Small-scale Patterns Research Articles

Use of thermal signal for the investigation of near-surface turbulence

Abstract. Organised motion of air in the roughness sublayer of the atmosphere was investigated using novel temperature sensing and data science methods. Despite accuracy drawbacks, current fibre-optic distributed temperature sensing (DTS) and thermal imaging (TIR) instruments offer frequent, moderately precise and highly localised observations of thermal signal in a domain geometry suitable for micrometeorological applications near the surface. The goal of this study was to combine DTS and TIR for the investigation of temperature and wind field statistics. Horizontal and vertical cross-sections allowed a tomographic investigation of the spanwise and streamwise evolution of organised motion, opening avenues for analysis without assumptions on scale relationships. Events in the temperature signal on the order of seconds to minutes could be identified, localised, and classified using signal decomposition and machine learning techniques. However, small-scale turbulence patterns at the surface appeared difficult to resolve due to the heterogeneity of the thermal properties of the vegetation canopy, which are not immediately evident visually. The results highlight a need for physics-aware data science techniques that treat scale and shape of temperature structures in combination, rather than as separate features.

When Imagery and Physical Sampling Work Together: Toward an Integrative Methodology of Deep-Sea Image-Based Megafauna Identification

Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selected taxa (Pisces, Crustacea, Echinoidea, and Asteroidea), which are good candidates for identification from images. Taxonomic identification ranks obtained for the images varied among these taxa (e.g., family/order for fishes, genus for echinoderms). At these ranks, imagery provided a higher taxonomic richness for hard-bottom and complex habitats, partially explained by the poor performance of trawling on these rough substrates. For the same reason, the gamma diversity of Pisces and Crustacea was also higher from images, but no difference was observed for echinoderms. On soft bottoms, physical sampling provided higher alpha and gamma diversity for fishes and crustaceans, but these differences tended to decrease for crustaceans identified to the species/morphospecies level from images. Physical sampling and imagery were selective against some taxa (e.g., according to size or behavior), therefore providing different facets of biodiversity. In addition, specimens collected at a larger scale facilitated megafauna identification from images. Based on this complementary approach, we propose a robust methodology for image-based faunal identification relying on a taxonomic framework, from collaborative work with taxonomists. An original outcome of this collaborative work is the creation of identification keys dedicated specifically to in situ images and which take into account the state of the taxonomic knowledge for the explored sites.

The dynamics and temperature regime of the crater lakes in the Nevado de Toluca volcano, Mexico

Volcanic lakes are unique ecosystems with complex relationships between atmospheric variables and crater lake dynamics. In two adjacent tropical, high mountain lakes, spectral analysis of coupled in situ meteorological and hydrodynamic measurements revealed strong diurnal fluctuations in water temperature due to wind-forced internal gravity waves and free seiche oscillations. Although the amplitudes of these internal motions were small, they contribute to the transfer of momentum and mixing, with large potential impacts on lake productivity. During daytime heating, in both lakes, a thermocline formed in the near-surface layer (2−3 m depth) but eroded at night. The heat penetration into each lake within the crater differed significantly, even though they were ∼ 500 m apart, driven by differences in water transparency and algal growth. Analyses of coupling between local meteorology and lake hydrodynamics revealed complex forcing of small-scale patterns which are important to incorporate into future studies to understand how ecosystem productivity is modulated.

Nighttime migrations and behavioral patterns of Pempheris schwenkii.

