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Sedimentary interfaces between contrasting hydrogeological facies in alluvial aquifers drive the development of biogeochemical interfaces that influence subsurface and surface water quality. Here, we calibrate a reactive transport model on a series of dual-domain column experiments, where centimeter-scale, low-permeability, organic-rich anoxic lenses are embedded in coarser-grained aquifer material. Simulations explicitly account for C, Fe, and S cycling at the interface between the lenses and the aquifer in water-saturated conditions. Our results highlight the role of fine-grained, organic-rich inclusions not only as sources or sinks for redox-sensitive species, but also as exporters of nutrients that stimulate downgradient biogeochemical cycling. By releasing large amounts of organic carbon into the surrounding aquifer, such lenses drive the development of proximal secondary reduction zones (“halos”), characterized by high microbial activity (e.g., sulfate reduction) and accumulation of reduced reaction products (e.g., iron sulfide). If similar secondary reduction zones develop within the hydraulically conductive domain of an aquifer, they would be highly susceptible to changes in hydrologic conditions, for instance oxygen pulses associated with seasonal snowmelt. Our results also emphasize the limitations of relying solely on aqueous species measurements to inform reactivity in systems where fast redox cycling and/or sizeable particulate transport may limit the signature of reactivity in the dissolved phase.

The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

Three clearly defined abrupt cooling events (ACEs) can be observed within Greenland Interstadial (GI)‐1 in the Greenland ice‐core records. However, the spatial variation in amplitude and timing of these ACEs is poorly understood due to the paucity of well‐dated records with quantified temperature reconstructions. This study presents high‐resolution chironomid‐inferred July air temperature (TJul) and oxygen isotope (δ18O) records from Crudale Meadow (Orkney Isles, UK). Three centennial‐scale ACEs punctuate the Windermere Interstadial at Crudale Meadow. The largest ACE shows an amplitude of 5.4 °C and a 1% isotopic decline and is centred on ~14.0 ka BP, consistent with the timing of the GI‐1d event in the Greenland stratigraphy. The two other observed ACEs are of smaller magnitude and are centred on ~13.6 ka BP and ~13.2 ka BP, with these smaller magnitude events tentatively correlated with the GI‐1cii and GI‐1b events, respectively, but lack sufficient chronological constraint to fully assess their timing. When comparing the Crudale Meadow record with other locations in the British Isles a strong relationship can be observed between the magnitude of TJul cooling and latitude, with a reduced signal in more southerly locations, indicating that oceanic forcing may be a key driver of the ACEs.

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

Second messenger signaling is required for cellular processes. We previously reported that extracellular vesicles (EVs) from stimulated cultured endothelial cells contain the biochemical second messenger, cAMP. In the current study, we sought to determine whether cAMP-enriched EVs induce second messenger signaling pathways in naïve recipient cells. Our results indicate that cAMP-enriched EVs increase cAMP content sufficient to stimulate PKA activity. The implications of our work are that EVs represent a novel intercellular mechanism for second messenger, specifically cAMP, signaling.

Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO(2) assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.

The influence of the North Atlantic on the margins of Europe means the region is particularly sensitive to changes in the ocean–atmospheric system. During the Last Glacial–Interglacial Transition (16–8 cal ka bp) this system was repeatedly disrupted, leading to a series of abrupt and short-lived shifts in climate. Despite much research, the number and magnitude of these ‘centennial-scale’ events is not well understood. To address this, we expand upon investigations at Quoyloo Meadow, Orkney, Scotland, one of the best chronologically constrained palaeoclimate records in northern Britain. By coupling stable isotope and chironomid fossil analyses with existing data, this study identifies multiple phases of centennial-scale disturbance at: c. 14.0, 11.1, 10.8, 10.5, 10.45 and 10.3 cal ka bp, with the events at 14.0 and 10.3 exhibiting a particularly pronounced cold-climate signature. During the Holocene, the strongest response to climate forcing was at c. 10.3–10.0 cal ka bp, expressed as a two-stage drop in mean July temperatures, a shift in pollen spectra indicative of ‘less-stable’ climatic regimes, and a depletion in δ18O values. We interpret this as the first reliably dated incidence of the ‘10.3-ka event’ in the British Isles and consider the wider impact of this climatic reversal in other Holocene records.

