggest that some lineages of B. paralicheniformis are halothermophilic.IMPORTANCE Deep-subsurface aquifers, buried thousands of meters down the Earth's crust, belong to the most underexplored microbial habitats. Although a few studies revealed the existence of microbial life at the depths, the knowledge about the microbial life in the deep hydrosphere is still scarce due to the limited access to such environments. Studying the subsurface microbiome provides unique information on microbial diversity, community structure, and geomicrobiological processes occurring under extreme conditions of the deep subsurface. Our study shows that low-diversity microbial assemblages in subsurface hot brines were dominated by the bacteria involved in biogeochemical cycles of sulfur and nitrogen. Based on genomic and physiological analyses, we found that the Bacillus paralicheniformis isolate obtained from the brine under study differed from the mesophilic species in the presence of specific adaptations to harsh environmental conditions. We indicate that some lineages of B. paralicheniformis are halothermophilic, which was not previously reported.

Plutonium Oxidation States in the Waste Isolation Pilot Plant Repository

The Waste Isolation Pilot Plant (WIPP), a deep geologic repository located 660 meters underground in bedded salt, is designed to isolate U.S. defense-related transuranic waste from the accessible environment. Plutonium isotopes are the most important radionuclides in WIPP waste. Plutonium solubility in WIPP brines (ionic strengths from 5.3 to 7.4) is strongly dependent on its oxidation state, with much lower solubilities associated with Pu(III) and Pu(IV) than with the higher Pu(V) and Pu(VI) oxidation states. The large quantity of metallic iron in WIPP waste and waste containers is expected to undergo anoxic corrosion, producing strongly reducing conditions and high hydrogen gas pressures after repository closure and brine intrusion. Because reducing conditions will prevail in the WIPP repository, the most important long-term oxidation states will be Pu(III) and Pu(IV). We performed a literature review to evaluate the effects of WIPP chemical and physical processes (not colloidal) on plutonium oxidation states that included reactions with reducing agents such as iron solids and aqueous species and radiolysis of solids and aqueous species. The results of this review indicate that equilibrium between Pu(III) solids and aqueous species will control dissolved plutonium concentrations in WIPP brines. We also performed geochemical modeling calculations using the ThermoChimie database to support this assessment of plutonium oxidation states in the long-term WIPP repository. Control of plutonium solubilities by Pu(III) solid instead of Pu(IV) solid may lead to higher predicted plutonium concentrations in brines potentially released to the ground surface by an inadvertent drilling intrusion into the long-term WIPP repository. The results of this study demonstrate that Pu(III) solid solubilities provide a reasonable upper bound for dissolved plutonium concentrations in WIPP brines.

Community dynamics and activity of nirS-harboring denitrifiers in sediments of the Indus River Estuary

Denitrification is an important pathway for reactive nitrogen removal from aquatic ecosystems. In this study, the biodiversity, abundance, and activity of cytochrome cd₁-type nitrate reductase gene (nirS)-harboring denitrifiers in the sediments of the Indus River Estuary were examined by molecular and isotope-tracing techniques. Results showed that the nirS-harboring denitrifier communities showed significant geographical variations along the estuarine salinity gradient. Real-time quantitative PCR showed that the abundance of nirS-harboring denitrifiers ranged from 5.3 × 10⁶ to 2.5 × 10⁸ copies g^-1, without significant spatiotemporal variation. The potential rates of denitrification varied from 0.01 to 6.27 μmol N kg^-1 h^-1 and correlated significantly to TOC and Fe(II) (P < 0.05). On the basis of ¹⁵N isotope-tracing experiments, the denitrification process contributed 18.4-99.4% to the total nitrogen loss in the sediments of the Indus River Estuary. This study provides novel insights into the microbial mechanism of nitrogen removal process in estuarine ecosystems.

Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy

Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L^-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidation of arsenite, in combination with arsenate-adsorbing materials, could be employed for metalloid removal.

NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats

NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.