BackgroundAlthough the biomass of the nocturnal fishes is almost same as that of diurnal fishes, most of the ecological studies that examine feeding or reproductive behaviors are on diurnal fishes. Therefore, there is limited ecological information regarding the nocturnal fishes. This fact may be attributed to the difficulty in observing them during darkness. Members of the genus Pempheris (Pempheridae) are one of the most abundant nocturnal fishes on coral reefs.MethodsThe nighttime migrations of Pempheris schwenkii were observed by attaching a chemical luminescent tag. Tagged fishes were followed by an observer without torch and SCUBA, and their positions and estimated depths were plotted on an underwater topographic map. Aquarium tank observation was carried out to further describe their habits during the night.ResultsThe new tagging method provided good data for observing the migration behavior. In all five observations, the target fishes started nighttime migration from the entrance of their cave within 1 h after sunset. All of them immediately left the inner reef and spent most of the observation time near the surface (0–5 m depth) or shallow (5–15 m depth) water-columns of the outer reef. Their migration pattern varied between days, but they migrated long distance (379–786 m/h) during each observation. The behavior observed in the aquarium tank was categorized into five patterns: schooling, shaking, migrating, spawning, and feeding. Shaking and spawning were observed during one of three observation days.DiscussionThe present study firstly clarified the small-scale but dynamic nocturnal migration pattern of P. schwenkii in nature by a new method using chemical luminescent tags. In addition, combined observations from nature and an aquarium could be used to estimate the behavior of this species. Pempheris schwenkii may reduce their predation risk of eggs and adults by spawning at outer reef in nighttime. It was estimated that they can potentially migrate 4–7 km/night. The rapid growth known for this species may have been supported by their feeding behavior where they can fill up their stomach every night with rich zooplankton in outer reefs. Furthermore, the behavior of this species indicates the possibility that they make an important contribution to the flow of energy and materials in their coral reef ecosystem.

Internal wave intensity and angle of propagation modulate small-scale settlement patterns of intertidal barnacles during peak recruitment

The settlement of intertidal barnacles Chthamalus spp. was measured for an entire recruitment season at 3 sites separated by 100 m in Baja California, Mexico. During a 10 d pulse that accounted for nearly 30% of yearly settlement, coastal wind speed and direction, nearshore water column temperature, and current velocities were also measured. During this period, strong internal tidal forcing was observed, with short episodes (1-1.5 h) of rapid fluctuations in water column temperature, stratification, and currents. Chthamalus spp. settlement was significantly and positively correlated with cumulative high-frequency fluctuations in temperature, thermal stratification, and surface current flows, but not with onshore winds. Furthermore, the spatial pattern in the number of settlers was correlated with the angle of propagation estimated for onshore-moving internal waves, potentially modulated by nearshore bathymetry. This relationship between Chthamalus spp. settlement and high-frequency changes in water column temperature was also shown for a site in La Jolla, California, USA, but not for a similar barnacle, Balanus glandula, suggesting that interspecific differences in larval behavior and nearshore depth distribution may translate into differences in transport. Our results suggest that both the number of settlers at shore and their spatial pattern can be modulated by the intensity and direction of internal wave events, at least during peak settlement periods. Future research should consider both the intensity and geometry of internal-wave-induced variability in the nearshore, as well the small-scale features of coastal geomorphology and bathymetry.

Small-scale patterns in a larger picture

Abstract Telling apart family-internal developments from contact-induced changes and socio-geographically conditioned areal trends is still one of the main challenges in tracing the development - and stability - of languages. Notably prima facie contact phenomena might turn out to have resulted from the interaction of a variety of sources upon closer inspection; assessing their interaction is a crucial requirement for comprehending the dynamics of change. Based on the example of simplification patterns in the system of short personal pronouns observed in the Balkan Slavic dialects located in the territory of North Macedonian and Greece, the present paper illustrates the necessity of identifying the multiplicity of triggers and their interaction, thereby making a case for the relevance of small-scale, transient patterns in understanding diachronic processes. In particular, it places the simplifications within the pronominal system into the larger context of differential object indexing by preverbal pronominal elements in the Balkan languages. With the loss of agreement distinctions on pronouns being characteristic for the last phase in the emergence of object indexing, both processes appear to be closely related. Obviously, in this case, the convergence of various different processes has created a favorable environment for the mutual reinforcement and stabilization of two otherwise highly volatile phenomena.

Living, dead, and absent trees-How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline?

