Associations between redox‐sensitive trace metals and microbial communities in a Proterozoic ocean analogue

Constraints on Precambrian ocean chemistry are dependent upon sediment geochemistry. However, diagenesis and metamorphism can destroy primary biosignatures, making it difficult to consider biology when interpreting geochemical data. Modern analogues for ancient ecosystems can be useful tools for identifying how sediment geochemistry records an active biosphere. The Middle Island Sinkhole (MIS) in Lake Huron is an analogue for shallow Proterozoic waters due to its low oxygen water chemistry and microbial communities that exhibit diverse metabolic functions at the sediment–water interface. This study uses sediment trace metal contents and microbial abundances in MIS sediments and an oxygenated Lake Huron control site (LH) to infer mechanisms for trace metal burial. The adsorption of trace metals to Mn‐oxyhydroxides is a critical burial pathway for metals in oxic LH sediments, but not for the MIS mat and sediments, consistent with conventional understanding of Mn cycling. Micronutrient trace metals (e.g., Zn) are associated with organic matter regardless of oxygen and sulfide availability. Although U and V are conventionally considered to be organically complexed in suboxic and anoxic conditions, U and organic covary in oxic LH sediments, and Mn‐oxyhydroxide cycling dominates V deposition in the anoxic MIS sediments. Significant correlations between Mo and organic matter across all redox regimes have major implications for our interpretations of Mo isotope systematics in the geologic record. Finally, while microbial groups vary between the sampling locales (e.g., the cyanobacteria in the MIS microbial mat are not present in LH sediments), LH and MIS ultimately have similar relationships between microbial assemblages and metal burial, making it difficult to link trace metal burial to microbial metabolisms. Together, these results indicate that bulk sediment trace metal composition does not capture microbiological processes; more robust trace metal geochemistry such as isotopes and speciation may be critical for understanding the intersections between microbiology and sediment geochemistry.     

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea

The stratified water column of the Black Sea produces a vertical succession of redox zones, stimulating microbial activity at the interfaces. Our study of intact polar membrane lipids (IPLs) in suspended particulate matter and sediments highlights their potential as biomarkers for assessing the taxonomic composition of live microbial biomass. Intact polar membrane lipids in oxic waters above the chemocline represent contributions of bacterial and eukaryotic photosynthetic algae, while anoxygenic phototrophic bacteria and sulfate-reducing bacteria comprise a substantial amount of microbial biomass in deeper suboxic and anoxic layers. Intact polar membrane lipids such as betaine lipids and glycosidic ceramides suggest unspecified anaerobic bacteria in the anoxic zone. Distributions of polar head groups and core lipids show planktonic archaea below the oxic zone; methanotrophic archaea are only a minor fraction of archaeal biomass in the anoxic zone, contrasting previous observations based on the apolar derivatives of archaeal lipids. Sediments contain algal and bacterial IPLs from the water column, but transport to the sediment is selective; bacterial and archaeal IPLs are also produced within the sediments. Intact polar membrane lipid distributions in the Black Sea are stratified in accordance with geochemical profiles and provide information on vertical successions of major microbial groups contributing to suspended biomass. This study vastly extends our knowledge of the distribution of complex microbial lipids in the ocean.     

Microbial diversity and stratification of South Pacific abyssal marine sediments

Abyssal marine sediments cover a large proportion of the ocean floor, but linkages between their microbial community structure and redox stratification have remained poorly constrained. This study compares the downcore gradients in microbial community composition to porewater oxygen and nitrate concentration profiles in an abyssal marine sediment column in the South Pacific Ocean. Archaeal 16S rRNA clone libraries showed a stratified archaeal community that changed from Marine Group I Archaea in the aerobic and nitrate-reducing upper sediment column towards deeply branching, uncultured crenarchaeotal and euryarchaeotal lineages in nitrate-depleted, anaerobic sediment horizons. Bacterial 16S rRNA clone libraries revealed a similar shift on the phylum and subphylum level within the bacteria, from a complex community of Alpha-, Gamma- and Deltaproteobacteria, Actinobacteria and Gemmatimonadetes in oxic surface sediments towards uncultured Chloroflexi and Planctomycetes in the anaerobic sediment column. The distinct stratification of largely uncultured bacterial and archaeal groups within the oxic and nitrate-reducing marine sediment column provides initial constraints for their microbial habitat preferences.     