Oxidation of Fe(II)-Organic Matter Complexes in the Presence of the Mixotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacterium Acidovorax sp. BoFeN1

Fe(II)-organic matter (Fe(II)-OM) complexes are abundant in the environment and may play a key role for the behavior of Fe and pollutants. Mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOx) reduce nitrate coupled to the oxidation of organic compounds and Fe(II). Fe(II) oxidation may occur enzymatically or abiotically by reaction with nitrite that forms during heterotrophic denitrification. However, it is unknown whether Fe(II)-OM complexes can be oxidized by NRFeOx. We used cell-suspension experiments with the mixotrophic nitrate-reducing Fe(II)-oxidizing bacterium Acidovorax sp. strain BoFeN1 to reveal the role of nonorganically bound Fe(II) (aqueous Fe(II)) and nitrite for the rates and extent of oxidation of Fe(II)-OM complexes (Fe(II)-citrate, Fe(II)-EDTA, Fe(II)-humic acid, and Fe(II)-fulvic acid). We found that Fe(II)-OM complexation inhibited microbial nitrate-reducing Fe(II) oxidation; large colloidal and negatively charged complexes showed lower oxidation rates than aqueous Fe(II). Accumulation of nitrite and fast abiotic oxidation of Fe(II)-OM complexes only happened in the presence of aqueous Fe(II) that probably interacted with (nitrite-reducing) enzymes in the periplasm causing nitrite accumulation in the periplasm and outside of the cells, whereas Fe(II)-OM complexes probably could not enter the periplasm and cause nitrite accumulation. These results suggest that Fe(II) oxidation by mixotrophic nitrate reducers in the environment depends on Fe(II) speciation, and that aqueous Fe(II) potentially plays a critical role in regulating microbial denitrification processes.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats.IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.

Use of Bacteria To Stabilize Archaeological Iron

Iron artifacts are common among the findings of archaeological excavations. The corrosion layer formed on these objects requires stabilization after their recovery, without which the destruction of the item due to physicochemical damage is likely. Current technologies for stabilizing the corrosion layer are lengthy and generate hazardous waste products. Therefore, there is a pressing need for an alternative method for stabilizing the corrosion layer on iron objects. The aim of this study was to evaluate an alternative conservation-restoration method using bacteria. For this, anaerobic iron reduction leading to the formation of stable iron minerals in the presence of chlorine was investigated for two strains of Desulfitobacterium hafniense (strains TCE1 and LBE). Iron reduction was observed for soluble Fe(III) phases as well as for akaganeite, the most troublesome iron compound in the corrosion layer of archaeological iron objects. In terms of biogenic mineral production, differential efficiencies were observed in assays performed on corroded iron coupons. Strain TCE1 produced a homogeneous layer of vivianite covering 80% of the corroded surface, while on the coupons treated with strain LBE, only 10% of the surface was covered by the same mineral. Finally, an attempt to reduce iron on archaeological objects was performed with strain TCE1, which led to the formation of both biogenic vivianite and magnetite on the surface of the artifacts. These results demonstrate the potential of this biological treatment for stabilizing archaeological iron as a promising alternative to traditional conservation-restoration methods.IMPORTANCE Since the Iron Age, iron has been a fundamental material for the building of objects used in everyday life. However, due to its reactivity, iron can be easily corroded, and the physical stability of the object built is at risk. This is particularly true for archaeological objects on which a potentially unstable corrosion layer is formed during the time the object is buried. After excavation, changes in environmental conditions (e.g., higher oxygen concentration or lower humidity) alter the stability of the corrosion layer and can lead to the total destruction of the object. In this study, we demonstrate the feasibility of an innovative treatment based on bacterial iron reduction and biogenic mineral formation to stabilize the corrosion layer and protect these objects.

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis

Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS) (34% salinity), demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs) assigned to 15 different genera from two orders, Halobacteriales and Haloferacales. All retrieved sequences were related to culturable halophiles or unculturable clones from saline (mostly hypersaline) niches. New sequences represented 53.9% of archaeal OTUs. Some of them formed separate branches with 90% similarity to the closest neighbor. Present results significantly differed from the previous investigations in regard to the number of presented genera, the domination of some genera not reported before in such extreme niche, and the identification of previously undiscovered 16S rRNA sequences.

Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment

Nitrate-reducing Fe(II)-oxidizing microorganisms were described for the first time ca. 20 years ago. Most pure cultures of nitrate-reducing Fe(II) oxidizers can oxidize Fe(II) only under mixotrophic conditions, i.e., when an organic cosubstrate is provided. A small number of nitrate-reducing Fe(II)-oxidizing cultures have been proposed to grow autotrophically, but unambiguous evidence for autotrophy has not always been provided. Thus, it is still unclear whether or to what extent Fe(II) oxidation coupled to nitrate reduction is an enzymatically catalyzed and energy-yielding autotrophic process or whether Fe(II) is abiotically oxidized by nitrite from heterotrophic nitrate reduction. The aim of the present study was to find evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. Microcosm incubations showed that with increasing incubation times, the stoichiometric ratio of reduced nitrate/oxidized Fe(II) [NO₃⁻_reduced/Fe(II)_oxidized] decreased, indicating a decreasing contribution of heterotrophic denitrification and/or an increasing contribution of autotrophic nitrate-reducing Fe(II) oxidation over time. After incubations of sediment slurries for >10 weeks, nitrate-reducing activity ceased, although nitrate was still present. This suggests that heterotrophic nitrate reduction had ceased due to the depletion of readily available organic carbon. However, after the addition of Fe(II) to these batch incubation mixtures, the nitrate-reducing activity resumed, and Fe(II) was oxidized, indicating the activity of autotrophic nitrate-reducing Fe(II) oxidizers. The concurrent reduction of ¹⁴C-labeled bicarbonate concentrations unambiguously proved that autotrophic C fixation occurred during Fe(II) oxidation and nitrate reduction. Our results clearly demonstrated that autotrophic nitrate-reducing Fe(II)-oxidizing bacteria were present in the investigated coastal marine sediments.

IMPORTANCE Twenty years after the discovery of nitrate-reducing Fe(II) oxidizers, it is still controversially discussed whether autotrophic nitrate-reducing Fe(II)-oxidizing microorganisms exist and to what extent Fe(II) oxidation in this reduction/oxidation process is enzymatically catalyzed or which role abiotic side reactions of Fe(II) with reactive N species play. Most pure cultures of nitrate-reducing Fe(II) oxidizers are mixotrophic; i.e., they need an organic cosubstrate to maintain their activity over several cultural transfers. For the few existing autotrophic isolates and enrichment cultures, either the mechanism of nitrate-reducing Fe(II) oxidation is not known or evidence for their autotrophic lifestyle is controversial. In the present study, we provide evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. The evidence is based on stoichiometries of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and the incorporation of carbon from CO₂ under conditions that favor the activity of nitrate-reducing Fe(II) oxidizers.

An overview of siderophores for iron acquisition in microorganisms living in the extreme

Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.

Geochemistry and Mineralogy of Western Australian Salt Lake Sediments: Implications for Meridiani Planum on Mars

Hypersaline lakes are characteristic for Western Australia and display a rare combination of geochemical and mineralogical properties that make these lakes potential analogues for past conditions on Mars. In our study, we focused on the geochemistry and mineralogy of Lake Orr and Lake Whurr. While both lakes are poor in organic carbon (<1%), the sediments' pH values differ and range from 3.8 to 4.8 in Lake Orr and from 5.4 to 6.3 in Lake Whurr sediments. Lake Whurr sediments were dominated by orange and red sediment zones in which the main Fe minerals were identified as hematite, goethite, and tentatively jarosite and pyrite. Lake Orr was dominated by brownish and blackish sediments where the main Fe minerals were goethite and another paramagnetic Fe(III)-phase that could not be identified. Furthermore, a likely secondary Fe(II)-phase was observed in Lake Orr sediments. The mineralogy of these two salt lakes in the sampling area is strongly influenced by events such as flooding, evaporation, and desiccation, processes that explain at least to some extent the observed differences between Lake Orr and Lake Whurr. The iron mineralogy of Lake Whurr sediments and the high salinity make this lake a suitable analogue for Meridiani Planum on Mars, and in particular the tentative identification of pyrite in Lake Whurr sediments has implications for the interpretation of the Fe mineralogy of Meridiani Planum sediments.

KEY WORDS

Western Australia-Salt lakes-Jarosite-Hematite-Pyrite-Mars analogue. Astrobiology 16, 525-538.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.

Microbial communities in riparian soils of a settling pond for mine drainage treatment

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage.

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia

We investigated the microbial community compositions in two sediment samples from the acidic (pH ∼3) and hypersaline (>4.5% NaCl) surface waters, which are widespread in Western Australia. In West Dalyup River, large amounts of NaCl, Fe(II) and sulfate are brought by the groundwater into the surface run-off. The presence of K-jarosite and schwertmannite minerals in the river sediments suggested the occurrence of microbial Fe(II) oxidation because chemical oxidation is greatly reduced at low pH. 16S rRNA gene diversity analyses revealed that sequences affiliated with an uncultured archaeal lineage named Aplasma, which has the genomic potential for Fe(II) oxidation, were dominant in both sediment samples. The acidophilic heterotrophs Acidiphilium and Acidocella were identified as the dominant bacterial groups. Acidiphilium strain AusYE3-1 obtained from the river sediment tolerated up to 6% NaCl at pH 3 under oxic conditions and cells of strain AusYE3-1 reduced the effects of high salt content by forming filamentous structure clumping as aggregates. Neither growth nor Fe(III) reduction by strain AusYE3-1 was observed in anoxic salt-containing medium. The detection of Aplasma group as potential Fe(II) oxidizers and the inhibited Fe(III)-reducing capacity of Acidiphilium contributes to our understanding of the microbial ecology of acidic hypersaline environments.