Mountain birch forests (Betula pubescens Ehrh. ssp. czerepanovii) at the subarctic treeline not only benefit from global warming, but are also increasingly affected by caterpillar outbreaks from foliage-feeding geometrid moths. Both of these factors have unknown consequences on soil organic carbon (SOC) stocks and biogeochemical cycles. We measured SOC stocks down to the bedrock under living trees and under two stages of dead trees (12 and 55years since moth outbreak) and treeless tundra in northern Finland. We also measured in-situ soil respiration, potential SOC decomposability, biological (enzyme activities and microbial biomass), and chemical (N, mineral N, and pH) soil properties. SOC stocks were significantly higher under living trees (4.1±2.1kg m²) than in the treeless tundra (2.4±0.6kg m²), and remained at an elevated level even 12 (3.7±1.7kg m²) and 55years (4.9±3.0kg m²) after tree death. Effects of tree status on SOC stocks decreased with increasing distance from the tree and with increasing depth, that is, a significant effect of tree status was found in the organic layer, but not in mineral soil. Soil under living trees was characterized by higher mineral N contents, microbial biomass, microbial activity, and soil respiration compared with the treeless tundra; soils under dead trees were intermediate between these two. The results suggest accelerated organic matter turnover under living trees but a positive net effect on SOC stocks. Slowed organic matter turnover and continuous supply of deadwood may explain why SOC stocks remained elevated under dead trees, despite the heavy decrease in aboveground C stocks. We conclude that the increased occurrence of moth damage with climate change would have minor effects on SOC stocks, but ultimately decrease ecosystem C stocks (49% within 55years in this area), if the mountain birch forests will not be able to recover from the outbreaks.

Fine-Scale Urban Heat Patterns in New York City Measured by ASTER Satellite—The Role of Complex Spatial Structures

Urban areas have very complex spatial structures. These spatial structures are primarily composed of a complex network of built environments, which evolve rapidly as the cities expand to meet the growing population’s demand and economic development. Therefore, studying the impact of spatial structures on urban heat patterns is extremely important for sustainable urban planning and growth. We investigated the relationship between surface temperature obtained by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER, at 90 m spatial resolution) and different urban components based on high-resolution QuickBird satellite imagery classification. We further investigated the relationships between ASTER-derived surface temperature and building footprint and land use information acquired by the New York City (NYC) Department of City Planning. The ASTER image reveals fine-scale urban heat patterns in the NYC metropolitan region. The impervious-medium and dark surfaces, along with bright covers, generate higher surface temperatures. Even with highly reflective urban surfaces, the presence of impervious materials leads to an increased surface temperature. At the same time, trees and shadows cast by buildings effectively reduce urban heat; on the contrary, grassland does not reduce or amplify urban heat. The data aggregated to the census tract reveals high-temperature hotspots in Queens, Brooklyn, and the Bronx region of NYC. These clusters are associated with industrial and manufacturing areas and multi-family walk-up buildings as dominant land use. The census tracts with more trees and higher building height variability showed cooling effects, consistent with shadows cast by high-rise buildings and trees. The results of this study can be valuable for urban heat island modeling on the impact of shadow generated by building heights variability and trees on small-scale surface temperature patterns since recent image reveals similar hotspot locations. This study further helps identify the risk areas to protect public health.