Microbiological and Geochemical Characterization of Fluvially Deposited Sulfidic Mine Tailings

The fluvial deposition of mine tailings generated from historic mining operations near Butte, Montana, has resulted in substantial surface and shallow groundwater contamination along Silver Bow Creek. Biogeochemical processes in the sediment and underlying hyporheic zone were studied in an attempt to characterize interactions consequential to heavy-metal contamination of shallow groundwater. Sediment cores were extracted and fractionated based on sediment stratification. Subsamples of each fraction were assayed for culturable heterotrophic microbiota, specific microbial guilds involved in metal redox transformations, and both aqueous- and solid-phase geochemistry. Populations of cultivable Fe(III)-reducing bacteria were most prominent in the anoxic, circumneutral pH regions associated with a ferricrete layer or in an oxic zone high in organic carbon and soluble iron. Sulfur- and iron-oxidizing bacteria were distributed in discrete zones throughout the tailings and were often recovered from sections at and below the anoxic groundwater interface. Sulfate-reducing bacteria were also widely distributed in the cores and often occurred in zones overlapping iron and sulfur oxidizers. Sulfate-reducing bacteria were consistently recovered from oxic zones that contained high concentrations of metals in the oxidizable fraction. Altogether, these results suggest a highly varied and complex microbial ecology within a very heterogeneous geochemical environment. Such physical and biological heterogeneity has often been overlooked when remediation strategies for metal contaminated environments are formulated.     

Bioturbation: impact on the marine nitrogen cycle

Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification-denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.     

Drought impacts on biogeochemistry and microbial processes in salt marsh sediments: a flow-through reactor approach

The effects of drought on salt marsh sediments from Sapelo Island, Georgia, were examined in flow-through reactor experiments. Three hydrological treatments were employed: a continuously flooded anoxic control, a periodic drought treatment that experienced alternate periods of flooding and drying, and a severe drought treatment, where sediment was exposed to drought (drying) for several weeks and then flooded; the effect of both buffered and non-buffered flooding solutions were examined. In permanently anoxic sediments as well as in sediments exposed to drought, organic carbon oxidation was dominated by SO₄ ^2? reduction (SR) and SR rates increased over time. The shift from anoxic to oxic conditions in drought treatments significantly altered sediment geochemistry and pathways of microbial metabolism. Drought conditions favored suboxic mineralization processes, such as Fe(III) reduction and denitrification, which was fueled by NH₄ ⁺ oxidation promoted by O₂ delivered during drought conditions. Other major drought-induced changes included pH decrease, and altered concentrations of solid phase adsorbed metals.     

The Effect of Sediment Type and pH-Adjustment on the Porewater Chemistry of Copper- and Zinc-Spiked Sediments

The spiking of metals into sediments lowers pH, raises the oxidative state, and exacerbates the partitioning of Fe, Mn, and spiked metal to the porewater. This study reports the geochemical response of three sediments of varying metal-binding capacity to Cu-/Zn-additions and the influence of pH-adjustment on the major metal-partitioning processes. The increase in redox potential and porewater metal concentrations observed in metal-spiked sediment was minimized by sediment neutralization to pH 7 irrespective of sediment type. In the presence of minimal sulfide concentrations, porewater metal concentrations suggested a greater affinity of copper for organic carbon than zinc, which was thought more dependent on iron oxyhydroxide phases. The amount of iron in the porewater of metal-spiked pH adjusted sediment was, in turn, affected by the type and concentration of spiked metal in the porewater. Increasing porewater concentrations of copper and zinc corresponded to decreasing and increasing porewater iron concentrations, respectively. Porewater copper appeared to act as a toxicant of Fe(III) reducing bacteria, while porewater zinc is thought to have had a stimulatory effect. The present study provides further insight on geochemical changes occurring to metal-spiked sediments and their implications for the interpretation of toxicity tests.     