Beach aquifers, located in the subsurface of sandy beaches, are unique ecosystems with steep chemical and physical gradients resulting from the mixing of terrestrial fresh groundwater and saline groundwater from the sea. While work has rapidly progressed to understand the physics and chemistry in this environment, much less is known about the microorganisms present despite the fact that they are responsible for vital biogeochemical processes. This paper presents a review of the current state of knowledge of microbes within beach aquifers and the mechanisms that control the beach aquifer microbiome. We review literature describing the distribution and diversity of microorganisms in the freshwater-saltwater mixing zone of beach aquifers, and identify just 12 papers. We highlight knowledge gaps, as well as future research directions: The understanding of beach aquifer microorganisms is informed primarily by 16S ribosomal RNA gene sequences. Metagenomics and metatranscriptomics have not yet been applied but are promising approaches for elucidating key metabolic and ecological roles of microbes in this environment. Additionally, variability in field sampling and analytical methods restrict comparison of data across studies and geographic locations. Further, documented evidence on the migration of microbes within the beach aquifer is limited. Taking into account the physical transport of microbes through sand by flowing groundwater may be critical for understanding the structure and dynamics of microbial communities. Quantitative measurements of rates of elemental cycling in the context of microbial diversity need further investigation, in order to understand the roles of microbes in mediating biogeochemical fluxes from the beach aquifer to the coastal ocean. Lastly, understanding the current state of beach aquifers in regulating carbon stocks is critical to foster a better understanding of the contribution of the beach aquifer microbiome to global climate models.

The Windermere Interstadial (GI-1; c. 14.7-12.9 kyr ago), a relatively warm period at the end of the last glaciation, provides an excellent opportunity to study past abrupt cooling events (ACEs). These events, commonly known as GI-1d and GI-1b, are clearly expressed in the Greenland ice cores and offer some of our best analogues for future events caused by anthropogenic warming. Such ACEs have variable expression in terms of their magnitude across Europe and the North Atlantic region which is likely to reflect the forcing factors which drive them. However, relatively few, spatially uneven, quantitative temperature reconstructions of ACEs exist for NW Europe. Between-site differences in sampling resolution applied and calibration datasets used makes inter-comparisons problematic. We applied chironomid and oxygen-isotope analysis at a high temporal resolution (~decadal) to a number of Windermere Interstadial lake sequences from spatially diverse locations across the British Isles. This dual proxy approach allows for quantitative reconstructions of past climate change and provides insight into seasonal temperature change as well as hydrological regime shifts. Several chironomid calibration datasets were tested to ascertain which provided the most reliable reconstruction. Even across a relatively restricted area such as the British Isles, clear spatial patterns can be observed in ACE strength. GI-1d exhibits greatest magnitude in the North of the region whilst GI-1b is most strongly expressed in the South. The results highlight the pivotal location of the British Isles in further refining our understanding of the forcing mechanism driving ACEs.

BACKGROUND Internet-delivered cognitive behavioral therapy (ICBT) is an effective treatment that can overcome barriers to mental health care. Various research groups have suggested that unguided ICBT (ie, ICBT without therapist support) and other eHealth interventions can be designed to enhance user engagement and thus outcomes. The persuasive systems design framework captures most design recommendations for eHealth interventions, but there is little empirical evidence that persuasive design is related to clinical outcomes in unguided ICBT. OBJECTIVE This study aims to provide an updated meta-analysis of randomized controlled trials of unguided ICBT for depression and anxiety, describe the frequency with which various persuasive design principles are used in such interventions, and use meta-regression to explore whether a greater number of persuasive design elements predicts efficacy in unguided ICBT for depression and anxiety. METHODS We conducted a systematic review of 5 databases to identify randomized controlled trials of unguided ICBT for depression and anxiety. We conducted separate random effects meta-analyses and separate meta-regressions for depression and anxiety interventions. Each meta-regression included 2 steps. The first step included, as a predictor, whether each intervention was transdiagnostic. For the meta-regression of ICBT for depression, the first step also included the type of control condition. The number of persuasive design principles identified for each intervention was added as a predictor in the second step to reveal the additional variance in effect sizes explained by persuasive design. RESULTS Of the 4471 articles we identified in our search, 46 (1.03%) were eligible for inclusion in our analyses. Our meta-analyses showed effect sizes (Hedges g) ranging from 0.22 to 0.31 for depression interventions, depending on the measures taken to account for bias in the results. We found a mean effect size of 0.45 (95% CI 0.33-0.56) for anxiety interventions, with no evidence that the results were inflated by bias. Included interventions were identified as using between 1 and 13 persuasive design principles, with an average of 4.95 (SD 2.85). The meta-regressions showed that a greater number of persuasive design principles predicted greater efficacy in ICBT for depression (R2 change=0.27; B=0.04; P=.02) but not anxiety (R2 change=0.05; B=0.03; P=.17). CONCLUSIONS These findings show wide variability in the use of persuasive design in unguided ICBT for depression and anxiety and provide preliminary support for the proposition that more persuasively designed interventions are more efficacious, at least in the treatment of depression. Further research is needed to clarify the role of persuasive design in ICBT. CLINICALTRIAL