Detailed Patterns of Methane Distribution in the German Bight

Although methane is a widely studied greenhouse gas, uncertainties remain with respect to the factors controlling its distribution and diffusive flux into the atmosphere, especially in highly dynamic coastal waters. In the southern North Sea, the Elbe and Weser rivers are two major tributaries contributing to the overall methane budget of the southern German Bight. In June 2019, we continuously measured methane and basic hydrographic parameters at a high temporal and spatial resolution (one measurement per minute every 200–300 m) on a transect between Cuxhaven and Helgoland. These measurements revealed that the overall driver of the coastal methane distribution is the dilution of riverine methane-rich water with methane-poor marine water. For both the Elbe and Weser, we determined an input concentration of 40–50 nmol/L compared to only 5 nmol/L in the marine area. Accordingly, we observed a comparatively steady dilution pattern of methane concentration toward the marine realm. Moreover, small-scale anomalous patterns with unexpectedly higher dissolved methane concentrations were discovered at certain sites and times. These patterns were associated with the highly significant correlations of methane with oxygen or turbidity. However, these local anomalies were not consistent over time (days, months). The calculated diffusive methane flux from the water into the atmosphere revealed local values approximately 3.5 times higher than background values (median of 36 and 128 μmol m–2 d–1). We evaluate that this occurred because of a combination of increasing wind speed and increasing methane concentration at those times and locations. Hence, our results demonstrate that improved temporal and spatial resolution of methane measurements can provide a more accurate estimation and, consequently, a more functional understanding of the temporal and spatial dynamics of the coastal methane flux.

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity

Montane cloud forests are fragile biodiversity hotspots. To attain their conservation, disentangling diversity patterns at all levels of ecosystem organization is mandatory. Biotic communities are regularly structured by environmental factors even at small spatial scales. However, studies at this scale have received less attention with respect to larger macroscale explorations, hampering the robust view of ecosystem functioning. In this sense, fungal small-scale processes remain poorly understood in montane cloud forests, despite their relevance. Herein, we analyzed soil fungal diversity and ecological patterns at the small-scale (within a 10 m triangular transect) in a pristine montane cloud forest of Mexico, using ITS rRNA gene amplicon Illumina sequencing and biogeochemical profiling. We detected a taxonomically and functionally diverse fungal community, dominated by few taxa and a large majority of rare species (81%). Undefined saprotrophs represented the most abundant trophic guild. Moreover, soil biogeochemical data showed an environmentally heterogeneous setting with patchy clustering, where enzymatic activities suggest distinctive small-scale soil patterns. Our results revealed that in this system, deterministic processes largely drive the assemblage of fungal communities at the small-scale, through multifactorial environmental filtering.

Tracing the horizontal transport of microplastics on rough surfaces

Occurrence and distribution of microplastics in different ecosystems have recently become subjects of numerous studies. However, to date the research has focused mainly on marine and freshwater ecosystems and widely neglected terrestrial environments. Only recently, first studies investigated the microplastics contamination of soils. Therefore, we know little about the transport mechanisms of microplastics in soils and sediments and virtually nothing about their surface transport. In this study we investigate surface transport mechanisms by tracking fluorescent, irregularly shaped polymethyl methacrylate (PMMA) particles in real time in a laboratory setup. In 108 experimental runs, we vary the irrigation rates, inclinations and surface roughnesses. Additionally, we simulate the small-scale flow patterns to resolve the role of the roughness-induced microrelief. Our results suggest that microplastics are transported along preferential pathways resulting from the micro- and macrorelief, which can be correlated to the flow pattern observed in the computer simulation. Our model study facilitates a deeper insight into microplastic transport on different soil surfaces and serves as a pilot for investigating mechanisms of horizontal microplastic transport. However, microplastics are a diverse group of contaminants with varying shapes, densities and sizes. Therefore, for a full understanding of transport of microplastics in terrestrial environments, it is important to address these properties as well as more variable surfaces for horizontal migration and to include vertical transport mechanisms in future research.

Environmental drivers of reef manta ray (Mobula alfredi) visitation patterns to key aggregation habitats in the Maldives.

