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Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.
The world’s coastlines are spatially highly variable, coupled-human-natural systems that comprise a nested hierarchy of component landforms, ecosystems, and human interventions, each interacting over a range of space and time scales. Understanding and predicting coastline dynamics necessitates frequent observation from imaging sensors on remote sensing platforms. Machine Learning models that carry out supervised (i.e., human-guided) pixel-based classification, or image segmentation, have transformative applications in spatio-temporal mapping of dynamic environments, including transient coastal landforms, sediments, habitats, waterbodies, and water flows. However, these models require large and well-documented training and testing datasets consisting of labeled imagery. We describe “Coast Train,” a multi-labeler dataset of orthomosaic and satellite images of coastal environments and corresponding labels. These data include imagery that are diverse in space and time, and contain 1.2 billion labeled pixels, representing over 3.6 million hectares. We use a human-in-the-loop tool especially designed for rapid and reproducible Earth surface image segmentation. Our approach permits image labeling by multiple labelers, in turn enabling quantification of pixel-level agreement over individual and collections of images.
In the United States (U.S.), waste byproducts generated from the treatment of municipal waste (biosolids), production of livestock (livestock waste), and drilling of oil and gas wells (drilling waste) are commonly applied to agricultural lands. Although this can be a cost-effective reuse/disposal practice, there is limited research on the potential for contaminant exposures and effects on ecosystems, wildlife, and human health from such land applications. In this study, we conducted extensive chemical, microbial, and toxicity analyses of biosolid, livestock, and drilling wastes just prior to land application on agricultural lands at 34 sites across the U.S. Twenty-two analytical methods were used to determine potential contaminant exposures profiles for 452 organic and 114 inorganic chemicals, nine microbial groups, estrogenicity, and cytotoxicity. Analytical results document unique and substantial chemical, microbial, and toxicity profiles for these land-applied wastes. Of the three waste byproducts, biosolids contained the greatest concentrations of household chemicals, pesticides, pharmaceuticals, per-/polyfluoroalkyl substances, calcium, and phosphorus. Livestock waste contained the greatest concentrations of total and leachable dissolved organic carbon, biogenic hormones, mycotoxins, plant estrogens, total inorganic nitrogen, and potassium. Drilling waste contained the greatest concentrations of BTEX compounds (benzene, toluene, ethylbenzene, and xylenes), polycyclic aromatic hydrocarbons, rare-earth elements, barium, strontium, and uranium–thorium series radioisotopes. Biosolid and livestock wastes had greater culturable heterotrophic bacteria, halophilic bacteria, Escherichia coli ( E. coli ), enterococci, and staphylococci concentrations, and greater microbial diversity than drilling waste. Bioassay analyses indicated that exposure to contaminants in livestock wastes and biosolids could result in estrogenic effects, whereas exposure to contaminants in drilling waste could result in cytotoxic effects. Our study documents that current reuse/disposal practices for biosolid, livestock, and drilling wastes on agricultural lands could provide a potential pathway for the redistribution of unique and complex contaminant mixtures into the environment that have bioactive, endocrine disrupting, and carcinogenic characteristics. Results of this study provide a snapshot of chemical compositions and concentrations that can be used to inform the development of best-management practices to help maximize beneficial reuse of these wastes and minimize risk to the environment and human health.
In order to investigate the effects of nearshore discharges of water quality degrading substances and bacteria in coastal environments, models capable of predicting nearshore circulation due to local wave and tide conditions are required. One of the larger challenges to nearshore coastal modeling is accurately reproducing nearshore circulation due to wave action. Local wave action not only drives circulation through processes such as longshore transport and rip currents, but also contributes significantly to the mixing of water quality constituents. In the present work, a wave model was used to calculate radiation shear stresses and dissipation due to wave action. The shear stresses and dissipation were incorporated into a hydrodynamic model to force circulation in the nearshore environment. The model was applied to a site in Santa Cruz, CA where site specific current data was available. The model reproduces the nearshore current structure observed in the region and was used to study the transport of dredge disposal plumes in the region which could have deleterious effects on local beaches. This presentation will outline the nearshore circulation model development and application.