Objectives Lymphatic malformations are benign vascular anomalies comprised of lymphatic elements and most commonly occur in the neck. They may be diagnosed prenatally on ultrasound, and, in addition to confirming the diagnosis, fetal MRI can delineate the presence and extent of airway involvement. A variety of therapies are available for the treatment of lymphatic malformations including medical management, sclerotherapy, and surgery. Case presentation We report a case of a 28 year-old pregnant female diagnosed with a fetal neck mass by ultrasound at 21 weeks gestation. A fetal MRI was performed which demonstrated a multiseptated cystic neck mass most suggestive of a lymphatic malformation. The mass was noted to be intimately associated with the fetal airway. Follow up ultrasounds showed continued growth of the lesion throughout pregnancy. The baby was born by EXIT procedure and the lymphatic malformation was ultimately treated by a combination of medical treatment, sclerotherapy, and surgery. Conclusions Cervical lymphatic malformations have a classic imaging appearance and can enlarge throughout gestation as well as after delivery. The treatment plan typically involves a multidisciplinary approach.

Since the 1980s, the San Francisco Bay Delta ecosystem has experienced large declines in primary production. Hypothesized reasons for this decline include (1) suppression of nitrate (NO3−) uptake, and thus phytoplankton growth, due to high concentrations of ammonium (NH4+), and (2) wastewater NH4+-induced changes in phytoplankton community composition away from large-celled diatoms. These twin hypotheses implicate NH4+ loading from the Sacramento Regional Wastewater Treatment Plant effluent outfall in explaining declines in primary production in the region. They have been controversial within the water resources management community and have stimulated a lengthy public scientific and regulatory debate. Here, in an effort to resolve this debate, we present results from a 48-h incubation experiment with surface water from both upstream and downstream of the Sacramento Regional Wastewater Treatment Plant effluent outfall, a major source of NH4+ loading to the ecosystem. We amended this water with either NH4+, NO3−, or full wastewater effluent. All assays were incubated under high light (52% of incident irradiance) or low light (6% of incident irradiance). NO3− uptake rates were suppressed to near zero in all treatments with either added NH4+, added wastewater effluent, or high in situ NH4+ concentrations. Yet, phytoplankton uniformly grew well on all dissolved inorganic nitrogen sources, including effluent and NH4+. Diatom species were the most abundant taxa at all stations, and diatom cell abundances increased at greater rates than all other taxa over the course of the experiment. Among all treatments, the light treatment had the greatest effects on chlorophyll a accumulation and phytoplankton growth rates. Our results suggest that high NH4+ loading is not a driver of the lower productivity in the San Francisco Bay Delta. Although phytoplankton preferred NH4+ to NO3− when both were available in our experiment, the form of dissolved inorganic nitrogen had no effect on growth rates or species composition.