A detailed understanding of the dynamics of small-scale (10s km) habitat use by the reef manta ray (Mobula alfredi) in the Maldives Archipelago is required to develop an effective national conservation management plan for this wide-ranging species. Here, a combination of photo-ID sightings data and acoustic telemetry were used to investigate both long-term M. alfredi visitation trends and small-scale movement patterns to key habitats on the eastern side of Baa Atoll (Hanifaru Bay feeding area, Dhigu Thila multifunctional site, and Nelivaru Thila cleaning station). All tagged and most of the sighted M. alfredi exhibited high affinity to the eastern side of Baa Atoll, where 99% of detections occurred, and 69% of individuals were re-sighted in multiple years. Sightings data suggests that visitation patterns may be associated with differences in habitat use by sex and maturity status. Boosted regression trees indicated that tag detection probability at Hanifaru Bay increased with increased westerly wind speed (>5ms-1) during the day, close to a new and full moon just after high tide, and when the tidal range was low. Interaction effects between predictors suggest that wind-driven oceanographic processes, such as Langmuir Circulation, maybe working to increase zooplankton concentration at this location. Tag detection probability increased at Dhigu Thila under similar conditions. At Nelivaru Thila, it increased at lower wind speeds (<5ms-1), close to a full moon, three hours after high tide. These results suggest that M. alfredi may utilise cleaning stations during the day when environmental conditions are not suitable for feeding. There was a high level of connectivity between these three locations, which suggests they form part of a network of key habitats that provide essential services to M. alfredi locally. Future conservation efforts should focus on identifying all areas of key habitat use for this species within the Maldives; applying strict protective measures to these sites and any connecting migration corridors which link them.

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi.

Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.

Movement patterns of juvenile Atlantic tarpon (Megalops atlanticus) in Brewers Bay, St. Thomas, U.S. Virgin Islands

BackgroundAtlantic tarpon (Megalops atlanticus) are a highly migratory species ranging along continental and insular coastlines of the Atlantic Ocean. Due to their importance to regional recreational and sport fisheries, research has been focused on large-scale movement patterns of reproductively active adults in areas where they are of high economic value. As a consequence, geographically restricted focus on adults has left significant gaps in our understanding of tarpon biology and their movements, especially for juveniles in remote locations where they are common. Our study focused on small-scale patterns of movement and habitat use of juvenile tarpon using acoustic telemetry in a small bay in St. Thomas, US Virgin Islands.ResultsFour juvenile tarpon (80–95 cm FL) were tracked from September 2015 to February 2018, while an additional eight juveniles (61–94 cm FL) left the study area within 2 days after tagging and were not included in analysis. Four tarpon had > 78% residency and average activity space of 0.76 km2 (range 0.08–1.17 km2) within Brewers Bay (1.8 km2). Their vertical distribution was < 18 m depth with occasional movements to deeper water. Activity was greater during day compared to night, with peaks during crepuscular periods. During the day tarpon used different parts of the bay with consistent overlap around the St. Thomas airport runway and at night tarpon typically remained in a small shallow lagoon. However, when temperatures in the lagoon exceeded 30 °C, tarpon moved to cooler, deeper waters outside the lagoon.ConclusionOur results, although limited to only four individuals, provide new baseline data on the movement ecology of juvenile Atlantic tarpon. We showed that juvenile tarpon had high residency within a small bay and relatively stable non-overlapping daytime home ranges, except when seasonally abundant food sources were present. Fine-scale acoustic tracking showed the effects of environmental conditions (i.e., elevated seawater temperature) on tarpon movement and habitat use. These observations highlight the need for more extensive studies of juvenile tarpon across a broader range of their distribution, and compare the similarities and differences in behavior among various size classes of individuals from small juveniles to reproductively mature adults.

Freshwater Mussel Assemblages in the Black River, Missouri and Arkansas

Freshwater mussel assemblages show predictable variation according to large-scale biogeographic factors and stream-size gradients, but smaller-scale assemblage patterns are less well known. The goal of this study was to classify and delineate mussel assemblages of the Black River, Missouri and Arkansas, USA, along an upstream–downstream gradient and with regard to physiography and biogeographical regions. We analyzed mussel assemblages using nonmetric multidimensional scaling and indicator-species analysis. Our results yielded three assemblage groupings distributed along the upstream–downstream gradient and thereby considered aquatic ecological systems (100–1,000 km2) in a hierarchical spatial classification scheme. These groupings also support previously proposed biogeographical differences for mussels and fishes between the Ozark Highlands and Mississippi Alluvial Plain physiographic regions. Each group was characterized by 2–13 indicator species. Our demonstration of small-scale patterns of mussel assemblage change will be useful for conservation planning and for a better understanding of mussel assemblage dynamics.