Carbon dioxide (CO 2 ) in fresh-water environments is poorly understood, yet in marine environments CO 2 can affect fish behaviour, including predator–prey relationships. To examine changes in predator success in elevated CO 2 , we experimented with predatory Micropterus salmoides and Pimephales promelas prey. We used a two-factor fully crossed experimental design; one factor was 4-day (acclimation) CO 2 concentration and the second factor CO 2 concentration during 20-min predation experiments. Both factors had three treatment levels, including ambient partial pressure of CO 2 ( p CO 2 ; 0–1000 μatm), low p CO 2 (4000–5000 μatm) and high p CO 2 (8000–10 000 μatm). Micropterus salmoides was exposed to both factors, whereas P. promelas was not exposed to the acclimation factor. In total, 83 of the 96 P. promelas were consumed ( n = 96 trials) and we saw no discernible effect of CO 2 on predator success or time to predation. Failed strikes and time between failed strikes were too infrequent to model. Compared with marine systems, our findings are unique in that we not only saw no changes in prey capture success with increasing CO 2 , but we also used CO 2 treatments that were substantially higher than those in past experiments. Our work demonstrated a pronounced resiliency of freshwater predators to elevated CO 2 exposure, and a starting point for future work in this area.
For Pacific salmon, estuaries are typically considered transitional staging areas between freshwater and marine environments, but their potential as rearing habitat has only recently been recognized. The objectives of this study were two-fold: (1) to determine if Coho Salmon Oncorhynchus kisutch were rearing in estuarine habitats, and (2) to characterize and compare the body length, age, condition, and duration and timing of estuarine occupancy of juvenile Coho Salmon between the two contrasting estuaries. We examined use of estuary habitats with analysis of microchemistry and microstructure of sagittal otoliths in two watersheds of south-central Alaska. Juvenile Coho Salmon were classified as estuary residents or nonresidents (recent estuary immigrants) based on otolith Sr : Ca ratios and counts of daily growth increments on otoliths. The estuaries differed in water source (glacial versus snowmelt hydrographs) and in relative estuarine and watershed area. Juvenile Coho Salmon with evidence of estuary rearing were greater in body length and condition than individuals lacking evidence of estuarine rearing. Coho Salmon captured in the glacial estuary had greater variability in body length and condition, and younger age-classes predominated the catch compared with the nearby snowmelt-fed, smaller estuary. Estuary-rearing fish in the glacial estuary arrived later and remained longer (39 versus 24 d of summer growth) during the summer than did fish using the snowmelt estuary. Finally, we observed definitive patterns of overwintering in estuarine and near shore environments in both estuaries. Evidence of estuary rearing and overwintering with differences in fish traits among contrasting estuary types refute the notion that estuaries function as only staging or transitional habitats in the early life history of Coho Salmon.
The paper develops approaches and methods of modeling and mapping land and water productivity of rain-fed crops in semi-arid environments of India using hyperspectral, hyperspatial, and advanced multispectral remote sensing data and linking the same to field-plot data and climate station data. The overarching goal is to provide information to advance water harvesting technologies in the agricultural croplands of the semi-arid environments of India by conducting research in a representative pilot site in Jodhpur, Rajasthan, India. ?? 2011 IEEE.
The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.
Climate-induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. Rocky Mountains, hybridization between native cutthroat trout and non-native rainbow trout has increased in recent decades due, in part, to climate-driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate-induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout. Here, we assessed whether invasive hybridization improves cardiac performance response to acute water temperature stress of native wild trout populations. We collected trout from four streams with a wide range of non-native admixture among individuals and with different temperature and streamflow regimes in the upper Flathead River drainage, USA. We measured individual cardiac performance (maximum heart rate, “MaxHR”, and temperature at arrhythmia, “ArrTemp”) during laboratory trials with increasing water temperatures (10–28°C). Across the study populations, we observed substantial variation in cardiac performance of individual trout when exposed to thermal stress. Notably, we found significant differences in the cardiac response to thermal regimes among native cutthroat trout populations, suggesting the importance of genotype-by-environment interactions in shaping the physiological performance of native cutthroat trout. However, rainbow trout admixture had no significant effect on cardiac performance (MaxHR and ArrTemp) within any of the three populations. Our results indicate that invasive hybridization with a warmer-adapted species does not enhance the cardiac performance of native trout under warming conditions. Maintaining numerous populations across thermally and hydrologically diverse stream environments will be crucial for native trout to adapt and persist in a warming climate.
Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon ( C. nelsonii ) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent ( C. nelsonii ), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent .
Modern microfossil distributions reflect site-specific habitats and provide an opportunity to assess sediment transport pathways in the nearshore environment. When applied to overwash deposits in the geological record, they provide insight into sediment provenance and transport, factors important for understanding patterns of frequency and intensity of past storms and tsunamis. Modern distribution studies are rare and often the first established ones occur immediately after an overwash event as part of a post-event field survey. This is problematic because it is unclear what effect overwash events have on nearshore microfossil assemblages and what time interval is necessary for them to return to pre-event conditions. This study documents the impacts of Hurricane Irma on nearshore sediments off the coast of Anegada, British Virgin Islands, using distributions of Homotrema rubrum , an encrusting foraminifer with a defined provenance in coral reefs. At four sampling intervals spanning two years, from six months pre-Hurricane Irma to eighteen months after, surface sediment was collected from three transects on the northern and southern shores of the island. Partitioning Around Medoids cluster analysis revealed that Hurricane Irma introduced an influx of well-preserved fragments into the reef flat and made the sediments more uniform, limiting the foraminifer’s utility as a known sediment transport indicator. The mixing of sediments along the two northern transects (reef proximal) persisted for seven to eighteen months before returning to near pre-hurricane conditions. However, the southern transect (absence of reef), where Homotrema rubrum concentrations are significantly less, failed to recover within the time period assessed by this study, indicating a variable recovery period between Atlantic Ocean and Caribbean Sea facing shorelines. Results from this study suggest that a waiting period of at least eighteen months after a major storm is recommended before collecting surface sediment from the nearshore environments of reef-dominated coastlines.
In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria . Unlike the type strain, Geobacter metallireducens , three of the five isolates could use H 2 as an electron donor for Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.
The Curiosity rover is exploring Hesperian-aged stratigraphy in Gale crater, Mars, where a transition from clay-bearing units to a layered sulfate-bearing unit has been interpreted to represent a major environmental transition of unknown character. We present the first description of key facies in the sulfate-bearing unit, recently observed in the distance by the rover, and propose a model for changes in depositional environments. Our results indicate a transition from lacustrine mudstones into thick aeolian deposits, topped by a major deflation surface, above which strata show architectures likely diagnostic of a subaqueous environment. This model offers a reference example of a depositional sequence for layered sulfate-bearing strata, which have been identified from orbit in other locations globally. It differs from the idea of a monotonic Hesperian climate change into long-term aridity on Mars and instead implies a period characterized by multiple transitions between sustained drier and wetter climates.
We examined three classes of factors that may influence brown treesnake (Boiga irregularis) trappability on Guam: (1) attributes of the snake, (2) attributes of the environment and (3) attributes of the trap. The attributes of the snake we considered included body condition, length and sex. Heavier snakes for a given size (better body condition) moved less and were less easily trapped. Longer snakes were easier to trap. Males were also slightly more easily trapped than females. We compared brown treesnake trappability between two study sites that differed greatly in the abundance of diurnal skinks, an important prey item for smaller snakes. We predicted that snakes, especially small individuals (<800 mm snout-vent length), would be more easily trapped in the low prey environment, a result that received only weak support from our data. However, small snakes were rarely trapped under any circumstance. We also predicted that diurnal foraging would be observed in the site with a higher density of diurnal prey, but daytime snake captures were negligible at both sites. Two attributes of traps that we varied were attractant (mouse vs. skink) and entrance flaps (present vs. absent). Traps with mice as attractant registered 6-16 fold more snake captures. We found little influence of entrances on captures. These modulators of brown treesnake trappability may have analogues in a variety of species, especially species that undergo an ontogenetic shift in diet. ?? 2008 Brill Academic Publishers.