Prokaryotic diversity in a Tunisian hypersaline lake, Chott El Jerid

Prokaryotic diversity was investigated in a Tunisian salt lake, Chott El Jerid, by quantitative real-time PCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting methods targeting the 16S rRNA gene and culture-dependent methods. Two different samples S1-10 and S2-10 were taken from under the salt crust of Chott El Jerid in the dry season. DGGE analysis revealed that bacterial sequences were related to Firmicutes, Proteobacteria, unclassified bacteria, and Deinococcus-Thermus phyla. Anaerobic fermentative and sulfate-reducing bacteria were also detected in this ecosystem. Within the domain archaea, all sequences were affiliated to Euryarchaeota phylum. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of bacteria was 5 × 10(6) DNA copies g(-1) whereas archaea varied between 5 × 10(5) and 10(6) DNA copies g(-1) in these samples. Eight anaerobic halophilic fermentative bacterial strains were isolated and affiliated with the species Halanaerobium alcaliphilum, Halanaerobium saccharolyticum, and Sporohalobacter salinus. These data showed an abundant and diverse microbial community detected in the hypersaline thalassohaline environment of Chott El Jerid.

Bioremediation of nitrate and Fe(ii) combined contamination in groundwater by heterotrophic denitrifying bacteria and microbial community analysis

The optimal condition range was determined for the simultaneous removal of nitrate and Fe(ii) in groundwater mediated by denitrifying Betaproteobacterial communities.

Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.

Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation

Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.

Predominance of biotic over abiotic formation of halogenated hydrocarbons in hypersaline sediments in Western Australia

Volatile halogenated organic compounds (VOX) contribute to ozone depletion and global warming. There is evidence of natural VOX formation in many environments ranging from forest soils to salt lakes. Laboratory studies have suggested that VOX formation can be chemically stimulated by reactive Fe species while field studies have provided evidence for direct biological (enzymatic) VOX formation. However, the relative contribution of abiotic and biotic processes to global VOX budgets is still unclear. The goals of this study were to quantify VOX release from sediments from a hypersaline lake in Western Australia (Lake Strawbridge) and to distinguish between the relative contributions of biotic and abiotic VOX formation in microbially active and sterilized microcosms. Our experiments demonstrated that the release of organochlorines from Lake Strawbridge sediments was mainly biotic. Among the organochlorines detected were monochlorinated, e.g., chloromethane (CH3Cl), and higher chlorinated VOX compounds such as trichloromethane (CHCl3). Amendment of sediments with either Fe(III) oxyhydroxide (ferrihydrite) or a mixture of lactate/acetate or both ferrihydrite and lactate/acetate did not stimulate VOX formation. This suggests that although microbial Fe(III) reduction took place, there was no stimulation of VOX formation via Fe redox transformations or the formation of reactive Fe species under our experimental conditions.

Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture

Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle.

Fe(III) reduction during pyruvate fermentation by Desulfotomaculum reducens strain MI-1

Desulfotomaculum reducens MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing several metals, among which is Fe(III). Very limited knowledge is available on the potential mechanism(s) of metal reduction among Gram-positive bacteria, despite their preponderance in the microbial communities that inhabit some inhospitable environments (e.g., thermal or hyperthermal ecosystems, extreme pH or salinity environments, heavy metal or radionuclide contaminated sediments). Here, we show that in the presence of pyruvate, this micro-organism is capable of reducing both soluble Fe(III)-citrate and solid-phase hydrous ferric oxide, although growth is sustained by pyruvate fermentation rather than Fe(III) respiration. Despite the fact that Fe(III) reduction does not support direct energy conservation, D. reducens uses it as a complementary means of discarding excess reducing equivalent after H2 accumulation in the culture headspace renders proton reduction unfavorable. Thus, Fe(III) reduction permits the oxidation of greater amounts of pyruvate than fermentation alone. Fe(III) reduction by D. reducens is mediated by a soluble electron carrier, most likely riboflavin. Additionally, an intracellular electron storage molecule acts as a capacitor and accumulates electrons during pyruvate oxidation for slow release to Fe(III). The reductase responsible for the transfer of electrons from the capacitor to the soluble carrier has not been identified, but data presented here argue against the involvement of c-type cytochromes.

Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers

The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly, Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deinococcus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.