Distribution and Rate of Methane Oxidation in Sediments of the Florida Everglades

Rates of methane emission from intact cores were measured during anoxic dark and oxic light and dark incubations. Rates of methane oxidation were calculated on the basis of oxic incubations by using the anoxic emissions as an estimate of the maximum potential flux. This technique indicated that methane oxidation consumed up to 91% of the maximum potential flux in peat sediments but that oxidation was negligible in marl sediments. Oxygen microprofiles determined for intact cores were comparable to profiles measured in situ. Thus, the laboratory incubations appeared to provide a reasonable approximation of in situ activities. This was further supported by the agreement between measured methane fluxes and fluxes predicted on the basis of methane profiles determined by in situ sampling of pore water. Methane emissions from peat sediments, oxygen concentrations and penetration depths, and methane concentration profiles were all sensitive to light-dark shifts as determined by a combination of field and laboratory analyses. Methane emissions were lower and oxygen concentrations and penetration depths were higher under illuminated than under dark conditions; the profiles of methane concentration changed in correspondence to the changes in oxygen profiles, but the estimated flux of methane into the oxic zone changed negligibly. Sediment-free, root-associated methane oxidation showed a pattern similar to that for methane oxidation in the core analyses: no oxidation was detected for roots growing in marl sediment, even for roots of Cladium jamaicense, which had the highest activity for samples from peat sediments. The magnitude of the root-associated oxidation rates indicated that belowground plant surfaces may not markedly increase the total capacity for methane consumption. However, the data collectively support the notion that the distribution and activity of methane oxidation have a major impact on the magnitude of atmospheric fluxes from the Everglades.     

Cable bacteria extend the impacts of elevated dissolved oxygen into anoxic sediments

Profound biogeochemical responses of anoxic sediments to the fluctuation of dissolved oxygen (DO) concentration in overlaying water are often observed, despite oxygen having a limited permeability in sediments. This contradiction is indicative of previously unrecognized mechanism that bridges the oxic and anoxic sediment layers. Using sediments from an urban river suffering from long-term polycyclic aromatic hydrocarbons (PAHs) contamination, we analyzed the physicochemical and microbial responses to artificially elevated DO (eDO) in the overlying water over 9 weeks of incubation. Significant changes in key environmental parameters and microbial diversity were detected over the 0–6 cm sediment depth, along with accelerated degradation of PAHs, despite that eDO only increased the porewater DO in the millimeter subfacial layer. The dynamics of physicochemical and microbial properties coincided well with significantly increased presence of centimeter-long sulfide-oxidizing cable bacteria filaments under eDO, and were predominantly driven by cable bacteria metabolic activities. Phylogenetic ecological network analyses further revealed that eDO reinforced cable bacteria associated interspecific interactions with functional microorganisms such as sulfate reducers, PAHs degraders, and electroactive microbes, suggesting enhanced microbial syntrophy taking advantage of cable bacteria metabolism for the regeneration of SO₄²⁻ and long-distance electron transfer. Together, our results suggest cable bacteria may mediate the impacts of eDO in anaerobic sediments by altering sediment physiochemical properties and by reinforcing community interactions. Our findings highlight the ecological importance of cable bacteria in sediments.Subject terms: Freshwater ecology, Water microbiology, Community ecology     

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4‐region gene fragments obtained by PCR amplification of community genomic DNA with bacterial‐ or archaeal‐specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158 686 bacterial and 225 591 archaeal sequences from 20 sediment samples, representing five 2‐cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor‐joining analysis using Chao–Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96–99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus‐related sequence abundance was correlated with high solid‐phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.     