Arsenic is toxic to most living cells. The two soluble inorganic forms of arsenic are arsenite (+3) and arsenate (+5), with arsenite the more toxic. Prokaryotic metabolism of arsenic has been reported in both thermal and moderate environments and has been shown to be involved in the redox cycling of arsenic. No arsenic metabolism (either dissimilatory arsenate reduction or arsenite oxidation) has ever been reported in cold environments (i.e. < 10°C). Results : Our study site is located 512 kilometres south of the Arctic Circle in the Northwest Territories, Canada in an inactive gold mine which contains mine waste water in excess of 50 mM arsenic. Several thousand tonnes of arsenic trioxide dust are stored in underground chambers and microbial biofilms grow on the chamber walls below seepage points rich in arsenite-containing solutions. We compared the arsenite oxidisers in two subsamples (which differed in arsenite concentration) collected from one biofilm. 'Species' (sequence) richness did not differ between subsamples, but the relative importance of the three identifiable clades did. An arsenite-oxidising bacterium (designated GM1) was isolated, and was shown to oxidise arsenite in the early exponential growth phase and to grow at a broad range of temperatures (4-25°C). Its arsenite oxidase was constitutively expressed and functioned over a broad temperature range. Conclusions : The diversity of arsenite oxidisers does not significantly differ from two subsamples of a microbial biofilm that vary in arsenite concentrations. GM1 is the first psychrotolerant arsenite oxidiser to be isolated with the ability to grow below 10°C. This ability to grow at low temperatures could be harnessed for arsenic bioremediation in moderate to cold climates.
The recent destruction of thousands of homes by lava flows from La Palma volcano, Canary Islands, and Nyiragongo volcano, Democratic Republic of Congo, serves as a reminder of the devastating impact that lava flows can have on communities living in volcanically active regions. Damage to buildings and infrastructure can have widespread and long-lasting effects on rehabilitation and livelihoods. Our understanding of how lava flows interact with buildings is limited and based upon sparse empirical data. Often a binary impact is assumed (destroyed when in contact with the flow and intact when not in contact with the flow), although previous events have shown this to be an oversimplification. Empirical damage data collected after past events provide an evidence base from which to better understand lava flow impacts across a range of building types, environments, and eruption styles, as well as to explore the temporal and spatial trends in these impacts. However, information on lava flow impacts is scattered across literature, reports, and maps; no comprehensive dataset of lava flow impacts exists. In this study, we compile and standardise lava flow impact information from previously compiled data, eruption records, and published literature to create the first comprehensive global dataset of impacts on the built environment from lava flows. We found that since the first recorded event between 5494 yr B.P. and 5387 yr B.P., lava flows from at least 155 events have impacted buildings or infrastructure (e.g., roads, electricity pylons, ski-lifts), with most (47%, n = 73) recorded as located in Europe. Over the last century, there have been approximately seven lava flow impact events per decade ( n = 71 total). This greatly expands on the past compilations of lava flow impact events. Since ca. 1800 CE, impacts have been consistently documented for less than 14% of recorded eruptions with lava flows globally; prior to 1800 CE, impacts were recorded much more variably (between 0 and 70% of lava flows in any 10-year time bin). The most destructive recorded events were the 1669 CE lava flows at Etna volcano, Italy, which destroyed up to 12 villages and part of the city of Catania, and the 2002 CE lava flows at Nyiragongo volcano, Democratic Republic of Congo, which destroyed up to 14,000 buildings. We found that few studies in the dataset report building typology, damage severity, or hazard intensity at the building-level scale, limiting our ability to assess past building-lava interactions. Future collection of building-level hazard and impact data, supplemented with non-English language records, can be used to inform models that forecast future impacts, support lava flow risk assessments, and develop potential mitigation measures.
Design of the nomogram is based on effective stress and combines consolidation theory as applicable to depositional environments with the infinite-slope model of slope-stability analysis. The link between the two combined theories is a term representing the effective overburden stress, which may be predicted from consolidation theory and a knowledge of sedimentation rate, time, and the coefficient of consolidation. In turn, if infinite-slope conditions are assumed to exist, the effective overburden stress can be used to derive a factor of safety against static slope failure by using the angle of internal friction and the slope angle. The nomogram applies to depostitional settings in which fine-grained sediment has accumulated at a relatively constant rate upon a base that is essentially impermeable. The model further assumes that the lateral extent of sediment affected by any mass movement will be great compared to its thickness and that no outside agents (e.g., cements, gas) are influencing the section. The nomogram is applicable to static conditions (inherent stability of the slope) and certain dynamic conditions (such as earthquakes). It may be used to investigate mass movements in the geologic past as well as those in modern environments.--Modified journal abstract.