Mapping bias: A rhizomatic critique of the National Literacy Panel Report

ABSTRACT The Report of the National Literacy Panel on Language-Minority Children and Youth was designed to be a definitive review of research on the literacy development of language-minoritized students. We adopt conceptual methods from rhizomatic mapping to replicate the report’s literature searches and critically examine studies eliminated based on the panel’s inclusion criteria. Our analyses demonstrate that epistemological bias disproportionately excluded small-scale, qualitative studies, and mapping citation patterns of scholarly impact demonstrates ongoing stratification and territorialization of scholarship since the report was published.

Tectonically conditioned record of continental interior paleoclimate during the Carnian Pluvial Episode: The Upper Triassic Los Rastros Formation, Argentina

Abstract Discerning paleoclimate parameters in depositional systems of the continental interior is challenging because the system response and stratigraphic record of climate are controlled by tectonic processes and are mediated through landscape and hydrological evolution of fluvial lacustrine systems. Climate and tectonic signals cannot be deconvolved from stratigraphic patterns alone but require additional information or data sets that directly record climate or tectonic influence. The Carnian Los Rastros Formation in northwest Argentina provides an excellent case study that integrates an appropriate range of information in a system with strong climate and tectonic signals, being deposited in part during the Carnian Pluvial Episode and spanning the active rift phase of the Ischigualasto–Villa Unión Basin. We examined the stratigraphic and spatial patterns of carbon (C) and oxygen (O) stable isotopes in lacustrine carbonates from the Los Rastros Formation in multiple parts of the basin to constrain paleohydrological conditions and paleotemperatures. Practically all C and O isotope values are characterized by negative values: δ18Ocarb –11.6&amp;#x89; and –15.7&amp;#x89; (χ average –13.1&amp;#x89;; 1σ = 1.6) and δ13Ccarb –2.6&amp;#x89; to –8.0&amp;#x89; (χ average –5.1&amp;#x89;; 1σ = 2.1), reflecting the latitude, altitude, and continentality of the lake system and its vegetated and humid catchment area. Stratigraphic patterns of stable isotope data from two different localities (Cerro Bola North and Cerro Bola South) show a change from short water-residence time to long residence time and back to short residence time. This contrasts with sedimentologic, organic geochemical, and small-scale stratigraphic patterns that indicate an overfilled lake basin, which is expected to contain a completely open-hydrology isotopic signature. Paleotemperatures calculated from marginal lacustrine carbonates show a warm and quite variable paleothermal range consonant with their continental interior position and with Global Climate Models estimates for high paleolatitudes. Warmer paleotemperatures (linked to aridity, probably smaller lake size, and less thermal mass) precede the Carnian Pluvial Episode, whereas relatively cooler paleotemperatures coincide with the Carnian Pluvial Episode (linked to humidity, probably larger lake size, and more thermal mass). Carbon and oxygen stable isotope signatures integrated with sedimentologic and physiographic information allow us to propose that tectonics, specifically, half-graben tilting during the active synrift phase, dominated over climate effects as the cause of hydrological fluctuations of this system, even during the Carnian Pluvial Episode. Without appropriate stratigraphic-tectonic context, single-proxy reconstructions of continental-interior paleoclimate can be misleading. A robust interpretation of climate effects requires characterization of tectonic effects, geomorphology, paleohydrology, and sedimentary system responses.