Riparian floodplains represent an interaction zone between the terrestrial subsurface and rivers, where regional groundwater flows, infiltration, and evapotranspiration drive mixing of water and import/export of nutrients and contaminants. These dynamics create seasonally transient redox conditions that drive biogeochemical transformations, which strongly modify groundwater quality. Microbial responses to changing hydrological conditions are perhaps the critical step connecting hydrology to geochemical transformations and groundwater quality, yet are not well understood. We aimed to address this knowledge gap by monitoring seasonal transitions at the United States Department of Energy legacy uranium ore processing site in Riverton, WY, through spring-summer-fall hydrological transitions. Our goal was to characterize the microbial community throughout the soil profile, down to the saturated aquifer, and observe its response to wet-dry transitions across a full season and compare to changes in geochemistry and hydrology. Next-generation sequencing was employed to identify biogeochemically relevant microbial taxa based on the 16S rRNA gene; we found a broad diversity of microbial clades including taxa involved in sulfur and metal cycling, as well as nitrification. These data were paired with measurements of soil moisture, major nutrients and cations, and trace elements. Overall microbial community composition was dependent on soil depth or type, with seasonal effects only observed in the topsoil or subsurface aquifer. This finding indicates that microbial communities in the transiently reduced center of the soil profile at the Riverton, WY site are remarkably stable, despite moisture and redox inversions. In addition, these communities likely impact the communities in surrounding soil horizons through export of metabolites and solutes as the water table rises and falls throughout the season.

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (

Autotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO2-fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition.Significance statementAutotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.

Summary Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity, and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modeling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems. This article is protected by copyright. All rights reserved.

Nitrogen (N) is one of the primary nutrients required to build biomass and is therefore in high demand in aquatic ecosystems. Estuaries, however, are frequently inundated with high concentrations of anthropogenic nitrogen, which can lead to substantially degraded water quality. Understanding drivers of biogeochemical N cycling rates and the microbial communities responsible for these processes is critical for understanding how estuaries are responding to human development. Estuaries are notoriously complex ecosystems: not only do individual estuaries by definition encompass gradients of salinity and other changing environmental conditions, but differences in physical parameters (e.g., bathymetry, hydrodynamics, tidal flushing) lead to a tremendous amount of variability in estuarine processes between ecosystems, as well. Here, we review the current knowledge of N cycling processes in estuaries carried out by bacteria and archaea, including both biogeochemical rate measurements and molecular characterizations of N cycling microbial communities. Particular attention is focused on identifying key environmental factors associated with distinct biogeochemical or microbial regimes across numerous estuaries. Additionally, we describe novel metabolisms or organisms that have recently been discovered but have not yet been fully explored in estuaries to date. While the majority of research has been conducted in the benthos, we also describe data from estuarine water columns. Understanding both the common patterns and the differences between estuaries has important implications for how these critical ecosystems respond to changing environmental conditions.

Ecological factors contributing to depth-related diversification of marine Thaumarchaeota populations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity-water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters-were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeota and heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobia and Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and Nitrospina OTUs. Even at depths where WCB-like Thaumarchaeota dominated, Nitrospina OTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.

The Last Glacial-Interglacial Transition (ca 16–8 ka BP) in north-west Europe is an important period of climatic change where millennial-scale climatic evolution led to environmental reorganisation. Imprinted upon these long-term changes are a series of short-lived, centennial-scale events that appear to be spatially and temporally complex across Europe. The complexity of environmental change in response to these climatic events is poorly understood because of a paucity of paired investigations that provide evidence of both driver and response variables. We present a high-resolution palynological, charcoal and stable isotopic record alongside chironomid-inferred temperature data from Tirinie, south-east Grampian Highlands, Scotland. The record is stratigraphically and chronologically constrained using tephra and radiocarbon dating. The isotopic and chironomid data reveal centennial-scale climatic deteriorations at ca 14.0; 13.2 and 11.4 cal ka BP. In response to these cooling events, vegetation became more open, fire frequency increased and landscape erosion was common. The reconstruction of both climate and environment reveals asynchrony in the phasing of annual and summer temperature variability, vegetation change and fire for each climatic event. Whilst responses appear strongest following the convergence of annual and summer temperature variability across all events, the ca 13.2 ka BP event reveals a two-stage environmental and fire response to climatic change, and the ca 11.4 ka BP event exhibits environmental change in the absence of summer temperature variability. The data further suggests that fire is an integral component of abrupt climatic change in this part of north-west Europe.