Small-scale distribution of interstitial nitrite in freshwater sediment microcosms: the role of nitrate and oxygen availability,and sediment permeability

The spatial distribution of interstitial NO2(-) concentrations was studied in NO3(-)-exposed freshwater sediment microcosms, using pore water extractions as well as ion-selective microsensors. Porewater extractions revealed ecotoxicologically critical NO2(-) concentrations in hypoxic and anoxic sediment layers in which significant NO3(-) consumption took place. In contrast, the use of ion-selective microsensors demonstrated the high capacity of the thin oxic surface layer of the sediments to consume NO2(-) and to produce NO3(-). Two modes of NO3(-) supply to the sediments were compared: In treatments with NO3(-) supply to the overlying water, a subsurface maximum of NO2(-) concentration was observed, coinciding with the site of maximum NO3(-) consumption. When NO3(-) was perfused up through the sediment cores, however, NO2(-) accumulated throughout the entire sediment column. Such spatially extensive NO2(-) accumulations were only observed in sediments poor in organic matter with a relatively high permeability. By manipulating the O2 content of the overlying water, the release of NO2(-) from the sediments could be influenced: In treatments with air-saturated overlying water, the sediments did not release detectable amounts of NO2(-) into the water phase. When kept hypoxic (25% air saturation) instead, significant NO2(-) accumulations were recorded in the overlying water. These findings suggest that in treatments with air-saturated overlying water, NO2(-) that was produced in deeper sediment layers (denitrifying conditions) was completely consumed at the oxic sediment surface (nitrifying conditions) before it could reach the overlying water.     

Benthic pH gradients across a range of shelf sea sediment types linked to sediment characteristics and seasonal variability

This study used microelectrodes to record pH profiles in fresh shelf sea sediment cores collected across a range of different sediment types within the Celtic Sea. Spatial and temporal variability was captured during repeated measurements in 2014 and 2015. Concurrently recorded oxygen microelectrode profiles and other sedimentary parameters provide a detailed context for interpretation of the pH data. Clear differences in profiles were observed between sediment type, location and season. Notably, very steep pH gradients exist within the surface sediments (10–20 mm), where decreases greater than 0.5 pH units were observed. Steep gradients were particularly apparent in fine cohesive sediments, less so in permeable sandier matrices. We hypothesise that the gradients are likely caused by aerobic organic matter respiration close to the sediment–water interface or oxidation of reduced species at the base of the oxic zone (NH₄ ⁺, Mn²⁺, Fe²⁺, S^?). Statistical analysis suggests the variability in the depth of the pH minima is controlled spatially by the oxygen penetration depth, and seasonally by the input and remineralisation of deposited organic phytodetritus. Below the pH minima the observed pH remained consistently low to maximum electrode penetration (ca. 60 mm), indicating an absence of sub-oxic processes generating H⁺ or balanced removal processes within this layer. Thus, a climatology of sediment surface porewater pH is provided against which to examine biogeochemical processes. This enhances our understanding of benthic pH processes, particularly in the context of human impacts, seabed integrity, and future climate changes, providing vital information for modelling benthic response under future climate scenarios.     

Viruses, prokaryotes and DNA in the sediments of a deep-hypersaline anoxic basin (DHAB) of the Mediterranean Sea

Viral and prokaryote abundance were investigated in a deep-hypersaline anoxic basin of the Eastern Mediterranean Sea (DHAB Atalante basin at c. 3000 m depth). This system was compared with two nearby deep-sea sites characterized by oxic conditions. Viral abundance and virus to prokaryote abundance ratio in hypersaline anoxic sediments displayed values close to those reported in oxic sites. The analysis of vertical profiles of viral abundance in the Atalante basin revealed the lack of significant changes with depth in the sediment, suggesting that benthic viruses in these anoxic and hypersaline conditions are preserved or resistant to decay. The anoxic basin displayed also very high concentrations of labile organic components (proteins and lipids) and extracellular DNA. These findings suggest that the DHAB sediments represent a reservoir for long-term preservation of benthic viruses and nucleic acids.     