Horizontal and vertical small-scale patterns of protist communities at the Atlantic deep-sea floor

Spatial distribution patterns of protists in the deep sea are not yet understood and due to the remoteness of the deep-sea biome this is a challenging task. Here, we investigated the structure and dispersal of protist communities in abyssal sediments at three sites in the Caribbean Sea (15°53.21′N/68°55.73′W), the northwestern Atlantic (23°33.23′N/48°05.04′W) and the central Atlantic Ocean (10°20.38′N/36°57.76′W), focusing especially on small horizontal (~1 m) and vertical (1 cm) spatial scales. High-throughput sequencing of the V9 SSU rDNA, revealed diverse protist communities dominated by diplonemids and dinoflagellates. Only 12% of OTUs were shared between the three deep-sea regions (4000–5134 m deep), indicating patterns of protistan distribution at large spatial scales in deep-sea sediments. The analyses of sediment samples taken from cores of the same Multi-Corer deployment, separated by ~1 m, showed differences in the community structure, indicating a distinct microbial eukaryotic diversity even at a local horizontal scale. At a vertical scale, in different sediment depth layers (upper 2 mm layer, 1 cm, 2 cm, 3 cm) of the same core, only 4–11% of OTUs were shared. We could show, that already at small spatial scales protist communities varied strongly, indicating an underestimated complexity of deep-sea microbial food webs.

Identifying forecast uncertainties for biogenic gases in the Po Valley related to model configuration in EURAD-IM during PEGASOS 2012

Abstract. Forecasts of biogenic trace gases in the planetary boundary layer (PBL) are highly affected by simulated emission and transport processes. The Po region during the PEGASOS campaign in summer 2012 provides challenging, yet common, conditions for simulating biogenic gases in the PBL. This study identifies and quantifies principal sources of forecast uncertainties induced by various model configurations under these conditions. Specifically, the effects of model configuration on different processes affecting atmospheric distributions of biogenic trace gas distributions are analyzed based on a priori available information. The investigation is based on the EURopean Air pollution Dispersion – Inverse Model (EURAD-IM) chemistry transport model employing the Model for Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN 2.1) biogenic emission module and Regional Atmospheric Chemistry Mechanism – Mainz Isoprene Mechanism (RACM-MIM) as the gas phase chemistry mechanism. Two major sources of forecast uncertainties are identified in this study. Firstly, biogenic emissions appear to be exceptionally sensitive to land surface properties inducing total variations in local concentrations of up to 1 order of magnitude. Moreover, these sensitivities are found to be highly similar for different gases and almost constant during the campaign, varying only diurnally. Secondly, the model configuration also highly influences regional flow patterns with significant effects on pollutant transport and mixing. This effect was corroborated by diverging source regions of a representative air mass and thus applies also to non-biogenic gases. As a result, large sensitivities to model configuration are found for surface concentrations of isoprene, as well as OH, affecting reactive atmospheric chemistry. Especially in areas with small-scale emission patterns, changes in the model configuration are able to induce significantly different local concentrations. The amount and complexity of sensitivities found in this study demonstrate the need to consider forecast uncertainties in chemical transport models with a special focus on biogenic emissions and pollutant transport.

ReHiC: Enhancing Hi-C data resolution via residual convolutional network.

High-throughput chromosome conformation capture (Hi-C) is one of the most popular methods for studying the three-dimensional organization of genomes. However, Hi-C protocols can be expensive since they require large amounts of sample material and may be time-consuming. Most commonly used Hi-C data are low-resolution. Such data can only be used to identify large-scale genomic interactions and are not sufficient to identify the small-scale patterns. We propose a novel deep learning-based computational approach (named ReHiC) that enhances the resolution of Hi-C data and allows us to achieve high-resolution Hi-C data at a relatively low cost. Our model only requires 1/16 down-sampling ratio of the original sequence reading to predict higher resolution Hi-C data. This is very close to high-resolution data in terms of numerical distribution and interaction distribution. More importantly, our framework stacks deeper and converges faster due to residual blocks in the core of the network. Extensive experiments show that ReHiC performs better than HiCPlus and HiCNN, two recently developed and frequently used methods to look at the spatial organization of chromatin structure in the cell. Moreover, the portability of our framework verified by extensive experiments shows that the trained model can also enhance the Hi-C matrix of other cell types efficiently. In conclusion, ReHiC offers more accurate high-resolution image reconstruction in a broad field.