Enhancement of the optical and electrical properties of Cd-rich NixCd1−xO alloys was achieved through an electrochemical procedure – their biasing at a constant negative potential into an electrolyte. Depending on the conductivity of the film (correlated to x), the films changed their color from transparent-yellowish to black. For a certain bias, the coloration became permanent and irreversible. Electron concentration for some samples increased for better than two orders of magnitude upon the coloration, while as the mobility decreased for a factor of 2–10. Rutherford Back Scattering (RBS) analysis revealed oxygen deficiency for the colored samples. The XRD analysis showed that the coloration could be associated to a partial reduction of CdO2 to CdO. XPS analysis suggested complex red-ox transitions of the two Ni and two Cd-oxides within the alloy. Ni2p electrons suggested that a partial NiO (transparent) transition to Ni2O3 (black) is likely the responsible process for the occurrence of the intensive light trapping. Since the NixCd1−xO band gap is tunable with x, one may conclude that this electrochemical procedure is motivating for tuning/modification/enhancement of the both, the absorption and conductivity of NixCd1−xO films for their possible application as integrated film photoanodes (TCO and PEC cell in one) within a hybrid water splitting device.

Understanding rates of nitrogen cycling in estuaries is crucial for understanding their productivity and resilience to eutrophication. Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, links reduced and oxidized forms of inorganic nitrogen and is therefore an important step of the nitrogen cycle. However, rates of nitrification in estuary waters are poorly characterized. In fall and winter of 2011–2012, we measured nitrification rates throughout the water column of all major regions of San Francisco Bay, a large, turbid, nutrient-rich estuary on the west coast of North America. Nitrification rates were highest in regions furthest from the ocean, including many samples with rates higher than those typically measured in the sea. In bottom waters, nitrification rates were commonly at least twice the magnitude of surface rates. Strong positive correlations were found between nitrification and both suspended particulate matter and ammonium concentration. Our results are consistent with previous studies documenting high nitrification rates in brackish, turbid regions of other estuaries, many of which also showed correlations with suspended sediment and ammonium concentrations. Overall, nitrification in estuary waters appears to play a significant role in the estuarine nitrogen cycle, though the maximum rate of nitrification can differ dramatically between estuaries.

Pelagic marine Thaumarchaea play a primary role in ammonia oxidation, an integral part of nitrification and the nitrogen cycle. This study examines how physicochemical and biological variables influence rates of nitrification and the distribution, abundance and activity of ammonia oxidizers throughout the dark northeast Pacific Ocean. Nitrification rates are highest near the epipelagic-upper mesopelagic transition and decrease with depth according to a Martin-like power function, suggestive of a coupling to the organic matter flux. In contrast, archaeal and bacterial ammonia monooxygenase (amoA) gene abundance remains fairly constant throughout the upper mesopelagic. Density-based composites reveal nitrification to be highest in the upper pycnocline, within the nitrate:silica and ammonium maxima, while ammonia-oxidizing archaea (AOA) abundances are highest in the lower pycnocline. Water column group A (WCA) and B (WCB) AOA amoA genes are present throughout the dark ocean but have no relationship to nitrification rates. WCA comprise the majority of the AOA community above 200 m and WCB comprise the majority of it below 500 m, largely because WCA abundances decrease precipitously from 200 m to 500 m. WCA and WCB amoA genes are actively transcribed throughout the dark ocean, irrespective of conditions. Thaumarchaeal urease (ureC) genes are also present throughout, implying a widespread capacity for mixotrophy; however, unlike amoA, their expression is not detectable. Together, the results support a strong linkage between organic matter flux and nitrification rates, identify density as an important control over AOA distributions, and suggest that WCA and WCB distributions are influenced by the availability of their preferred substrates in the dark ocean.

Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH(4)(+)), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH(4)(+) in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH(4)(+) availability, with broad implications for comparisons of ecologically distinct populations.

Nitrite (NO2−) is a substrate for both oxidative and reductive microbial metabolism. NO2− accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2− production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3−) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3− reduction to NO2− were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2− production in the PNM. Sensitive (< 10 nmol L−1), precise measurements of [NH4+] and [NO2−] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2− producing process, with rates of NH3 oxidation to NO2− of up to 31 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2− production from NO3− was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2− production from NO3− were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2− production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2− just below the PNM was not captured in the incubations. Residence time estimates of NO2− within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.