Dynamics of Dimethyl Sulfide in a Marine Microbial Mat

Abstract The microbial mat was chosen as a model ecosystem to study dynamics of dimethyl sulfide (DMS) in marine sediments in order to gain insight into key processes and factors which determine emission rates. A practical advantage, compared to open ocean ecosystems, is that microbial mats contain high biomasses of different functional groups of bacteria involved in DMS dynamics, and that DMS concentrations are generally high enough to allow direct measurement of emission rates. Field data showed that, during the seasonal development of microbial mats, concentrations of chlorophyll a corresponded to dimethylsulfoniopropionate (DMSP). DMSP is an important precursor of DMS. It was demonstrated, with laboratory cultures, that various species of benthic diatoms produce substantial amounts of DMSP. The abundances of aerobic and anaerobic DMS- or DMSO-utilizing bacteria were estimated using the most-probable-number technique. Laboratory experiments with relatively undisturbed sediment cores showed that microbial mats act as a sink for DMS under oxic/light (day) conditions, and as a source of DMS under anoxic/dark (night) conditions. Axenic culture studies with Chromatium vinosum M2 and Thiocapsa pfennigii M8 (isolated from a microbial mat) showed that, under anoxic/light conditions, DMS was quantitatively converted to dimethylsulfoxide (DMSO). T. roseopersicina M11 converted DMSP to DMS and acrylate, apparently without use of either substrate. Received: 5 May 1997; Accepted: 21 August 1997     

Microbial Community Response to Seawater Amendment in Low-Salinity Tidal Sediments

Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater–saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375–408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more “marine-like” through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of the microbial community.     

Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.     

A Michaelis–Menten type equation for describing methylmercury dependence on inorganic mercury in aquatic sediments

Methylation of mercury (Hg) is the crucial process that controls Hg biomagnification along the aquatic food chains. Aquatic sediments are of particular interest because they constitute an essential reservoir where inorganic divalent Hg (Hg^II) is methylated. Methylmercury (MeHg) concentrations in sediments mainly result from the balance between methylation and demethylation reactions, two opposite natural processes primarily mediated by aquatic microorganisms. Thus, Hg availability and the activity of methylating microbial communities control the MeHg abundance in sediments. Consistently, some studies have reported a significant positive correlation between MeHg and Hg^II or total Hg (Hg_T), taken as a proxy for Hg^II, in aquatic sediments using enzyme-catalyzed methylation/demethylation mechanisms. By compiling 1,442 published and unpublished Hg_T–MeHg couples from lacustrine, riverine, estuarine and marine sediments covering various environmental conditions, from deep pristine abyssal to heavily contaminated riverine sediments, we show that a Michaelis–Menten type relationship is an appropriate model to relate the two parameters: MeHg = aHg_T/(K _m  + Hg_T), with a = 0.277 ± 0.011 and K _m  = 188 ± 15 (R ² = 0.70, p < 0.001). From K _m variations, which depend on the various encountered environmental conditions, it appears that MeHg formation and accumulation are favoured in marine sediments compared to freshwater ones, and under oxic/suboxic conditions compared to anoxic ones, with redox potential and organic matter lability being the governing factors.     

Bioturbation and the role of microniches for sulfate reduction in coastal marine sediments

The effects of bioturbation in marine sediments are mainly associated with an increase in oxic and oxidized zones through an influx of oxygen‐rich water deeper into the sediment and the rapid transport of particles between oxic and anoxic conditions. However, macrofaunal activity also can increase the occurrence of reduced microniches and anaerobic processes, such as sulfate reduction. Our goal was to determine the two‐dimensional distribution of microniches associated with burrows of a ghost shrimp (Neotrypaea californiensis) and to determine microbial activities. In laboratory experiments, detailed measurements of sulfate reduction rates (SRR) were measured by injecting, in a 1 cm grid, radiolabelled sulfate directly into a narrow aquarium (40 cm × 30 cm × 3 cm) containing the complex burrow of an actively burrowing shrimp. Light‐coloured oxidized burrow walls, along with black reduced microniches, were clearly visible through the aquarium walls. Direct injection of radiotracers allowed for whole‐aquarium incubation to obtain two‐dimensional documentation of sulfate reduction. Results indicated SRR were up to three orders of magnitude higher (140–790 nmol SO₄^2? cm^?3 day^?1) in reduced microniches associated with burrows when compared with the surrounding sediment. Additionally, some of the subsurface sulfate‐reducing microniches associated with the burrow system appeared to be zones of dinitrogen fixation. Bioturbation may also lead to decreased sulfate reduction in other microniches and the sum of the activity in all microniches might not result in a total increase of sulfate reduction compared with non‐bioturbated control sediments.     

Nitrogen‐cycling bacteria and archaea in the carbonate sediment of a coral reef

In the coarse‐grained carbonate sediments of coral reefs, advective porewater flow and the respiration of organic matter establish redox zones that are the scene of microbially mediated transformations of N compounds. To investigate the geobiology of N cycling in reef sediments, the benthic microbiota of Checker Reef in Kaneohe Bay, Hawaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes (napA, narG, nrfA, amoA) and ribotypes (unique RNA sequences) of anammox‐like 16S rRNA. Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of napA (≥202 in anoxic sediment) and narG (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of nrfA hosts in interfacial reef sediment was dominated by Vibrio species. The identified members of the aerobic ammonium oxidizing guild (amoA hosts) were Crenarchaeota or close relatives of Nitrosomonadales. Putative anammox bacteria were detected in the RNA pool of Checker Reef sediment. More than half of these ribotypes show ≥90% identity with homologous sequences of Scalindua spp., while no evidence was found for members of the genera Brocadia or Kuenenia. In addition to exploring the diversity of these four nitrogen‐cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers (amoA), nitrite oxidizers (nxrAB), ammonifying nitrite reducers (nrfA) and denitrifiers (nosZ) were estimated using real‐time PCR. Representatives of all targeted guilds were detected, suggesting that most processes of the biogeochemical N cycle can be catalyzed by the benthic microbiota of tropical coral reefs.     

Sedimentary pyrite sulfur isotope compositions preserve signatures of the surface microbial mat environment in sediments underlying low-oxygen cyanobacterial mats

The sedimentary pyrite sulfur isotope (δ³⁴S) record is an archive of ancient microbial sulfur cycling and environmental conditions. Interpretations of pyrite δ³⁴S signatures in sediments deposited in microbial mat ecosystems are based on studies of modern microbial mat porewater sulfide δ³⁴S geochemistry. Pyrite δ³⁴S values often capture δ³⁴S signatures of porewater sulfide at the location of pyrite formation. However, microbial mats are dynamic environments in which biogeochemical cycling shifts vertically on diurnal cycles. Therefore, there is a need to study how the location of pyrite formation impacts pyrite δ³⁴S patterns in these dynamic systems. Here, we present diurnal porewater sulfide δ³⁴S trends and δ³⁴S values of pyrite and iron monosulfides from Middle Island Sinkhole, Lake Huron. The sediment–water interface of this sinkhole hosts a low-oxygen cyanobacterial mat ecosystem, which serves as a useful location to explore preservation of sedimentary pyrite δ³⁴S signatures in early Earth environments. Porewater sulfide δ³⁴S values vary by up to ~25‰ throughout the day due to light-driven changes in surface microbial community activity that propagate downwards, affecting porewater geochemistry as deep as 7.5 cm in the sediment. Progressive consumption of the sulfate reservoir drives δ³⁴S variability, instead of variations in average cell-specific sulfate reduction rates and/or sulfide oxidation at different depths in the sediment. The δ³⁴S values of pyrite are similar to porewater sulfide δ³⁴S values near the mat surface. We suggest that oxidative sulfur cycling and other microbial activity promote pyrite formation in and immediately adjacent to the microbial mat and that iron geochemistry limits further pyrite formation with depth in the sediment. These results imply that primary δ³⁴S signatures of pyrite deposited in organic-rich, iron-poor microbial mat environments capture information about microbial sulfur cycling and environmental conditions at the mat surface and are only minimally affected by deeper sedimentary processes during early diagenesis.